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Smelt Protections/Pumping Restrictions Findings May 27, 2010

Smelt Protections/Pumping Restrictions Findings May 27, 2010

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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 I. INTRODUCTION Plaintif fs, San Luis & Delta Mendota Water Author ity (the “Au thority”) an d Westlands Water District (“Westla nds”), move for a preliminary injunction (“PI” ) against the implemen tation of Reasonable and Prud ent Alternat ive (“RPA”) Component 2 set forth in the United States F ish and Wild life Service’s (“FWS”) Decemb er 15, 2008 Bio logical Opin ion, which addresses the impa cts of the coor dinated oper ations of the federal Central Valley Project (“CVP”) and State Water Project (“SWP”) o n the threaten ed delta sme lt (Hypom esus transpacificus) (“20 08 1 The Cons olidated Del ta Smelt Cases UNITED STATES DISTRI CT CO URT FOR THE EASTERN DISTRICT OF C ALIFORNIA

1:09-CV-00407 OWW DL B 1:09-cv-00480-OWW-GS A 1:09-cv-00422-OWW-GS A 1:09-cv-00631-OWW-DL B 1:09-cv-00892-OWW-DL B FINDINGS OF FA CT AND CONCLUSIONS OF LAW R E PLAINTIFFS’ RE QUEST FOR PRELIMINARY IN JUNCTI ON AGAINST IMPLEM ENTATI ON OF RPA COMPONE NT 2 (a/k/a Action 3)(Doc . 433)

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Smelt Bi Op” or “BiOp ”).

Doc. 433.

Plaintif fs State Wat er Contractors; Metropolitan Water Di strict of So uthern California; Kern Count y Water Agency a nd Coalition for a Sustainable; Stewart & Jasper Orchards , et al.; an d the Family Farm Alliance jo in in the moti on. Docs. 4 49, 451 & 453. Plaintiff-Int erven or

Departme nt of Water Resources (“DWR”), the operator of the SWP, partially j oins. Doc. 452.

Federal Defendants a nd Defendant Intervenors oppo sed. Docs. 46 9, 473. 495, 497 & 507. Pla intiffs replied. Docs. 487, 491,

The motion came on for an eviden tiary Doc s. 644, 652 ,

hearing on April 2, 5, 6, and 7, 2010 . 653 & 65 4.

The part ies were represented by couns el, as

noted in the record. After co nsideration of the testimony of the witnesse s, the exhib its received in evidence, the written briefs o f the partie s, oral arguments, and the parties ’ proposed findings of fact and conclusions of law, the followin g findings o f fact and conclusions of law concerni ng the motio n for interim relief/prelimin ary injuncti on are enter ed. To the e xtent any fi nding of fact may be interpre ted as a con clusio n of law or any conclusion of law may be interpre ted as a fin ding of fact, it is so intend ed. 2

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II. BACKGROUND The 2008 Smelt BiOp, prepared pursuant to Section 7 of the E ndangered Sp ecies Act (“ESA”), 16 U.S.C. § 1536(a)( 2), co nclude d tha t “the coordinated operations of the CVP and SWP, as proposed, are likely to jeopa rdize the cont inued existe nce of the delta smelt” and “adverse ly modify de lta smelt critical habitat.” 276-78. BiOp at

As re quired by law, the BiOp includes an RPA

designed to allow the pro jects to continue operat ing without causing jeop ardy to the species or advers e modifica tion to its critical habitat. Id. at 279. Th e

RPA incl udes various operational components desig ned to reduce e ntrainment o f smelt during critical times of the year by contro lling exports out of and water flows into the Delt a. Id . at 279-85.

Componen t 1 (P rotection of the Adult Delta Smelt Life Stage) c onsists of t wo Actions related to Old and Middle River (“ OMR”) flows. • Action 1 , which is d esigned to protec t upmigrating delta sm elt, is trig gered during low and high entrainm ent risk per iods based on physical and biologic al monitorin g. Action 1 requires OMR flo ws

to be no more negati ve than -2,000 cubic fe et per second ( “cfs”) on a 14-day average and no more 3

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negative than -2,500 cfs for a 5-day runnin g average. Id. at 2 81, 329. Action 2 of Componen t 1 is designed t o protect ad ult delta sm elt that hav e migrated upstream and are residing in the Delt a prior to spawning. Action 2 is

triggere d immediatel y after Action 1 ends o r if recommen ded by the S melt Working Group (“SWG”). Flows un der Action 2 can be set within a range fr om -5,000 t o -1,2 50 cfs, depending on a complex set of biologic al and envir onmental parameters. 82, 352- 56. At issue here is Component 2 (Action 3) (Protecti on of Larva l and Juveni le Delta Smelt), which requir es OMR flows to remain betw een - 1,250 and -5,000 c fs, be ginni ng when Com ponent 1 is completed, when Delta water temperat ures reach 1 2° Celcius (“C”), or when a s pent female s melt is dete cted in trawls or at salvage faciliti es. I d. at 282, 357-58. Component 2 rem ains in Id. at 281-

place un til June 30 or when the Clifton Court For ebay water te mperature re aches 25° C. Id. at 28 2, 368 .

Componen t 3 (I mprove Habitat for Delta Smelt Grow th and Rear ing) require s sufficient Delta outflow to maintain average mix ing point locations of Delta outflow and estu arine water inflow (“X2”) from September to 4

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December , depending on water year type, in accord ance with a s pecifically described “adaptive management process” overseen by FWS. Id. at 282-83, 3 69.

Under Co mponent 4 (H abitat Restoratio n), DWR is t o create o r restore 8, 000 acres of intertidal and s ubtidal habitat in the Delta and Suisun Marsh within 10 y ears. Id. at 2 83-84, 379. Under Co mponent 5 (M onitoring and Rep orting), the Projects gather and report information to ensure proper implemen tation of th e RPA actions, achievement of physical results, an d evaluation of the effective ness of the acti ons on the t argeted life stages of delta smelt, so that the ac tions can be refined, if needed. 284-85, 328, 3 75. III. SUMMARY OF MOT ION Plaintif fs’ request temporary injunctive relief o n the foll owing ground s: 1) the d istrict cour t has already found that the United S tates Bureau of Reclamation (“Reclamation”) failed t o comply wit h the National Environmental Policy A ct (“NEPA”) in implementing the 2008 Smel t BiOp RPA ; and. 2) the 2 008 Smelt Bi Op violates the ESA and is arbitrar y, capriciou s, and contrary to law becaus e: 5 Id. at

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a) vario us aspects o f the BiOp’s baseline a nd effects analysis are flawed, undermining the overall jeopardy con clusion, causing overstat ement of the effects of the proposed action a nd impositio n of overly-broad and overly-r estrictive R PA Components; b) the s evere OMR fl ow restrictions in RPA Componen ts 1 and 2 a re unsupported by the best availabl e science an d the data in the 2008 Smelt BiOp; an d c) Compo nent 3 (“The Fall X2 Action”) is arbitrar y and capric ious, because it is without factual or scientifi c justification and/or is not supp orted by the best available science, compelli ng a finding of likelihood of success on the meri ts. Plainti ffs further claim that the implementation of RPA Comp onents 1 and 2 will cause them continuing irrepara ble harm and that the public interest and bala nce of hards hips favor i njunctive relief. RPA Comp onent 1 has ended for the 2009-2010 water year, mo oting any re quest for injunctive relief a gainst its impo sition. Com ponent 3 is not set to begin until

Septembe r, and Plain tiffs do not presently seek 6

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injuncti ve relief ag ainst its operation.

Barring

unforese en circumsta nces, the parties’ cross-motions for summary judgment wil l be heard and decided before Septembe r. decision . 1 Plaintif fs’ in junction request has be en modified over time. O riginally, P laintiffs sought an inj unctio n Componen ts 1 and 3 are not addressed in this

against implementati on of RPA Component 2 and enf orcement of the i ncidental ta ke limits in the BiOp. at 2-4. • In place of Componen t 2, Plaintiffs sought to req uire Federal Defend ants a nd DWR to use a Potential Entrainm ent Index (“ PEI”) to estimate cumulative entrainm ent loss of delta smelt. If the PEI esti mate See Doc. 435

of cumul ative loss i s less than or equal to 7%, n o pumping restrictions should be imposed; if the PE I estimate of cumulati ve entrainment loss exceeds 7 %, FWS shal l be respons ible for setting OMR flows un der the rang e specified in Component 2 of the BiOp. 435 at 3 .
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 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 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 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 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 thi s ti me .
1

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Plaintif fs requested that the Inciden tal Take Statemen t (“IT S”) be recalculated bas ed on a higher Cumulati ve Salvage I ndex (“CSI”) of 11.36 for adu lts. Doc. 435 at 4.

