$5 27 10 Findings of Fact Re PI Motion Smelt

Case 1:09-cv-00407-OWW-DLB Document 704 Filed 05/27/2010 Page 1 of 126
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UNITED STATES DISTRI CT CO URT
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FOR THE EASTERN DISTRICT OF C ALIFORNIA
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1:09-CV-00407 OWW DL B
8 1:09-cv-00480-OWW-GS A
1:09-cv-00422-OWW-GS A
9 1:09-cv-00631-OWW-DL B
The Cons olidated Del ta Smelt 1:09-cv-00892-OWW-DL B
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Cases
11 FINDINGS OF FA CT AND
CONCLUSIONS OF LAW R E
12 PLAINTIFFS’ RE QUEST FOR
PRELIMINARY IN JUNCTI ON
13 AGAINST IMPLEM ENTATI ON
OF RPA COMPONE NT 2
14 (a/k/a Action 3)(Doc .
15 433)
16
I. INTRODUCTION
17
Plaintif fs, San Luis & Delta Mendota Water Author ity
18
19 (the “Au thority”) an d Westlands Water District
20 (“Westla nds”), move for a preliminary injunction (“PI” )
21 against the implemen tation of Reasonable and Prud ent

22 Alternat ive (“RPA”) Component 2 set forth in the United
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States F ish and Wild life Service’s (“FWS”) Decemb er 15,
24
2008 Bio logical Opin ion, which addresses the impa cts of
25
the coor dinated oper ations of the federal Central Valley
26
Project (“CVP”) and State Water Project (“SWP”) o n the
27
28 threaten ed delta sme lt (Hypom esus transpacificus) (“20 08
1
1 Smelt Bi Op” or “BiOp ”). Doc. 433.

2 Plaintif fs State Wat er Contractors; Metropolitan
3
Water Di strict of So uthern California; Kern Count y Water
4
Agency a nd Coalition for a Sustainable; Stewart & Jasper
5
Orchards , et al.; an d the Family Farm Alliance jo in in
6
the moti on. Docs. 4 49, 451 & 453. Plaintiff-Int erven or
7
8 Departme nt of Water Resources (“DWR”), the operator of
9 the SWP, partially j oins. Doc. 452.
10 Federal Defendants a nd Defendant Intervenors oppo sed.

11 Docs. 46 9, 473. Pla intiffs replied. Docs. 487, 491,
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495, 497 & 507. The motion came on for an eviden tiary
13
hearing on April 2, 5, 6, and 7, 2010 . Doc s. 644, 652 ,
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653 & 65 4. The part ies were represented by couns el, as
15
noted in the record.
16
17 After co nsideration of the testimony of the
18 witnesse s, the exhib its received in evidence, the written

19 briefs o f the partie s, oral arguments, and the parties ’
20
proposed findings of fact and conclusions of law, the
21
followin g findings o f fact and conclusions of law
22
concerni ng the motio n for interim relief/prelimin ary
23
injuncti on are enter ed.
24
25 To the e xtent any fi nding of fact may be interpre ted
26 as a con clusio n of law or any conclusion of law may be
27 interpre ted as a fin ding of fact, it is so intend ed.

28
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1 II. BACKGROUND
2 The 2008 Smelt BiOp, prepared pursuant to Section 7
3 of the E ndangered Sp ecies Act (“ESA”), 16 U.S.C. §
4
1536(a)( 2), co nclude d tha t “the coordinated operations of
5
the CVP and SWP, as proposed, are likely to jeopa rdize
6
the cont inued existe nce of the delta smelt” and
7
“adverse ly modify de lta smelt critical habitat.” BiOp at
8
9 276-78. As re quired by law, the BiOp includes an RPA
10 designed to allow the pro jects to continue operat ing
11 without causing jeop ardy to the species or advers e

12 modifica tion to its critical habitat. Id. at 279. Th e
13
RPA incl udes various operational components desig ned to
14
reduce e ntrainment o f smelt during critical times of the
15
year by contro lling exports out of and water flows into
16
the Delt a. Id . at 279-85.
17
18 Componen t 1 (P rotection of the Adult Delta Smelt Life
19 Stage) c onsists of t wo Actions related to Old and Middle

20 River (“ OMR”) flows.
21
• Action 1 , which is d esigned to protec t upmigrating
22
delta sm elt, is trig gered during low and high
23
entrainm ent risk per iods based on physical and
24
biologic al monitorin g. Action 1 requires OMR flo ws
25
26 to be no more negati ve than -2,000 cubic fe et per
27 second ( “cfs”) on a 14-day average and no more
28
3
1 negative than -2,500 cfs for a 5-day runnin g average.

2 Id. at 2 81, 329.
3
• Action 2 of Componen t 1 is designed t o protect ad ult
4
delta sm elt that hav e migrated upstream and are
5
residing in the Delt a prior to spawning. Action 2 is
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triggere d immediatel y after Action 1 ends o r if
7
8 recommen ded by the S melt Working Group (“SWG”).
9 Flows un der Action 2 can be set within a range fr om
10 -5,000 t o -1,2 50 cfs, depending on a complex set of

11 biologic al and envir onmental parameters. Id. at 281-
12
82, 352- 56.
13
At issue here is Component 2 (Action 3) (Protecti on
14
of Larva l and Juveni le Delta Smelt), which requir es OMR
15
flows to remain betw een - 1,250 and -5,000 c fs, be ginni ng
16
17 when Com ponent 1 is completed, when Delta water
18 temperat ures reach 1 2° Celcius (“C”), or when a s pent

19 female s melt is dete cted in trawls or at salvage
20
faciliti es. I d. at 282, 357-58. Component 2 rem ains in
21
place un til June 30 or when the Clifton Court For ebay
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water te mperature re aches 25° C. Id. at 28 2, 368 .
23
Componen t 3 (I mprove Habitat for Delta Smelt Grow th
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25 and Rear ing) require s sufficient Delta outflow to
26 maintain average mix ing point locations of Delta outflow
27 and estu arine water inflow (“X2”) from September to

28
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1 December , depending on water year type, in accord ance

2 with a s pecifically described “adaptive management
3
process” overseen by FWS. Id. at 282-83, 3 69.
4
Under Co mponent 4 (H abitat Restoratio n), DWR is t o
5
create o r restore 8, 000 acres of intertidal and s ubtidal
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habitat in the Delta and Suisun Marsh within 10 y ears.
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8 Id. at 2 83-84, 379.
9 Under Co mponent 5 (M onitoring and Rep orting), the
10 Projects gather and report information to ensure proper

11 implemen tation of th e RPA actions, achievement of
12
physical results, an d evaluation of the effective ness of
13
the acti ons on the t argeted life stages of delta smelt,
14
so that the ac tions can be refined, if needed. Id. at
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284-85, 328, 3 75.
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III. SUMMARY OF MOT ION
18
Plaintif fs’ request temporary injunctive relief o n
19
the foll owing ground s:
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1) the d istrict cour t has already found that the
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22 United S tates Bureau of Reclamation (“Reclamation”)
23 failed t o comply wit h the National Environmental
24 Policy A ct (“NEPA”) in implementing the 2008 Smel t

25 BiOp RPA ; and.
26
2) the 2 008 Smelt Bi Op violates the ESA and is
27
arbitrar y, capriciou s, and contrary to law becaus e:
28
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1 a) vario us aspects o f the BiOp’s baseline a nd

2 effects analysis are flawed, undermining the
3
overall jeopardy con clusion, causing
4
overstat ement of the effects of the proposed
5
action a nd impositio n of overly-broad and
6
overly-r estrictive R PA Components;
7
8 b) the s evere OMR fl ow restrictions in RPA
9 Componen ts 1 and 2 a re unsupported by the best
10 availabl e science an d the data in the 2008 Smelt

11 BiOp; an d
12
c) Compo nent 3 (“The Fall X2 Action”) is
13
arbitrar y and capric ious, because it is without
14
factual or scientifi c justification and/or is
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not supp orted by the best available science,
16
17 compelli ng a finding of likelihood of success on
18 the meri ts.

19 Plainti ffs further claim that the implementation of
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RPA Comp onents 1 and 2 will cause them continuing
21
irrepara ble harm and that the public interest and bala nce
22
of hards hips favor i njunctive relief.
23
RPA Comp onent 1 has ended for the 2009-2010 water
24
25 year, mo oting any re quest for injunctive relief a gainst
26 its impo sition. Com ponent 3 is not set to begin until
27 Septembe r, and Plain tiffs do not presently seek

28
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1 injuncti ve relief ag ainst its operation. Barring

2 unforese en circumsta nces, the parties’ cross-motions for
3
summary judgment wil l be heard and decided before
4
Septembe r. Componen ts 1 and 3 are not addressed in this
5
decision . 1
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Plaintif fs’ in junction request has be en modified over
7
8 time. O riginally, P laintiffs sought an inj unctio n
9 against implementati on of RPA Component 2 and enf orcement
10 of the i ncidental ta ke limits in the BiOp. See Doc. 435

11 at 2-4.
12
• In place of Componen t 2, Plaintiffs sought to req uire
13
Federal Defend ants a nd DWR to use a Potential
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Entrainm ent Index (“ PEI”) to estimate cumulative
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entrainm ent loss of delta smelt. If the PEI esti mate
16
17 of cumul ative loss i s less than or equal to 7%, n o
18 pumping restrictions should be imposed; if the PE I

19 estimate of cumulati ve entrainment loss exceeds 7 %,
20
FWS shal l be respons ible for setting OMR flows un der
21
the rang e specified in Component 2 of the BiOp. Doc.
22
435 at 3 .
23
1
Du ri ng t he e vi de nt ia ry he ar in g, P l ain ti ff s ar gu ed t ha t
24 tes ti mo ny r eg ar di ng C omp on en t 3 sh o uld b e he ar d be ca us e it is
rel ev an t to t he ir l ik eli ho od o f su c ces s on t he m er it s. But , ev en i f
25 Pla in ti ff s we re l ik el y t o su cc ee d o n t he ir c la im t ha t Co mpo ne nt 3 i s
arb it ra ry a nd c ap ri ci ous , su ch a f i ndi ng w ou ld h av e no b ear in g on
26 the p ro pr ie ty o f is su ing a n in ju nc t ion a ga in st t he o pe ra tio n of
Com po ne nt 2 . T he f ac tua l an d le ga l ar gu me nt s co nc er ni ng Co mp on en t 3
27 are v ol um in ou s. In l igh t of P la in t iff s’ r eq ue st t ha t th is mo ti on b e
res ol ve d wi th a ll d el ibe ra te h as te , Co mp on en t 3 is n ot a ddr es se d at
28 thi s ti me .
7
1 • Plaintif fs requested that the Inciden tal Take

2 Statemen t (“IT S”) be recalculated bas ed on a higher
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Cumulati ve Salvage I ndex (“CSI”) of 11.36 for adu lts.
4
Doc. 435 at 4.
5
• In the a lternative, if the above remedies are not
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imposed, DWR request ed th at t hat the Court impose the
7
8 interim remedial ope rational conditio ns imposed
9 followin g summary ju dgment in NRDC v. Kempthorne,
10 1:05-cv- 1207. Doc. 452 at 2.

11 Although Plaintiffs never filed a written
12
modifica tion of thei r request for relief, at the
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evidenti ary hearing Plaintiffs withdrew their req uest to
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enjoin e nforcement o f the ITS and their request t o
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implemen t the PEI in place of RPA Component 2 of the R PA.
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17 4/2/10 T r. 90:4-12; 4/7/10 Tr. 243:23 -244:8 . Instead,
18 Plaintif fs now propo se that Component 2 be replac ed by a

19 flat -5, 600 cfs ceil ing on negative O MR flows during the
20
remainde r of t he implementation period for Component 2 .
21
Id.; see 4/2/10 Tr. 208.
22
23 IV. STANDARD OF DE CISION
24 Injuncti ve relief, w hether temporary or permanent , is
25 an “extr aordinary re medy, never awarded as of rig ht.”
26
Winter v . Natural Re sources Defense Council, 129 S. Ct .
27
365, 376 (2008); Weinberg er v. Romero-Barce lo, 456 U.S.
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1 305, 312 (1982). Fo ur factors must be establishe d by a

2 preponde rance of the evidence to qualify for temp orary
3
injuncti ve relief:
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1. Likeliho od of succes s on the merits;
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2. Likeliho od the movin g party will suffer
6
irrepara ble harm abs ent injunctive re lief;
7
8 3. The bala nce of equit ies tips in the moving
9 parties’ favor; and
10 4. An injun ction is in the public interest.

11 Winter, 129 S. Ct. a t 374; Am. Trucking Ass ’n v. City of
12
Los Ange les, 5 59 F.3d 1046, 1052 (9th Cir. 2009).
13
14 V. FINDINGS OF FA CT
15 A. The Agen cy Action.
16 1. The agen cy action is the coordinated operation
17 of the C VP and SWP, pursuant to an Agreement for the

18 Coordina ted Operatio n of the two projects (“COA”) .
19
2. Accordin g to the Riv ers and Harbors A ct of 1937,
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the dams and reservo irs of the CVP “shall be used , first,
21
for rive r regulation , improvement of navigation a nd flood
22
23 control; second, for irrigation and domestic uses ; and,
24 third, f or power.” 50 St at. 844, 850.
25 3. The CVP was reauthor ized in 1 992 through th e

26 Central Valley Impro vement Act (“CVPIA”), which m odified
27
the 1937 Act and add ed mitigation, protection, an d
28
9
1 restorat ion of fish and wildlife as co-equal project

2 purposes . Pub. L. 1 02-575 § 3402, 106 Stat. 4600 , 4706
3
(1992). One of the stated purposes of the CVPIA is to
4
address impacts of t he CVP on fish and wildlife. §
5
3406(a). The CVPIA made environmental protection and
6
water de liveries co- purpo ses.
7
8 4. This cas e presents a critical conflict between
9 these du al legislati ve purposes, providing water service
10 for agri cultural, do mestic, and industrial use, v ersus

11 enhancin g environmen tal protection for fish speci es whose
12
habitat is maintaine d in rivers, estuaries, canal s, and
13
other wa terways that comprise the Sacramento-San Joaquin
14
Delta.
15
5. It is of manifest si gnificance to the public
16
17 interest that DWR, a co-opera tor and the State
18 contract ual partner of Reclamation, disagrees wit h at

19 least so me portions of the RPA and seeks injuncti ve
20
relief a gainst the calendar-based cei ling in RPA
21
Componen t 2.
22
23 B. Facts Re levant to NE PA Claim.
24 6. It is un disputed tha t neither FWS nor
25 Reclamat ion engaged in any NEPA analysis in conne ction
26
with pre paration or implementation of the 2008 Sm elt
27
BiOp.
28
10
1 7. It is al so undispute d that on Novembe r 13, 2009,

2 the Cour t entered an Order granting San Luis Plai ntiffs’
3
motion f or summary j udgment on their claim that F ederal
4
Defendan ts violated NEPA when they implemented th e 2008
5
Smelt Bi Op without c onducting the required NEPA a nalys is.
6
Doc. 399 .
7
8 8. FWS did not engage i n a systematic consideration
9 of impac ts to the hu man environment and/or consid erati on
10 of alter natives that took into account those impa cts,

11 ordinari ly performed as part of a NEPA revi ew.
12
13 C. Facts Re levant to ES A Challenges.
14 (1) Status o f the Specie s.
15 9. The delt a smelt was listed as a threatened
16 species under the ES A on March 5, 1993. 58 Fed. Reg.
17 12,584 ( March 5, 199 3). Critical habitat was des ignated

18 for the delta smelt on De cemb er 19, 1994. 59 Fed . Reg.
19
65,256 ( Dec. 19, 199 4).
20
10. The thre atened delta smelt, one of the most
21
abundant species in the Bay-Delta eco system as re cently
22
23 as thirt y years ago, is in imminent danger of ext inction.
24 Doc. 94, Findings of Fact Re Plaintiffs’ Motion f or
25 Prelimin ary Injuncti on, ## 1-2. The expert s agre e that

26 there is no current population count for de lta smelt.
27
4/2/10 T r. 174 (Feyr er); 4/5/10 Tr. 67 (Newman); 4/5/10
28
11
1 Tr. 231 (Hilborn); 4 /6/10 Tr. 95 (Deriso). Howev er, the

2 species’ relative ab undance from year-to-year is
3
monitore d using the Fall Midwater Trawl index (“F MWT”)
4
prepared by the California Department of Fi sh and Game
5
(“CDFG”) , as well as other abundance indices. 4/2/10 Tr.
6
174-75. The F MWT shows a continuously and precip itous ly
7
8 declinin g trend in d elta smelt abundance in recen t years,
9 register ing a series of record-breaking low s. 4/ 2/10 Tr.
10 176-78. That trend has continued in the last two years,

11 with the FMWT declin ing from 23 in 2008 to 17 in 2009,
12
the lowe st val ue ever recorded. Id. The p opulat ion
13
growth r ate for delt a smelt has been “quite negat ive” for
14
the last ten years. 4/5/10 Tr. 232. The stock-
15
recruitm ent relation ship for delta smelt, which s hows the
16
17 relation ship between adults (i.e., the “stock” of the
18 populati on) to juven iles recruited into the popul ation,

19 is “tren ding t oward the origin,” the opposi te directio n
20
from rec overy. 4/2/ 10 Tr. 187-88. “There’ s no q uesti on
21
that [th e present ab undance levels of delta smelt ] are
22
very low .” 4/5/10 T r. 232 (Hilborn).
23
11. FWS rece ntly determi ned that delta smelt
24
25 warrante d uplisting from threatened to endangered , but
26 that the action was currently precluded by higher
27 priority listing act ions. 4/7/10 Tr. 163; 75 Fed . Reg.

28
12
1 17,667 ( Apr. 7, 2010 ). The direct mo rtality of delta

2 smelt by entrainment at the CVP and SWP pumps, as well as
3
the dest ruction and adverse modification of its h abitat
4
caused b y water expo rts, were important factors i n this
5
determin ation. 75 F ed. Reg. at 17,671 (“The oper ation of
6
State an d Fede ral export facilities constitute a
7
8 signific ant and ongo ing threat to delta smelt thr ough
9 direct m ortality by entrainment”). As a result o f the
10 “immedia te and high magnitude threats” confrontin g the

11 species, the delta s melt was assigned a listing priority
12
number o f 2. 2 Id. at 17,675.
13
12. Evidence submitted d uring trial indicates that,
14
as of th e dates of t he March Spring Kodiak Trawl (March
15
8-11, 20 10) an d 20 m m surveys (March 15-18, 2010) , del ta
16
17 smelt we re collected in the northern and western porti ons
18 of the D elta, not in the danger zones of the central or

19 south De lta. SWC Exs. 91 8 & 919. Through March 28,
20
2010, th e SWP had an expanded salvage of 16 delta smelt,
21
and the CVP had an e xpanded salvage of 28 delta s melt.
22
SWC Ex. 915.
23
13. Plaintif fs are corre ct that during the three
24
25 years th at restricti ons on spring exports have be en in
26 place, t he FMWT inde x has continued t o trend downward.
27 2
“W ar ra nt ed b ut p re cl ude d” s pe ci es are a ss ig ne d li st in g
pri or it y nu mb er s fr om 1 to 1 2, w it h 1 be in g th e hi gh es t pri or it y.
28 Id. a t 17 ,6 74 .
13
1 4/7/10 T r. 94:8-14. However, Mr. Gri maldo testif ied t hat

2 improved conditions may not immediate ly translate into
3
improved survival an d population growth. 4/7/10 Tr.
4
120:9-25 .
5
6 (2) Baseline Issues.
7 a. Comparis on of CalSim and Dayflow Data.
8 14. CalSim I I (“CalSim”) is a com puter model
9 develope d jointly by DWR and Reclamation. The mo del
10
simulate s SWP and CV P ope rati ons and is the standard
11
planning tool for ev aluating project operat ions. 4/2/ 10
12
Tr. 101: 24-102 :6. The first version of the CalSi m model
13
was avai lable in May 2002. It is continuously up dated.
14
15 4/2/10 T r. 102:7-13.
16 15. CalSim s imulates SWP and CVP reservoir
17 operatio ns, project exports and water deliveries, flow

18 through the Delta, a nd salinity requirements in t he
19
Delta, i ncluding the location of X2. 4/2/1 0 Tr. 102:1 4-
20
20; BiOp at 207.
21
16. X2 is th e location in the Delta where the
22
23 salinity is two part s per thousand. It is measur ed as
24 the dist ance u pstream from the Golden Gate. 4/2/10 Tr .
25 102:21-2 4.
26 17. The CalS im model ass umes 82 years of hydrology,
27
4/2/10 T r. 101:23-102:3, 103:14-18, 1 61:2-6, prov ides the
28
14
1 model wi th data rega rding inflow to r eservo irs and oth er

2 informat ion affectin g the water supply, 4/2 /10 Tr .
3
103:19-2 3. The mode l also assumes a level of
4
developm ent, which reflects water dem and resultin g from a
5
particul ar urban pop ulation level, agricultural
6
producti on, and wild life refuge needs, 4/2/10 Tr. 104:1-
7
8 7, as we ll as the existence and effect of environmenta l
9 regulati ons and envi ronmental program s, 4/2/10 Tr.
10 103:14-1 8. The assu mptions used in the CalSim st udies

11 were dev eloped by represe ntatives from FWS, the N ation al
12
Oceanic and Atmosphe ric Administration (“NOAA”),
13
Reclamat ion, C DFG, and DW R. 4/2/10 Tr. 105 :8-12.
14
18. The CalS im model ass ists scientists in making
15
planning decisions b y allowing comparisons betwee n
16
17 studies based on dif fering as sumptions. See 4/2/ 10 Tr .
18 102:25-1 03:6. Accor ding to Aaron Miller, P.E., a n expert

19 qualifie d to offer o pinions on the subject of the
20
formulat ion and appl ication of CalSim, CalSim is not
21
designed , or intende d to be used, to compare CalS im st udy
22
outputs to act ual “h istoric” data or to out puts from
23
differen t models, in cluding the Dayflow model. 4 /2/10
24
25 Tr. 95:7 -14; DWR Ex. 511 at ¶8.
26 19. CalSim s tudy 7.0 was developed as the baseline
27 study fo r the 2008 OCAP Biolo gical Assessment (“2008 OCAP

28
15
1 BA” or “ BA”). Study 7.0 represents existing condition s,

2 and assu mes a 2005 l evel of development and a ful l
3
environm ental water account (“EWA”). 4/2/10 Tr. 104:8-
4
20; 123: 21-24, 146:3-6; BiOp at 207. Study 7.1 is a
5
near-fut ure co nditions study. It assumes a 2005 level of
6
developm ent and a li mited EWA. 4/2/10 Tr. 104:8- 23;
7
8 123:21-2 5; BiOp at 2 07-08. Study 8.0 is a future
9 conditio ns stu dy. I t ass umes a 2030 level of developm ent
10 and a li mited EWA. 4/2/10 Tr. 104:8-25; 123:21-124:2;

11 BiOp at 208.
12
20. CalSim s tudy 6.0 was designed to look at the
13
differen ces between the prior CalSim model used i n the
14
2004 OCA P BA a nd the new model used in the 2008 OCAP BA.
15
4/2/10 T r. 104:8-15, 157: 11-18.
16
17 21. Study 6.1 is similar to 6.0 , but did not
18 include the EW A and used an older version of the X2

19 estimate . 4/2/10 Tr . 104:8-17. Study 6.1 was prepare d
20
at the r equest of Re clamation biologists to asses s
21
changes in water pro ject operations during the pe lagic
22
organism decline (“P OD”) era. 4/2/10 Tr. 149:18- 24,
23
150:16-1 51:17, 158:8-13. Reclamation biolo gists compa red
24
25 study 6. 1 against th e 7.0 and 8.0 studies on pages 13- 10
26 though 1 3-17 o f the 2008 OCAP BA. 4/ 2/10 T r. 149:12-24;
27 AR 01105 7-0110 64.

28
16
1 22. Mr. Mi ller testified th at study 6.1 shoul d not

2 have bee n used for c omparison because it was not
3
comparab le to the ot her studies. 4/2/10 Tr. 156: 25-
4
157:8. Study 6.1 us ed the Kimmerer Monismith equ ation to
5
estimate X2 and it, as well as study 6.0, did not
6
complete ly reflect the ne w enhancements in the Ca lSim
7
8 model de veloped afte r the 2004 OCAP BA. 4/ 2/10 Tr.
9 157:10-1 8; SLDMWA Ex . 12 at 205-206.
10 23. The CalS im 9.0 serie s of studies represents

11 climate change scena rios. Study 9.0 represents a future
12
conditio n to serve as a basis of comparison of the
13
effects of climate c hange to sea level rise, with out the
14
inclusio n of (b)(2) or EWA. Study 9.1 represents a one-
15
foot sea level rise, without the inclusion of (b) (2) and
16
17 EWA. St udies 9.2 th rough 9.5 look at predicted c hanges
18 in preci pitation and temperature for the period 2 010 to

19 2030, re lative to conditions for the period 1971 to 20 00.
20
The 9.0 climate chan ge scenarios were not intende d to be
21
directly compared to studies 7.0–8.0. 4/2/ 10 Tr. 105: 1-
22
5; BiOp at 208. Suc h a comparison is not v alid becaus e
23
the stud ies make dif ferent assumptions regarding
24
25 environm ental progra ms. 4/2/10 Tr. 123:10-16.
26 24. In the B iOp, CalSim studies were compared to
27 simulati ons of histo ric conditions generated usin g the

28
17
1 Dayflow model. 4/2/10 Tr. 107:4-7, 142:6-9. Day flow is

2 a model that estimat es historic outflow based on historic
3
precipit ation, inflo w, and exports, and estimates of
4
delta is land diversi ons. Dayflow also provides a n
5
estimate for the loc ation of X2. 4/2/10 Tr. 107: 8-14.
6
25. In the B iOp, FWS pur ports to quantify adult
7
8 entrainm ent by compa ring OMR flows from CalSim st udies to
9 historic OMR flows d uring 1967-2007. BiOp at 21 2-13.
10 The BiOp depicts the se results in Tables E-5b and E-5c in

11 the BiOp , whic h are labeled “differen ce from hist oric
12
median v alue to CalS im II model median value” and
13
“differe nce from his toric median salvage to predi cted
14
salvage based on ... CalSim II,” respectively. Id. at
15
214. Ta bles E-5b and E-5c purport to quant ify, as
16
17 effects of the actio n, changes in OMR flows and
18 entrainm ent using th e Day flow-generat ed his toric data as

19 the base line and com paring that to CalSim study r esults.
20
Based on these compa risons of CalSim data and Day flow-
21
generate d hist oric data, the BiOp concludes, “adu lt
22
entrainm ent is likel y to be higher than it has be en in
23
the past under most operating scenarios, resultin g in
24
25 lower po tential prod uction of early life history stages
26 in the s pring in som e years.” BiOp at 213.
27 26. In anoth er analysis in the Bi Op, FWS purpor ts to

28
18
1 quantify the effects of the action on delta smelt habitat

2 by compa ring CalSim model projections of the loca tion of
3
X2 under the propose d action to the median locati on of X2
4
over the historical period 1967-2007, as si mulate d by
5
Dayflow. BiOp at 23 5-36. Ba sed on this comparis on, t he
6
BiOp con cludes “[t]h e median X2 [loca tions] acros s the
7
8 CalSim I I modeled sc enarios were 10-15 perc ent fu rther
9 upstream than actual historic X2 (Figure E-19).” Id. at
10 235. In reliance on these percent differen ces be tween

11 CalSim-c reated data and historical data, the BiOp
12
conclude s “proposed action operations are likely to
13
negative ly affect th e abundance of delta smelt.” Id. at
14
236.
15
27. In the B iOp, F WS per forme d similar comparisons
16
17 of CalSi m data to Dayflow -sim ulated historic base line
18 data to quanti fy the effects of the action on lar val a nd

19 juvenile delta smelt . See, e.g., BiOp at 2 19 (examini ng
20
effect o f action on larval and juvenile entrainme nt and
21
stating “[t]he analy sis is based on compari son of
22
historic al (1967-2007) OM R and X2 to the pr oposed
23
action’s predictions of these variables provided in ...
24
25 [CalSim] studies 7.0 , 7.1, 8.0, and 9.0-9.5 ”).
26 28. Mr. Mill er explained that outputs from a CalSim
27 study sh ould not be compared to outputs fro m the Dayfl ow

28
19
1 model be cause the as sumptions used in the two mod els are
2 signific antly differ ent. 4/2/10 Tr. 107:18-23, 1 36:10 -
3
18.
4
a. The CalS im model ass umes a constant level of
5
developm ent. In con trast, the Dayflow model inco rporates
6
a contin uous c hange in the level of development because
7
8 the Dayf low model is using historical information as
9 input. When compari ng models to determine the ef fect of
10 project operations, the best scientific practice is to

11 keep the assumed level of development constant. 4/2/1 0
12
Tr. 107: 15-108 :15.
13
b. A CalSim study also assumes a constant
14
regulato ry environme nt, whereas Dayflow uses a re gulatory
15
environm ent that has changed over time. This dif ference
16
17 renders any co mparison between CalSim and Dayflow outp uts
18 unreliable. 4 /2/10 Tr. 1 08:16-109:23.

19 c. CalSim a lso operates on a monthly time step,
20
whereas Dayflow oper ates on a daily time step. T he two
21
models a lso operate to different guidelines. The Dayflow
22
model in corporates a conservative operation to av oid
23
violating a re gulation. In contrast, the CalSim model
24
25 operates strictly to that regulation. 4/2/10 Tr. 107: 23-
26 108:3, 1 09:24- 110:9. Operating conservatively results in
27 higher m odeled outfl ow. 4/2/10 Tr. 110:10-14.

28
20
1 d. The diff erences in t he model assumptions an d

2 in the w ay the model s operate, as described above , cannot
3
be quant ified to cal ibrate the models. CalSim do es not
4
model or simulate hi storical conditions, so it ca nnot be
5
calibrat ed to histor y. 4/2/10 Tr. 121:18-122:6, 161:2 -6.
6
Calibrat ion would be “ver y di fficult, nearl y impossible,
7
8 to do wi thout [] developi ng a model designe d to simulate
9 historic al condition s.” 4/2/10 Tr. 110:15-111:1. The
10 CalSim m odel cannot currently predict X2 for hist oric

11 years be cause it wou ld require a new model. 4/2/ 10 Tr.
12
122:7-16 .
13
e. The Dayf low historic time window that FWS
14
reported using in th e BiOp was 1967 to 2007. Cal Sim
15
studies model water years 1992 through 2003. The BiOp’s
16
17 comparis on of CalSim-modeled data to Dayflow-modeled data
18 resulted in comparin g differe nt sets of wat er yea rs. Mr.

19 Miller t estified tha t the best scientific practic e
20
regardin g years of c omparison would have been to use
21
consiste nt tim e windows. 4/2/10 Tr. 116:18-117:2 1;
22
142:13-1 5.
23
f. The arti ficial neura l network (“ANN”) and
24
25 the Kimm erer M onismi th eq uation (“KM equati on”) are tw o
26 methods of estimatin g X2. 4/2/10 Tr. 111:2-16. The
27 CalSim s tudies used ANN to estimate the position of X2,

28
21
1 because ANN can be a dapted to address sea level r ise.

2 4/2/10 T r. 111:19-25. Th e Dayflow model us es the KM
3
equation to estimate X2. 4/2/10 Tr. 111:2-8; DWR Ex. 510
4
at Fig. 2; DWR Ex. 5 11 at ¶15. The KM equation w as
5
develope d using hist orical data, making the KM equatio n
6
invalid for a sea le vel rise study. 4/2/10 Tr. 1 11:19-
7
8 25.
9 g. At locat ions less than 75 kilometers (“km”)
10 from the Golden Gate , the KM equation results in an X2

11 estimate greater tha n (or farther upstream than) the ANN
12
estimate . In contra st, at locations greater than 75 km
13
from the Golden Gate , the KM equation provides an
14
estimate less than the ANN estimate. 4/2/10 Tr. 112:1-
15
113:18, DWR Ex. 510 at Fig. 2.
16
17 29. Mr. Mill er calculate d the magnitude of error
18 introduc ed into the BiOp by FWS’s application of both the

19 KM and t he ANN metho ds of estimating X2. He repl icated
20
the 87 k m value as t he median estimat e of X2 from CalSim
21
study 7. 0 using the ANN method, and, consistent w ith the
22
BiOp, ca lculated the difference between the repor ted
23
historic median of X 2 [79 km] and the study 7.0 m edian
24
25 [87 km] to be 10% [( 87 km - 79 km)/79]. He then
26 calculat ed the media n X2 for the CalSim 7.0 study using
27 the KM e quation (ins tead of using ANN) to be 84 k m

28
22
1 (instead of 87 km). Finally, he identified the p ercent

2 differen ce between t he reported historic median e stimate
3
of X2 us ing the KM e quation [79 km] and the CalSi m stu dy
4
7.0 medi an estimate of X2 using the KM equation [ 84 km]
5
to be 6% [(84 km–79 km)/7 9 km]. 4/2/10 Tr. 114:6 -25; DWR
6
Ex. 511 at ¶¶ 14-16; BiOp at 235-36.
7
8 30. FWS did not calculat e X2 using the KM equation
9 for the CalSim studies, as did Mr. Miller. Inste ad, i t
10 undertoo k a direct c omparison. DWR Ex. 511 at ¶1 5. The

11 BiOp rep orted a 10% difference between the report ed
12
historic median X2 a nd the CalSim study 7.0 X2 me dian.
13
Calculat ing the perc ent difference between the hi storical
14
median X 2 and study 7.0 median X2 using the KM eq uation
15
resulted in only a 6 % difference. From this, Mr. Mill er
16
17 conclude d that 40% o f the difference between X2 a s
18 estimate d by study 7 .0 and the historical X2 base line

19 reported in the BiOp is error attributed en tirely to t he
20
use of t he KM equati on to calculate the historica l
21
baseline X2 and the ANN equation to calculate the CalSim
22
study 7. 0 baseline. 4/2/10 Tr. 114:6-25; D WR Ex 511 ¶
23
15.
24
25 31. Mr. Mill er testified that the differences in the
26 KM equat ion and the ANN method of estimating X2 h as an
27 effect o n the BiOp’s analysis of habi tat ar ea, which i n

28
23
1 turn eff ects the BiO p’s prediction of smelt abund ance (as
2 measured by the Summer Townet Survey Index). 4/2/10 T r.
3
113:19-1 14:5; BiOp a t 235–236 , 266-269.
4
32. Mr. Mill er explained that correcting for the
5
differen ces between the use of the KM and ANN met hods to
6
estimate X2 does not correct for all the biases i nherent
7
8 in compa ring CalSim data to “historic” data. It is
9 unknown which portion of the remaining 60% of difference
10 is attri butable to t he proposed action, and which portion

11 is due t o the other identified biases. 4/2/10 Tr. 115:1-
12
8; DWR E x. 511 at ¶16.
13
33. Mr. Mill er testified that when using CalSim
14
study 7. 0 -- d esigned as a current conditio ns bas eline --
15
instead of the “hist orical” baseline in the BiOp, and
16
17 comparin g study 7.0 to the near-futur e 7.1 study, X2
18 moved up stream 0.7 k m. T he percentage change in X2 from

19 current to near-current conditions was 0.8% . Fur ther,
20
when com paring study 7.0 to study 8.0 (a 2030 lev el of
21
developm ent scenario ), X2 moved upstream only 1.1 km,
22
with a r esultant percenta ge change in X2 of 1.2% from
23
current to future conditi ons. 4/2/10 Tr. 1 28:18- 129:11;
24
25 DWR Ex. 511 at ¶20; BiOp at 235, 265. The 0.7 km chan ge
26 and the 1.1 km chang e, respectively, were vastly
27 differen t from the a pproximately 8.7 km and 9.1 k m

28
24
1 changes shown in the BiOp (Figure E-19) usi ng his toric al

2 Dayflow as the basel ine. BiOp at 265; DWR Ex. 51 1 at ¶7.
3
34. Using th e equation i dentified in Figure E-20 in
4
the BiOp , Mr. Miller calculated the reduction in suitable
5
habitat consistent w ith the change in the positio n of X2.
6
A compar ison of CalS im study 7.0 with study 7.1 y ielded a
7
8 reductio n in habitat area of 128 hect ares, and a
9 comparis on of study 7.0 with study 8.0 yielded a
10 reductio n in habitat area of 289 hectares. 4/2/10 Tr.

11 129:12-1 30:5; DWR Ex . 511 at ¶20; BiOp at 266.
12
35. Plaintif fs assert th at, prior to issuance of the
13
BiOp, FW S was put on noti ce t hat comparing histor ical
14
data to CalSim simul ated data was an inappropriate and
15
invalid methodology. 4/2 /10 Tr. 133:15-134 :11, 1 37:16 -
16
17 138:16, 138:21-139:14; SLDMWA Ex. 351 at 7; SLDMWA Ex.
18 261 at 5 ; SWC Ex. 93 3 at 3.

19 a. The 2008 OCAP BA did raise so me cautionary
20
notes:
21
CalSim I I is intende d to be used in a
22 comparat ive mode. Th e results from a “proposed
operatio n” scenario are compared to the results
23 of a “ba se” scenario , to determine the
incremen tal effects. The model should be used
24 with cau tion t o pres cribe sea sonal or to gu ide
real-tim e operations, predict flows or wate r
25 deliveri es for any r eal-time operations. T he
results from a singl e simulation may not
26 necessar ily represen t the exact operations for a
specific month or ye ar, but should reflect long-
27 term tre nds.
28 DWR Ex. 518.

25
1 b. DWR Depu ty Director Jerry Johns, on October

2 24, 2008 , submitted comments to FWS on the draft effects
3
analysis , generally cautioning against the compar ison of
4
modeled data with ac tual data:
5
USFWS is using histo ric data for comparison to
6 CalSim I I simulation s. Great caution should be
taken wh en comparing actual data to modeled
7 data. Ca lSim II mode ling should be used in a
8 comparat ive mode. In other words, it should be
used to compare one set of model runs to
9 another. For example , it would be app ropriate to
compare CalSim II mo deling of one demand
10 alternat ive to anoth er to analyze the
incremen tal effects.
11
12 AR 8671; see also AR 8668 (further explaini ng
13 unreliab ility proble ms comparing historic and mod eled
14 data).
15 c. The Stat e Water Cont ractors also cited a
16
letter t hat th ey sent to FWS before the BiO p was
17
complete d. However, that letter only critiqued t he
18
comparis on of simula ted data to historical salvag e data,
19
and did not dispute with the comparison of CalSim -
20
21 simulate d to Dayflow-simulated histor ic dat a. 4/2/10 Tr.
22 133-34.
23 d. Mr. Mill er acknowled ged that, despite his

24 heavy in volvement in the modeling analysis underl ying the
25
BiOp, he did not pre sent his current critic ism of the use
26
of the d ata to FWS d uring preparation of th e BiOp .
27
4/2/10 T r. 115-16.
28
26
1 36. FWS was not on notic e of Mr. Miller’s critiques

2 regardin g comparing simulated Calsim runs to simu lated
3
Dayflow runs, and was not put on notice by him that they
4
were imp roperly usin g the spe cialized models. FW S did
5
not have an op portunity to correct its modeling or
6
address Plaintiffs’ concerns.
7
8 37. The BiO p explains w hy FWS looked beyond CalSim.
9 When Cal Sim was used to identify current Project
10 operatio ns, and thes e results were then compared to th e

11 results of a CalSim modeling run purportedly simu lating
12
past ope rations, the results “were nearly identic al”
13
despite significant operational changes in curren t
14
operatio ns as compar ed to past. BiOp at 204-05. The
15
BiOp exp lains that “ [t]he inaccuracie s in CalSim [led
16
17 FWS] to use actual d ata to develop an empirical
18 baseline .” Id . at 206. FWS “also developed historical

19 time ser ies data for hydrologic variables used in this
20
effects analysis bas ed on the Dayflow database .. . and
21
OMR data obtained from US GS.” Id.
22
38. Mr. Mil ler asserts that best scientific
23
practice would precl ude FWS from comparing CalSim output
24
25 to histo ric da ta generated by Dayflow. How ever, Mr.
26 Miller a cknowledged that in the 2008 OCAP BA, DWR and
27 Reclamat ion co mpared CalSim output to histo ric da ta,

28
27
1 albeit f or a differe nt purpose, namel y to show that th e

2 timing a nd magnitude of reservoir and export oper ations
3
were sim ilar to hist oric operations. 4/2/1 0 Tr. 119-20.
4
Mr. Mill er acknowled ged that other modelers invol ved in
5
preparin g the BA exp ressed concerns about using o nly
6
CalSim d ata, and tha t the BA itself questioned th e use of
7
8 that dat a alone, as CalSi m simulations did not pr ovide
9 “an espe cially satis factory representation of pre -POD
10 water pr oject operat ions.” Id. at 150-51. The BA,

11 prepared by DWR and Reclamation, states: “While we ha ve
12
not adop ted an alter native statistical approach [ to the
13
use of C alSim model runs] in this biological asse ssment,
14
we belie ve it would be a useful way to further as sess
15
changes in water pro ject operations during the PO D era
16
17 and we r ecommend tha t [FW S] consider such a n anal ysis as
18 further refinement t o this BA.” Id. Other reputed

19 scientis ts in the fi eld agree with FWS and the BA that
20
the CalS im-gen erated modeling studies did not “ge nerat e[]
21
baseline s with a hig h degree of reliability.” Id. at
22
160. Ne ither Mr. Mi ller nor DWR offered any alte rnative
23
to Dayfl ow to FWS to address that serious shortco ming
24
25 during p reparation o f the BiOp. Id. at 160-61.
26 39. Mr. Mil ler acknowle dged that , even if the
27 CalSim c omparison ha d been conducted in the manne r he

28
28
1 recommen ds, it would have confirmed FWS’s conclus ions

2 that Pro ject operati ons as proposed in the BA mov e X2
3
further upstream in the fall, reducing the amount of
4
habitat for de lta smelt and modifying the quality of
5
critical habitat by shifting the low salinity zon e away
6
from hig her-qu ality habitat and further into the centr al
7
8 Delta. Id. at 130. Mr. Miller did not suggest t hat this
9 revision would resul t in a de minimis shift of X2.
10 40. Mr. Mill er presents substantive criticisms of

11 the BiOp ’s CalSim ru ns. These specific con cerns were not
12
raised b efore the ag ency prior to the BiOp’ s issuance.
13
Moreover , FWS expressed legitimate concerns, shar ed with
14
other sc ientists, about the exclusive reliance on CalSim
15
runs. M r. Miller co ncedes that even if his recommende d
16
17 approach had been ta ken, the same fundamental res ult
18 would ha ve obtained: project operations shift th e

19 position of X2 upstr eam. 3
20
41. This hi ghly technical dispute was not raised
21
before t he agency, a nd there were legitimate conc erns
22
about co mparing Cals im modeling runs to other Cal sim
23
runs. T his choice o f competing methodologies is not
24
25 sufficie ntly clear e rror to justify the court’s
26 interven tion.
27 3
Th e ma gn it ud e of t he sh if t, n ot i t s e xi st en ce , an d wh at sh ou ld
be do ne a bo ut i t ma y be re le va nt t o th e ne ed f or a nd j us tif ic at io n
28 of RP A Co mp on en t 3.
29
1 b. Treatment of “Other Stressors.”

2 42. Plaintif fs raise a generic concern about ho w the
3 BiOp tre ated the man y other factors that are unde niably
4
contribu ting to the decline of delta smelt includ ing: (a)
5
presence of aquatic macrophytes (submerged aquati c
6
vegetati on such as Egeria densa that may ov erwhel m del ta
7
smelt ha bitat); (b) predation; (c) introduction a nd
8
9 propagat ion of invas ive species, incl uding inland
10 silversi des and the overbite clam that compete wi th the
11 delta sm elt; (d) pre sence of contamin ants, such as

12 pesticid es and waste water , in the Delta; and (e) presence
13
of large blooms of b lue-green algae toxic to the copep ods
14
eaten by delta smelt . BiOp at 182-86; 4/7/10 Tr. 148: 17-
15
19, 149: 20-25.
16
43. Plaintif fs take part icular issue with a
17
18 statemen t in the ver y first paragraph of a sectio n of the
19 BiOp ent itled “Effec ts of the Proposed Action.”

20 The Stat us of the Sp ecies/Environmental Baseline
section of this docu ment described the multitude
21 of facto rs that affe ct delta smelt population
dynamics including p redation, contaminants,
22 introduc ed species, entrainment, habitat
suitabil ity, food su pply, aquatic macrophytes,
23 and micr ocystis. The extent to which these
factors adversely af fect delta smelt is related
24 to hydro dynamic cond itions in the Delta, wh ich
in turn are controll ed to a large extent by CVP
25 and SWP operations. Other sources of water
diversio n (NBA, CCWD , local agricultural
26 diversio ns, power pl ants) adversely affect delta
smelt la rgely throug h entrainment (see following
27 discussi on), but when taken together do not
control hydrodynamic conditions throughout the
28
30
1 Delta to any degree that approaches the

influenc e of the Ban ks and Jones export
2 faciliti es. So while many of the other stressors
that hav e been ident ified as adversely affecting
3 delta sm elt were not caused by CVP and SWP
operatio ns, the like lihood and extent to which
4 they adv ersely affec t delta smelt is highly
influenc ed by how th e CVP/SWP are operated in
5 the cont ext of annua l and seasonal hydrologic
conditio ns. While re search indicates that there
6 is no si ngle primary driver of delta smelt
populati on dynamics, hydrodynamic conditions
7 driven o r influenced by CVP/SWP operations in
turn inf luence the d ynamics of delta smelt
8 interact ion with, th ese other stressors (Bennett
and Moyl e 1996 ).
9
BiOp at 202 (emphasi s added).
10
44. The BiOp concludes t hat “the CVP and SWP have
11
12 played a n indirect r ole in the delta smelt’s decl ine by
13 creating an altered environment in the Delta that has
14 fostered the establi shment of nonindigenous speci es an d

15 that exa cerbates the se and other stressors that a re
16
adversel y impacting delta smelt.” BiOp at 203; 4 /7/10
17
Tr. 152: 5-12. Ms. G oude further testified that it is not
18
possible to quantify the level of effects of thos e other
19
factors. 4/7/10 Tr. 150:1-3.
20
21 45. When ask ed by the Co urt to identify a ny
22 informat ion in the r ecord that supports the BiOp’ s
23 conclusi on that proj ect operations exacerbate the effect

24 of other stressors, Dr. Thomas Quinn, an ex pert appointed
25
under Fe deral Rule o f Evidence 706, c oncluded that “there
26
does not appear to b e evidence in the record
27
demonstr ating that p roject operations exacerbate the
28
31
1 effect/i mpact of oth er stressors.” Doc. 633, Ord er

2 Transmit ting R esponses from 706 Experts, Ex. A, at 20.
3
Ms. Goud e testified that she disagreed with this
4
conclusi on, but coul d not identify any evidence f rom the
5
record t o support he r assertion. See 4/7/1 0 Tr. 201:22-
6
203:9.
7
8 46. Dr. Andr e Punt, anot her court-appoint ed exp ert,
9 further explained th e BiOp’s notion that indirect effe cts
10 of the P rojects may contribute to effects such as high

11 water to xicity, supp ression of phytoplankton, inc rease of
12
overbite clams, and increase in encounters with
13
unscreen ed agricultu ral diversions in the Delta a re
14
plausibl e hypotheses , but that “there are n o dire ct da ta
15
availabl e to test th em.” Doc. 633 at 21.
16
17 47. In contr ast to the BiOp’s general statements
18 assignin g the blame for at least some, unquantifi ed

19 portion of the negat ive effects cause by these “o ther
20
stressor s” to the project s, elsewhere, the BiOp
21
acknowle dges that th ere is “no single primary dri ver of
22
delta sm elt populati on dynamics,” id. at 202, but rath er
23
that the re are “mult iple factors” and that “not a ll ar e
24
25 directly influenced by operations of the CVP/SWP. ” Id .
26 at 328. “Other stres sors” are discussed in detail
27 througho ut the BiOp. See , e. g., id. at 182-88, 1 98, 2 01-

28
32
1 2. Spec ifically, FW S considered the effects of

2 “predati on, contamin ants, introduced species..., habitat
3
suitabil ity, food su pply, aquatic macrophytes, an d
4
microcys tis.” Id. at 202 , 277. The BiOp express ly
5
recogniz es that the long- term decline of the spec ies “was
6
very str ongly affect ed by ecosystem changes cause d by
7
8 non-indi genous species invasions and other factors....”
9 Id. at 189.
10 48. Although the BiOp ac knowledges that “not all” of

11 the mult iple factors negatively impacting the spe cies
12
“are dir ectly influe nced” by Project operations, the
13
general assertion in the BiOp that other stressor s are
14
the resu lt of (or at least exacerbated by) Project
15
operatio ns is not supported by the record. This error
16
17 compound s the agency ’s failure to address alterna tive
18 approach es to avoidi ng jeopardy, incl uding whether oth er

19 stressor s can be mit igated or eliminated, which NEPA
20
requires .
21
22 (3) Challeng es to Compon ent 2 (Action 3).
23 49. Componen t 2 (P rotect ion o f La rval and Juven ile
24 Delta Sm elt) require s OMR flows to remain between -1,250

25 and -5,0 00 cfs beginning when Component 1 i s comp leted ,
26
when Del ta water tem peratures reach 12° Celsius, or when
27
a spent female smelt is detected in trawls or at salvage
28
33
1 faciliti es. I d. at 282, 357-358. Componen t 2 re mains in

2 place un til June 30 or when Clifton Court Forebay water
3
temperat ure reaches 25° Celsius, whichever first occurs.
4
Id. at 2 82, 368.
5
50. The obje ctive of Com ponent 2 (which corresponds
6
to Actio n 3 in Attac hment B of the BiOp), is to “ improve
7
8 flow con ditions in t he Central and South Delta so that
9 larval a nd juvenile delta smelt can successfully rear in
10 the Cent ral Delta an d move downstream when appropriate .”