In the a lternative, if the above remedies are not imposed, DWR request ed th at t hat the Court impose the interim remedial ope rational conditio ns imposed followin g summary ju dgment in NRDC v. Kempthorne, 1:05-cv- 1207. Doc. 452 at 2.

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

Plaintif fs now propo se that Component 2 be replac ed by a flat -5, 600 cfs ceil ing on negative O MR flows during the remainde r of t he implementation period for Component 2 . Id.; see 4/2/10 Tr. 208. IV. STANDARD OF DE CISION Injuncti ve relief, w hether temporary or permanent , is an “extr aordinary re medy, never awarded as of rig ht.” Winter v . Natural Re sources Defense Council, 129 S. Ct . 365, 376 (2008); Weinberg er v. Romero-Barce lo, 456 U.S. 8

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305, 312 (1982).

Fo ur factors must be establishe d by a

preponde rance of the evidence to qualify for temp orary injuncti ve relief: 1. 2. Likeliho od of succes s on the merits; Likeliho od the movin g party will suffer

irrepara ble harm abs ent injunctive re lief; 3. The bala nce of equit ies tips in the moving

parties’ favor; and 4. An injun ction is in the public interest.

Winter, 129 S. Ct. a t 374; Am. Trucking Ass ’n v. City of Los Ange les, 5 59 F.3d 1046, 1052 (9th Cir. 2009). V. FINDINGS OF FA CT A. The Agen cy Action. 1. The agen cy action is the coordinated operation

of the C VP and SWP, pursuant to an Agreement for the Coordina ted Operatio n of the two projects (“COA”) . 2. Accordin g to the Riv ers and Harbors A ct of 1937,

the dams and reservo irs of the CVP “shall be used , first, for rive r regulation , improvement of navigation a nd flood control; second, for irrigation and domestic uses ; and, third, f or power.” 3. 50 St at. 844, 850.

The CVP was reauthor ized in 1 992 through th e

Central Valley Impro vement Act (“CVPIA”), which m odified the 1937 Act and add ed mitigation, protection, an d 9

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restorat ion of fish and wildlife as co-equal project purposes . (1992). Pub. L. 1 02-575 § 3402, 106 Stat. 4600 , 4706 One of the stated purposes of the CVPIA is to §

address impacts of t he CVP on fish and wildlife. 3406(a).

The CVPIA made environmental protection and

water de liveries co- purpo ses. 4. This cas e presents a critical conflict between

these du al legislati ve purposes, providing water service for agri cultural, do mestic, and industrial use, v ersus enhancin g environmen tal protection for fish speci es whose habitat is maintaine d in rivers, estuaries, canal s, and other wa terways that comprise the Sacramento-San Joaquin Delta. 5. It is of manifest si gnificance to the public

interest that DWR, a co-opera tor and the State contract ual partner of Reclamation, disagrees wit h at least so me portions of the RPA and seeks injuncti ve relief a gainst the calendar-based cei ling in RPA Componen t 2. B. Facts Re levant to NE PA Claim. 6. It is un disputed tha t neither FWS nor

Reclamat ion engaged in any NEPA analysis in conne ction with pre paration or implementation of the 2008 Sm elt BiOp. 10

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7.

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

the Cour t entered an Order granting San Luis Plai ntiffs’ motion f or summary j udgment on their claim that F ederal Defendan ts violated NEPA when they implemented th e 2008 Smelt Bi Op without c onducting the required NEPA a nalys is. Doc. 399 . 8. FWS did not engage i n a systematic consideration

of impac ts to the hu man environment and/or consid erati on of alter natives that took into account those impa cts, ordinari ly performed as part of a NEPA revi ew. Facts Re levant to ES A Challenges. (1) 9. Status o f the Specie s. The delt a smelt was listed as a threatened 58 Fed. Reg.

species under the ES A on March 5, 1993. 12,584 ( March 5, 199 3).

Critical habitat was des ignated 59 Fed . Reg.

for the delta smelt on De cemb er 19, 1994. 65,256 ( Dec. 19, 199 4). 10.

The thre atened delta smelt, one of the most

abundant species in the Bay-Delta eco system as re cently as thirt y years ago, is in imminent danger of ext inction. Doc. 94, Findings of Fact Re Plaintiffs’ Motion f or Prelimin ary Injuncti on, ## 1-2. The expert s agre e that

there is no current population count for de lta smelt. 4/2/10 T r. 174 (Feyr er); 4/5/10 Tr. 67 (Newman); 4/5/10 11

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Tr. 231 (Hilborn); 4 /6/10 Tr. 95 (Deriso).

Howev er, the

species’ relative ab undance from year-to-year is monitore d using the Fall Midwater Trawl index (“F MWT”) prepared by the California Department of Fi sh and Game (“CDFG”) , as well as other abundance indices. 174-75. 4/2/10 Tr.

The F MWT shows a continuously and precip itous ly

declinin g trend in d elta smelt abundance in recen t years, register ing a series of record-breaking low s. 176-78. 4/ 2/10 Tr.

That trend has continued in the last two years,

with the FMWT declin ing from 23 in 2008 to 17 in 2009, the lowe st val ue ever recorded. Id. The p opulat ion

growth r ate for delt a smelt has been “quite negat ive” for the last ten years. 4/5/10 Tr. 232. The stock-

recruitm ent relation ship for delta smelt, which s hows the relation ship between adults (i.e., the “stock” of the populati on) to juven iles recruited into the popul ation, is “tren ding t oward the origin,” the opposi te directio n from rec overy. 4/2/ 10 Tr. 187-88. “There’ s no q uesti on

that [th e present ab undance levels of delta smelt ] are very low .” 11. 4/5/10 T r. 232 (Hilborn).

FWS rece ntly determi ned that delta smelt

warrante d uplisting from threatened to endangered , but that the action was currently precluded by higher priority listing act ions. 4/7/10 Tr. 163; 75 Fed . Reg. 12

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17,667 ( Apr. 7, 2010 ).

The direct mo rtality of delta

smelt by entrainment at the CVP and SWP pumps, as well as the dest ruction and adverse modification of its h abitat caused b y water expo rts, were important factors i n this determin ation. 75 F ed. Reg. at 17,671 (“The oper ation of

State an d Fede ral export facilities constitute a signific ant and ongo ing threat to delta smelt thr ough direct m ortality by entrainment”). As a result o f the

“immedia te and high magnitude threats” confrontin g the species, the delta s melt was assigned a listing priority number o f 2. 2 12. Id. at 17,675.

Evidence submitted d uring trial indicates that,

as of th e dates of t he March Spring Kodiak Trawl (March 8-11, 20 10) an d 20 m m surveys (March 15-18, 2010) , del ta smelt we re collected in the northern and western porti ons of the D elta, not in the danger zones of the central or south De lta. SWC Exs. 91 8 & 919. Through March 28,

2010, th e SWP had an expanded salvage of 16 delta smelt, and the CVP had an e xpanded salvage of 28 delta s melt. SWC Ex. 915. 13. Plaintif fs are corre ct that during the three

years th at restricti ons on spring exports have be en in place, t he FMWT inde x has continued t o trend downward.
“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. Id. a t 17 ,6 74 .
2

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4/7/10 T r. 94:8-14.

However, Mr. Gri maldo testif ied t hat

improved conditions may not immediate ly translate into improved survival an d population growth. 120:9-25 . (2) Baseline Issues. a. 14. Comparis on of CalSim and Dayflow Data. 4/7/10 Tr.

CalSim I I (“CalSim”) is a com puter model The mo del

develope d jointly by DWR and Reclamation.

simulate s SWP and CV P ope rati ons and is the standard planning tool for ev aluating project operat ions. Tr. 101: 24-102 :6. 4/2/ 10

The first version of the CalSi m model It is continuously up dated.

was avai lable in May 2002. 4/2/10 T r. 102:7-13. 15.

CalSim s imulates SWP and CVP reservoir

operatio ns, project exports and water deliveries, flow through the Delta, a nd salinity requirements in t he Delta, i ncluding the location of X2. 20; BiOp at 207. 16. X2 is th e location in the Delta where the It is measur ed as 4/2/10 Tr . 4/2/1 0 Tr. 102:1 4-

salinity is two part s per thousand.

the dist ance u pstream from the Golden Gate. 102:21-2 4. 17.