11 BiOp 282 .
12
51. The most recent smel t working group
13
recommen dation for t he week of April 12, 2010 rec ommends
14
OMR flow s no more ne gative than -5,000 cfs because the
15
“risk to larval delt a smelt was low, given that n o
16
17 salvage of larvae ha s occurred so far this year and the
18 latest s urvey data s uggest that the greatest dens ities of

19 delta sm elt are in t he Sacramento River and downs tream of
20
the conf luence, and, therefore, outside the influ ence of
21
the pump s.” 4
22
//
23
//
24
25 //
26
4
Ju di ci al n ot ic e is t ake n of t he e x ist en ce a nd c on te nt o f t he
27 Sme lt W or ki ng G ro up R eco mm en da ti on , da te d Ap ri l 12 , 20 10 , a va il ab le
at: ht tp :/ /w ww .f ws .g ov/ sa cr am en to / es/ do cu me nt s/ ds _w or ki ng_ gr ou p/ 4-
28 12- 10 %2 0n ot es .p df .
34
1 a. Use of R aw Salvage t o Jus tify the

Quantita tive Flow Re strictions.
2
52. The BiOp quantitativ ely analyzed the effects of
3
pumping at the Banks and Jones pumping plants. 4 /6/10
4
5 Tr. 19:1 -3; BiOp at 208-209.
6 53. The resu lts of that quantitative analysis, which
7 compared OMR flows w ith gross salvage numbers, ar e

8 describe d in Figures B-13 and B-14 of the B iOp. BiOp at
9
348, 350 . These fig ures were presented as part o f a
10
three an d-a-ha lf page section of the BiOp entitled
11
“Justifi cation for F low Prescriptions in Action 1.” BiOp
12
at 347-5 1. It also appears that this analysis was rel ied
13
14 upon to set the cale ndar- based flow prescription in
15 Componen t 2 (Action 3), as no other basis for the -5,000
16 cfs ceil ing is prese nted. Because this por tion o f the
17 BiOp is critic al to the p resent challenge, it is
18
reproduc ed here in i ts entirety:
19
Justification for Flow Prescriptions in Action 1
20
21 Understanding the relationship between OMR flows and delta smelt salvage allows
a determination of what flows will result in salvage. The OMR-Salvage analysis
22 herein was initiated using the relationship between December to March OMR flow
and salvage provided by P. Smith and provided as Figure B-13, below. Visual
23
review of the relationship expressed in Figure B-13 indicates what appears to be a
24 “break” in the dataset at approximately -5,000 OMR; however, the curvilinear fit
to the data suggest that the break is not real and that the slope of the curve had
25 already begun to increase by the time that OMR flows reached -5,000 cfs.
26
27
28
35
2
3
4
5
6
7
8
9
10
11
12
13
14
15 Further, a nonlinear regression was performed on the dataset, and the resulting
pseudo-R2 value was 0.44—suggesting that although the curvilinear fit is a
16
reasonable description of the data, other functional relationships also may be
17 appropriate for describing the data. Fitting a different function to the data could
also determine the location where salvage increased, i.e. identify the “break point”
18 in the relationship between salvage and OMR flows. Consequently, an analysis
19 was performed to determine if the apparent break at -5,000 cfs OMR was real. A
piecewise polynomial regression, sometimes referred to as a multiphase model,
20 was used to establish the change (break) point in the dataset.
21
A piecewise polynomial regression analysis with a linear-linear fit was performed
22 using data from 1985 to 2006. The linear-linear fit was selected because it was the
analysis that required the fewest parameters to be estimated relative to the amount
23 of variation in the salvage data. Piecewise polynomial regressions were performed
24 using Number Cruncher Statistical Systems (© Hintz, J., NCSS and PASS,
Number Cruncher Statistical Systems, Kaysville UT).
25
The piecewise polynomial regression analysis resulted in a change point of -1162,
26 i.e. at -1162 cfs OMR, the slope changed from 0 to positive (Figure B-14). These
27 results indicate that there is a relatively constant amount of salvage at all flows
more positive than -1162 cfs but that at flows more negative than -1162, salvage
28
36
1 increases. The pseudo-R2 value was 0.42, a value similar to that obtained by P.
Smith in the original analysis.
2
3 To verify that there was no natural break at any other point, the analysis was
performed using a linear-linear-linear fit (fitting two change points). The linear-
4 linear-linear fit resulted in two change points, -1,500 cfs OMR and -2,930 cfs
5 OMR. The -1,500 cfs value is again the location in the dataset at which the slope
changes from 0 to positive. The pseudo-R2 value is 0.42 indicating that this
6 relationship is not a better description of the data. Because of the additional
parameters estimated for the model, it was determined that the linear-linear-linear
7
fit was not the best function to fit the data, and it was rejected. No formal AIC
8 analysis was performed because of the obvious outcome.
9 A major assumption of this analysis is that as the population of Delta smelt

10 declined, the number of fish at risk of entrainment remained constant. If the
number of fish in the vicinity of the pumps declined, fewer fish would be entrained
11 and more negative OMR flows would result in lower salvage. This situation would
result in an overestimate, i.e. the change point would be more positive. In fact, if
12
the residuals are examined for the relationship in Figure B-13 above, the salvage for
13 the POD years 2002, 2004, 2005, and 2006 are all below the line. 2003 is above
the line although the line is not extended to the points at the top of the figure, and
14 these data points occur when the curve becomes almost vertical. The negative
15 residuals could be a result of a smaller population size available for entrainment
and salvage. This could be verified by normalizing the salvage data by the
16 estimated population size based on the FMWT data.
17
18
19
20
21
22
23
24
25
26
27
28
37
1
The original values of OMR and salvage could have been measured with error due
2 to a number of causes, consequently the values used in the original piecewise
3 polynomial analysis could be slightly different than the “true” values of salvage
and OMR flow. Consequently, a second analysis was undertaken to examine the
4 effect of adding stochastic variation to the OMR and salvage values in the
piecewise polynomial regression analysis. The correlation between OMR and
5
salvage in the original dataset was -0.61 indicating that the more negative the
6 OMR, the greater the salvage. Consequently, it was necessary to maintain the
original covariance structure of the data when adding the error terms and
7 performing the regressions. The original covariance structure of the OMR–salvage
8 data was maintained by adding a random error term to both parameters. The
random error term was added to OMR and a correlated error term was added to
9 salvage. The expected value of the correlated errors was -0.61.
10
The error terms were selected from a normal distribution with a mean of 1.0 and a
11 standard deviation of 0.25 which provided reasonable variability in the original
data. Operationally this process generated a normal distribution of OMR and
12 salvage values in which the mean of the distributions were the original data points.
13 Additional analyses were performed with standard deviations of 0.075, 0.025, and
0.125. Smaller standard deviations in the error term resulted in estimates of the
14 change point nearer to the original estimate of -1,162 cfs. This is to be expected as
the narrower the distribution of error terms, the more likely the randomly selected
15
values would be close to the mean of the distribution. The process was repeated
16 one hundred times, each time a new dataset was generated and a new piecewise
polynomial regression was performed. The software package @Risk (© Palisade
17 Decision Tools) was used to perform the Monte Carlo simulations. Latin
18 hypercube sampling was used to insure that the distributions of OMR and salvage
values were sampled from across their full distributions. The parameter of interest
19 in the simulations was the change point, the value of the OMR flow at which the
amount of salvage began to increase. Incorporating uncertainty into the analysis
20
moved the change point to -1,800 cfs OMR, indicating that at flows above -1683,
21 the baseline level of salvage occurred but with flows more negative than -1683,
salvage increased.
22
BiOp 347 -51 (emphasi s added).
23
24 54. The BiOp does not us e this information to assert
25 that ent rainment has a statistically significant effect
26 on the p opulation of delta smelt every year. 4/7/10 Tr.

27 172. Ra ther, this information appears to be used to s et
28
38
1 “break p oints” above and below which entrainment rates

2 noticeab ly change. In turn, these break points w ere
3
utilized in the form ation of the flow restriction s in the
4
RPAs.
5
55. It is un disputed tha t the use of gross salv age
6
does not account for the size (or relative size) of the
7
8 smelt po pulation, as estimated by reliable abunda nce
9 indexes. 4/6/10 Tr. 22:10-11, 23:19. The BiOp a dmits as
10 much, an d concedes t hat the analysis “assumes that as the

11 populati on of Delta smelt declined, the number of fish at
12
risk of entrainment remained constant.” See emph asize d
13
text abo ve.
14
56. Consider ing gross sa lvage numbers alone provides
15
no means of distingu ishing an event in which 10,000 fish
16
17 are salv aged out of a population of 20,000 from a n event
18 in which 10,000 fish are salvaged from a populati on of 20

19 million. 4/6/10 Tr. 24:19-22.
20
57. FWS was aware of the problems with using gross
21
salvage numbers befo re the completion of the BiOp. Th e
22
August 2 6, 2008, dra ft meeting notes of FWS’s Del ta Smelt
23
Action E valuation Te am state:
24
25 When ana lyzing the i mportance of entrainment to
the spec ies populati on structure or decline, the
26 relevant fact to con sider is the percentage of
the popu lation being removed via entrainmen t.
27 Salvage data, by its elf, may not be sufficient
to help one understa nd the percentage of the
28 populati on being rem oved via entrainment.
39
1
MWD Ex. 633 at 5.
2
58. The Inde pendent Peer Review of FWS’s draft
3
4 Effects Analys is for the BiOp also recommended to FWS
5 that it “normalize[] ” salvage to population size:
6 The pane l suggests t hat the use of predicted

salvage of adult sme lt should be normalized for
7 populati on size. To tal number salvaged is
influenc ed by a variety o f factors, particu larly
8 the numb er of fish i n the population....
Expressi ng salvage a s a normalized index may
9 help rem ove some of the confounding of the
temporal trends duri ng the baseline.
10
MWD Ex. 608 at 8.
11
59. However, notwithstan ding the recommen dation of
12
13 the Inde pendent Peer Review and its own internal staff’s
14 recognit ion that sal vage data should be normalize d, FWS
15 persiste d in using r aw salvage data and did not normal ize

16 or index the salvage data to the population size. BiOp
17
at 348, 350. As a result, salvage numbers relied upon to
18
justify the RPAs do not relate to any information
19
regardin g population-level effects. 4/6/10 Tr. 22:10- 11,
20
23:19. This was unr easonable, not based on the b est
21
22 availabl e science, a rbitrary, and capriciou s.
23 60. This con clusion was supported by explanatory

24 testimon y of the exp erts. There was agreement am ong the
25
testifyi ng scientifi c experts that the use of nor malized
26
salvage data rather than gross salvage data is th e
27
standard accepted scientific methodology among
28
40
1 professi onals in the fields of fisheries

2 biology/ management. 4/5/10 Tr. 97:4-10, 143:25-144:1;
3
4/6/10 T r. 30:15-22; Doc. 633, Ex. A, at 7, 10; 4/6/10
4
Tr. 31:1 1-16; MWD Ex . 608 at 6; Fed. Gov’t Smelt Ex. 17
5
at ¶11.
6
a. The Fede ral Defendants’ expert on biological
7
8 statisti cs, Dr. Kenn eth Newman, stated in his dec laration
9 that Fed eral Defenda nts should have “scale[ed] sa lvage by
10 some mea sure of popu lation abundance” and stated in his

11 oral tes timony that without indexing salvage to
12
population the re is “nothing to go on.” Fed. Gov’t Sm elt
13
Ex. 17 a t ¶11; 4/5/10 Tr. 143:25-144:1.
14
b. Dr. Newm an went on t o state that the
15
relevant factor to c onsider is the percentage of the
16
17 smelt po pulation bei ng removed by entrainment and that
18 salvage data b y itself is not sufficient. 4/5/10 Tr.

19 97:4-10. Dr. Newman also stated that becau se Fig ure B -13
20
relates raw salvage to combined OMR flows, it doe s not
21
enable t he agency to determine the effect on the
22
populati on of a part icular OMR flow. 4/5/10 Tr. 100:11-
23
15.
24
25 c. Dr. Punt found that “it was unreasonable
26 (given t hat appropri ate data and analysis methods were
27 availabl e to account for population size) to have only

28
41
1 relied o n the inform ation in Fig. B-13 and Fig. B -14

2 rather t han on an an alysis in which salvage is expressed
3
relative to populati on size.” Doc. 633, Ex. A, a t 7.
4
Dr. Deri so agreed. 4/6/10 Tr. 30:15-31:2.
5
d. Dr. Thom as Quinn, the oth er 706 exper t,
6
stated: “it is not c lear why such an adjustment [ of
7
8 salvage to populatio n size] was not made for the data
9 examined in this rep ort.” Doc. 633, Ex. A, at 10 . Dr.
10 Deriso a greed. 4/6/ 10 Tr. 31:11-19.

11 61. The BiOp itself reco gnized the necessity of
12
normaliz ing raw salv age data:
13
To provi de context t o determine the magnitude of
14 effect o f pre- spawning adult direct mortality
through entrainment within any given season (as
15 measured by salvage) , it is necessary to
consider two importa nt factors.....¶ The second
16 factor t o consider w hen relating salvage to
populati on-lev el sig nific ance is that the total
17 number s alvaged at t he facilities does not
necessar ily indicate a negative impact on the
18 overall delta smelt population.
19 BiOp at 338.
20 62. August 2 6, 2008 meet ing notes of the Delta Smelt

21 Action E valuation Te am also indicate that FWS recognized
22
and was aware of the need to analyze the percenta ge of
23
the popu lation remov ed by salvage, but neither th ese
24
notes no r the BiOp e xplain why this analysis was not
25
26 performe d. MWD Ex. 633 at 5; 4/5/10 Tr. 96-97:14 -10.
27 63. The BiOp , in fact, u sed n orma lized salvage data
28 for othe r parts of i ts analysis, including the In cidental

42
1 Take Sta tement, evid encing its ability to do so. BiOp at

2 386; 4/7 /10 Tr. 196: 18-20; see also 4/7/10 Tr. 19 9:14- 21
3
(Cay Gou de testifyin g that FWS understood the imp ortance
4
of using normalized salvage data and chose to use it i n
5
parts of the BiOp).
6
64. FWS did not explain its decision in the BiOp to
7
8 use gros s salvage nu mbers in Figures B-13 and B-14, an d
9 did not explain why it selectively used normalize d
10 salvage data i n some parts of the BiOp but not in others.

11 4/6/10 T r. 28:5-8, 32:5-9.
12
65. FWS pres ented no cre dible, scientifically based
13
explanat ion for the decision to use gross salvage numbers
14
instead of normalize d salvage data in Figures B-13 and B-
15
14, eith er in the Bi Op or at the hearing. Other than
16
17 endeavor ing to struc ture a result, there is no
18 explanat ion for this departure from best availabl e

19 science. This raise s the spectre of bad faith.
20
66. For the purposes of (a) demonstrating the
21
differen ce bet ween t he analysis presented i n the BiOp and
22
a popula tion-n ormalized analysis and (b) identifying an
23
appropri ate interim remedy, Dr. Deriso analyzed t he
24
25 relation ship between normalized salvage and OMR f lows.
26 This ana lysis reveal ed that there were no detecta ble
27 trends i n the juveni le salvage rate at flows up t o -5, 600

28
43
1 cfs, whi ch is the mo st negative salvage weighted flow

2 rate con tained in th e data. 4/6/10 Tr. 55:18-24; Fed.
3
Gov’t Sm elt Ex. 18 a t ¶25.
4
67. Federal Defendants critic ize Dr. Deriso’s
5
alternat ive analysis in a number of ways:
6
a. Dr. Newm an explained that Dr. Deriso’s
7
8 analysis is more app ropriately characterized as a “first
9 cut” at an analysis that fails to correct for pot entially
10 large “o bservation e rrors.” 4/5/10 Tr. 73, 77-78. Those

11 “errors” include fac tors and variability that wou ld tend
12
to confo und the resu lts if not accounted for, suc h as
13
temperat ure variatio ns, geographic distribution,
14
turbidit y, or predat ion, all of which can “distor t[,]
15
confuse or con found” the relationship between the factors
16
17 one is t rying to exa mine. Id. at 51 (Dr. Newman’s
18 testimon y regarding the factors he will be addres sing and

19 includin g in his for thcoming delta smelt life cyc le
20
model). He opined t hat some of these confounding factors
21
are very important a nd ignoring them could lead o ne
22
“[e]ithe r to wrongly assume that there is a relat ionship
23
or to as sume that th ere is [one] when there isn’t .” Id.
24
25 at 82. This concern was reiterated by Dr. Rose i n his
26 2000 pap er, and by D r. Hilborn. Id. at 160-61.
27 b. Dr. Newm an ran his o wn analysis, applying a

28
44
1 differen t standard s tatistical methodology, on th e same

2 cumulati ve salvage i ndex versus OMR flow data use d by Dr.
3
Deriso, and got diff erent results regarding the
4
“inflect ion point” w here OMR flows had an increasing
5
impact o n the popula tion- normalized salvage rate. 4/5/10
6
Tr. 63-6 4. Ultimate ly, Dr. Newman testified that he
7
8 would ha ve performed a statistical analysis diffe rent
9 from tho se performed by both Dr. Deriso and in th e BiOp.
10 Id. at 7 9-80. Dr. N ewman nev er suggested that an

11 analysis utilizing r aw salvage numbers (i.e., not
12
adjusted for relativ e population size) is scienti fically
13
appropri ate. This i s not just a scientific dispu te among
14
experts, particularl y in view of FWS’s concession in the
15
BiOp.
16
17 c. Dr. Deri so admitted that he is not a delta
18 smelt bi ologist, 4/6 /10 Tr. 125, and that his ana lysis
19 does not account for a number of pote ntially confounding
20
factors, such as: th e large amount of pumping-rel ated
21
mortalit y that is no t measure d by salvage, id. at 89;
22
116, pum ping-r elated changes to delta smelt habitat, id.
23
at 116, 140; pumping-related impacts on foo d supply, id.
24
25 at 143; pumping-related impacts of spatial confin ement of
26 delta sm elt to the S acramento River, id. at 144-45;
27 whether the de ath of some individuals such as fec und

28
45
1 females may have a d isproportionate impact on the

2 populati on (the so-called “big mama” hypoth esis) id. a t
3
116; and whether the relationship between OMR flo ws and
4
populati on abundance could change depending on populat ion
5
size, id . at 146.
6
d. Nor did Dr. Deriso’s analysis distinguish
7
8 between years pre-dating or post-dating the POD, thoug h
9 he ackno wledged that there is evidence of drastic changes
10 in the e stuary durin g that period. Id. at 123-24, 165.

11 Reputable scie ntists in the field, including Drs. Peter
12
Moyle an d Bill Benne tt, have opined that statisti cal
13
“correla tions [in th e Delta] seem to be los ing some of
14
their fo rmer predict ive value in recent years for some
15
desirabl e species (K immerer et al. 2009). This, in pa rt,
16
17 may be d ue to ... th e extremely low abundance of
18 desirabl e fishes, wh ich may not be tracked as eff ectively

19 by the t raditional m onitoring programs.” Id. at 119-20.
20
e. In the a bsence of re liable population
21
estimate s for delta smelt, Dr. Deriso utili zed th e FMW T
22
index as a proxy for population when conducting h is
23
analysis of the popu lation-level effects of salva ge on
24
25 adult de lta smelt. However, Dr. Newman noted tha t there
26 are seve ral biases i n the FMWT data, particularly
27 selectio n bias, such that he would not rely purely on

28
46
1 FMWT dat a “when it c omes to analyzing salvage.” 4/5/10

2 Tr. 118.
3
e. In addit ion, Dr. Der iso’s analysis accounts
4
in only a very limit ed way for spatial distributi on (by
5
excludin g years with low turbidity from the analysis).
6
Spatial distribution reflects the increased vulne rability
7
8 of delta smelt to en trainment as they move closer to the
9 pumps. 4/5/10 Tr. 8 0-82. In contrast, Component s 1 and
10 2 of the BiOp accoun t for spatial distribution to a much

11 greater extent by allowing for modification of th e lev el
12
of OMR f lows based o n the location of delta smelt in the
13
estuary. 4/7/10 Tr. 55-56, 6 9-71. Dr. Der iso’s analy sis
14
looks so lely at the relationship between populati on-
15
weighted salvage and OMR flows, excluding all other
16
17 factors and consider ations.
18 68. Neverthe less, even a ssuming all of these

19 critique s of D r. Der iso’s opinion are valid, they do
20
nothing to justify t he BiOp’s election to base it s flow
21
prescrip tions on an analysis that uses raw salvag e
22
numbers. Even if Dr . Deriso’s “first cut” needs
23
refineme nt to addres s these critiques, the BiOp’s
24
25 analysis in Figure B-13 does not account fo r any of th e
26 issues o n which Fede ral Defendants criticize Dr. Deriso’s
27 analysis .
28
47
1 69. Federal Defendants note that Dr. Deriso

2 presente d his conclu sions and analysis regarding the BiOp
3
to the N ational Rese arch Council of the National Academy
4
of Scien ces panel th at peer-reviewed the BiOp. 4 /2/10
5
Tr. 193; 4/6/10 Tr. 137. After reviewing the inf ormation
6
presente d by D r. Deriso, that panel explicitly di sagreed
7
8 with his conclusion that FWS’s analysis in the Bi Op was
9 not base d on the bes t available science or one th at a
10 “reasona ble biologis t” would perform. Instead, t he NRC

11 Panel co nfirmed the analysis performed by FWS and its
12
biologis ts, stating that:
13
Although there are s cientifically based
14 argument s that raise legitimate questions about
this act ion, the com mittee concludes that until
15 better m onitoring da ta and comprehensive life
cycle mo dels are ava ilable, it is scientifically
16 reasonab le to conclu de that high negative OMR
flows in winter prob ably adversely affect smelt
17 populati ons. Thus th e concept of reducing OMR
and nega tive flows t o reduce mortality of smelt
18 at the S WP and CVP f acilities is scientifically
justifie d.
19
4/2/10 T r. 194. The NRC analysis justifies its
20
conclusi on by recogn izing better monitoring is no t
21
availabl e, a compreh ensive life cycle model does not
22
23 exist, a nd that high negative OMR flows in winter
24 “probabl y” adversely affect smelt populations.

25 70. The NRC’ s equivocal conclusion is in no way
26
inconsis tent with a finding that the BiOp failed to
27
utilize the best ava ilable scientific methods by relying
28
48
1 on a qua ntitative an alysis using raw salvage to select

2 the uppe r ceil ing for negative OMR flows un der Co mpone nt
3
2. The Federal Defe ndants have not told the whol e NRC
4
Panel st ory. The NR C Panel expressly found that “there
5
is substantial uncertainty re garding the amount of flo w
6
that sho uld trigger a reduction in exports,” (emphasis
7
8 added) a nd dec lined to decide whether alternative RPAs
9 would “ provide equa l or greater protections for the
10 species while requir ing less disruptions of Delta water

11 diversio ns,” conclud ing that the panel had received
12
insuffic ient documen tation on such alternatives. Id. at
13
200-01. Having fail ed to perform the required NE PA
14
analysis , it is cert ain that Federal Defendants c ould not
15
and did not take the requisite hard look at RPA
16
17 alternat ives.
18 71. Federal Defendants a rgue that the district court

19 previous ly heard and rejected similar statistical
20
analysis of fish pop ulation dynamics presented by Mr.
21
B.J. Mil ler during t he 2007 interim remedy hearin g.
22
a. Mr. Mill er “conclude d that there was no
23
statisti cal signific ance in the relationship betw een
24
25 Delta sm elt abundance and salvage and expor t oper ation s
26 in the p umps.” 4/6/ 10 Tr. 114. Another of Plain tiffs’
27 witnesse s in that pr oceeding, Dr. Charles Hanson, then

28
49
1 explaine d that even if Mr. Miller’s statistical a nalyses

2 were cor rect and “re flect the low significance of that
3
salvage mortality to the population,” it did not suggest
4
that reg ulatory acti on to minimize salvage at the pumps
5
was not justified:
6
On the o ther side, Y our Honor, the fact that we
7 are salv aging Delta smelt represents a source of
mortalit y to this populat ion. And one of th e
8 approach es that's be ing made, given the low
populati on abundance , is to identify those
9 sources of mortality that we know of and to try
and redu ce those. My feeling is that we have
10 such a c omplex estua ry with so many interacting
variable s that chang e from year to ye ar and
11 within y ears, that i t's difficult to rely solely
on stati stical analy ses. I think we're at a
12 point wh ere we need to say do we have a
substant ial source o f mortality and is there
13 somethin g we can do to help reduce that.
14 4/6/10 T r. 114-15.
15
b. Plaintif fs’ expert, Dr. Hilborn, expr essed
16
similar opinions dur ing the most recent evidentia ry
17
hearings , acknowledg ing that, while he criticized the
18
BiOp for lacking “a basis for population level ef fects of
19
20 the prop osed actions... i t’s pretty clear t hat th ere a re
21 viabilit y concerns a bout Delta smelt.” 4/5/10 Tr . 224.
22 Dr. Hilb orn also ack nowledged “it’s very clear th at large
23 negative flows have an impact on the number of fi sh that
24
are impi nged and ent rained.” Id. at 228. He did not
25
quantify what he mea nt by “large negative flows.” Dr.
26
Hilborn agrees that there is no doubt that the po pulation
27
28 size of delta smelt is currently at an historic l ow and
50
1 that ent rainment at project facilities results in direct

2 mortalit y. Id . at 249-50. Dr. Hilborn explained that he
3
does not deny that a long-ter m relationship between
4
populati on growth ra te and salvage may exist, onl y that
5
he has n ot see n “any evidence of that in any of the
6
analysis I've seen so far .” Id. at 2 28. D r. Hilborn
7
8 acknowle dged t hat he “couldn’t exclude the possib ility ”
9 that a f uture salvag e event could eliminate 100% of the
10 populati on, even if there was no relationship bet ween the

11 amount o f delta smel t salvaged and long-ter m popu latio n
12
dynamics . Id. at 229.
13
c. Assuming, argu endo, the “ possibility” canno t
14
be “exclude[d] ” that a future salvage event could
15
eliminat e 100% of th e population, FWS did n ot justify its
16
17 selectio n of - 5,000 cfs on th e basis of that ceiling’s
18 ability to prevent s uch a catastrophic salvage ev ent.

19 Faced wi th express c oncerns from inside and outsi de the
20
agency a bout drawing conclusions from analyses us ing raw
21
salvage, FWS complet ely failed to explain why it
22
nonethel ess did so. None of the post-hoc
23
rational izations off ered by Federal Defendants, e .g. t he
24
25 “big mam a” hypothesi s, was mentioned in the BiOp as ba ses
26 for sele cting -5,000 cfs as the ceiling for negative OMR
27 flows.
28
51
1 72. FWS’s re liance on an alyses that utilize raw (as

2 opposed to populatio n-nor mali zed) salvage data is an
3
undeniab le fai lure to use the best available scientifi c
4
methodol ogy.
5
6 b. Other Da ta Supportin g the General Conclusion
that Neg ative OMR fl ows Jeopardize the
7 Smelt.
8 73. There is far more di spute over the sufficiency
9 of evide nce supporti ng the BiOp’s general conclusion t hat
10
the nega tive OMR flo ws predicted to take place un der
11
planned Project oper ations will jeopardize the sm elt
12
(referre d to in this subsection as the “jeopardy
13
conclusi on”).
14
15
(1) Sporadic ally Signifi cant Take.
16
74. One of t he key ratio nales for the jeopardy
17
conclusi on is the as sertion that entrainment has a
18
“sporadi cally signif icant” effect on smelt abunda nce.
19
BiOp at 210. This a ssertion was based on the est imates
20
21 of propo rtional entr ainment in Kimmerer 2008. Bi Op at
22 210; Fed . Gov’ t Smelt Ex. 38. Kimmer er 200 8 states th at:
23 Delta sm elt may suff er substantial losses to
export p umping both as pre-spawning adults and
24 as larva e and early juveniles. In contrast to
the situ ation for sa lmon, pre-salvage morta lity
25 has been constrained in the calculations for
adult De lta smelt, a nd its effects eliminated
26 from the calculation s for larval/juvenile Delta
smelt. C ombining the results for both life
27 stages, losses may b e on the order of zero to 40
percent of the popul ation throughout winter and
28
52
1 spring.
2 4/7/10 T r. 42- 43; AR 018877.
3 75. Dr. Grim aldo confirm ed that the Kimmerer (2008)
4
and Kimm erer and Nob riga (2008) studies represent ed the
5
“best av ailable scie nce” when the BiOp was prepar ed.
6
4/7/10 T r. 63- 64. The BiOp cites Kimmerer (2008) (and
7
other pe er-rev iewed studies) for the propositions that
8
9 entrainm ent can affe ct the abundance of delta sme lt in
10 certain years; may p revent recovery when habitat
11 conditio ns are suita ble; and that high entrainmen t of

12 adults i n the winter appears to have played a role in the
13
decline of delta sme lt in the POD years. BiOp at 158- 59.
14
76. Dr. Deri so questions whether Kimmerer (2008)
15
should b e interprete d as standing for the proposi tion
16
that ent rainment mor tality can kill a subst antial portion
17
18 of the p opulat ion in some years. For examp le, he
19 testifie d that the K immerer (2008) article relied on a

20 number o f assumption s to calculate the percentage
21
entrainm ent figures incorporated into the BiOp, i ncluding
22
the assu mption that a proportional relationship exists
23
between OMR flow lev els and entrainment. 4/6/10 Tr.
24
131:12-1 6; Fed . Gov’t Smelt Ex. 29 at ¶19; Fed. Gov’t
25
26 Smelt Ex . 38 at 0188 75-018876. Because the Kimme rer
27 (2008) a rticle began with this assumption, Dr. De riso
28
53
1 opined t hat it could not reasonably b e used by FWS as

2 evidence that a prop ortional relationship exists between
3
OMR flow level and s melt entrainment. Fed. Gov’t Smel t
4
Ex. 29 a t ¶19.
5
77. But, the BiOp did no t rely on Kimmerer (2008)
6
for this purpose. D r. Grimaldo explained that “w hat t he
7
8 Kimmerer 2008 paper actually showed was that ther e was a
9 populati on response [to entrainment] within life stage s.”
10 4/7/10 T r. 98. 5 Dr. Newman explained that this

11 informat ion is “cert ainly pertinent to understand ing
12
what’s h appening wit h the pop ulation.” 4/5/10 Tr. 135 -
13
136.
14
78. Dr. Newm an, who did not participate in the
15
preparat ion of the B iOp, agreed that FWS’s conclu sion in
16
17 the BiOp that entrai nment affects subsequent year
18
5
K im me re r (2 00 8) a ck now le dg es t ha t “. .. de sp it e su bs ta nt ial
19 var ia bi li ty i n ex po rt fl ow i n ye ar s si nc e 19 82 , no e ff ec t o f ex po rt
flo w on s ub se qu en t mi dwa te r tr aw l a bun da nc e is e vi de nt ,” bu t re fu se s
20 to “d is mi ss t he r at he r l ar ge p ro po r tio na l lo ss es o f de lt a s me lt t ha t
occ ur i n so me y ea rs ; rat he r, i t su g ges ts t ha t th es e lo ss es ha ve
21 eff ec ts t ha t ar e ep is odi c an d th er e for e th ei r ef fe ct s sh oul d be
cal cu la te d ra th er t ha n i nf er re d fr o m c or re la ti on a na ly se s.” Fe d.
22 Gov ’t S me lt 3 8 at 2 5 (AR 0 18 87 8) . Dr. Q ui nn o pi ne d th at “e vi de nc e
sho ul d ha ve b ee n pr es ent ed i n th e B iOp t o de mo ns tr at e su ch ef fe ct s,
23 bas ed o n so me c al cu la tio n. ” D oc . 6 33 at 2 . F or e xa mp le , h e as ks :
“In w hi ch y ea rs w er e the re l ar ge l o sse s th at c an b e di re ctl y
24 att ri bu te d to t he p um pin g op er at io n s, an d wh at w er e th e eff ec ts o n
sub se qu en t re cr ui tm en t? Be ca us e th e sm el t ar e la rg el y an nua l fi sh , a
25 cat as tr op he i n a si ng le ye ar c ou ld put t he m at g re at r is k o f
ext in ct io n an d tw o ba d y ea rs i n a r ow co ul d ac co mp li sh i t. Th e ri sk
26 inh er en t in t he s ta ti sti ca l an d ec o log ic al u nc er ta in ty i s b or ne
hea vi ly b y th e sp ec ie s b ut t he re s t ill s ho ul d be s om e ev ide nc e in
27 the r ec or d to r ev ea l the se e ff ec ts . ” Id . I t is n ot c le ar wh et he r
the B iO p re li es o n Ki mme re r 20 08 a s ev id en ce o f th es e ef fec ts o r
28 sim pl y as e vi de nc e th at th es e ef fe c ts ma y be s ig ni fi ca nt .
54
1 abundanc e of Delta s melt even sporadically is sup porte d

2 by gener ally accepte d scientific standards. 4/5/ 10 Tr.
3
89-90. It is undisputed that very large salvage events
4
can and have occurre d at OMR flows of less than - 5,000
5
cfs. In May and Jun e of 1999 alone, 58,929 and 7 3,368
6
delta sm elt, respect ively, were salva ged at the Projec t
7
8 export f acilities. 4/6/10 Tr. 111. Average OMR flows
9 during t hose months were -1,0 62 cfs and -3,814 cfs,
10 respecti vely. Id. at 112 . While Dr. Deris o test ified

11 that the significanc e of such an event depends on the
12
size of the population, he also could not state whethe r
13
the curr ent populati on was large enough to surviv e
14
similar salvage even ts, or whether such an event would
15
jeopardi ze the conti nued existence of the smelt. Id.
16
17 Dr. Hans on, another of Plaintiffs’ expert fish bi ologist
18 witnesse s, testified in 2007 that salvage of 1,30 0-1,400

19 delta sm elt would be “a very high level of salvag e”
20
“under t he current p opulation levels.” Id. at 113.
21
Delta sm elt abundanc e levels have further decline d since
22
Dr. Hans on made that statement. Id.
23
79. It was n ot unreasona ble for FWS to conclude that
24
25 salvage events may b e “sporadically significant.”
26 //
27 //
28
55
1 (2) Dr. Benn ett’s Work.

2 (a) Impact of VAMP on Po pulat ion
Dynamics.
3
80. Dr. Ben nett’s unpub lished research
4
“demonst rated that the number of larv ae tha t survived to
5
6 the fall is related to when they hatch in the spr ing....
7 [and] th at larvae th at hatched during the VAMP .. .
8 protecti ve period[] were the ones that survived t o the

9 fall in the pe riod that he examined.” 4/7/ 10 Tr. 93.
10
81. The BiOp concluded:
11
Based on Bennett’s u npublished analysis,
12 reduced spring expor ts resulting from VAMP
have sel ectively enh anced the survival of
13 delta sm elt larvae s pawned in the Central
14 Delta th at emerge du ring VAMP by reducing
their entrainment. Initial ot olith studies
15 by Benne tt’s lab sug gest that these spring-
spawned fish dominat e subsequent recruitment
16 to adult life stages . By contrast, delta
smelt sp awned prior to and after the VAMP
17 have bee n poorly-rep resented in the adult
stock in recent years. The da ta suggests
18
that the differentia l fate of early, middle
19 and late cohorts aff ects sizes of delta
smelt in fall becaus e the later cohorts have
20 a shorte r growing se ason. The se findings
suggest that direct entrainment of larvae
21 and juve nile d elta s melt duri ng the spring
are rele vant to popu lation dynamics.
22
23 BiOp at 170 (emphasi s added). Nothing in the rec ord
24 suggests this conclu sion was unreasonable.
25
(b) Big Mama Hypot hesis.
26
82. Federal Defendants a nd Defendant Intervenors
27
also sug gest that Dr . Bennett’s work provided “ev idence”
28
56
1 to suppo rt the “big mama” hypothesis that Project

2 operatio ns may affec t delta smelt abundance by en training
3
the most fecund indi viduals in the population, th ereby
4
creating a dispropor tionate impact on the reproductive
5
potentia l and growth rate of the population.
6
83. However, the BiOp do es not suggest Bennett’s
7
8 work pro vides evidence of thi s hypothesis; rather , the
9 BiOp con sistently in dicates that the “big mama”
10 hypothes is is just t hat -- a hypothesis:

11 Another possible con tributing driver of reduced
12 delta sm elt survival , health, fecundity, and
resilien ce that occu rs during winter is the “Big
13 Mama Hyp othesis” (Bi ll Bennett, UC Davis, pers.
comm. an d various or al presentations). As a
14 result o f his synthesis of a variety of studies,
Bennett proposed tha t the largest delta smelt
15 (whether the fastest growing age-1 fish or fish
that man age to spawn at age-2) could have a
16
large in fluence on p opulation trends. Delta
17 smelt la rvae spawned in the South Delta hav e
high ris k of entrain ment under most hydrologic
18 conditio ns (Kimmerer 2008), but water
temperat ures often w arm earlier in the South
19 Delta th an the Sacra mento River (Nobriga and
Herbold 2008). Thus, delta smelt spawning often
20
starts a nd ends earl ier in the Central and South
21 Delta th an elsewhere . This differential warming
may contribute to the “Big Mama Hypothesis” by
22 causing the earliest ripening females to spawn
dispropo rtionately i n the South Delta, putting
23 their of fspring at h igh risk of entrainment.
Although water diver sion strategies have been
24 changed to better pr otect the ‘average’ larva,
25 the resi lience histo rically provided by variable
spawn ti ming may be reduced by water divers ions
26 and othe r factors that covary with Delta inflows
and outf lows.
27
BiOp at 158 (emphasi s added). This hypothe sis ha s not
28
57
1 been pro ved.

2
(3) Consider ation of Lif e Stage and
3 Geograph ic Dis tribut ion.
4 84. The BiOp considers t he life stage of delta smelt
5
and wher e the popula tion is located in the estuar y, to
6
help ass ess en trainment risk. Dr. Grimaldo expla ined:
7
[I]n the fall [and] winter, we have very low
8 entrainm ent risk. Bu t once the first flush
events h appen, begin ning sometime in mid
9 December , Delta smel t often migrate upstream. So
they’re vulnerable a t this part of th e life
10 stage. After they m igrate upstream, they stage
for a li ttle bit. An d they’re vulnerable to
11 entrainm ent during t he staging period. And then
after th e staging pe riod, they spawn. And their
12 progeny are vulnerab le to entrainment at this
period.
13
So there ’s vulnerabi lity to different life
14 stages a s -- and, in general, as they become
distribu ted closer t o the central and south
15 Delta ce ntral and so uth Delta, their entrainment
risk goe s up.
16
4/7/10 T r. 50- 51. The RPA takes into account these
17
spatial and li fe sta ge fa ctors by breaking actions int o
18
19 differen t components over different periods of ti me. Id.
20 at 64-65 .
21 85. Mr. Feyr er and Dr. G rimaldo testified that the

22 export p umps affect the geographic distribution o f delta
23
smelt, a nd that prev entin g th e fish from coming n ear the
24
pumps re duces the ri sk of entraining those fish. 4/2/10
25
Tr. 180; 4/7/10 Tr. 64. Larval and juvenile delt a smelt,
26
in parti cular, are “ neutrally buoyant” and thus f ollow
27
28 the flow in the Delt a in a manner similar to part icles.
58
1 4/7/10 T r. 54- 55. Particle-tracking modeling sho ws that

2 many of the particle s are “lost” to the pumps whe n
3
export-i nflow ratios are increased. Id. at 59-60.
4
Kimmerer and Nobriga (2008), relied on in the BiO p,
5
asserts that these s tudies “suggest a direc t link between
6
the posi tion of the smelt population as determine d by
7
8 outflow and losses a s determined by export flow” and “may
9 be enoug h to recomme nd strong protective measures for
10 Delta sm elt in sprin g (March-May) of low ou tflow years

11 when the y are highly vulnerable to export losses.” Id .
12
at 60-62 . Non-export factors influence entrainment too,
13
“such as river inflo ws, the position of X2 and wh ere the
14
fish are distributed .” Id. However, as Mr . Feyr er
15
testifie d, “essentia lly the closer [the fish] are , the
16
17 more vul nerable [the y] will be” to the effects of
18 entrainm ent. 6 Id.

19
20
21 6
En tr ai nm en t in cl ud es mo re t ha n ju s t s al va ge m ea su re d at th e
pum ps . A s Mr . Fe yr er ex pl ai ne d, s a lva ge i s a sm al l su bs et of
22 ent ra in me nt : “ Sa lv ag e i s es se nt ia l ly th e fi sh t ha t ar e obs er ve d at
the . .. s al va ge f ac il iti es . T ho se are t he f ac il it ie s th at ar e
23 loc at ed a t bo th t he s tat e an d fe de r al ex po rt o pe ra ti on f aci li ti es .
And t ho se f ac il it ie s are d es ig ne d t o e ss en ti al ly f il te r the f is h ou t
24 of th e wa te r be fo re t hey a re e nt ra i ned i nt o th e pu mp s. And t he n
the y’ re r el ea se d ba ck in to t he e st u ary . A nd s o th os e ar e t he f is h
25 tha t yo u ac tu al ly o bs erv e in s al va g e. H ow ev er , en tr ai nm ent r ef er s
to th e fi sh t ha t ar e not o bs er ve d p lus t ho se f is h th at a re
26 obs er ve d. ” 4 /2 /1 0 Tr . 1 80 -8 1. Fi s h t ha t ar e no t ob se rv ed in cl ud e
tho se t ha t su ff er f ro m p re -s cr ee n m ort al it y at C li ft on C our t
27 For eb ay , id . at 1 82 , and t ho se t ha t ar e no t de te ct ed d ue to l ou ve r
ine ff ic ie nc y. Pu mp in g p ul ls f is h i nto t he F or eb ay , in cr eas in g th ei r
28 exp os ur e to t he se s ou rce s of m or ta l ity . I d. a t 18 3.
59
1 c. Life Cyc le Analysis.

2 86. Studies cited in the BiOp failed to demonstrate
3 that wat er exports a ffect the delta smelt populat ion
4
growth r ate. Kimmer er (2008), for example, noted a “l ack
5
of evide nce for popu lation-level effects” o f the water
6
projects and stated that “no effect of export flo w on
7
subseque nt midwater trawl is evident.” AR 018878 ,
8
9 018855; MWD Ex. 600 at 53; MWD Ex. 600 at 28. Be nnett
10 (2005) f ound that “i t is unlikely that losses of young
11 fish to the export f acilities consistently reflec t a

12 direct i mpact on rec ruitment success later in the year.”
13
AR 01700 4; MWD Ex. 6 07; SLDMWA Ex. 240.
14
87. All expe rts agree th at applic ation of a lif e-
15
cycle mo del 7 is accep ted method for evaluating the
16
effects of an action upon a population’s growth r ate.
17
18 a. The Delt a Smelt Acti on Evaluation Team
19 recogniz ed that such a model should be developed and

20 utilized . MWD Ex. 6 33 at 5, 9, 10, 11.
21
b. Dr. Deri so testified that a population
22
growth r ate analysis is the method by which fishe ries
23
biologis ts normally evaluate the impact of a stre ssor on
24
a popula tion. 4/6/1 0 Tr. 38:11-18.
25
26 c. Dr. Hilb orn similarl y testified that life-
27 7
Th e ex pe rt s us e th e ter m “p op ul at i on dy na mi cs m od el ,” “ lif e
his to ry m od el ,” a nd “ lif e cy cl e mo d el” i nt er ch an ge ab ly . Se e, e .g .,
28 4/2 T r. 2 55 ; 4/ 6 Tr . 41.
60
1 cycle mo dels are the accepted method in population

2 dynamics to evaluate anthropogenic effects on the
3
probabil ity of growt h or decline of a species. 4 /5/10
4
Tr. 154: 16-24. Dr. Hilborn testified that develo pment of
5
such a m odel is “sta ndard operating procedure” fo r
6
fisherie s management agencies to evaluate human impact s
7
8 on fish species. 4/ 5/10 Tr. 155:20-25.
9 d. FWS’s ex pert, Dr. Ne wman, stated in his
10 declarat ion that he “agreed with the utility of l ife

11 history models for a ssessing population level eff ects of
12
SWP/CVP operations.” Fed. Go v’t Smelt Ex. 17 at ¶8.
13
e. Dr. Newm an said he w ould have developed a
14
life-cyc le mod el for the BiOp. 4/5/10 Tr. 107:21 -108:5.
15
Dr. Newm an stated th e methodology employed in the BiOp
16
17 was “qui te a differe nt way of doing things” from the
18 statisti cal analysis he was “familiar with” and

19 “comfort able with.” 4/5/10 Tr. 107:21-108:5.
20
f. Federal Defendants’ expert, Mr. Feyrer,
21
testifie d that, once developed, a life-cycle model wou ld
22
be the b est availabl e science to evaluate the pop ulation-
23
level im pacts of the water projects on the delta smelt .
24
25 4/2/10 T r. 253:4-10.
26 g. Accordin g to Mr. Fey rer, use of a life-cycle
27 modeling methodology in the BiOp would have reduc ed the

28
61
1 uncertai nty in the R PAs. 4/2/10 Tr. 258:22-259:8 .

2 88. How long it would ha ve taken FWS to develop an
3
appropri ate li fe cyc le model is a matter of consi derable
4
debate.
5
a. Life-cyc le modeling is an analytical
6
techniqu e that has b een known and available to sc ientists
7
8 for year s. 4/5/10 T r. 109:19-110:3. Numerous textboo ks
9 and refe rence articl es explain how to devel op a life-
10 cycle mo del, which a re a standard tool used by fi sheries

11 scientis ts to evalua te population-lev el impacts. 4/2/10
12
Tr. 254: 23-255 :14. Basic growth rate models such as the
13
Ricker m odel and the Beverton-Holt mo del were develope d
14
in the 1 950s. 4/6/10 Tr. 41:22-42:4; 49:16 -22.
15
b. Dr. Deri so testified that sufficient data
16
17 existed at the time of the creation of the BiOp t o enable
18 FWS to p erform a qua ntitative life-cycle modeling

19 analysis . 4/6/10 Tr . 46:16-47:16.
20
c. Dr. Deri so testified that a basic
21
quantita tive life-cycle m odeling analysis c ould b e
22
performe d in less th an an hour, while a more comp licated
23
modeling effort coul d be completed in a few weeks .
24
25 4/6/10 T r. 43:2-7.
26 d. Mr. Feyr er testified that FWS could have
27 complete d a life-cycle mo deling analy sis within 1 8

28
62
1 months. 4/2/10 Tr. 263:15-24.