The CalS im model ass umes 82 years of hydrology,

4/2/10 T r. 101:23-102:3, 103:14-18, 1 61:2-6, prov ides the 14

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model wi th data rega rding inflow to r eservo irs and oth er informat ion affectin g the water supply, 4/2 /10 Tr . 103:19-2 3. The mode l also assumes a level of

developm ent, which reflects water dem and resultin g from a particul ar urban pop ulation level, agricultural producti on, and wild life refuge needs, 4/2/10 Tr. 104:17, as we ll as the existence and effect of environmenta l regulati ons and envi ronmental program s, 4/2/10 Tr. 103:14-1 8. The assu mptions used in the CalSim st udies

were dev eloped by represe ntatives from FWS, the N ation al Oceanic and Atmosphe ric Administration (“NOAA”), Reclamat ion, C DFG, and DW R. 18. 4/2/10 Tr. 105 :8-12.

The CalS im model ass ists scientists in making

planning decisions b y allowing comparisons betwee n studies based on dif fering as sumptions. 102:25-1 03:6. See 4/2/ 10 Tr .

Accor ding to Aaron Miller, P.E., a n expert

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

study fo r the 2008 OCAP Biolo gical Assessment (“2008 OCAP 15

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BA” or “ BA”).

Study 7.0 represents existing condition s,

and assu mes a 2005 l evel of development and a ful l environm ental water account (“EWA”). 20; 123: 21-24, 146:3-6; BiOp at 207. near-fut ure co nditions study. developm ent and a li mited EWA. 123:21-2 5; BiOp at 2 07-08. conditio ns stu dy. and a li mited EWA. BiOp at 208. 20. CalSim s tudy 6.0 was designed to look at the 4/2/10 Tr. 104:8Study 7.1 is a

It assumes a 2005 level of 4/2/10 Tr. 104:8- 23;

Study 8.0 is a future

I t ass umes a 2030 level of developm ent 4/2/10 Tr. 104:8-25; 123:21-124:2;

differen ces between the prior CalSim model used i n the 2004 OCA P BA a nd the new model used in the 2008 OCAP BA. 4/2/10 T r. 104:8-15, 157: 11-18. 21. Study 6.1 is similar to 6.0 , but did not

include the EW A and used an older version of the X2 estimate . 4/2/10 Tr . 104:8-17. Study 6.1 was prepare d

at the r equest of Re clamation biologists to asses s changes in water pro ject operations during the pe lagic organism decline (“P OD”) era. 150:16-1 51:17, 158:8-13. 4/2/10 Tr. 149:18- 24,

Reclamation biolo gists compa red

study 6. 1 against th e 7.0 and 8.0 studies on pages 13- 10 though 1 3-17 o f the 2008 OCAP BA. AR 01105 7-0110 64. 16 4/ 2/10 T r. 149:12-24;

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22.

Mr. Mi ller testified th at study 6.1 shoul d not

have bee n used for c omparison because it was not comparab le to the ot her studies. 157:8. 4/2/10 Tr. 156: 25-

Study 6.1 us ed the Kimmerer Monismith equ ation to

estimate X2 and it, as well as study 6.0, did not complete ly reflect the ne w enhancements in the Ca lSim model de veloped afte r the 2004 OCAP BA. 157:10-1 8; SLDMWA Ex . 12 at 205-206. 23. The CalS im 9.0 serie s of studies represents Study 9.0 represents a future 4/ 2/10 Tr.

climate change scena rios.

conditio n to serve as a basis of comparison of the effects of climate c hange to sea level rise, with out the inclusio n of (b)(2) or EWA. Study 9.1 represents a one-

foot sea level rise, without the inclusion of (b) (2) and EWA. St udies 9.2 th rough 9.5 look at predicted c hanges

in preci pitation and temperature for the period 2 010 to 2030, re lative to conditions for the period 1971 to 20 00. The 9.0 climate chan ge scenarios were not intende d to be directly compared to studies 7.0–8.0. 5; BiOp at 208. 4/2/ 10 Tr. 105: 1-

Suc h a comparison is not v alid becaus e

the stud ies make dif ferent assumptions regarding environm ental progra ms. 24. 4/2/10 Tr. 123:10-16.

In the B iOp, CalSim studies were compared to

simulati ons of histo ric conditions generated usin g the 17

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Dayflow model.

4/2/10 Tr. 107:4-7, 142:6-9.

Day flow is

a model that estimat es historic outflow based on historic precipit ation, inflo w, and exports, and estimates of delta is land diversi ons. Dayflow also provides a n 4/2/10 Tr. 107: 8-14.

estimate for the loc ation of X2. 25.

In the B iOp, FWS pur ports to quantify adult

entrainm ent by compa ring OMR flows from CalSim st udies to historic OMR flows d uring 1967-2007. BiOp at 21 2-13.

The BiOp depicts the se results in Tables E-5b and E-5c in the BiOp , whic h are labeled “differen ce from hist oric median v alue to CalS im II model median value” and “differe nce from his toric median salvage to predi cted salvage based on ... CalSim II,” respectively. 214. Id. at

Ta bles E-5b and E-5c purport to quant ify, as

effects of the actio n, changes in OMR flows and entrainm ent using th e Day flow-generat ed his toric data as the base line and com paring that to CalSim study r esults. Based on these compa risons of CalSim data and Day flowgenerate d hist oric data, the BiOp concludes, “adu lt entrainm ent is likel y to be higher than it has be en in the past under most operating scenarios, resultin g in lower po tential prod uction of early life history stages in the s pring in som e years.” 26. BiOp at 213.

In anoth er analysis in the Bi Op, FWS purpor ts to 18

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quantify the effects of the action on delta smelt habitat by compa ring CalSim model projections of the loca tion of X2 under the propose d action to the median locati on of X2 over the historical period 1967-2007, as si mulate d by Dayflow. BiOp at 23 5-36. Ba sed on this comparis on, t he

BiOp con cludes “[t]h e median X2 [loca tions] acros s the CalSim I I modeled sc enarios were 10-15 perc ent fu rther upstream than actual historic X2 (Figure E-19).” 235. Id. at

In reliance on these percent differen ces be tween

CalSim-c reated data and historical data, the BiOp conclude s “proposed action operations are likely to negative ly affect th e abundance of delta smelt.” 236. 27. In the B iOp, F WS per forme d similar comparisons Id. at

of CalSi m data to Dayflow -sim ulated historic base line data to quanti fy the effects of the action on lar val a nd juvenile delta smelt . See, e.g., BiOp at 2 19 (examini ng

effect o f action on larval and juvenile entrainme nt and stating “[t]he analy sis is based on compari son of historic al (1967-2007) OM R and X2 to the pr oposed action’s predictions of these variables provided in ... [CalSim] studies 7.0 , 7.1, 8.0, and 9.0-9.5 ”). 28. Mr. Mill er explained that outputs from a CalSim

study sh ould not be compared to outputs fro m the Dayfl ow 19

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model be cause the as sumptions used in the two mod els are signific antly differ ent. 18. a. developm ent. The CalS im model ass umes a constant level of In con trast, the Dayflow model inco rporates 4/2/10 Tr. 107:18-23, 1 36:10 -

a contin uous c hange in the level of development because the Dayf low model is using historical information as input. When compari ng models to determine the ef fect of

project operations, the best scientific practice is to keep the assumed level of development constant. Tr. 107: 15-108 :15. b. A CalSim study also assumes a constant 4/2/1 0

regulato ry environme nt, whereas Dayflow uses a re gulatory environm ent that has changed over time. This dif ference

renders any co mparison between CalSim and Dayflow outp uts unreliable. c. 4 /2/10 Tr. 1 08:16-109:23. CalSim a lso operates on a monthly time step, T he two The Dayflow

whereas Dayflow oper ates on a daily time step. models a lso operate to different guidelines.

model in corporates a conservative operation to av oid violating a re gulation. In contrast, the CalSim model 4/2/10 Tr. 107: 23-

operates strictly to that regulation. 108:3, 1 09:24- 110:9.

Operating conservatively results in 4/2/10 Tr. 110:10-14. 20

higher m odeled outfl ow.

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d.

The diff erences in t he model assumptions an d

in the w ay the model s operate, as described above , cannot be quant ified to cal ibrate the models. CalSim do es not

model or simulate hi storical conditions, so it ca nnot be calibrat ed to histor y. 4/2/10 Tr. 121:18-122:6, 161:2 -6.