2 e. In a 200 5 research a rticle Dr. Bennett
3
employed a life-cycle model to evaluate a n umber of
4
impacts on the delta smelt. 4/2/10 Tr. 46:16-47: 16.
5
f. Dr. Hilb orn testifie d that a life-cycle
6
modeling effor t could have been performed for the delt a
7
8 smelt wi thin a matte r of months. 4/5/10 Tr. 175: 5-21.
9 He furth er testified that even an incomplete life -cycle
10 modeling analysis, s uch as the one found in Benne tt

11 (2005), would be sup erior to simply relying on
12
professi onal or expe rt opinion withou t use of any such
13
model. 4/5/10 Tr. 2 12:23-213 :6. How ever, Dr. Hi lborn
14
admitted that when h e and Dr. Maunder actually en deavored
15
to build a quantitat ive population dynamics model for
16
17 delta sm elt over 18 months ago, they abandoned that
18 particul ar modeling effort as too complicated and time-

19 consumin g. Id . at 217-18.
20
g. Dr. Punt stated “[i] t is surprising that a
21
populati on dynamics model was not developed for d elta
22
smelt fo r the BiOp.. .. The model developed by Ben nett
23
could ha ve bee n exte nded to more fully account fo r the
24
25 biology of delta sme lt and fitted to data to asse ss the
26 populati on-lev el effects of impact of the project .”
27 4/6/10 T r. 44:16-21; Doc. 633, Ex. A, at 3.

28
63
1 89. Yet, a quantitative population dynamics mo del

2 for delt a smelt is “ not something that you go to the
3
store an d just buy [ like] a piece of equipment,” but
4
rather w ould consist of a large amount of formula s.
5
4/2/10 T r. 254; 4/5/ 10 Tr. 48 (Dr. Newman concurr ing that
6
“there’s not off-the-shelf software to buil d such
7
8 models”) . Dr. Newma n testified that previous eff orts to
9 build su ch models in which he has been involved h ave
10 taken tw o to three y ears, 4/5/10 Tr. 50, and have

11 involved numerous pe ople because you need experti se in
12
biology, statistics, and modeling. Id. at 131. Mr.
13
Feyrer s tated that “ the construction of a full bl own high
14
quality life cycle m odel is no simple task.” 4/2 /10 Tr.
15
255, 258 .
16
17 90. Mr. Fey rer also poi nted out the importance of
18 construc ting an appr opriate and well-calibrated model:

19 “even fo r individual s with the amazing skills of [Drs.
20
Maunder, Deriso and Hilborn], it still takes a lo t of
21
time to develop thos e to where you have the confi dence in
22
them so that you can actually apply them in a sit uation
23
where, y ou know, the re's obviously a lot at stake here.
24
25 You don' t want to ap ply something prematurely wit hout
26 really u nderstanding how well it works.” Id. at 258.
27 Dr. Deri so, in contr ast, applied a generic “textb ook”

28
64
1 version of a life hi story model in the analysis h e

2 presente d to the Cou rt, without modifying it to a pply
3
specific ally to delt a smelt biology and character istics.
4
4/6/10 T r. 42. Sign ificant disagreement exists a mong
5
competen t experts as to what constitutes a reliab le
6
quantita tive populat ion dynamics model for delta smelt .
7
8 91. Federal Defendants w ere aware of the value of a
9 life-cyc le mod el. At a March 8, 2007 meeti ng regardin g
10 the OCAP ESA Re-consultation, attended by a numbe r of FWS

11 employee s, the impor tance of using a life cycle m odel was
12
recogniz ed and the p rogress to date was inquired into.
13
4/7/10 T r. 183:9-188:4; S WC Ex. 960. Likewise, during
14
the Delt a Smelt Acti on Evaluation Team meeting on August
15
8, 2008, the Team re cognized that population mode ls for
16
17 delta sm elt already had been developed, and that it wa s
18 possible to use thos e models as a starting point for

19 quantita tive analyse s with appropriate assumption s added
20
as bound s to the ana lysis. 4/7/10 Tr. 188:9-190:22.
21
92. Neverthe less, it is undisputed that, despite
22
over thr ee yea rs of controversy regarding t he spe cies, no
23
quantita tive life cy cle model adapted to the delt a smelt
24
25 was avai lable to or used by FWS at th e time the B iOp was
26 issued. A quantitat ive population dynamics model for
27 delta sm elt does not currently exist, although there a re

28
65
1 several efforts unde rway to develop one. 4/2/10 Tr. 189;

2 4/5/10 T r. 44. Rese archers from a number of
3
universi ties, includ ing Drs. Wim Kimmerer, Bill B ennett,
4
Kenny Ro se and Steve Monismith, have been working on
5
developi ng such a mo del for a number of yea rs. Id. at
6
189-90; 4/5/10 Tr. 46. Dr. Mark Maunder has also been
7
8 working on such a mo del for delta smelt since at least
9 March 20 08, with the assistance of Dr. Hilborn an d Dr.
10 Deriso. Id. a t 258; 4/5/10 Tr. 47. Dr. Newman, who h as

11 previous ly developed three quantitative life hist ory
12
models, is currently working with the National Ce nter for
13
Ecologic al Analysis and Synthesis (“NCEAS”) to de velop
14
one for delta smelt, an effort that has been unde rway
15
since Oc tober 2007. 4/5/10 Tr. 44-46.
16
17 93. No party who partici pated in the preparation of
18 the BA o r commented on the public review drafts o f the

19 BiOp sub mitted a qua ntitative life cycle model or the
20
results of such an a nalysis using a life cycle mo del for
21
delta sm elt to FWS d uring the consultation. 4/5/ 10 Tr.
22
16-18.
23
94. It is no table that F WS did make use of the
24
25 relative ly simple an d limited life-cycle model describ ed
26 by Dr. B ennett in hi s 2005 paper. 4/2/10 Tr. 256 -57. It
27 utilized that existi ng model by conducting the effects

28
66
1 analysis in the BiOp according to a similar conce ptual

2 life-cyc le mod el. Id. at 258 . The agency then c onducted
3
analyses on specific components of those life sta ges that
4
would be affected by the proposed Project operati ons.
5
Id. Dr. Hilbo rn asserts that FWS erred by not us ing t he
6
Bennett model to jus tify the export limitations i n the
7
8 RPA, 4/5 /10 Tr. 241, but the Bennett 2005 paper a nd Dr.
9 Bennett himself caut ioned that the life-cyc le mod el it
10 presente d is “premat ure for management purposes.” Id. at

11 18, 115, 240-4 1.
12
95. In sum, although all agree that a quantitative
13
life-cyc le mod el would help FWS evaluate im pacts on de lta
14
smelt, F WS had not d eveloped an appropriate model , and no
15
such mod el was avail able for FWS’s use (or otherw ise
16
17 presente d to FWS) pr ior to the issuance of the Bi Op.
18
d. Incident al Take Stat ement.
19
96. Plaintif fs inc luded propo sed findings of fa ct
20
concerni ng FWS’s for mulation of the Incidental Ta ke
21
22 Statemen t (“ITS”). However, at the evidentiary h earing,
23 Plaintif fs aba ndoned their request to enjoin
24 implemen tation of th e ITS. 4/7/10 Tr. 243-44

25 (“Plaint iffs do not seek modification of the inci dental
26
take lim it at this t ime. Even though the current low ITS
27
limits a re not suppo rted by the data and applicat ion of
28
67
1 quantita tive populat ion dynamics analysis, that v ery

2 conserva tive limit, Your Honor, plaintiffs believ e will
3
serve as a back stop that will provide an additio nal
4
level of assurance t o the Court that during the c omponent
5
two peri od, which en ds in June, the surviva l of the sm elt
6
will not be jeopardi zed by project operations.”).
7
8
e. Critical Habitat.
9
97. Federal Defendants a nd Defendant Intervenors
10
maintain , in the alt ernative, that negative OMR f lows
11
adversel y modify cri tical habitat and Component 2 can be
12
upheld b ecause it ad dresses this adverse modifica tion.
13
14 4/7/10 T r. 272:8-273:3; 4 /6/10 Tr. 93:2-6; 4/5/10 Tr.
15 225:18-2 26:22.
16 98. However, the specifi c quantitative criteria

17 establis hed for RPA Component 2 are not derived f rom or
18
justifie d by a ny independent analysis of adverse
19
modifica tion of delt a smelt critical habitat. Bi Op at
20
344-68.
21
22 99. Discussi on of habita t in the justific ations for
23 RPA Comp onents 2 def ines habitat solely in terms of
24 entrainm ent risk. B iOp at 34 4-368. The on ly

25 quantita tive analysi s of entrainment risk is foun d in
26
Figures B-13 a nd B-14 of the BiOp. B iOp at 348, 350.
27
28
68
1 f. Indirect Harm.
2 100. Federal Defendants c laim that Component 2 also
3 protects against ind irect harm. However, the
4
quantita tive analysi s used to derive the flow levels does
5
not ment ion indirect harm as a basis for the flow
6
restrict ions imposed .
7
8 g. The Role of RPA Comp onent 2 in Avoiding
Jeopardy to the Spec ies and Adverse
9 Modifica tion of Crit ical Habitat.
10 101. All of t he experts q ualified in delta smelt
11
biology concurred th at enjoining parts or all of
12
Componen t 2 would ca use jeopardy or adverse impac ts to
13
delta sm elt and desi gnated critical habitat.
14
102. Dr. Grim aldo explain ed that entrainment risk is
15
16 particul arly h igh from March to May because delta smelt
17 larvae a nd juveniles are most likely to behave li ke
18 neutrall y buoyant pa rticles during this time peri od.

19 4/7/10 T r. 68.
20
103. Ms. Goud e testified that the Projects exert a
21
direct e ntrainment effect on delta sm elt, a s well as
22
indirect impacts upo n the species’ food supply, r isk of
23
24 predatio n, and expos ure to contaminants and other
25 stressor s, and affec t critical habitat by changin g the
26 amount a nd location of habitat in winter, spring and

27 fall. I d. at 150-51. In her opinion, enjo ining Actio n 3
28
69
1 of the R PA would res ult in irreparable harm to th e delta

2 smelt du e to very lo w abundance levels and the ri sk of a
3
“huge” e ntrainment e vent causing “catastrophic ev ents.”
4
Id. at 169-70.
5
104. However, none of these experts offered any
6
quantita tive or qual itative analysis, apart from that
7
8 discusse d above, whi ch utilized raw salvage data, to
9 specific ally justify the imposition of a -5,000 c fs
10 ceiling on negative OMR flows .

11
h. Alternat ive Proposal to Limit negative OMR
12 Flow to -5,600 cfs.
13 105. Plaintif fs suggest i mposition of a -5,600
14
ceiling on OMR flows . This is based entirely on Dr.
15
Deriso’s analysis of population-index ed sal vage rates
16
versus n egative OMR flows. Although Dr. Deriso’s
17
analysis corre cts for the fundamental error of re lying on
18
19 raw salv age figures, given the large number of va riables
20 not accounted for in Dr. Deriso’s analysis, it is unclear
21 whether the -5 ,600 break- point he suggests is any more or

22
less app ropriate as a ceiling than th e -5,0 00 fig ure
23
utilized in the BiOp .
24
106. Mr. Feyr er opined th at operating the Project
25
pumps to meet OMR fl ows no less negative than -5,600 cfs,
26
27 the alte rnative OMR ceiling proposed by Plaintiff s,
28 during t he spring wo uld not avoid jeopardy to the delta

70
1 smelt or adverse mod ification of its critical hab itat.

2 4/2/10 T r. 208.
3
107. Regardle ss of the ap propriate upper limit for
4
negative OMR flows, RPA Component 2 defines a ran ge of
5
OMR flow s within whi ch the Projects may operate d uring
6
designat ed time peri ods. This range of flows “pr ovides
7
8 flexibil ity in [] wa ter operations [and] the abil ity to
9 be prote ctive when t heir conditions are not favor able --
10 or when entrainment risk increases.... So it max imizes

11 protecti on for the s pecies while providing flexib ility
12
for wate r operations .” 4/7/10 Tr. 66-67. According to
13
Dr. Grim aldo, operat ing to a “unitary” flow, as
14
recommen ded by Plain tiffs, “removes your flexibil ity from
15
managing that risk”:
16
17 So there may be time s when the fish become
distribu ted in the s outh Delta or the central
18 Delta. And perhaps a lot of them, like we saw
in April 2002 and Ap ril 2003 were large number
19 of the l arvae were i n the central and south
Delta. If you were at a fixed number, that your
20
risk wou ld be high a nd you would have
21 substant ial losses, which were demonstrated in
Kimmerer 2008 during that time period.
22
Id. at 67.
23
108. Both the BiOp and su bsequent peer reviews have
24
25 acknowle dged that th e specific OMR flow triggers and the
26 implemen tation of th e OMR -flo w related requirements of
27 the RPA “need[] to b e accompanied by careful moni toring,

28
71
1 adaptive management and additional analyses that permit

2 regular review and a djustment of strategies as kn owledge
3
improves .” 4/2/10 T r. 195; BiOp at 279 (“[t]he speci fic
4
flow req uirements, a ction triggers and monitoring
5
stations prescribed in the RPA will be continuous ly
6
monitore d and evalua ted consistent with the adapt ive
7
8 process. As new inf ormation becomes available, t hese
9 action t riggers may be modified without necessarily
10 requirin g re-c onsultation on the overall proposed

11 action.” ).
12
109. Althoug h the record shows that FWS’s -5,00 0 OMR
13
ceiling is not based on the best available scienc e, the
14
record d oes not cont ain sufficient information to
15
conclude that the imposition of Plaintiff’s suggested
16
17 -5,600 O MR ceiling w ould be sufficien tly pr otective of
18 the smel t, particula rly in light of the fact that

19 Plaintif fs do not pr opose any flexibility in the
20
manageme nt regime th at would permit greater restr ictions
21
if a large sal vage event was approaching or ongoing.
22
110. Providi ng flexibili ty to permit adaptive
23
manageme nt for delta smelt is justified.
24
25
D. Irrepara ble Harm.
26
111. The reco rd evidence has established a variety of
27
adverse impacts to h umans and the human environme nt from
28
72
1 reduced CVP and SWP deliveries, including irretri evable

2 resource losses (per manent crops, fallowed lands,
3
destruct ion of famil y and entity farming business es);
4
social d isruption an d dislocation; as well as
5
environm ental harms caused by, among other things ,
6
increase d groundwate r consumption and overdraft, and
7
8 possible air quality reduction.
9
(1) Water Su pply Impacts .
10
112. Any lost pumping cap acity directly attributable
11
to the 2 008 Smelt Bi Op will contribute to and exa cerbate
12
the curr ently catast rophic situation faced by Pla intiffs,
13
14 whose fa rms, busines ses, water service areas, and
15 impacted cities and counties, are dependent, some
16 exclusiv ely, upon CV P and/or SWP water deliveries .

17 113. Every ac re-foo t of p umping fo regone during
18
critical time period s is an acre-foot that does not re ach
19
the San Luis Reservo ir where it can be stored for future
20
delivery to users du ring times of peak demand in the
21
22 water ye ar.
23 114. It is un disputed tha t, in the three water y ears
24 prior to the 2009-2010 wa ter year, Californ ia has

25 experien ced three co nsecutive years of drought
26
conditio ns. Gov’t S almon Ex. 5 at (internal) Exh ibit 1
27
at 18. This influen ces the amount of run-off for ecast ed
28
73
1 for 2010 and is indi cative of why reservoir storages w ere

2 at a low state enter ing the 2009-2010 water year. 4/1 /10
3
Tr. 208: 7-15. Hydro logic conditions are no t within th e
4
control of the parti es and have materially contri buted to
5
water se rvice reduct ions to contractors.
6
115. It is al so undispute d that other, non-project
7
8 factors, such as tid es, wind events, storm surges , San
9 Joaquin River flows, Contra Costa Water District
10 operatio ns, and dive rsions by in-Delta wate r users eff ect
11 how Recl amation must operate the project to meet flow
12
targets. See id. at 202:12-204:1.
13
116. The proj ects are sub ject to export reductions
14
required to protect species listed under the Cali fornia
15
Endanger ed Species A ct, including longfin smelt, delta
16
17 smelt, w inter- run Chinook salmon, and spring-run Chinook
18 salmon, which subjec t the water project operators to

19 controls under state law that are similar, and, i n some
20
cases, i dentical to those contained in the 2008 S melt
21
BiOp and the Nationa l Marine Fisheries Service’s (“NFMS”)
22
June 4, 2009 Biologi cal Opinion (“2009 Salmonid B iOp”)
23
concerni ng various E SA-listed anadromous and ocea nic
24
25 species. See id. at Tr. 212:4-213:8. In t he abs ence of
26 the BiOp s’ RPAs, tho se protections are argued to have
27 likely l imited expor t pumping to levels below tho se

28
74
1 allowabl e unde r State Water Resources Contr ol Boa rd

2 Decision 1641 (“D-1641”), whi ch also limits Project
3
pumping at certain t imes of the year. See, e.g., SWC Ex.
4
938 (DWR ’s 3/30/10 a llocation announcement consid ered
5
several “SWP operati onal constraints” including “ the
6
incident al take perm it for longfin smelt”).
7
8 117. Plaintif fs’ estimate s of water losses do not
9 account for or other wise offset losses attributab le to
10 proposed remedies in the consolidated Delta Smelt and

11 Salmon c ases. See 4/7/10 Tr. 17:10-20:14.
12
118. The quan tity of expo rtabl e wa ter has been
13
reduced by the imple mentation of the Salmonid and Smelt
14
BiOp’s R PAs. Id. From J anuary 20 through March 24,
15
2010, Mr . Erlewine t estified that potential and a ctual
16
17 exports were diminis hed by 522,561 acre fee t (“AF ”), o f
18 which a 433,000 AF l oss was attributable to the S WP and a

19 89,000 A F loss was a ttributable to the CVP. 4/6/ 10 Tr.
20
185:16-1 9; SWC Demon strative Ex. 903.
21
119. DWR made its initial water supply allocation
22
announce ment o n November 30, 2009, allocating 5% of Table
23
A contra cted amounts for SWP water contractors. 4/6/10
24
25 Tr. 240: 16-22; SWC Ex. 923, Ex. B. As of March 3 0, 2010,
26 DWR incr eased the SW P allocation for 2010 to 20%. 4/6/10
27 Tr. 189: 15-17; SWC Ex. 938; 4/1/10 Tr. 249:22-25. On

28
75
1 April 23 , 2010, DWR again increased its allocatio n of SWP

2 deliveri es to 30%. See Doc. 323-2 (DWR Pre ss Release) .
3
120. Reclamat ion announce d its initial allocation of
4
CVP wate r on Februar y 26, 2010. Fed. Gov’t Salmo n Ex. 5
5
(Third M illiga n Decl.) at ¶11. Under the 90% exceedance
6
forecast , Reclamatio n allocated CVP agricultural users 5%
7
8 of their contract am ounts, and CVP municipal and
9 industri al (“M&I”) c ontractors 55% of their contr act
10 amounts. Id. at ¶12. Under the 50% exceedance foreca st,

11 north-of -Delta agric ultural and M&I contractors w ere
12
allocate d 100% of th eir contract amounts, while s outh- of-
13
Delta ag ricultural c ontractors were allocated 30% and M&I
14
contract ors 75%. Id.
15
121. CVP wate r users face d similar reducti ons to
16
17 their in dividual all ocations. Farmers on the wes t side
18 of the S an Joaquin V alley have received reduced C VP water

19 supply a llocations i n the 2007-2008, 2008-2009, a nd 20 09-
20
2010 wat er years, an d face similar reductions in 2010-
21
2011. S LDMWA Ex. 153 at ¶3; SLDMWA E x. 154 at ¶4; SLD MWA
22
Ex. 156 at ¶4. In 2 007-2008, Reclamation allocated to
23
Westland s 40% of its contract supply. In 2008-2009, that
24
25 allocati on was 10%. SLDMWA Ex. 155 at ¶8. For t he 2009-
26 2010 wat er year, Wes tlands was advised the initial
27 allocati on was zero percent. SLDMWA Ex. 155 at ¶ 9.

28
76
1 122. On March 16, 2010, R eclamation raised the

2 allocati on for south-of-Delta agricultural users to 25 %
3
under a 90% forecast and 30% under a 50% forecast .
4
4/1/10 T r. 210:14-22; Fed . Gov’t Salm on Exh . 13.
5
123. These in cremental in creases do not alter the
6
fact tha t water deli veries will likely increase f urther
7
8 if the t wo RPAs are enjoined. 4/1/10 Tr. 213:14- 20
9 (acknowl edging that deliveries would increase by 5% - 10%
10 if the R PAs we re enjoined).

11 124. The quan tity of wate r lost through pumping
12
reductio ns translate s directly into water losses for
13
urban an d agricultur al water users. In the SWP s ervice
14
area, on e acre-foot of water serves about five to seven
15
people f or one year. 4/6/10 Tr. 186:25-187 :1-3. An S WP
16
17 loss of 433,000 AF, if available to urban users, would
18 have sup plied approx imately 2.6 million people fo r one

19 year. 4 /6/10 Tr. 18 7:8-11. Seventy-five to eighty-fi ve
20
percent of SWP suppl y is provided for urban uses, with
21
the rema inder provid ed to agricultural users. 4/ 6/10 Tr.
22
187:15-1 7. The Metr opolitan Water District of So uthern
23
Californ ia alone ser ves approximately 20 million urban
24
25 users.
26 125. Water lo ss for agric ultural users results in
27 reductio n in t he num ber o f acres that may b e sustained

28
77
1 with act ual water su pply. Water duty is the amou nt of

2 water th at a crop ne eds per acre for a growing se ason.
3
4/6/10 T r. 187:21-22. DW R information indi cates that for
4
the SWP service area , the water duty is approxima tely
5
three AF per acre. 4/6/10 Tr. 187:22-25. If 433,000 AF
6
were wit hheld from a lmond crops, for example, alm ond
7
8 producti on would be reduced by approximately 140, 000
9 acres. 4/6/10 Tr. 1 88:1- 4.
10 126. Reduced CVP and SWP water supply allocations

11 have inc reased the c ost of supplemental water. F armers
12
have bee n forced to purchase supplemental water a t
13
drastica lly increase d cost. SLDMWA Ex. 154 at ¶7 ; SLDMWA
14
Ex. 155 at ¶17; SLDM WA Ex. 156 at ¶6. Since 2007 , the
15
cost of securing sup plemental water has mor e than
16
17 tripled. SLDMWA Ex. 156 at ¶6; SLDMWA Ex. 154 at ¶7. As
18 of Janua ry 2010, the cost for buying replacement water

19 for tran sfer in a dr y year is at least $300 per a cre
20
foot, pl us transport ation costs. SLDMWA Ex. 157 at ¶12.
21
127. Increase d water allo cations may lessen this
22
increase d cost, and will mitigate anticipated har ms from
23
reduced water alloca tions. Farmers anticipate th at
24
25 increase d water allo cations would mitigate antici pated
26 damage t o crops in p roportion to the amount of wa ter
27 received and prevent further layoffs of farm empl oyees.

28
78
1 SLDMWA E x. 156 at ¶1 0.
2 128. In 2009, the Federal Defendants accounted for
3
actions taken under the Delta smelt biological op inion as
4
(b)(2) a ctions, purs uant to section 3406(b)(2) of the
5
CVPIA. 4/1/10 Tr. 2 13:24-214 :2. Federal Defendants h ave
6
indicate d their inte nt to follow the same account ing
7
8 procedur e for federa l export reductions related t o both
9 BiOps in 2010, to th e extent that (b)(2) assets a re
10 availabl e at the tim e the act ion is taken. Id. at 214:3-

11 7.
12
13 (2) Other Re source Impac ts Caused or Exacerbated by
the 2008 Smelt BiOp RPA Actions.
14
129. Plaintif fs attribute a number of other human
15
impacts to reduction s in the water supply. There is
16
consider able dispute among the parties rega rding the
17
extent t o which the 2008 Smelt BiOp RPA is respon sible
18
19 for thes e other impa cts. It is undisputed that t he RPA
20 is, at t he very leas t, exacerbating the following
21 impacts.
22
23 (1) Permanen t Crops.
24 130. Reductio ns in the qu antity of water supply
25 deliveri es have resu lted in changes to farming pr actices,
26 includin g an increas ed reliance on permanent crop s.