Calibrat ion would be “ver y di fficult, nearl y impossible, to do wi thout [] developi ng a model designe d to simulate historic al condition s.” 4/2/10 Tr. 110:15-111:1. The

CalSim m odel cannot currently predict X2 for hist oric years be cause it wou ld require a new model. 122:7-16 . e. The Dayf low historic time window that FWS Cal Sim The BiOp’s 4/2/ 10 Tr.

reported using in th e BiOp was 1967 to 2007. studies model water years 1992 through 2003.

comparis on of CalSim-modeled data to Dayflow-modeled data resulted in comparin g differe nt sets of wat er yea rs. Miller t estified tha t the best scientific practic e regardin g years of c omparison would have been to use consiste nt tim e windows. 142:13-1 5. f. The arti ficial neura l network (“ANN”) and 4/2/10 Tr. 116:18-117:2 1; Mr.

the Kimm erer M onismi th eq uation (“KM equati on”) are tw o methods of estimatin g X2. 4/2/10 Tr. 111:2-16. The

CalSim s tudies used ANN to estimate the position of X2, 21

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because ANN can be a dapted to address sea level r ise. 4/2/10 T r. 111:19-25. Th e Dayflow model us es the KM 4/2/10 Tr. 111:2-8; DWR Ex. 510 The KM equation w as

equation to estimate X2.

at Fig. 2; DWR Ex. 5 11 at ¶15.

develope d using hist orical data, making the KM equatio n invalid for a sea le vel rise study. 25. g. At locat ions less than 75 kilometers (“km”) 4/2/10 Tr. 1 11:19-

from the Golden Gate , the KM equation results in an X2 estimate greater tha n (or farther upstream than) the ANN estimate . In contra st, at locations greater than 75 km

from the Golden Gate , the KM equation provides an estimate less than the ANN estimate. 113:18, DWR Ex. 510 at Fig. 2. 29. Mr. Mill er calculate d the magnitude of error 4/2/10 Tr. 112:1-

introduc ed into the BiOp by FWS’s application of both the KM and t he ANN metho ds of estimating X2. He repl icated

the 87 k m value as t he median estimat e of X2 from CalSim study 7. 0 using the ANN method, and, consistent w ith the BiOp, ca lculated the difference between the repor ted historic median of X 2 [79 km] and the study 7.0 m edian [87 km] to be 10% [( 87 km - 79 km)/79]. He then

calculat ed the media n X2 for the CalSim 7.0 study using the KM e quation (ins tead of using ANN) to be 84 k m 22

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(instead of 87 km).

Finally, he identified the p ercent

differen ce between t he reported historic median e stimate of X2 us ing the KM e quation [79 km] and the CalSi m stu dy 7.0 medi an estimate of X2 using the KM equation [ 84 km] to be 6% [(84 km–79 km)/7 9 km]. 4/2/10 Tr. 114:6 -25; DWR

Ex. 511 at ¶¶ 14-16; BiOp at 235-36. 30. FWS did not calculat e X2 using the KM equation Inste ad, i t The

for the CalSim studies, as did Mr. Miller. undertoo k a direct c omparison.

DWR Ex. 511 at ¶1 5.

BiOp rep orted a 10% difference between the report ed historic median X2 a nd the CalSim study 7.0 X2 me dian. Calculat ing the perc ent difference between the hi storical median X 2 and study 7.0 median X2 using the KM eq uation resulted in only a 6 % difference. From this, Mr. Mill er

conclude d that 40% o f the difference between X2 a s estimate d by study 7 .0 and the historical X2 base line reported in the BiOp is error attributed en tirely to t he use of t he KM equati on to calculate the historica l baseline X2 and the ANN equation to calculate the CalSim study 7. 0 baseline. 15. 31. Mr. Mill er testified that the differences in the 4/2/10 Tr. 114:6-25; D WR Ex 511 ¶

KM equat ion and the ANN method of estimating X2 h as an effect o n the BiOp’s analysis of habi tat ar ea, which i n 23

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turn eff ects the BiO p’s prediction of smelt abund ance (as measured by the Summer Townet Survey Index). 113:19-1 14:5; BiOp a t 235–236 , 266-269. 32. Mr. Mill er explained that correcting for the 4/2/10 T r.

differen ces between the use of the KM and ANN met hods to estimate X2 does not correct for all the biases i nherent in compa ring CalSim data to “historic” data. It is

unknown which portion of the remaining 60% of difference is attri butable to t he proposed action, and which portion is due t o the other identified biases. 8; DWR E x. 511 at ¶16. 33. Mr. Mill er testified that when using CalSim 4/2/10 Tr. 115:1-

study 7. 0 -- d esigned as a current conditio ns bas eline -instead of the “hist orical” baseline in the BiOp, and comparin g study 7.0 to the near-futur e 7.1 study, X2 moved up stream 0.7 k m. T he percentage change in X2 from Fur ther,

current to near-current conditions was 0.8% .

when com paring study 7.0 to study 8.0 (a 2030 lev el of developm ent scenario ), X2 moved upstream only 1.1 km, with a r esultant percenta ge change in X2 of 1.2% from current to future conditi ons. 4/2/10 Tr. 1 28:18- 129:11; The 0.7 km chan ge

DWR Ex. 511 at ¶20; BiOp at 235, 265.

and the 1.1 km chang e, respectively, were vastly differen t from the a pproximately 8.7 km and 9.1 k m 24

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changes shown in the BiOp (Figure E-19) usi ng his toric al Dayflow as the basel ine. 34. BiOp at 265; DWR Ex. 51 1 at ¶7.

Using th e equation i dentified in Figure E-20 in

the BiOp , Mr. Miller calculated the reduction in suitable habitat consistent w ith the change in the positio n of X2. A compar ison of CalS im study 7.0 with study 7.1 y ielded a reductio n in habitat area of 128 hect ares, and a comparis on of study 7.0 with study 8.0 yielded a reductio n in habitat area of 289 hectares. 4/2/10 Tr.

129:12-1 30:5; DWR Ex . 511 at ¶20; BiOp at 266. 35. Plaintif fs assert th at, prior to issuance of the

BiOp, FW S was put on noti ce t hat comparing histor ical data to CalSim simul ated data was an inappropriate and invalid methodology. 4/2 /10 Tr. 133:15-134 :11, 1 37:16 -

138:16, 138:21-139:14; SLDMWA Ex. 351 at 7; SLDMWA Ex. 261 at 5 ; SWC Ex. 93 3 at 3. a. notes: CalSim I I is intende d to be used in a comparat ive mode. Th e results from a “proposed operatio n” scenario are compared to the results of a “ba se” scenario , to determine the incremen tal effects. The model should be used with cau tion t o pres cribe sea sonal or to gu ide real-tim e operations, predict flows or wate r deliveri es for any r eal-time operations. T he results from a singl e simulation may not necessar ily represen t the exact operations for a specific month or ye ar, but should reflect longterm tre nds. DWR Ex. 518. 25 The 2008 OCAP BA did raise so me cautionary

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b.

DWR Depu ty Director Jerry Johns, on October

24, 2008 , submitted comments to FWS on the draft effects analysis , generally cautioning against the compar ison of modeled data with ac tual data: USFWS is using histo ric data for comparison to CalSim I I simulation s. Great caution should be taken wh en comparing actual data to modeled data. Ca lSim II mode ling should be used in a comparat ive mode. In other words, it should be used to compare one set of model runs to another. For example , it would be app ropriate to compare CalSim II mo deling of one demand alternat ive to anoth er to analyze the incremen tal effects. AR 8671; see also AR 8668 (further explaini ng unreliab ility proble ms comparing historic and mod eled data). c. The Stat e Water Cont ractors also cited a

letter t hat th ey sent to FWS before the BiO p was complete d. However, that letter only critiqued t he

comparis on of simula ted data to historical salvag e data, and did not dispute with the comparison of CalSim simulate d to Dayflow-simulated histor ic dat a. 133-34. d. Mr. Mill er acknowled ged that, despite his 4/2/10 Tr.

heavy in volvement in the modeling analysis underl ying the BiOp, he did not pre sent his current critic ism of the use of the d ata to FWS d uring preparation of th e BiOp . 4/2/10 T r. 115-16. 26

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36.

FWS was not on notic e of Mr. Miller’s critiques

regardin g comparing simulated Calsim runs to simu lated Dayflow runs, and was not put on notice by him that they were imp roperly usin g the spe cialized models. FW S did

not have an op portunity to correct its modeling or address Plaintiffs’ concerns. 37. The BiO p explains w hy FWS looked beyond CalSim.

When Cal Sim was used to identify current Project operatio ns, and thes e results were then compared to th e results of a CalSim modeling run purportedly simu lating past ope rations, the results “were nearly identic al” despite significant operational changes in curren t operatio ns as compar ed to past. BiOp at 204-05. The

BiOp exp lains that “ [t]he inaccuracie s in CalSim [led FWS] to use actual d ata to develop an empirical baseline .” Id . at 206. FWS “also developed historical

time ser ies data for hydrologic variables used in this effects analysis bas ed on the Dayflow database .. . and OMR data obtained from US GS.” 38. Id.

Mr. Mil ler asserts that best scientific

practice would precl ude FWS from comparing CalSim output to histo ric da ta generated by Dayflow. How ever, Mr.

Miller a cknowledged that in the 2008 OCAP BA, DWR and Reclamat ion co mpared CalSim output to histo ric da ta, 27

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albeit f or a differe nt purpose, namel y to show that th e timing a nd magnitude of reservoir and export oper ations were sim ilar to hist oric operations. 4/2/1 0 Tr. 119-20.

Mr. Mill er acknowled ged that other modelers invol ved in preparin g the BA exp ressed concerns about using o nly CalSim d ata, and tha t the BA itself questioned th e use of that dat a alone, as CalSi m simulations did not pr ovide “an espe cially satis factory representation of pre -POD water pr oject operat ions.” Id. at 150-51. The BA, “While we ha ve

prepared by DWR and Reclamation, states:

not adop ted an alter native statistical approach [ to the use of C alSim model runs] in this biological asse ssment, we belie ve it would be a useful way to further as sess changes in water pro ject operations during the PO D era and we r ecommend tha t [FW S] consider such a n anal ysis as further refinement t o this BA.” Id. Other reputed

scientis ts in the fi eld agree with FWS and the BA that the CalS im-gen erated modeling studies did not “ge nerat e[] baseline s with a hig h degree of reliability.” 160. Id. at

Ne ither Mr. Mi ller nor DWR offered any alte rnative

to Dayfl ow to FWS to address that serious shortco ming during p reparation o f the BiOp. 39. Id. at 160-61.

Mr. Mil ler acknowle dged that , even if the

CalSim c omparison ha d been conducted in the manne r he 28

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recommen ds, it would have confirmed FWS’s conclus ions that Pro ject operati ons as proposed in the BA mov e X2 further upstream in the fall, reducing the amount of habitat for de lta smelt and modifying the quality of critical habitat by shifting the low salinity zon e away from hig her-qu ality habitat and further into the centr al Delta. Id. at 130. Mr. Miller did not suggest t hat this

revision would resul t in a de minimis shift of X2. 40. Mr. Mill er presents substantive criticisms of These specific con cerns were not

the BiOp ’s CalSim ru ns.

raised b efore the ag ency prior to the BiOp’ s issuance. Moreover , FWS expressed legitimate concerns, shar ed with other sc ientists, about the exclusive reliance on CalSim runs. M r. Miller co ncedes that even if his recommende d

approach had been ta ken, the same fundamental res ult would ha ve obtained: project operations shift th e

position of X2 upstr eam. 3 41. This hi ghly technical dispute was not raised

before t he agency, a nd there were legitimate conc erns about co mparing Cals im modeling runs to other Cal sim runs. T his choice o f competing methodologies is not

sufficie ntly clear e rror to justify the court’s interven tion.
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 of RP A Co mp on en t 3.
3

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b.

Treatment of “Other Stressors.”

Plaintif fs raise a generic concern about ho w the

BiOp tre ated the man y other factors that are unde niably contribu ting to the decline of delta smelt includ ing: (a) presence of aquatic macrophytes (submerged aquati c vegetati on such as Egeria densa that may ov erwhel m del ta smelt ha bitat); (b) predation; (c) introduction a nd propagat ion of invas ive species, incl uding inland silversi des and the overbite clam that compete wi th the delta sm elt; (d) pre sence of contamin ants, such as pesticid es and waste water , in the Delta; and (e) presence of large blooms of b lue-green algae toxic to the copep ods eaten by delta smelt . 19, 149: 20-25. 43. Plaintif fs take part icular issue with a BiOp at 182-86; 4/7/10 Tr. 148: 17-

statemen t in the ver y first paragraph of a sectio n of the BiOp ent itled “Effec ts of the Proposed Action.” The Stat us of the Sp ecies/Environmental Baseline section of this docu ment described the multitude of facto rs that affe ct delta smelt population dynamics including p redation, contaminants, introduc ed species, entrainment, habitat suitabil ity, food su pply, aquatic macrophytes, and micr ocystis. The extent to which these factors adversely af fect delta smelt is related to hydro dynamic cond itions in the Delta, wh ich in turn are controll ed to a large extent by CVP and SWP operations. Other sources of water diversio n (NBA, CCWD , local agricultural diversio ns, power pl ants) adversely affect delta smelt la rgely throug h entrainment (see following discussi on), but when taken together do not control hydrodynamic conditions throughout the 30

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Delta to any degree that approaches the influenc e of the Ban ks and Jones export faciliti es. So while many of the other stressors that hav e been ident ified as adversely affecting delta sm elt were not caused by CVP and SWP operatio ns, the like lihood and extent to which they adv ersely affec t delta smelt is highly influenc ed by how th e CVP/SWP are operated in the cont ext of annua l and seasonal hydrologic conditio ns. While re search indicates that there is no si ngle primary driver of delta smelt populati on dynamics, hydrodynamic conditions driven o r influenced by CVP/SWP operations in turn inf luence the d ynamics of delta smelt interact ion with, th ese other stressors (Bennett and Moyl e 1996 ). BiOp at 202 (emphasi s added). 44. The BiOp concludes t hat “the CVP and SWP have

played a n indirect r ole in the delta smelt’s decl ine by creating an altered environment in the Delta that has fostered the establi shment of nonindigenous speci es an d that exa cerbates the se and other stressors that a re adversel y impacting delta smelt.” Tr. 152: 5-12. BiOp at 203; 4 /7/10

Ms. G oude further testified that it is not

possible to quantify the level of effects of thos e other factors. 45. 4/7/10 Tr. 150:1-3. When ask ed by the Co urt to identify a ny

informat ion in the r ecord that supports the BiOp’ s conclusi on that proj ect operations exacerbate the effect of other stressors, Dr. Thomas Quinn, an ex pert appointed under Fe deral Rule o f Evidence 706, c oncluded that “there does not appear to b e evidence in the record demonstr ating that p roject operations exacerbate the 31

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effect/i mpact of oth er stressors.”

Doc. 633, Ord er

Transmit ting R esponses from 706 Experts, Ex. A, at 20. Ms. Goud e testified that she disagreed with this conclusi on, but coul d not identify any evidence f rom the record t o support he r assertion. 203:9. 46. Dr. Andr e Punt, anot her court-appoint ed exp ert, See 4/7/1 0 Tr. 201:22-

further explained th e BiOp’s notion that indirect effe cts of the P rojects may contribute to effects such as high water to xicity, supp ression of phytoplankton, inc rease of overbite clams, and increase in encounters with unscreen ed agricultu ral diversions in the Delta a re plausibl e hypotheses , but that “there are n o dire ct da ta availabl e to test th em.” 47. Doc. 633 at 21.

In contr ast to the BiOp’s general statements

assignin g the blame for at least some, unquantifi ed portion of the negat ive effects cause by these “o ther stressor s” to the project s, elsewhere, the BiOp acknowle dges that th ere is “no single primary dri ver of delta sm elt populati on dynamics,” id. at 202, but rath er that the re are “mult iple factors” and that “not a ll ar e directly influenced by operations of the CVP/SWP. ” at 328. “Other stres sors” are discussed in detail througho ut the BiOp. See , e. g., id. at 182-88, 1 98, 2 0132 Id .

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2.

Spec ifically, FW S considered the effects of

“predati on, contamin ants, introduced species..., habitat suitabil ity, food su pply, aquatic macrophytes, an d microcys tis.” Id. at 202 , 277. The BiOp express ly

recogniz es that the long- term decline of the spec ies “was very str ongly affect ed by ecosystem changes cause d by non-indi genous species invasions and other factors....” Id. at 189. 48. Although the BiOp ac knowledges that “not all” of

the mult iple factors negatively impacting the spe cies “are dir ectly influe nced” by Project operations, the general assertion in the BiOp that other stressor s are the resu lt of (or at least exacerbated by) Project operatio ns is not supported by the record. This error

compound s the agency ’s failure to address alterna tive approach es to avoidi ng jeopardy, incl uding whether oth er stressor s can be mit igated or eliminated, which NEPA requires . (3) 49. Challeng es to Compon ent 2 (Action 3). Componen t 2 (P rotect ion o f La rval and Juven ile

Delta Sm elt) require s OMR flows to remain between -1,250 and -5,0 00 cfs beginning when Component 1 i s comp leted , when Del ta water tem peratures reach 12° Celsius, or when a spent female smelt is detected in trawls or at salvage 33

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faciliti es.

I d. at 282, 357-358.