27 SLDMWA E x. 154 at ¶6 ; SLDMWA Ex. 155 at ¶¶ 18, 22 ; SLDMWA
28
79
1 Ex. 157 at ¶11.

2 131. Permanen t crops plac e farmers at greater ri sk
3
than row crops, as f armers cannot cut back on the water
4
to perma nent crops w ithout destroying them. SLDM WA Ex.
5
154 at ¶ 6; SLDMWA Ex . 155 at ¶¶ 18, 22; SLDMWA Ex . 157 at
6
¶11.
7
8
(2) Fallowed Lands.
9
132. Because of reduced w ater forecasts and
10
uncertai nty regardin g future water supply, farmer s have
11
fallowed hundreds an d thousands of acres of field s.
12
13 SLDMWA E x. 155 at ¶1 0; SLDMWA Ex. 153 at ¶3; SLDM WA Ex.
14 156 at ¶ 5.
15 133. Fallowed lands and r educed water supply have

16 caused t he loss of thousa nds of acres of cr ops. Todd
17
Allen, a third-generation farmer in Fresno County, was
18
able to salvage and harvest only 40 acres of a wh eat crop
19
out of a total arabl e 616 acres on his farm in 20 09.
20
SLDMWA E x. 153 at ¶3 .
21
22 134. For ever y 1,000 AF of water lost by the San Luis
23 Plaintif fs’ member a gencies, approximately 400 ac res of
24 land may remain out of production. SLDMWA Ex. 15 7 at

25 ¶13.
26
135. Fallowin g fields als o negatively impacts the air
27
quality of the San J oaquin Valley by increasing dust a nd
28
80
1 particul ate matter. SLDMWA Ex. 155 at ¶20. Redu ced air
2 quality in turn impa irs major transportation rout es
3
through the valley. SLDMWA Ex. 155 at ¶20.
4
5 (3) Lack of Access to Cr edit.
6 136. The more unreliable the water supply, the more
7 difficul t it is for farmers to secure necessary f inancing

8 for thei r farming op erations. SLDMWA Ex. 153 at ¶4;
9
SLDMWA E x. 154 at ¶1 3; SLDMWA Ex. 155 at ¶26; SLD MWA Ex.
10
156 at ¶ 7; SLDMWA Ex . 157 at ¶15. In some cases, lenders
11
deny loa n applicatio ns becaus e of a lack of reliable
12
13 water su pply. SLDMW A Ex. 153 at ¶4; SLDMWA Ex. 1 54 at
14 ¶13; SLD MWA Ex. 155 at ¶26; SLDMWA Ex. 156 at ¶7; SLDMWA
15 Ex. 157 at ¶15. In others, lenders’ concerns abo ut

16 availabi lity to land s irrigated by federally-supplied
17
water ha s requ ired farmers to make a 50% down pay ment to
18
secure a ny loans. S LDMWA Ex. 156 at ¶7.
19
20 (4) Social D isruption an d Dislocation.
21 137. It is un disputed tha t farm employees and their
22 families have faced devastating losses due to red uctions
23
in the a vailab le water supply. The impact on the farm
24
economy from the com bination of a three-yea r drou ght a nd
25
diversio n limitation s relating to the delta smelt has
26
already been severe. SLDMWA Ex. 157 at ¶14.
27
28 138. Lost wat er supply ha s decreased the number of
81
1 producti ve agricultu ral acres, which has resulted in

2 reductio ns in employ ee hours, salaries, and posit ions,
3
devastat ing farm emp loyees and their families. S LDMWA
4
Ex. 154 at ¶11; SLDM WA Ex. 156 at ¶8.
5
139. The remo val of 250,0 00 acres from pro ductio n
6
translat es to a loss of approximately 4,200 perma nent
7
8 agricult ural worker positions. SLDMWA Ex. 155 at ¶19.
9 Water sh ortages also cause jobs to be lost in
10 agricult ure-re lated businesses, such as packing sheds,

11 processi ng plants, a nd other related servic es. Id. The
12
projecte d agricultur e-rel ated wage loss for the S an
13
Joaquin Valley stand s at $1.6 billion. Id.
14
140. Dr. Mich ael, Defenda nt Intervenors’ economist
15
with exp ertise in re gional and environmental econ omics,
16
17 counters that “[a]lthough water impacts hav e affected
18 parts of the west si de, there is no evidence that reduced

19 water de liveries hav e had a severe effect on farm or non-
20
farm emp loyment in t he Central Valley as a whole. ” D- I
21
Exh. 100 6 (Michael D ecl.) ¶10. Instead, it is a
22
combinat ion of facto rs, including the three-year droug ht,
23
the glob al economic recession, the foreclosure cr isis,
24
25 and the collapse of the real estate market and
26 construc tion industr y, not RPA Component 3, that are
27 mainly d riving crop and job losses, food bank nee ds, a nd
28
82
1 credit p roblems in t he Central Valley. Id. at ¶¶ 6-10 .

2 Dr. Mich ael estimate s that ESA-related pump ing
3
restrict ions have re sulted in the loss of less th an 2,000
4
jobs. S ee id. at ¶4.
5
141. Unemploy ment has led to hunger on the west side
6
of the S an Joaquin V alley. SLDMWA Ex. 158 at ¶8. The
7
8 Communit y Food Bank, serving Fresno, Madera and K ings
9 Counties , estimates 435,000 people in its service area do
10 not have a reliable source of food. SLDMWA Ex. 1 58 at

11 ¶4. The Chief Execu tive Offi cer of the Community Food
12
Bank, Da na Wilkie, b elieves that hunger in the
13
communit ies served b y the Food Bank in the wester n San
14
Joaquin Valley will continue to increase in 2010 because
15
of ongoi ng water sho rtages. SLDMWA Ex. 158 at ¶5 . Ms.
16
17 Wilkie u nderst ands that at least 42,000 people served by
18 the Food Bank in Oct ober 2009 were employed by fa rm-

19 related businesses b efore losing their jobs. SLD MWA Ex.
20
158 at ¶ 8.
21
22 (5) Groundwa ter Consumpt ion and Overdraft.
23 142. Reductio ns in the av ailable water supply have
24 caused w ater users t o increase groundwater pumpin g in

25 attempts to make up the difference between irriga tion
26
need and allocated w ater supplies. SLDMWA Ex. 15 5 at ¶¶
27
4, 7; SL DMWA Ex. 157 at ¶10; 4/6/10 Tr. 216:6-7.
28
83
1 143. However, groundwater is not always availabl e,

2 and cann ot be used i n all areas or for all crops. SLDMWA
3
Ex. 155 at ¶11. Inc reased groundwater pumping re duces
4
the qual ity of water applied to the soil by incre asing
5
soil sal inity. SLDM WA Id. at ¶15. Not all fields and
6
crops can be i rrigated with groundwater. Id. at ¶¶ 11 ,
7
8 15.
9 144. Increase d reliance o n and overuse of groundwater
10 has caus ed groundwat er overdraft, which occurs wh en

11 pumping exceeds the safe yield of an aquifer. Id. at
12
¶12. Ov erdraft caus es increased land subsidence and
13
potentia l damage to CVP conveyance facilities, id. at ¶¶
14
12-13, althoug h it is not clear that any subsidence of
15
Project facilities h as occurred as a result of th e
16
17 implemen tation of th e 2008 Smelt BiOp RPA Actions , as the
18 only rep orted incide nt of subsidence at a S WP conveyan ce

19 facility predates cu rrent implementation, 4/7/10 Tr.
20
16:1-13.
21
145. Increase d groundwate r pumping also increases
22
demand f or energy. SLDMWA Ex. 155 at ¶16. Due t o the
23
falling water table, wells require increase d amou nts o f
24
25 energy. Id. Westlands estimates that pumping of
26 groundwa ter in 2009 required approximately 425,00 0,000
27 kWh. Id . Adverse e nvironmental impacts are asso ciated

28
84
1 with suc h increased demand for and use of energy. Id.

2 146. Increase d groundwate r pumping has depleted
3
groundwa ter reserves . Groundwater reserves that were at
4
2 millio n AF in the beginning of 2007 are now les s than
5
900,000 AF. 4/6/10 Tr. 216:21-24. Within MWD’s servi ce
6
area, st orage levels are at 1.3 million AF, about half of
7
8 normal s torage level s. 4/6/10 Tr. 217:4-8.
9
(6) Related, Recent Impa cts on Naval Air
10 Station Lemoore.
11 147. Captain James Knapp testified as a fact witness
12 on behal f of Naval A ir Station Lemoore, which is located

13 approxim ately 30 miles south of Fresn o, eig ht miles we st
14
of the t own of Lemoo re, California. 4/7/10 Tr. 2 08:12-
15
14. Its daytime pop ulation is approximately 14,0 00
16
people, includ ing residents, who are sailors and
17
dependen t families. Id. at 2 08:15-21.
18
19 148. The air station’s lo cation was selected at a
20 time whe n the Navy w as transitioning from propell er-
21 driven a ircraft to j et aircraft, the latter being

22
incompat ible with ur ban environments such as the Naval
23
Air Stat ion Alameda in the San Francisco Bay Area . Id .
24
at 211:1 7-212: 21. T he ai r station’s 18,000 acres of
25
agricult ure-co mpatible land and neighboring land under
26
27 permanen t agricultur al easements help to ensure t here
28 will be no urban bui ld-out to interfere with the Navy’s

85
1 operatio ns. I d. at 211:17-212:21, 213:2-19. From its

2 location , the instal lation supports aircraft carr ier
3
activiti es along the Pacific Coast. Id.
4
149. Active a gricultural operations on the air
5
station’ s 18,000 acr es and in the surrounding are as also
6
serve “t o control bi rd and animal strike hazards, gras s
7
8 fires, r odent activi ty, dust, and the release of
9 Coccidio idomycosis ( Valley Fever) spores carried by
10 dust.” SLDMWA Ex. 3 90 at p. 3. These risks are

11 interrel ated; for ex ample, fallowed fields attrac t
12
rodents and predator y birds. 4/7/10 Tr. at 213:10-25.
13
An incre ased bird pr esence increases the chances of bird
14
strikes by naval air craft. Id. at 214:1-6.
15
150. Ongoing agricultural activities are v itally
16
17 importan t to the Nav y’s ability to safely train a nd
18 support flight operations at Naval Air Stat ion Le moore .

19 4/7/10 T r. at 214:7- 24; S LDMWA EX. 390 at p . 2.
20
151. Lemoore Naval Air St ation’s principal source of
21
municipa l, industria l, and agricultural water is
22
Westland s Water Dist rict. 4/7/10 Tr. 208:24-209:2.
23
152. The past water year began with a zero percent
24
25 water al location whi ch increased to a ten percent
26 allocati on, resultin g in 6,000 acres of fallow fi elds.
27 SLDMWA E x. 390 at p. 3. Pilots training at low a ltitude

28
86
1 witnesse d an increas e in bird activity, wit h one aircr aft

2 sufferin g thousands of dollars in damage as a res ult of a
3
bird str ike. Id.
4
43. Captain Knapp testif ied that Naval Air Station
5
Lemoore had requeste d and received emergency supp lemental
6
water al locations fr om Reclamation for these propertie s.
7
8 Id. at 2 10, 21 7-18; SLDMWA Ex. 391.
9 44. This pos t-reco rd evi dence is received for t he
10 limited purpose of s howing the action agency’s ab ility to

11 respond to condition s that pose imminent harm to the
12
human en vironment.
13
14 (3) Harm to Species.
15 45. To the extent such infor mation is in the r ecord,
16 the pote ntial harms to the species of enjoining C omponent

17 2 (Actio n 3) a re dis cusse d above.
18
19 VI. CONCLUSI ONS OF LAW 1.
20 A. Jurisdic tion.
21 1. Jurisdic tion over cl aims brought unde r NEPA
22 exists u nder 28 U.S. C. § 1331 (Federal Question) and the

23 Administ rative Proce dure Act (“APA”), 5 U.S.C. § 702 et
24
seq. Ju risdiction o ver the ESA claims exists und er the
25
ESA citi zen-su it provision, 16 U.S.C. § 1540(g)(1)(A).
26
Personal jurisdiction over all the pa rties exists by
27
virtue o f their part icipation in the lawsuit as
28
87
1 Plaintif fs, Defendan ts, and Intervenors.

2
B. Likeliho od of Succes s on the Merits: NEPA Claims.
3
2. Plaintif fs have alre ady succeeded on their NEPA
4
5 claim. See Do c. 399.
6 3. NEPA ins ures that fe deral agencies “make
7 informed decisions a nd ‘contemplate the environme ntal

8 impacts of [their] a ctions.’” Ocean Mammal Inst. v.
9
Gates, 5 46 F. Supp. 2d 960, 971 (D. Hi. 200 8) (qu oting
10
Idaho Sp orting Cong. v. Thomas, 137 F .3d 1146, 1149 (9 th
11
Cir. 199 8).
12
4. “NEPA em phasizes the importance of coherent and
13
14 comprehe nsive up-front en vironmental analys is to insure
15 informed decision-making to the end that th e agen cy wi ll
16 not act on incomplet e information, only to regret its

17 decision after it is too late to correct.” Ctr. for
18
Biologic al Diversity v. U.S. Forest Serv., 349 F.3d 11 57,
19
1166 (9t h Cir. 2003) .
20
5. Federal Defendants’ violations of NEPA prevented
21
22 the requ ired reasona ble evaluation, analysis, “ha rd look
23 at,” and disclosure of the harms of implementing the 2008
24 Smelt Bi Op RPA Actio ns to human health and safety , the

25 human en vironment, a nd other environments not inh abited
26
by the d elta smelt.
27
6. Harms th at have been caused by RPA water supply
28
88
1 reductio ns include b ut are not limite d to: destruction of

2 permanen t crops; fal lowed lands; increased ground water
3
consumpt ion; land su bsidence; reduction of air qu ality;
4
destruct ion of famil y and entity farming business es; and
5
social d isruption an d dislocation, such as increa sed
6
property crime and i ntra- family crimes of violenc e,
7
8 adverse effects on s chools, and increased unemplo yment
9 leading to hunger an d homelessness.
10 7. Where a federal agen cy takes action in violation

11 of NEPA, “that actio n will be set asi de.” High Sierra
12
Hikers A ss’n v. Blac kwell, 390 F.3d 630, 640 (9th Cir.
13
2004).
14
8. However, a court may not issue an injunction
15
under NE PA that woul d cause a violation of other
16
17 statutor y requiremen ts, such as those found in se ction 7
18 of the E SA. S ee United States v. Oakland Cannabis

19 Buyers’ Coop., 532 U.S. 483, 497 (2001) (“A district
20
court ca nnot, for ex ample, override Congress’ pol icy
21
choice, articulated in a statute, as to what beha vior
22
should b e prohibited .”). Nor should an injunctio n issue
23
under NE PA when enjo ining government action would result
24
25 in more harm to the environment than denying inju nctive
26 relief. Save Our Ec osystems v. Clarke, 747 F.2d 1240,
27 1250 (9t h Cir. 1984) ; Am. Motorcyclis t Ass’ n v. Watt, 714

28
89
1 F.2d 962 , 966 (9th C ir. 1983) (holding publ ic int erest
2 does not favor grant ing an injunction where “gove rnment
3
action a llegedly in violation of NEPA might actua lly
4
jeopardi ze natural r esources”); Alpin e Lake s Prot. Soc ’y
5
v. Schla pfer, 518 F.2d 1089, 1090 (9th Cir. 1975)
6
(denying injun ctive relief in NEPA case where more har m
7
8 could oc cur to fores t from disease if injunction was
9 granted) .
10
C. Likeliho od of Succes s on the Merits: ESA Claims.
11
(1) Legal St andards.
12
9. The Admi nistrative P rocedure Act (“APA”) requires
13
Plaintif fs to show t hat FWS’s action was “a rbitrary,
14
15 capricio us, an abuse of discretion, or otherwise not in
16 accordan ce with law. ” 5 U.S.C. § 706(2)(A).
17
a. Record R eview.
18
10. A court reviews a bi ological opinion “based upon
19
the evid ence contain ed in the administrative record.”
20
21 Arizona Cattle Growe rs’ Ass’n v. FWS, 273 F .3d 12 29, 1 245
22 (9th Cir . 2001). Ju dicial review under the APA m ust

23 focus on the adminis trative record already in exi stence,
24
not some new record made initially in a reviewing court.
25
Parties may not use “post -dec ision information as a ne w
26
rational ization eith er for sustaining or attackin g the
27
agency’s decision.” Ass’n of Pac. Fi sherie s v. EPA, 615
28
90
1 F.2d 794 , 811- 12 (9th Cir. 1980).

2 11. Exceptio ns to admini strative record review for
3
technica l info rmation or expert explanation make such
4
evidence admissible only for limited purposes, an d those
5
exceptio ns are narro wly construed and applied. Lands
6
Council v. Powell, 395 F. 3d 1019, 1030 (9th Cir. 2005).
7
8 12. Here, th e Court has considered expert testi mony
9 only for explanation of technical terms and compl ex
10 subject matter beyon d the Court’s knowledge; to

11 understa nd the agenc y’s explanations, or lack the reof,
12
underlyi ng the RPA; and to determine if any bad f aith
13
existed.
14
15 b. Deferenc e to Agency Exper tise.
16 13. The Cour t must defer to the agency on matters
17 within t he agency’s expertise, unless the agency
18
complete ly failed to address some factor, conside ration
19
of which was essenti al to making an informed deci sion.
20
Nat’l Wi ldlife Fed’n v. NMFS, 422 F.3 d 782, 798 ( 9th Cir.
21
22 2005). The court “m ay not substitute its judgmen t for
23 that of the agency c oncerning the wisdom or prude nce of
24 the agen cy’s action. ” River Runners for Wilderne ss v.

25 Martin, 593 F.3d 106 4, 1070 (9th Cir. 2009).
26
In condu cting an APA revi ew, the court must
27 determin e whether th e agency’s decision is
“founded on a ration al connection between the
28 facts fo und and the choices made ... and whether
91
1 [the age ncy] has com mitted a clear error of

judgment .” Ariz. Cattle Growers’ Ass’n v. U.S.
2 Fish & W ildlife, 273 F.3d 122 9, 1243 (9th C ir.
2001). “The [agency ’s] action ... need be only
3 a reason able, not th e best or most reasonable,
decision .” Nat’l Wildlife Fed. v. Burford, 871
4 F.2d 849 , 855 (9th C ir. 1989).
5 Id.
6 14. Although deferential , judicial review under the
7
APA “is designed to ensure that the agency consid ered all
8
of the r elevant fact ors and that its decision con tained
9
no clear error of ju dgment.” Arizona v. Thomas, 824 F.2d
10
745, 748 (9th Cir. 1 987) (internal citations omitted).
11
12 “The def erence accor ded an agency’s scientific or
13 technica l expertise is not unlimited.” Bro wer v. Evan s,
14 257 F.3d 1058, 1067 (9th Cir. 2001) (internal cit ations
15 omitted) . Deference is not owed when “the agency has
16
complete ly failed to address some fac tor consider ation of
17
which wa s essential to making an informed decisio n.” Id.
18
(interna l citations and quotations omitted).
19
[An agen cy’s decisio n is] arbitrary and
20 capricio us if it has relied on factors which
Congress has not int ended it to consider,
21 entirely failed to c onsider an important aspect
of the p roblem, offe red an explanation for its
22 decision that runs c ounter to the evidence
before t he agency, o r is so implausible that it
23 could no t be ascribe d to a difference in view or
the prod uct of agenc y expertise.
24
Motor Ve hicle Mfrs. Ass’n of U.S. v. State Farm M ut.
25
26 Auto. In s. Co., 463 U.S. 29, 43 (1983); see also Citiz ens
27 to Prese rve Overton Park, Inc. v. Volpe, 401 U.S. 402,

28
92
1 416 (197 1) (“A revie wing court may overturn an ag ency’s

2 action a s arbitrary and c apricious if the a gency failed
3
to consi der relevant factors, failed to base its decision
4
on those factors, an d/or made a clear error of
5
judgment .”).
6
7 c. General Obligations Under the ESA.
8 15. ESA Sect ion 7(a)(2) prohibits agency action that
9
is “like ly to jeopar dize the continued existence” of any
10
endanger ed or threat ened species or “result in th e
11
destruct ion or adver se modification” of its criti cal
12
habitat. 16 U.S.C. § 1536(a)(2).
13
14 16. To “jeop ardize the c ontinued existence of” means
15 “to enga ge in an act ion that reasonably would be
16 expected , directly o r indirectly, to reduce appre ciably

17 the like lihood of bo th the survival and recovery of a
18
listed s pecies in th e wild by reducing the reprod uction,
19
numbers, or distribu tion of that species.” 50 C.F.R. §
20
402.02; see also Nat ’l Wildlife Fed’n v. NMFS, 524 F.3d
21
22 917 (9th Cir. 2008) (“NWF v. NMFS II”) (rej ecting agen cy
23 interpre tation of 50 C.F.R. § 402.02 that in effe ct
24 limited jeopardy ana lysis to survival and did not

25 realisti cally evalua te recove ry, thereby avoiding an
26
interpre tation that reads the provision “and reco very”
27
entirely out of the text). An action is “jeopard izing”
28
93
1 if it ke eps recovery “far out of reach,” even if the

2 species is able to c ling to survival. Id. at 931 .
3
17. “[A]n a gency may no t take action that will tip
4
a specie s from a sta te of precarious survival int o a
5
state of likely exti nction. Likewise, even where
6
baseline conditions already jeopardize a species, an
7
8 agency m ay not take action that deepens the jeopa rdy by
9 causing additional h arm.” Id. at 930 .
10 18. To satis fy this obli gation, the federal agency

11 undertak ing the acti on (the “action agency”) must prepare
12
a “biolo gical assess ment” that evaluates the acti on’s
13
potentia l impacts on species and species’ h abitat . 16
14
U.S.C. § 1536(c); 50 C.F.R. § 402.12(a).
15
19. If the p roposed acti on “is likely to adversely
16
17 affect” a threatened or endangered species or adv ersely
18 modify i ts designate d critical habitat, the actio n agency

19 must eng age in “form al consul tation” with FWS to obtai n
20
its biol ogical opini on as to the impacts of the p roposed
21
action o n the listed species. 16 U.S.C. § 1536(a)(2),
22
(b)(3); see also 50 C.F.R. § 402.14(a), (g) . Onc e the
23
consulta tion process has been completed, FWS must give
24
25 the acti on age ncy a written biological opinion “setting
26 forth [F WS’s] opinio n, and a summary of the infor mation
27 on which the opinion is based, detailing how the agency

28
94
1 action a ffects the s pecies or its critical habita t.” 16

2 U.S.C. § 1536(b)(3)( A); see a lso 50 C.F.R. § 402.14(h) .
3
20. If FWS d etermines th at jeopardy or destruction
4
or adver se modificat ion of critical habitat is li kely,
5
FWS “sha ll suggest t hose reasonable and prudent
6
alternat ives which [ it] believes would not violat e
7
8 subsecti on (a)(2) of this section and can b e taken by the
9 Federal agency or ap plicant in implementing the a gency
10 action.” 16 U.S.C. § 153 6(b) (3)(A). “Following the

11 issuance of a ‘jeopa rdy’ opinion, the agency must either
12
terminat e the action , implement the proposed alte rnati ve,
13
or seek an exemption from the Cabinet-level Endangered
14
Species Committee pu rsuant to 16 U.S.C. § 1536(e) .”
15
National Ass’n of Ho me Builders v. Defenders of W ildlife,
16
17 551 U.S. 644, 652 (2 008).
18
d. Best Ava ilable Scien ce.
19
21. Under th e ESA, an ag ency’s actions mu st be based
20
on “the best scienti fic and commercial data avail able.”
21
22 16 U.S.C . § 1536(a)( 2); 50 C.F.R. § 402.14(g)(8) (“In
23 formulat ing its Biol ogical Opinion, any reasonabl e and
24 prudent alternatives , and any reasonable and prud ent

25 measures , the Servic e will use the best scientifi c and
26
commerci al data avai lable.”). “The obvious purpo se of
27
the [bes t available science requirement] is to en sure
28
95
1 that the ESA not be implemented haphazardly, on t he basis

2 of specu lation or su rmise.” Bennett v. Spear, 520 U.S.
3
154, 176 (1997). A failure by the agency to util ize the
4
best ava ilable scien ce is arbitrary and capriciou s. See
5
Gutierre z II, 606 F. Supp. 2d at 1144.
6
22. A decisi on about jeo pardy must be made based on
7
8 the best science ava ilable at the tim e of the dec ision;
9 the agen cy cannot wa it for or promise future stud ies.
10 See Ctr. for B iological Diversity v. Rumsfeld, 198 F.