Componen t 2 re mains in

place un til June 30 or when Clifton Court Forebay water temperat ure reaches 25° Celsius, whichever first occurs. Id. at 2 82, 368. 50. The obje ctive of Com ponent 2 (which corresponds

to Actio n 3 in Attac hment B of the BiOp), is to “ improve flow con ditions in t he Central and South Delta so that larval a nd juvenile delta smelt can successfully rear in the Cent ral Delta an d move downstream when appropriate .” BiOp 282 . 51. The most recent smel t working group

recommen dation for t he week of April 12, 2010 rec ommends OMR flow s no more ne gative than -5,000 cfs because the “risk to larval delt a smelt was low, given that n o salvage of larvae ha s occurred so far this year and the latest s urvey data s uggest that the greatest dens ities of delta sm elt are in t he Sacramento River and downs tream of the conf luence, and, therefore, outside the influ ence of the pump s.” 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 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/ 412- 10 %2 0n ot es .p df .

4

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a.

Use of R aw Salvage t o Jus tify the Quantita tive Flow Re strictions.

The BiOp quantitativ ely analyzed the effects of 4 /6/10

pumping at the Banks and Jones pumping plants. Tr. 19:1 -3; BiOp at 208-209. 53.

The resu lts of that quantitative analysis, which

compared OMR flows w ith gross salvage numbers, ar e describe d in Figures B-13 and B-14 of the B iOp. 348, 350 . BiOp at

These fig ures were presented as part o f a

three an d-a-ha lf page section of the BiOp entitled “Justifi cation for F low Prescriptions in Action 1.” at 347-5 1. BiOp

It also appears that this analysis was rel ied

upon to set the cale ndar- based flow prescription in Componen t 2 (Action 3), as no other basis for the -5,000 cfs ceil ing is prese nted. Because this por tion o f the

BiOp is critic al to the p resent challenge, it is reproduc ed here in i ts entirety: Justification for Flow Prescriptions in Action 1 Understanding the relationship between OMR flows and delta smelt salvage allows a determination of what flows will result in salvage. The OMR-Salvage analysis 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 review of the relationship expressed in Figure B-13 indicates what appears to be a “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 already begun to increase by the time that OMR flows reached -5,000 cfs.

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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 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 reasonable description of the data, other functional relationships also may be 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” in the relationship between salvage and OMR flows. Consequently, an analysis 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, was used to establish the change (break) point in the dataset. A piecewise polynomial regression analysis with a linear-linear fit was performed 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 of variation in the salvage data. Piecewise polynomial regressions were performed using Number Cruncher Statistical Systems (© Hintz, J., NCSS and PASS, Number Cruncher Statistical Systems, Kaysville UT). The piecewise polynomial regression analysis resulted in a change point of -1162, i.e. at -1162 cfs OMR, the slope changed from 0 to positive (Figure B-14). These 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 36

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increases. The pseudo-R2 value was 0.42, a value similar to that obtained by P. Smith in the original analysis. 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 linearlinear-linear fit resulted in two change points, -1,500 cfs OMR and -2,930 cfs 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 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 fit was not the best function to fit the data, and it was rejected. No formal AIC analysis was performed because of the obvious outcome. A major assumption of this analysis is that as the population of Delta smelt 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 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 the residuals are examined for the relationship in Figure B-13 above, the salvage for 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 these data points occur when the curve becomes almost vertical. The negative 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 estimated population size based on the FMWT data.

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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 54. The original values of OMR and salvage could have been measured with error due to a number of causes, consequently the values used in the original piecewise polynomial analysis could be slightly different than the “true” values of salvage and OMR flow. Consequently, a second analysis was undertaken to examine the effect of adding stochastic variation to the OMR and salvage values in the piecewise polynomial regression analysis. The correlation between OMR and salvage in the original dataset was -0.61 indicating that the more negative the OMR, the greater the salvage. Consequently, it was necessary to maintain the original covariance structure of the data when adding the error terms and performing the regressions. The original covariance structure of the OMR–salvage 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 salvage. The expected value of the correlated errors was -0.61. The error terms were selected from a normal distribution with a mean of 1.0 and a standard deviation of 0.25 which provided reasonable variability in the original data. Operationally this process generated a normal distribution of OMR and salvage values in which the mean of the distributions were the original data points. 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 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 values would be close to the mean of the distribution. The process was repeated one hundred times, each time a new dataset was generated and a new piecewise polynomial regression was performed. The software package @Risk (© Palisade Decision Tools) was used to perform the Monte Carlo simulations. Latin 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 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 moved the change point to -1,800 cfs OMR, indicating that at flows above -1683, the baseline level of salvage occurred but with flows more negative than -1683, salvage increased. BiOp 347 -51 (emphasi s added). The BiOp does not us e this information to assert

that ent rainment has a statistically significant effect on the p opulation of delta smelt every year. 172. 4/7/10 Tr.

Ra ther, this information appears to be used to s et 38

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“break p oints” above and below which entrainment rates noticeab ly change. In turn, these break points w ere

utilized in the form ation of the flow restriction s in the RPAs. 55. It is un disputed tha t the use of gross salv age

does not account for the size (or relative size) of the smelt po pulation, as estimated by reliable abunda nce indexes. 4/6/10 Tr. 22:10-11, 23:19. The BiOp a dmits as

much, an d concedes t hat the analysis “assumes that as the populati on of Delta smelt declined, the number of fish at risk of entrainment remained constant.” text abo ve. 56. Consider ing gross sa lvage numbers alone provides See emph asize d

no means of distingu ishing an event in which 10,000 fish are salv aged out of a population of 20,000 from a n event in which 10,000 fish are salvaged from a populati on of 20 million. 57. 4/6/10 Tr. 24:19-22. FWS was aware of the problems with using gross Th e

salvage numbers befo re the completion of the BiOp.

August 2 6, 2008, dra ft meeting notes of FWS’s Del ta Smelt Action E valuation Te am state: When ana lyzing the i mportance of entrainment to the spec ies populati on structure or decline, the relevant fact to con sider is the percentage of the popu lation being removed via entrainmen t. Salvage data, by its elf, may not be sufficient to help one understa nd the percentage of the populati on being rem oved via entrainment. 39

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MWD Ex. 633 at 5. 58. The Inde pendent Peer Review of FWS’s draft

Effects Analys is for the BiOp also recommended to FWS that it “normalize[] ” salvage to population size: The pane l suggests t hat the use of predicted salvage of adult sme lt should be normalized for populati on size. To tal number salvaged is influenc ed by a variety o f factors, particu larly the numb er of fish i n the population.... Expressi ng salvage a s a normalized index may help rem ove some of the confounding of the temporal trends duri ng the baseline. MWD Ex. 608 at 8. 59. However, notwithstan ding the recommen dation of

the Inde pendent Peer Review and its own internal staff’s recognit ion that sal vage data should be normalize d, FWS persiste d in using r aw salvage data and did not normal ize or index the salvage data to the population size. at 348, 350. BiOp

As a result, salvage numbers relied upon to

justify the RPAs do not relate to any information regardin g population-level effects. 23:19. 4/6/10 Tr. 22:10- 11,

This was unr easonable, not based on the b est

availabl e science, a rbitrary, and capriciou s. 60. This con clusion was supported by explanatory There was agreement am ong the

testimon y of the exp erts.

testifyi ng scientifi c experts that the use of nor malized salvage data rather than gross salvage data is th e standard accepted scientific methodology among 40

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professi onals in the fields of fisheries biology/ management. 4/5/10 Tr. 97:4-10, 143:25-144:1;

4/6/10 T r. 30:15-22; Doc. 633, Ex. A, at 7, 10; 4/6/10 Tr. 31:1 1-16; MWD Ex . 608 at 6; Fed. Gov’t Smelt Ex. 17 at ¶11. a. The Fede ral Defendants’ expert on biological

statisti cs, Dr. Kenn eth Newman, stated in his dec laration that Fed eral Defenda nts should have “scale[ed] sa lvage by some mea sure of popu lation abundance” and stated in his oral tes timony that without indexing salvage to population the re is “nothing to go on.” Ex. 17 a t ¶11; 4/5/10 Tr. 143:25-144:1. b. Dr. Newm an went on t o state that the Fed. Gov’t Sm elt

relevant factor to c onsider is the percentage of the smelt po pulation bei ng removed by entrainment and that salvage data b y itself is not sufficient. 97:4-10. 4/5/10 Tr.

Dr. Newman also stated that becau se Fig ure B -13

relates raw salvage to combined OMR flows, it doe s not enable t he agency to determine the effect on the populati on of a part icular OMR flow. 15. c. Dr. Punt found that “it was unreasonable 4/5/10 Tr. 100:11-

(given t hat appropri ate data and analysis methods were availabl e to account for population size) to have only 41

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relied o n the inform ation in Fig. B-13 and Fig. B -14 rather t han on an an alysis in which salvage is expressed relative to populati on size.” Dr. Deri so agreed. d. Doc. 633, Ex. A, a t 7.