11 Supp. 2d 1139, 1156 (D. Ariz. 2002).
12
23. The “bes t available science” mandate of the ESA
13
sets a b asic standard that “prohibits the [ agency] fro m
14
disregar ding availab le scientific evidence that i s in
15
some way better than the evidence [it] relies on. ” Am.
16
17 Wildland s v. Kemptho rne, 530 F.3d 991, 998 (D.C. Cir.
18 2008) (c itation omit ted).

19 24. What con stitutes the “best” available scien ce
20
implicat es core agen cy judgment and expertise to which
21
Congress requires th e courts to defer; a court sh ould be
22
especial ly wary of o verturning such a determinati on on
23
review. Baltimore G as & Elec. Co. v. Natural Res .
24
25 Defense Council, 462 U.S. 87, 103 (1983) (a court must be
26 “at its most deferen tial” when an agency is “maki ng
27 predicti ons within i ts area of special expertise, at the

28
96
1 frontier s of science ”). As explained by the en b anc

2 panel of the Ninth C ircuit in Lands C ouncil, 537 F.3d at
3
993, cou rts may not “impose on the agency their o wn
4
notion o f which proc edures are best or most likel y to
5
further some vague, undefined public good.” Id. In
6
particul ar, an agenc y’s “scientific methodology i s owed
7
8 substant ial deferenc e.” Gifford Pinc hot Task For ce v.
9 U.S. Fis h & Wildlife Serv., 3 78 F.3d 1059, 1066 (9th C ir.
10 2004).
11 25. This def erence exten ds to the use and
12
interpre tation of st atistical methodologies. As
13
explaine d by the D.C . Circuit in Appalachia n Power Co. v.
14
EPA, 135 F.3d 791 (D .C. Cir. 1998), i n reviewing a
15
challeng e to a decis ion of the Environmental Prot ection
16
17 Agency ( “EPA”) under the “arbitrary and capriciou s”
18 standard of review:
19 Statisti cal analysis is perhaps the prime
example of those are as of technical wildern ess
20 into whi ch judicial expeditions are best limited
to ascer taining the lay of the land. Although
21 computer models are “a useful and often
essentia l tool for p erforming the Herculean
22 labors C ongress impo sed on EPA in the Clean Air
Act,” [c itation] the ir scientific nature does
23 not easi ly lend itse lf to judicial review. Our
consider ation of EPA ’s use of a regression
24 analysis in this cas e must therefore comport
with the deference t raditionally given to an
25 agency w hen reviewin g a scientific analysis
within i ts area of e xpertise without abdicating
26 our duty to ensure t hat the application of this
model wa s not arbitr ary.
27
Id. at 802.
28
97
1 26. More gen erally, “[w] hen specialists express

2 conflict ing views, a n agency must have discretion to rely
3
on the r easona ble opinions of its own qualified experts
4
even if, as an origi nal matter, a court might fin d
5
contrary views more persuasive.” Lan ds Council, 537 F.3d
6
at 1000 (quoting Marsh v. Oregon Natural Re s. Cou ncil,
7
8 490 U.S. 360, 378 (1 989)).
9 27. Mere unc ertainty, or the fact that evidence may
10 be “weak ,” is not fa tal to an agency decision.

11 Greenpea ce Action v. Franklin, 14 F.3d 1324 , 1337 (9th
12
Cir. 199 2) (upholdin g biological opinion, despite
13
uncertai nty about th e effectiveness of management
14
measures , beca use decision was based on a reasonable
15
evaluati on of all av ailable data); Nat’l Wildlife Fed' n
16
17 v. Babbi tt, 12 8 F. S upp. 2d 1274, 1300 (E.D . Cal. 2000 )
18 (holding that the “m ost reasonable” reading of th e best

19 scientif ic data avai lable standard is that it “permits
20
the [FWS ] to take ac tion based on imperfect data, so long
21
as the d ata is the b est available”).
22
28. The defe rence afford ed under the best available
23
science standard is not unlimited. For example, Tucson
24
25 Herpetol ogical Socie ty v. Salazar, 566 F.3d 870, 879 ( 9th
26 Cir. 200 9), held tha t an agency may not rely on
27 “ambiguo us studies a s evidence” to support findin gs made

28
98
1 under th e ESA. Beca use the studies did not lead to the
2 conclusi on reached b y FWS, the Ninth Circuit held that
3
these st udies provided in adequate support i n the
4
administ rative recor d for the determination made by FWS.
5
Id.; see also Rock Creek Alliance v. U.S. F ish & Wildl ife
6
Service, 390 F. Supp . 2d 993 (D. Mont. 2005) (rej ecting
7
8 FWS’s re liance on a disputed scientific report, w hich
9 explicit ly stated it s analysis was not applicable to the
10 small po pulations ad dressed in the challenged opi nion);

11 Greenpea ce v. NMFS, 80 F. Supp. 2d 1137, 11 49-50 (W.D.
12
Wash. 20 00) (where a gency totally failed to devel op any
13
projecti ons regardin g population viability, it co uld n ot
14
use as a n excuse the fact that relevant data had not been
15
analyzed ).
16
17 29. The pres umption of a gency expertise may be
18 rebutted if the agen cy’s decisions, although base d on

19 scientif ic expertise , are not reasoned. Greenpeace, 80
20
F. Supp. 2d at 1147. Agencies cannot disregard a vailable
21
scientif ic evidence better than the evidence on w hich it
22
relies. Kern County Farm Bureau v. Allen, 450 F.3d 10 72,
23
1080 (9t h Cir. 2006) ; S.W . Ct r. for Biological Di versity
24
25 v. Babbi tt, 21 5 F.3d 58, 60 (D.C. Cir . 2000 ).
26 30. Courts r outinely per form substantive reviews of
27 record e vidence to e valuate the agency's treatmen t of

28
99
1 best ava ilable scien ce. The judicial review proc ess is
2 not one of blind acc eptance. See, e. g., Kern County, 450
3
F.3d 107 2 (thoroughl y reviewing three post-comment
4
studies and FWS’s tr eatment of those studies to d etermine
5
whether they “provid e[d] the sole, essential supp ort for”
6
or “mer ely suppleme nted” the data used to suppor t a
7
8 listing decision); Home Builders Ass’n of N . Cal. v. U .S.
9 Fish and Wildlife Se rv., 529 F. Supp. 2d 1110, 1120 (N .D.
10 Cal. 200 7) (examinin g substance of challenge to F WS’s

11 determin ation that c ertain data should be disrega rded);
12
Trout Un limited v. L ohn, 645 F. Supp. 2d 929 (D. Or.
13
2007) (f inding best available science standard had been
14
violated after thoro ugh examination of rationale for
15
NMFS’s d ecision to w ithdraw its proposal to list Oregon
16
17 Coast Co ho salmon); Ocean a, Inc. v. Evans, 384 F. Supp .
18 2d 203, 217-18 (D.D.C. 2005) (carefully considering

19 scientif ic underpinn ings of challenge to Service’ s use of
20
a partic ular model, including post decision evide nce
21
presente d by an expe rt, to help the court underst and a
22
complex model, apply ing one of several record rev iew
23
exceptio ns articulat ed in Esc h v. Yeutter, 876 F.2d 97 6,
24
25 991 (D.C . Cir. 1989) , which are similar to those
26 articula ted by the N inth Circuit).
27 31. Courts a re not requi red to defer to an agency

28
100
1 conclusi on that runs counter to that of other age ncies or

2 individu als with spe cialized expertise in a parti cular
3
technica l area. See, e.g ., Am. Turnb oat Ass’n v.
4
Baldrige , 738 F.2d 1 013, 1016-17 (9th Cir. 1984) (NMFS ’s
5
decision under the M arine Mammal Protection Act w as not
6
supporte d by substan tial evidence because agency ignored
7
8 data tha t was product of “many years’ effort by traine d
9 research personnel”) ; Sie rra Club v. U.S. Army Co rps of
10 Eng’rs, 701 F.2d 101 1, 1030 (2d Cir. 1983) (“court may
11 properly be skeptica l as to whether an EIS’s conc lusions
12
have a s ubstantial b asis in fact if the responsib le
13
agency h as apparentl y ignored the conflicting vie ws of
14
other ag encies havin g pertinent experience[]”) (i nternal
15
citation s omitted). A court should “reject concl usory
16
17 assertio ns of agency ‘expertise’ where the agency spurns
18 unrebutt ed expert op inions wi thout itself offering a

19 credible alternative explanation.” N. Spot ted Ow l v.
20
Hodel, 7 16 F. Supp. 479, 483 (W.D. Wash. 19 88) (c iting
21
Am. Turn boat Ass’n, 738 F .2d at 1016).
22
32. In Conner v. Burford, 848 F.2d 1441, 1453-54
23
(9th Cir . 1988), the agency attempted to de fend its
24
25 biologic al opinions by arguing that there was a l ack of
26 sufficie nt informati on. In rejecting this defens e, the
27 court he ld that “inc omplete information ... does not

28
101
1 excuse t he failure t o comply with the statutory

2 requirem ent of a comprehensive biological opinion usin g
3
the best information available,” and it noted tha t FWS
4
could ha ve completed more analysis with the infor mation
5
that was available. Id. at 1 454 (emphasis added). Th e
6
Ninth Ci rcuit stated :
7
8 In light of the ESA requi reme nt that the
agencies use the bes t scientific and commercial
9 data ava ilable ... t he FWS cannot ignore
availabl e biological info or fail to develop
10 projecti ons of ... a ctivities which may indicate
potentia l conflicts between development and the
11 preserva tion of prot ected species. W e hold that
the FWS violated the ESA by failing to use the
12 best inf ormation ava ilable to prepare
comprehe nsive biolog ical opinions.
13
848 F.2d at 1454 (em phasis added).
14
15 (2) Environm ental Baseli ne Challenges.
16 33. The rele vant regulat ory definition of the
17 “environ mental basel ine” is provided within the

18 definiti on of the “e ffects of the action”:
19
the dire ct and indir ect effects of an action on
20 the spec ies or criti cal habitat, together with
the effe cts of other activities that are
21 interrel ated or inte rdependent with that action,
that wil l be added t o the environmental
22 baseline . The envir onmental baseline includes
the past and present impacts of all Federal,
23 State, o r private ac tions and other human
activiti es in the ac tion area , the anticipa ted
24 impacts of all propo sed Federal projects in the
action a rea that hav e already undergone formal
25 or early section 7 c onsultation, and the impact
of State or private actions which are
26 contempo raneous with the consultation in
process.
27
50 C.F.R . § 402.02.
28
102
1 34. When det ermining the “effects of the action,”

2 the agen cy first mus t evaluate the status of the species
3
or criti cal habitat, which will involve “consider ation of
4
the pres ent environm ent” in which the species or habitat
5
exists a s well as “t he environment th at will exist when
6
the acti on is comple ted, in terms of the totality of
7
8 factors affecting th e species or critical habitat .” 51
9 Fed. Reg . 19,926, 19 ,932 (June 3, 1986). This ev aluation
10 is to se rve as the “ baseline” for determining the effe cts

11 of the a ction on the species or critical habitat. Id.
12
However, all of thes e elements are to be evaluate d
13
together as the “eff ects of the action.”
14
35. If addit ional data w ould provide a better
15
informat ion base fro m which to formul ate a biological
16
17 opinion, the consult ing agency (FWS or NMFS) may request
18 an exten sion of form al consultation and that the action

19 agency o btain additi onal data to determine how or to what
20
extent t he action ma y affect listed species or cr itical
21
habitat. 50 C.F.R. § 402.14(f); FWS and NMFS, En dangered
22
Species Consultation Handbook (March 1998) at 4-6. 8
23
36. The Nint h Circuit di rects the consulting agency
24
25 to consi der the effe cts of its actions “within th e
26 context of other exi sting human activities that impact
27 8
Ju di ci al n ot ic e ma y be ta ke n of t h is Ha nd bo ok , wh ic h is
ava il ab le a t:
28 htt p: // ww w. fw s. go v/ en dan ge re d/ co ns u lta ti on s/ s7 hn db k/ s7 hn dbk .h tm .
103
1 the list ed species.” NWF v. NMFS II, 524 F .3d at 930.

2 “[T]he p roper baseli ne analysis is not the propor tional
3
share of responsibil ity the federal agency bears for the
4
decline in the speci es, but what jeopardy might r esult
5
from the agency’s propose d actions in the p resent and
6
future h uman and nat ural contexts.” Id. The relevant
7
8 jeopardy analysis is whether this Project will ti p a
9 species into a state of “likely extinction.” 524 F.3d at
10 930.
11 Even und er the so-called aggregation approa ch
NMFS cha llenges, then, an agency only
12 “jeopard ize[s]” a sp ecies if it causes some new
jeopardy . An agency may still take action that
13 removes a species fr om jeopardy entirely, or
that les sens the deg ree of jeopardy. However, an
14 agency m ay not take action that will tip a
species from a state of precarious survival into
15 a state of likely ex tinction. Likewise, even
where ba seline condi tions already jeopardize a
16 species, an agency m ay not take action that
deepens the jeopardy by causing additional harm.
17
Our appr oach does not require NMFS to include
18 the enti re environme ntal baseline in the “agency
action” subject to r eview. It simply requires
19 that NMF S appropriat ely consider the effects of
its acti ons “within the context of other
20 existing human activ ities that impact the listed
species. ” [citation] . This approach is
21 consiste nt with our instruction (which NMFS does
not chal lenge) that “[t]he proper baseline
22 analysis is not the proportional share of
responsi bility the f ederal agency bears for the
23 decline in the speci es, but w hat jeopardy m ight
result f rom the agen cy's proposed actions in the
24 present and future h uman and natural contexts.”
[citatio n].
25
Id. (footnote omitted).
26
27 37. Plaintif fs’ es sentia l cri tiqu e of the BiOp’ s
28 baseline analysis is that the BiOp improperly conclude d

104
1 that “CV P and SWP op erations exacerbate the effec ts of

2 other fa ctors, such as food or predation on the d elta
3
smelt.” See D oc. 667, Pltf’s Proposed Conclusions of Law
4 9
## 316-1 8. Plaintiffs argue “FWS sim ply determined that
5
these fa ctors are attributable to CVP and SWP operations”
6
and ther efore “based the effects analysis of the 2008
7
8 BiOp upo n an unreaso ned premise.” Id. at Proposed
9 Conclusi on of Law # 343.
10 38. Plaintif fs are corre ct that the general

11 assertio n that Proje ct operations exa cerbate the effects
12
of these other stres sors is unsupported by the re cord.
13
However, the inclusi on of this unsupported assert ion does
14
not inva lidate the B iOp’s baseline analysis. BiOp at
15
140-189. FWS does discuss “other stressors” at length in
16
17 the BiOp . See , e.g., id. at 182-88, 198, 2 01-2.
18 Specific ally, FWS co nsidered the effects of “pred ation,

19 contamin ants, introd uced species..., habitat suitabili ty,
20
food sup ply, aquatic macrophytes, and microcystis .” Id.
21
at 202, 277. The CVP and SWP are not ident ified as th e
22
9
Pl ai nt if fs ’ mo ti on f or pr el im in ar y in ju nc ti on s pe ci fi ca lly
23 add re ss es t he t re at me nt of h at ch er i es an d gr av el l os s be low
Whi sk ey to wn D am . D oc . 1 64 a t 11 -1 2 . Ho we ve r, t hi s is su e w as n ot
24 pre se nt ed o r di sc us se d a t th e ev id e nti ar y he ar in g or i n Pla in ti ff s’
pro po se d fi nd in gs . T hes e sp ec if ic arg um en ts a pp ea r to h ave b ee n
25 aba nd on ed .
Pla in ti ff s al so a dv an ce an e la bo ra t e a rg um en t ba se d on t he
26 con te nt io n th at F WS m isa pp li ed t he “re as on ab ly c er ta in t o o cc ur ”
sta nd ar d ap pl ic ab le t o “ in di re ct e f fec ts ” an al ys es . B ec aus e
27 Com po ne nt 2 i s no t ex pli ci tl y ju st i fie d by a ny i nd ir ec t eff ec ts
ana ly si s, t hi s ar gu me nt is n ot d ir e ctl y re le va nt t o th e res ol ut io n
28 of th e pe nd in g mo ti on fo r pr el im in a ry in ju nc ti on .
105
1 sole sou rce of the d elta smelt’s problems. Rathe r, FWS

2 expressl y recognizes that the long-term decline of the
3
species “was very st rongly affected by ecosystem changes
4
caused b y nonindigenous species invasions and other
5
factors. ...” Id. at 189. The BiOp repeate dly
6
acknowle dges that th ere is “no single primary dri ver of
7
8 delta sm elt populati on dynamics,” id. at 202, but rath er
9 that the re are “mult iple factors” and that “not a ll are
10 directly influenced by operations of the CVP/SWP. ” Id .

11 at 328.
12
39. It is un disputed tha t uncertainty surrounding
13
the meas urement of t he other stressors makes it d ifficult
14
(if not impossible) to separate those effects fro m the
15
effects of joint Pro ject operations. Even if it were
16
17 possible to separate the quantitative effec t of the ot her
18 stressor s, which are part of the environmental ba seline,

19 the ESA does not req uire that FWS qua ntify and/or parc el
20
out the “proportiona l share” of harms among the b aseline
21
and the proposed act ion. See Pacific Coast Fed’n of
22
Fisherme n's Ass'ns v . U.S. Bureau of Reclamation, 426
23
F.3d 108 2, 1093 (9th Cir. 2005); see also P acific Coas t
24
25 Fed’n of Fishermen's Ass'ns v. U.S. Bureau of
26 Reclamat ion, 2 26 Fed . App x. 715, 718 (9th C ir. 2007)
27 (rejecti ng water use rs’ argument that agenc y acti on mu st

28
106
1 be the “ historical c ause” of the jeopardy to salm on).

2 40. FWS’s tr eatment of t he “other stressors” in the
3
BiOp did not violate the ESA’s baseline analysis
4
requirem ents because the ESA does not demand a
5
quantita tive separat ion of project st ressors from non-
6
project stressors. See NWF v . NMFS II, 524 F.3d at 930.
7
8 (“[T]he proper basel ine analysis is not the propo rtional
9 share of responsibil ity the federal agency bears for the
10 decline in the speci es, but what jeopardy might r esult

11 from the agenc y’s proposed actions in the present and
12
future h uman and nat ural contexts.”). FWS was re quired
13
to and d id describe the present and future federa l,
14
state, a nd private a ctions in the action area, wh ich
15
include the “other s tressors”. Whether it sufficiently
16
17 justifie d whether je opardy might result from the agency’s
18 proposed actions vie wed in this context is a sepa rate

19 question .
20
41. It is in equitable to put the entire burden of
21
the stre ssors on the water supply. However, this
22
decision goes beyond science to implicate the Exe cutiv e’s
23
(Departm ent of Inter ior) allocation of resources. A
24
25 court la cks authorit y to interfere with such a po licy
26 choice b y a coordina te branch of government.
27
28
107
1 a. Discreti onary v. Non-Discretionary.

2 42. Plaintif fs complain that the BiOp does not
3 distingu ish between discretionary and non-discret ionar y
4
actions. Home Build ers, 551 U.S. 644, held that ESA §
5
7’s cons ultation req uirements do not apply to non -
6
discreti onary action s. Where an agency is required by
7
law to p erform an ac tion, it lacks th e power to insure
8
9 that the action will not jeopardize the species. Id. at
10 667.
11 43. However, Home Builde rs sa ys n othing about

12 whether, once sectio n 7 consultation is triggered , the
13
jeopardy analysis sh ould segregate di scretionary and non-
14
discreti onary action s, relegating the non-discret ionar y
15
actions to the envir onmental baseline. Hom e Buil ders
16
fundamen tally concer ns whether the section 7 cons ultation
17
18 obligati on attaches to a particular agency action at all.
19 See Home Builders, 551 U. S. at 679-80 (“duty does not

20 attach t o actions... that an agency i s required by
21
statute to undertake ....”) (emphasis added).
22
23 b. Reclamat ion’s Treatm ent of the Coordinated
Operatio ns Agreement .
24
The same reasoning a pplies to Plaintiffs’ related
25
argument that Federa l Defendants acted unlawfully by
26
attribut ing to the p roject the effects of “mandat ory”
27
28 complian ce with the Coordinated Operations Agreem ent
108
1 (“COA”). Even assum ing, arguendo, th at any mandatory

2 obligati on exists un der the COA, a proposition that is
3
question able given t he open-ended wor ding of the COA and
4
language in the CVPI A subjecting project operatio ns to
5
the ESA, Home Builde rs do es n ot require the agenc y to
6
segregat e discretion ary from non-discretion ary activit ies
7
8 during a n ESA § 7 consultation. 10 Moreover, this argument
9 was not presented in Plaintiffs’ opening brief. See
10 Alaska C tr. for Envt . v. U.S. Forest Serv., 189 F .3d 8 51,
11 858 n. 4 (9th Cir. 1 999) (arguments not raised in opening
12
brief ar e waived).
13
14 c. Comparis on of CalSim Data aga inst Dayflow
Data.
15
44. Plaintif fs also argu e that FWS’s analysis is
16
flawed b ecause FWS c ompared CalSim data to Dayflo w Data.
17
As discu ssed in the Findings of Fact, although Mr. Miller
18
19 presents some substa ntive criticisms of the way t he BiOp
20 utilized CalSi m runs and compared those run s to other
21 types of data, these specific concerns were not raised

22
before t he agency pr ior to the issuance of the Bi Op. FWS
23
had legi timate concerns, shared by other scientists, w ith
24
the excl usive relian ce on CalSim data. Finally, Mr.
25
Miller c oncedes that even if the approach he reco mmends
26
27 10
T o th e ex te nt t ha t Pla in ti ff s su g ges t th at s ec ti on 7 d oes
not a pp ly t o th e pr oj ect s at a ll u n der H om e Bu il de rs , th is pa ra di gm -
28 shi ft in g ar gu me nt h as no t pr op er ly bee n ra is ed o r br ie fe d.
109
1 had been taken, the same fundamental result would have

2 obtained : project o perations shift the position of X2
3
upstream . The magni tude of this shift is relevan t to the
4
justific ation for and design of Component 3, which takes
5
effect i n September, but that need not be resolve d at
6
this tim e.
7
8
(3) Effects Analysis Cha llenges (Food Web).
9
45. Plaintif fs’ original motion attacked the BiOp’s
10
analysis regarding P. forbesi , a food item for de lta
11
smelt du ring the sum mer and fall seasons. Doc. 4 47 at
12
21-26. Plaint iffs appear to have abandoned this
13
14 argument , as it was not discussed during the evid entiary
15 hearing or in their proposed Findings of Fact or
16 Conclusi ons of Law.

17
(4) Challeng es to Component 2.
18
a. Use of R aw Salvage N umbers.
19
46. The evid ence describ ed in the Findings of Fact
20
21 establis hes that FWS ’s use of gross salvage numbe rs to
22 justify the quantita tive pumping restrictions in RPA

23 Componen t 2 did not utilize the best available sc ience.
24
47. There wa s agreement among all the experts that
25
the best available, scientifically accepted metho dology
26
is to us e normalized salvage data to analyze the effect
27
of OMR f lows on the delta smelt population. Norm alized
28
110
1 salvage data was ava ilable to FWS, bu t FWS failed to

2 incorpor ate any anal ysis of normalized salvage da ta into
3
its quan titative jus tification for the specific f low
4
prescrip tions impose d by RPA Component 2. To exa cerbate
5
this fai lure, FWS di d not explain why it did not.
6
48. FWS’s di sregard for an available scie ntific
7
8 methodol ogy that was “in some way better than the
9 evidence [the agency ] relied on” was a violation of th e
10 “best av ailable scie nce” standard of the ESA. Kern

11 County, 450 F.3d at 1080.
12
49. Addition ally, by ent irely failing to explain its
13
use of g ross salvage numbers despite internal dis cussions
14
indicati ng an awaren ess of the problem and critic ism from
15
the Inde pendent Peer Review, FWS “has entirely fa iled to
16
17 articula te a satisfa ctory explanation for its
18 conclusi ons.” Gutierrez II, 606 F. Supp. 2 d at 1 183.

19 50. Plaintif fs have show n a likelihood of success on
20
the meri ts of their claim that the use of gross s alvage
21
numbers in Figures B-13 and B -14 of t he BiOp was a
22
violatio n of the ESA , and was arbitra ry, capricio us, and
23
an abuse of discreti on.
24
25 51. However, Plaintiffs have not demonstrated that
26 Dr. Deri so’s alterna tive -5,6 00 cfs flow limit is any
27 more val id than the -5,000 cfs limit impose d by RPA

28
111
1 Componen t 2. The condition of the delta smelt continu es

2 to be no n-viab le and prec arious, with a lik ely risk of
3
extincti on if protec tions are not afforded. Plai ntiffs
4
must pro duce evidenc e that shows otherwise to jus tify a
5
flow res triction tha t permits negative OMR flows to
6
exceed - 5,000 cfs.
7
8
b. Failure to Use a Qua ntitative Life Cycle
9 Model.
10 52. The agen cy is not re quired to generate new
11 studies. For exampl e, in Sou thwest Center for Biologi cal
12 Diversit y v. Babbitt, 215 F.3d 58, 60-61 (D .C. Cir.

13 2000), t he district court found the availab le evi dence
14
regardin g FWS’s deci sion not to list the Queen Ch arlotte
15
goshawk “inconclusiv e” and held that the agency w as
16
obligate d to find be tter data on the species’ abu ndance.
17
The D.C. Circuit rev ersed, emphasizing that, alth ough
18
19 “the dis trict court’s vie w has a superficia l appe al .. .
20 this sup erficial app eal cannot circumvent the sta tute’s
21 clear wo rding: The secretary must make his decis ion as

22
to wheth er to list a species as threatened or end angered
23
‘solely on the basis of the best scientific and
24
commercial dat a available to him....’ 16 U.S.C. §
25
1533(b)( 1)(A).” Id. at 61.
26
27 53. The use of a quantit ative life cycle model is
28 the pref erred scient ific methodology. FWS made a

112
1 consciou s choice not to use expertise available w ithin

2 the agen cy to develop one, nor did it explain why it did
3
not. Ho wever, a com pleted life-cycle model was not
4
availabl e for FWS’s use prior to the issuance of the
5
BiOp, an d the Court does not have the authority t o
6
require the agency t o create one.
7
8
(5) Critical Habitat.
9
54. As requi red by the E SA, if FWS finds that the
10
proposed agency acti on will result in “jeopardy o r
11
adverse modification [of critical habitat] ... th e
12
Secretar y shall sugg est those reasonable and prud ent
13
14 alternat ives which [ it] believes would not violate
15 [Section 7(a)(2)] an d can be taken by the Federal agency
16 or appli cant in impl ementing the agency action.” 16

17 U.S.C. § 1536(b)(3)( A). Avoiding adverse modific ation of
18
critical habitat is an indepe ndent statutory basis for
19
the prom ulgation of an RPA.
20
55. The BiOp sets forth extensive findings regarding
21
22 the adve rse effects of export pumping on the crit ical
23 habitat of the delta smelt. See BiOp at 19 0-202, 239- 78.
24 For inst ance, the Bi Op found that the export pump s “alter
25 the hydr ologic condi tions wit hin spawning habitat
26
througho ut the spawn ing period for delta smelt by
27
impactin g various ab iotic factors including the
28
113
1 distribu tions of tur bidity, food, and contaminant s,” and

2 further adversely mo dify spawning habitat by
3
“contrib ut[ing] to u pstream movement of the LSZ [low
4
salinity zone],” whi ch in turn “reduc[es] the amo unt and
5
quality of spawning habitat available to delta sm elt.”
6
Id. at 239-40.
7
8 56. In light of such fin dings, the BiOp concluded
9 that the operations of the CVP and SWP “are likel y to
10 adversel y modify del ta smelt critical habitat” be cause

11 “[t]he p ast and pres ent operations of the CVP/SWP have
12
degraded [delta smel t] habitat elements (particul arly
13
PCEs 2-4 [“primary c onstituent elements” – water, wate r
14
flow, an d salinity]) to the extent th at their co-
15
occurren ce at the ap propriate places and times is
16
17 insuffic ient to supp ort successful delta smelt
18 recruitm ent at level s that will provide for the s pecies’

19 conserva tion.” Id. at 278.
20
57. Plaintif fs have not challenged the BiOp’s
21
findings on adverse modification of critical habi tat in
22
this mot ion. Plaint iffs’ experts Dr. Deriso and Dr.
23
Hilborn stated that their criticisms of the BiOp’ s OMR
24
25 flow res trictions di d not apply to critical habit at.
26 4/5/10 T r. 226; 4/6/ 10 Tr. 93. Rather, Pla intiff s arg ue
27 that the only stated rationale for the specific f low

28
114
1 prescrip tions impose d by Component 2 is to avoid

2 jeopardy , and that C omponent 2 does not itself in dicate
3
that it is necessary to prevent adverse modificat ion.
4
See Pls.’ Repl y (Doc. 491 ) at 1 n.1.
5
58. Federal Defendants r espond that “[t]h is arg ument
6
elevates form over s ubstance and needlessly
7
8 compartm entalizes po rtions of the BiOp that are d esigned
9 to work together as part of the same document.” Doc.
10 666, Pro posed Conclu sion of Law #187.

11 59. As a gen eral matter, Federal Defendan ts are
12
correct that the BiO p’s critical habitat modifica tion
13
finding operates as an independent justification for
14
imposing flow restri ctions on the projects. Howe ver, the
15
BiOp jus tifies the specific flow prescripti ons im posed by
16
17 Componen t 2 with a q uantitative analysis that say s
18 nothing whatsoever a bout critical habitat. Rathe r, an

19 improper analysis of raw salvage data is utilized to
20
generate a series of “break points,” including a -5,000
21
cfs ceil ing on negat ive OMR flows. There is no a nalysis
22
of criti cal habitat that independently justifies this
23
specific flow prescr iption, as opposed to the cei ling of
24
25 -5,600 p roposed by P laintiffs, or any other level.
26 //
27 //
28
115
1 (6) Reclamat ion’s ESA Re sponsibility.

2 60. The ESA regulations require the action agency to
3 “determi ne whether a nd in what manner to proceed with the
4
action i n light of i ts section 7 obligations and the
5
Service’ s biological opinion.” 50 C.F.R. § 402.1 5(a).
6
Prior to accepting a nd im plem enting the 2008 Smel t BiOp
7
RPA, Rec lamation had an independent obligation un der ESA
8
9 section 7(a)(2) to e nsure that it “use[d] the bes t
10 scientif ic and comme rcial data available.”
11 61. Reclamat ion, as the federal action agency, “may

12 not rely solely on a FWS biological opinion to es tablish
13
conclusi vely its com pliance with its substantive
14
obligati ons under se ction 7(a)(2).” Pyramid Lake Paiu te
15
Tribe of Indians v. U.S. Dept. of the Navy, 898 F .2d
16
1410, 14 15 (9th Cir. 1990). “[T]he action agency must
17
18 not blin dly adopt th e conclusions of the consulta nt
19 agency.” City of Ta coma v. Fed. Energy Reg ulatory

20 Comm’n, 460 F.3d 53, 76 (D.C. Cir. 20 06).
21
62. Reclam ation did no t ens ure that the RPA u tilize d
22
the best available s cience. Rather, it uncritica lly
23
accepted the RPA and did not independently identi fy an d
24
analyze alternative RPA Actions that minimized je opardy
25
26 to human s and the hu man environment while protect ing
27 threaten ed species.
28
116
1 D. Balancin g of the Har ms.

2 (1) Balancin g of the Har ms in ESA Cases.
3 63. The Supr eme Court he ld in TVA v. Hill, 437 U.S.
4 153, 194 (1978), tha t Congress struck the balance in
5
favor of affording e ndangered species the highest of
6
prioriti es. In adop ting the ESA, Congress intend ed to
7
“halt an d reverse th e trend toward species’ extin ction ,
8
whatever the cost.” Id. at 1 84 (emphasis added). TVA v.
9
10 Hill con tinues to be viable. See Hom e Builders, 551 U.S.
11 at 669-7 1; see also Oakland Cannabis Buyers’ Co-op., 532
12 U.S. 496 -97; A moco Prod. Co. v. Village of Gambell, 480

13 U.S. 531 , 543 n.9 (1 987).
14
64. Winter d oes not modi fy or discuss the TVA v.
15
Hill sta ndard. 11 Alth ough Winter altered the Ninth
16
Circuit’ s general pr eliminary injunctive relief s tandard
17
by makin g that stand ard more rigorous, Winter did not
18
19 address, nor c hange, the approach to the ba lancing of
20 economic hardships w here endangered s pecies and their
21 critical habitat are jeopardized. See Biodiversity Le gal

22
Found. v . Badgley, 309 F. 3d 1166, 1169 (9th Cir. 2002)
23
(Congres s removed th e courts’ traditional equitable
24
discreti on to balanc e parties’ competing interest s in ESA
25
injuncti on proceedin gs); Nat’l Wildlife Fed’n v.
26
27
11
Al th ou gh W in te r in vo lve d ES A- li st e d s pe ci es , th e Wi nt er
28 dec is io n di d no t ad dr ess a ny E SA c l aim s.
117
1 Burlingt on N. R.R., Inc., 23 F.3d 1508, 1510-11 (9th Cir.

2 1994)(sa me).
3
65. Prior de cisions invo lving the coordinated
4
projects ’ operations found that TVA v . Hill and relate d
5
Ninth Ci rcuit author ities foreclose the district court’s
6
traditio nal discreti on to balance economic equiti es under
7
8 the ESA. There is n o such bar in NEPA injunction
9 proceedi ngs.
10 66. Plaintif fs have adva nced a hu man welfare

11 exceptio n and conten d that unlike any of the prio r cases,
12
this cas e juxtaposes species’ survival against hu man
13
welfare, requiring a balancing of the BiOp’s thre ats of
14
harm to humans, heal th, safety, and protection of
15
affected communities. No case, including TVA v. Hill,
16
17 which co ncerned the competing economic interest i n the
18 operatio n of a hydro-electric project and p rohibited

19 federal courts from balancing the loss of funds s pent on
20
that pro ject against the loss of an endangered sp ecies,
21
expressl y addresses whether the ESA precludes bal ancing
22
of harms to humans a nd the human environment unde r the
23
circumst ances presen ted here.
24
25 67. This c ase in volves both harm to threatene d
26 species and to human s and their environment. Con gress
27 has not nor do es TVA v. Hill elevate species prot ection

28
118
1 over the health and safety of humans.

2
(2) Balancin g the Harms under NEPA.
3
68. Although it is undis puted that all harms may be
4
5 consider ed in evalua ting a claim for injunctive r elief
6 under NE PA, an injunction should not issue if enjoining
7 such gov ernment acti on would result in more harm to the

8 environm ent than den ying injunctive relief. Save Our
9
Ecosyste ms, 74 7 F.2d at 1 250.
10
11 E. The Publ ic Interest.
12 69. In adopt ing the ESA, Congress explicitly fo und
13 that all threatened and endangered species “are o f

14 esthetic , ecological , educational, historical,
15
recreati onal, and sc ientific value to the Nation and its
16
people.” 16 U.S.C. § 1531(a)(3). The ESA advanc es a
17
Congress ional policy to “halt and reverse the trend
18
toward s pecies extin ction, whatever the cost.” TVA v.
19
20 Hill, 43 7 U.S. at 184.
21 70. The publ ic policy un derlying NEPA favors

22 protecti ng the balan ce between humans and the
23
environm ent. See 42 U.S. C. § 4321 (declari ng a national
24
policy t o “enc ourage productive and enjoyable har mony
25
between man and his environment; to promote effor ts which
26
will pre vent or elim inate damage to the environme nt and
27
28 biospher e and stimul ate the health and welfare of man;
119
1 [and] to enrich the understanding of the ecologic al

2 systems and natural resources important to the
3
Nation.. ..”).
4
71. If both these object ives can be realized by
5
astute m anagement, i t is the government’s obligat ion to
6
do so.
7
8 72. It is in the publi c int erest that relief be
9 granted to Pla intiffs, who represent a subs tantia l
10 populati on of water users in California, to enhan ce the

11 water su pply to redu ce the adverse harms of destr uction
12
of perma nent crops; fallowed lands; increased gro undwater
13
consumpt ion; reducin g groundwater supplies; land
14
subsiden ce; reductio n of air quality; destruction of
15
family a nd entity fa rming businesses; and social
16
17 disrupti on and dislo cation, such as increased pro perty
18 crimes a nd intra-family c rimes of violence, adverse

19 effects on schools, and increased unemploym ent leading to
20
hunger a nd homelessn ess. This must be done witho ut
21
jeopardi zing the spe cies and their critical habit at.
22
23 VII. CONCLUSI ON 1.
24 1. Plaintif fs have succ eeded on the merits of their
25 NEPA cla im.
26
a. NEPA req uires that t he respon sible agency
27
take a h ard look at the environmental consequence s of its
28
120
1 actions, Robertson v . Methow Valley Citizen’s Cou nsel,

2 490 U.S. 332, 350 (1 989), obligating federal agen cies to
3
prepare an environme ntal impact statement (“EIS”) for all
4
“major f ederal actions significantly affecting the
5
quality of the human environment.” 42 U.S.C. §
6
4332(2)( C).
7
8 b. Federal Defendants a re required to evaluate
9 the impa ct of the co ordinated operations of the C VP and
10 SWP, whi ch constitut es major federal action. The

11 evidence overwhelmin gly establishes significant
12
detrimen tal effects visited on the quality of the human
13
environm ent by imple mentation of the BiOp’s RPA A ctions,
14
which im pose substan tial restrictions on the wate r supply
15
to Calif ornia to pro tect the delta smelt.
16
17 c. Where re quired, an EIS discloses
18 environm ental effects of a proposed action and considers

19 alternat ive courses of action. Id. Here, Federal
20
Defendan ts completel y abdicated their responsibil ity to
21
consider alternative remedies in formulating RPA Actions
22
that wou ld not only protect the species, but woul d also
23
minimize the adverse impact on humans and the hum an
24
25 environm ent.
26 d. In consi dering RPA a lternatives, the record
27 shows th e burden of other causes is allocated to the

28
121
1 water su pply, withou t the required an alysis whether

2 alternat ives, less h armful to humans and the huma n
3
environm ent, exist. Although this allocation of
4
resource s ultimately is the prerogative of the ag ency,
5
NEPA nev ertheless re quires a hard look.
6
2. Plaintif fs have also shown a likeliho od of
7
8 success on the merit s of their ESA claim. Althou gh the
9 premise underlying C omponent 2 -- that the species may be
10 jeopardi zed by incre ased negative flows occasione d by

11 export p umping -- has rec ord support, FWS h as failed to
12
adequate ly justify b y generally recog nized scientific
13
principl es the preci se flow prescriptions imposed by
14
Componen t 2. The ex act restrictions imposed, whi ch are
15
inflicti ng material harm to humans and the human
16
17 environm ent, are not supported by the record, mak ing it
18 impossib le to determ ine whether RPA Component 2 overly

19 protecti ve. Judicia l deference is not owed to ar bitrary,
20
capricio us, and scie ntifically unreasonable agenc y
21
action.
22
3. It is hi ghly signifi cant that the co-operat or of
23
the Proj ects, DWR, with access to scientifi c comp etenc e
24
25 in the f ields of fis h biology and ecology, and pr oject
26 operatio ns, does not oppose the motion for a prel iminary
27 injuncti on.
28
122
1 4. Under th e balance of hardships analysis,

2 Defendan ts’ contenti on that the ESA, under TVA v. Hill ,
3
preclude s equitable weighing of Plaintiffs’ inter ests is
4
not supp orted by tha t case, as evidence of harm t o the
5
human en vironment in the form of social dislocati on,
6
unemploy ment, and ot her threats to human welfare were not
7
8 present in Hil l. They are in this case.
9 5. Defendan ts argue tha t jeopardy to the species
10 cannot b e avoided wi thout continuing substantial

11 reductio n of pumping , with resultant reduction of water
12
supply t o Plaintiffs , representing over 20,000,00 0
13
persons, affec ted communities, and the agricultural
14
industry in Northern , Central, and Southern Calif ornia.
15
6. Congre ss created public exp ectations in the
16
17 Amended Reclamation Act by instructing Reclamatio n to
18 contract for water s ervice to hundreds of public- entity

19 water se rvice provid ers that supply water to mill ions of
20
people a nd thousands of acres of productive agric ultural
21
land. T he agencies have not fully discharged the ir
22
responsi bility to ef fectively allocate Project wa ter
23
resource s. Federal Defendants have acted a rbitra rily and
24
25 capricio usly in form ulating Component 2 of the RP A, wh ich
26 lacks fa ctual and sc ientific justification, while
27 effectiv ely ignoring the irreparable harm that pumping

28
123
1 restrict ions have in flicted and will inflict on humans

2 and the human enviro nment.
3
7. The sp ecies and its cri tica l habitats are
4
entitled to protecti on under the ESA. The specie s has
5
been and will be pro tected. That is the law.
6
Nonethel ess, FWS and Reclamation, as the consulti ng and
7
8 action a gencies, must tak e the hard look un der NE PA at
9 the seve re consequen ces visited upon Plaintiffs, the
10 water su pply of Cali fornia, the agricultural indu stry,

11 and the residents an d communities impacted by the water
12
supply l imitations i mposed by the Component 2. F ederal
13
Defendan ts have fail ed to comprehensi vely a nd competen tly
14
evaluate whether RPA alternatives can be prescrib ed that
15
will be mutually pro tective of all the statutory purposes
16
17 of the P rojects.
18 8. This i s a case of first imp ression. The stakes

19 are high , the harms to the affected human c ommuni ties
20
great, a nd the injur ies unacceptable if they can be
21
mitigate d. FWS and Reclamation have not complied with
22
NEPA. T his prevente d in- depth analysis of the po tential
23
RPA Acti ons through a properly focused study to identi fy
24
25 and sele ct alternati ve remedial measures that min imize
26 jeopardy to affected humans and their communities , as
27 well as protecting t he threatened species. No pa rty has

28
124
1 suggeste d that human s and their environment are l ess

2 deservin g of protect ion than the species. Until
3
Defendan t Agencies h ave complied with the law, so me
4
injuncti ve relief pe nding NEPA compliance may be
5
appropri ate, so long as it will not further jeopa rdize
6
the spec ies or their habitat.
7
8 9. Injunc tive relief also may be warra nted u nder the
9 ESA, bec ause, althou gh the general premises under lying
10 Componen t 2 find some support in the record , the preci se

11 flow pre scriptions i mposed on coordinated project
12
operatio ns are not s upported by the best availabl e
13
science and are not explained as the law requires .
14
10. Injunc tive r elief canno t be imposed witho ut
15
current evidence of the status of the species to assure
16
17 that alt ered operati ons will not deepen jeopardy to the
18 affected species or otherwise violate other laws. The

19 evidence has not suf ficiently focused on re medies to
20
provide a confidence level that Plaintiffs’ propo sed
21
remedy o f a flat -5,600 cfs ceiling o n negative O MR flows
22
will not jeopardize the continued existence of th e
23
species and/or adver sely modify its critical habi tat.
24
25 11. Legal and eq uitabl e gro unds for injunctiv e
26 relief h ave otherwis e been established by a prepo nderance
27 of the e vidence.
28
125
1 12. RPA componen t 2 su ffers fro m a lack of

2 populati on scaling i n violation of the requiremen t FWS
3
use the best availab le science. There is no reli able
4
lifecycl e model, whi ch best available science cal ls for,
5
even if the Court ca nnot require the agency to de velop
6
one. Co ntinuing evi dence of the extreme risk to the
7
8 continue d existence of the Delta smelt population has
9 been pre sented by De fendants. Absent a showing b y
10 Plaintif fs that Delt a smelt are not within immine nt risk

11 of entra inment by Pr oject pumping facilities and/ or not
12
within h ydraulic inf luence of the pumps in the da nger
13
area of the Central and South Delta, the -5,000 c fs fl ow
14
restrict ion cannot b e enjoined.
15
13. A telephonic confe rence to discuss whether
16
17 Plaintif fs have evid ence that imminence of harm t o Delta
18 smelt do es not exist to justify injunction of pum ping

19 restrict ions shall be held May 28, 2010 in Courtr oom 3 at
20
10:00 a. m.
21
22
SO ORDER ED
23
Dated: M ay 27, 2010
24
25 /s/ O liver W. Wanger
Oliver W. Wang er
26 United States Distri ct Ju dge
27
28
126

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Case 1:09-cv-00407-OWW-DLB Document 704 Filed 05/27/2010 Page 1 of 126

20 (“Westla nds”), move for a preliminary injunction (“PI” )

21 against the implemen tation of Reasonable and Prud ent

1 Smelt Bi Op” or “BiOp ”). Doc. 433.

9 the SWP, partially j oins. Doc. 452.

10 Federal Defendants a nd Defendant Intervenors oppo sed.

18 witnesse s, the exhib its received in evidence, the written

26 as a con clusio n of law or any conclusion of law may be

27 interpre ted as a fin ding of fact, it is so intend ed.

10 designed to allow the pro jects to continue operat ing

11 without causing jeop ardy to the species or advers e

19 Stage) c onsists of t wo Actions related to Old and Middle

27 second ( “cfs”) on a 14-day average and no more

1 negative than -2,500 cfs for a 5-day runnin g average.

9 Flows un der Action 2 can be set within a range fr om

10 -5,000 t o -1,2 50 cfs, depending on a complex set of

18 temperat ures reach 1 2° Celcius (“C”), or when a s pent

26 maintain average mix ing point locations of Delta outflow

27 and estu arine water inflow (“X2”) from September to

1 December , depending on water year type, in accord ance

9 Under Co mponent 5 (M onitoring and Rep orting), the

10 Projects gather and report information to ensure proper

23 failed t o comply wit h the National Environmental

24 Policy A ct (“NEPA”) in implementing the 2008 Smel t

1 a) vario us aspects o f the BiOp’s baseline a nd

9 Componen ts 1 and 2 a re unsupported by the best

10 availabl e science an d the data in the 2008 Smelt

18 the meri ts.

26 its impo sition. Com ponent 3 is not set to begin until

27 Septembe r, and Plain tiffs do not presently seek

1 injuncti ve relief ag ainst its operation. Barring

9 against implementati on of RPA Component 2 and enf orcement

10 of the i ncidental ta ke limits in the BiOp. See Doc. 435

18 pumping restrictions should be imposed; if the PE I

1 • Plaintif fs requested that the Inciden tal Take

9 followin g summary ju dgment in NRDC v. Kempthorne,

10 1:05-cv- 1207. Doc. 452 at 2.

18 Plaintif fs now propo se that Component 2 be replac ed by a

1 305, 312 (1982). Fo ur factors must be establishe d by a

9 parties’ favor; and

10 4. An injun ction is in the public interest.

15 A. The Agen cy Action.

16 1. The agen cy action is the coordinated operation

17 of the C VP and SWP, pursuant to an Agreement for the

24 third, f or power.” 50 St at. 844, 850.

25 3. The CVP was reauthor ized in 1 992 through th e

1 restorat ion of fish and wildlife as co-equal project

9 these du al legislati ve purposes, providing water service

10 for agri cultural, do mestic, and industrial use, v ersus

18 contract ual partner of Reclamation, disagrees wit h at

1 7. It is al so undispute d that on Novembe r 13, 2009,

9 of impac ts to the hu man environment and/or consid erati on

10 of alter natives that took into account those impa cts,

14 (1) Status o f the Specie s.

15 9. The delt a smelt was listed as a threatened

16 species under the ES A on March 5, 1993. 58 Fed. Reg.

17 12,584 ( March 5, 199 3). Critical habitat was des ignated

24 Doc. 94, Findings of Fact Re Plaintiffs’ Motion f or

25 Prelimin ary Injuncti on, ## 1-2. The expert s agre e that

1 Tr. 231 (Hilborn); 4 /6/10 Tr. 95 (Deriso). Howev er, the

9 register ing a series of record-breaking low s. 4/ 2/10 Tr.

10 176-78. That trend has continued in the last two years,

18 populati on) to juven iles recruited into the popul ation,