4/6/10 Tr. 30:15-31:2.

Dr. Thom as Quinn, the oth er 706 exper t,

stated: “it is not c lear why such an adjustment [ of salvage to populatio n size] was not made for the data examined in this rep ort.” Deriso a greed. 61. Doc. 633, Ex. A, at 10 . Dr.

4/6/ 10 Tr. 31:11-19.

The BiOp itself reco gnized the necessity of

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

Action E valuation Te am also indicate that FWS recognized and was aware of the need to analyze the percenta ge of the popu lation remov ed by salvage, but neither th ese notes no r the BiOp e xplain why this analysis was not performe d. 63. MWD Ex. 633 at 5; 4/5/10 Tr. 96-97:14 -10.

The BiOp , in fact, u sed n orma lized salvage data

for othe r parts of i ts analysis, including the In cidental 42

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Take Sta tement, evid encing its ability to do so.

BiOp at

386; 4/7 /10 Tr. 196: 18-20; see also 4/7/10 Tr. 19 9:14- 21 (Cay Gou de testifyin g that FWS understood the imp ortance of using normalized salvage data and chose to use it i n parts of the BiOp). 64. FWS did not explain its decision in the BiOp to

use gros s salvage nu mbers in Figures B-13 and B-14, an d did not explain why it selectively used normalize d salvage data i n some parts of the BiOp but not in others. 4/6/10 T r. 28:5-8, 32:5-9. 65. FWS pres ented no cre dible, scientifically based

explanat ion for the decision to use gross salvage numbers instead of normalize d salvage data in Figures B-13 and B14, eith er in the Bi Op or at the hearing. Other than

endeavor ing to struc ture a result, there is no explanat ion for this departure from best availabl e science. 66. This raise s the spectre of bad faith. For the purposes of (a) demonstrating the

differen ce bet ween t he analysis presented i n the BiOp and a popula tion-n ormalized analysis and (b) identifying an appropri ate interim remedy, Dr. Deriso analyzed t he relation ship between normalized salvage and OMR f lows. This ana lysis reveal ed that there were no detecta ble trends i n the juveni le salvage rate at flows up t o -5, 600 43

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cfs, whi ch is the mo st negative salvage weighted flow rate con tained in th e data. Gov’t Sm elt Ex. 18 a t ¶25. 67. Federal Defendants critic ize Dr. Deriso’s 4/6/10 Tr. 55:18-24; Fed.

alternat ive analysis in a number of ways: a. Dr. Newm an explained that Dr. Deriso’s

analysis is more app ropriately characterized as a “first cut” at an analysis that fails to correct for pot entially large “o bservation e rrors.” 4/5/10 Tr. 73, 77-78. Those

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

testimon y regarding the factors he will be addres sing and includin g in his for thcoming delta smelt life cyc le model). He opined t hat some of these confounding factors

are very important a nd ignoring them could lead o ne “[e]ithe r to wrongly assume that there is a relat ionship or to as sume that th ere is [one] when there isn’t .” at 82. Id.

This concern was reiterated by Dr. Rose i n his Id. at 160-61.

2000 pap er, and by D r. Hilborn. b.

Dr. Newm an ran his o wn analysis, applying a 44

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differen t standard s tatistical methodology, on th e same cumulati ve salvage i ndex versus OMR flow data use d by Dr. Deriso, and got diff erent results regarding the “inflect ion point” w here OMR flows had an increasing impact o n the popula tion- normalized salvage rate. Tr. 63-6 4. 4/5/10

Ultimate ly, Dr. Newman testified that he

would ha ve performed a statistical analysis diffe rent from tho se performed by both Dr. Deriso and in th e BiOp. Id. at 7 9-80. Dr. N ewman nev er suggested that an

analysis utilizing r aw salvage numbers (i.e., not adjusted for relativ e population size) is scienti fically appropri ate. This i s not just a scientific dispu te among

experts, particularl y in view of FWS’s concession in the BiOp. c. Dr. Deri so admitted that he is not a delta

smelt bi ologist, 4/6 /10 Tr. 125, and that his ana lysis does not account for a number of pote ntially confounding factors, such as: th e large amount of pumping-rel ated mortalit y that is no t measure d by salvage, id. at 89; 116, pum ping-r elated changes to delta smelt habitat, id. at 116, 140; pumping-related impacts on foo d supply, id. at 143; pumping-related impacts of spatial confin ement of delta sm elt to the S acramento River, id. at 144-45; whether the de ath of some individuals such as fec und 45

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females may have a d isproportionate impact on the populati on (the so-called “big mama” hypoth esis) id. a t 116; and whether the relationship between OMR flo ws and populati on abundance could change depending on populat ion size, id . at 146. d. Nor did Dr. Deriso’s analysis distinguish

between years pre-dating or post-dating the POD, thoug h he ackno wledged that there is evidence of drastic changes in the e stuary durin g that period. Id. at 123-24, 165.

Reputable scie ntists in the field, including Drs. Peter Moyle an d Bill Benne tt, have opined that statisti cal “correla tions [in th e Delta] seem to be los ing some of their fo rmer predict ive value in recent years for some desirabl e species (K immerer et al. 2009). This, in pa rt,

may be d ue to ... th e extremely low abundance of desirabl e fishes, wh ich may not be tracked as eff ectively by the t raditional m onitoring programs.” e. Id. at 119-20.

In the a bsence of re liable population

estimate s for delta smelt, Dr. Deriso utili zed th e FMW T index as a proxy for population when conducting h is analysis of the popu lation-level effects of salva ge on adult de lta smelt. However, Dr. Newman noted tha t there

are seve ral biases i n the FMWT data, particularly selectio n bias, such that he would not rely purely on 46

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FMWT dat a “when it c omes to analyzing salvage.” Tr. 118. e.

4/5/10

In addit ion, Dr. Der iso’s analysis accounts

in only a very limit ed way for spatial distributi on (by excludin g years with low turbidity from the analysis). Spatial distribution reflects the increased vulne rability of delta smelt to en trainment as they move closer to the pumps. 4/5/10 Tr. 8 0-82. In contrast, Component s 1 and

2 of the BiOp accoun t for spatial distribution to a much greater extent by allowing for modification of th e lev el of OMR f lows based o n the location of delta smelt in the estuary. 4/7/10 Tr. 55-56, 6 9-71. Dr. Der iso’s analy sis

looks so lely at the relationship between populati onweighted salvage and OMR flows, excluding all other factors and consider ations. 68. Neverthe less, even a ssuming all of these

critique s of D r. Der iso’s opinion are valid, they do nothing to justify t he BiOp’s election to base it s flow prescrip tions on an analysis that uses raw salvag e numbers. Even if Dr . Deriso’s “first cut” needs

refineme nt to addres s these critiques, the BiOp’s analysis in Figure B-13 does not account fo r any of th e issues o n which Fede ral Defendants criticize Dr. Deriso’s analysis . 47

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69.

Federal Defendants note that Dr. Deriso

presente d his conclu sions and analysis regarding the BiOp to the N ational Rese arch Council of the National Academy of Scien ces panel th at peer-reviewed the BiOp. Tr. 193; 4/6/10 Tr. 137. 4 /2/10

After reviewing the inf ormation

presente d by D r. Deriso, that panel explicitly di sagreed with his conclusion that FWS’s analysis in the Bi Op was not base d on the bes t available science or one th at a “reasona ble biologis t” would perform. Instead, t he NRC

Panel co nfirmed the analysis performed by FWS and its biologis ts, stating that: Although there are s cientifically based argument s that raise legitimate questions about this act ion, the com mittee concludes that until better m onitoring da ta and comprehensive life cycle mo dels are ava ilable, it is scientifically reasonab le to conclu de that high negative OMR flows in winter prob ably adversely affect smelt populati ons. Thus th e concept of reducing OMR and nega tive flows t o reduce mortality of smelt at the S WP and CVP f acilities is scientifically justifie d. 4/2/10 T r. 194. The NRC analysis justifies its

conclusi on by recogn izing better monitoring is no t availabl e, a compreh ensive life cycle model does not exist, a nd that high negative OMR flows in winter “probabl y” adversely affect smelt populations. 70. The NRC’ s equivocal conclusion is in no way

inconsis tent with a finding that the BiOp failed to utilize the best ava ilable scientific methods by relying 48

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on a qua ntitative an alysis using raw salvage to select the uppe r ceil ing for negative OMR flows un der Co mpone nt 2. The Federal Defe ndants have not told the whol e NRC The NR C Panel expressly found that “there

Panel st ory.

is substantial uncertainty re garding the amount of flo w that sho uld trigger a reduction in exports,” (emphasis added) a nd dec lined to decide whether alternative RPAs would “ provide equa l or greater protections for the

species while requir ing less disruptions of Delta water diversio ns,” conclud ing that the panel had received insuffic ient documen tation on such alternatives. 200-01. Id. at

Having fail ed to perform the required NE PA

analysis , it is cert ain that Federal Defendants c ould not and did not take the requisite hard look at RPA alternat ives. 71. Federal Defendants a rgue that the district court

previous ly heard and rejected similar statistical analysis of fish pop ulation dynamics presented by Mr. B.J. Mil ler during t he 2007 interim remedy hearin g. a. Mr. Mill er “conclude d that there was no

statisti cal signific ance in the relationship betw een Delta sm elt abundance and salvage and expor t oper ation s in the p umps.” 4/6/ 10 Tr. 114. Another of Plain tiffs’

witnesse s in that pr oceeding, Dr. Charles Hanson, then 49

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explaine d that even if Mr. Miller’s statistical a nalyses were cor rect and “re flect the low significance of that salvage mortality to the population,” it did not suggest that reg ulatory acti on to minimize salvage at the pumps was not justified: On the o ther side, Y our Honor, the fact that we are salv aging Delta smelt represents a source of mortalit y to this populat ion. And one of th e approach es that's be ing made, given the low populati on abundance , is to identify those sources of mortality that we know of and to try and redu ce those. My feeling is that we have such a c omplex estua ry with so many interacting variable s that chang e from year to ye ar and within y ears, that i t's difficult to rely solely on stati stical analy ses. I think we're at a point wh ere we need to say do we have a substant ial source o f mortality and is there somethin g we can do to help reduce that. 4/6/10 T r. 114-15. b. Plaintif fs’ expert, Dr. Hilborn, expr essed

similar opinions dur ing the most recent evidentia ry hearings , acknowledg ing that, while he criticized the BiOp for lacking “a basis for population level ef fects of the prop osed actions... i t’s pretty clear t hat th ere a re viabilit y concerns a bout Delta smelt.” 4/5/10 Tr . 224.

Dr. Hilb orn also ack nowledged “it’s very clear th at large negative flows have an impact on the number of fi sh that are impi nged and ent rained.” Id. at 228. He did not Dr.

quantify what he mea nt by “large negative flows.”

Hilborn agrees that there is no doubt that the po pulation size of delta smelt is currently at an historic l ow and 50

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that ent rainment at project facilities results in direct mortalit y. Id . at 249-50. Dr. Hilborn explained that he

does not deny that a long-ter m relationship between populati on growth ra te and salvage may exist, onl y that he has n ot see n “any evidence of that in any of the analysis I've seen so far .” Id. at 2 28. D r. Hilborn

acknowle dged t hat he “couldn’t exclude the possib ility ” that a f uture salvag e event could eliminate 100% of the populati on, even if there was no relationship bet ween the amount o f delta smel t salvaged and long-ter m popu latio n dynamics . c. Id. at 229. Assuming, argu endo, the “ possibility” canno t

be “exclude[d] ” that a future salvage event could eliminat e 100% of th e population, FWS did n ot justify its selectio n of - 5,000 cfs on th e basis of that ceiling’s ability to prevent s uch a catastrophic salvage ev ent. Faced wi th express c oncerns from inside and outsi de the agency a bout drawing conclusions from analyses us ing raw salvage, FWS complet ely failed to explain why it nonethel ess did so. None of the post-hoc

rational izations off ered by Federal Defendants, e .g. t he “big mam a” hypothesi s, was mentioned in the BiOp as ba ses for sele cting -5,000 cfs as the ceiling for negative OMR flows. 51

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72.

FWS’s re liance on an alyses that utilize raw (as

opposed to populatio n-nor mali zed) salvage data is an undeniab le fai lure to use the best available scientifi c methodol ogy. b. Other Da ta Supportin g the General Conclusion that Neg ative OMR fl ows Jeopardize the Smelt.

73.

There is far more di spute over the sufficiency

of evide nce supporti ng the BiOp’s general conclusion t hat the nega tive OMR flo ws predicted to take place un der planned Project oper ations will jeopardize the sm elt (referre d to in this subsection as the “jeopardy conclusi on”). (1) 74. Sporadic ally Signifi cant Take.

One of t he key ratio nales for the jeopardy

conclusi on is the as sertion that entrainment has a “sporadi cally signif icant” effect on smelt abunda nce. BiOp at 210. This a ssertion was based on the est imates Bi Op at

of propo rtional entr ainment in Kimmerer 2008. 210; Fed . Gov’ t Smelt Ex. 38.

Kimmer er 200 8 states th at:

Delta sm elt may suff er substantial losses to export p umping both as pre-spawning adults and as larva e and early juveniles. In contrast to the situ ation for sa lmon, pre-salvage morta lity has been constrained in the calculations for adult De lta smelt, a nd its effects eliminated from the calculation s for larval/juvenile Delta smelt. C ombining the results for both life stages, losses may b e on the order of zero to 40 percent of the popul ation throughout winter and 52

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spring. 4/7/10 T r. 42- 43; AR 018877. 75. Dr. Grim aldo confirm ed that the Kimmerer (2008)

and Kimm erer and Nob riga (2008) studies represent ed the “best av ailable scie nce” when the BiOp was prepar ed. 4/7/10 T r. 63- 64. The BiOp cites Kimmerer (2008) (and

other pe er-rev iewed studies) for the propositions that entrainm ent can affe ct the abundance of delta sme lt in certain years; may p revent recovery when habitat conditio ns are suita ble; and that high entrainmen t of adults i n the winter appears to have played a role in the decline of delta sme lt in the POD years. 76. BiOp at 158- 59.

Dr. Deri so questions whether Kimmerer (2008)

should b e interprete d as standing for the proposi tion that ent rainment mor tality can kill a subst antial portion of the p opulat ion in some years. For examp le, he

testifie d that the K immerer (2008) article relied on a number o f assumption s to calculate the percentage entrainm ent figures incorporated into the BiOp, i ncluding the assu mption that a proportional relationship exists between OMR flow lev els and entrainment. 4/6/10 Tr.

131:12-1 6; Fed . Gov’t Smelt Ex. 29 at ¶19; Fed. Gov’t Smelt Ex . 38 at 0188 75-018876. Because the Kimme rer

(2008) a rticle began with this assumption, Dr. De riso 53

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opined t hat it could not reasonably b e used by FWS as evidence that a prop ortional relationship exists between OMR flow level and s melt entrainment. Ex. 29 a t ¶19. 77. But, the BiOp did no t rely on Kimmerer (2008) D r. Grimaldo explained that “w hat t he Fed. Gov’t Smel t

for this purpose.

Kimmerer 2008 paper actually showed was that ther e was a populati on response [to entrainment] within life stage s.” 4/7/10 T r. 98. 5 Dr. Newman explained that this

informat ion is “cert ainly pertinent to understand ing what’s h appening wit h the pop ulation.” 136. 78. Dr. Newm an, who did not participate in the 4/5/10 Tr. 135 -

preparat ion of the B iOp, agreed that FWS’s conclu sion in the BiOp that entrai nment affects subsequent year
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 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 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 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. 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, 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 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 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 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 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 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 .
5

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abundanc e of Delta s melt even sporadically is sup porte d by gener ally accepte d scientific standards. 89-90. 4/5/ 10 Tr.

It is undisputed that very large salvage events

can and have occurre d at OMR flows of less than - 5,000 cfs. In May and Jun e of 1999 alone, 58,929 and 7 3,368

delta sm elt, respect ively, were salva ged at the Projec t export f acilities. 4/6/10 Tr. 111. Average OMR flows

during t hose months were -1,0 62 cfs and -3,814 cfs, respecti vely. Id. at 112 . While Dr. Deris o test ified

that the significanc e of such an event depends on the size of the population, he also could not state whethe r the curr ent populati on was large enough to surviv e similar salvage even ts, or whether such an event would jeopardi ze the conti nued existence of the smelt. Id.

Dr. Hans on, another of Plaintiffs’ expert fish bi ologist witnesse s, testified in 2007 that salvage of 1,30 0-1,400 delta sm elt would be “a very high level of salvag e” “under t he current p opulation levels.” Id. at 113.

Delta sm elt abundanc e levels have further decline d since Dr. Hans on made that statement. 79. Id.

It was n ot unreasona ble for FWS to conclude that

salvage events may b e “sporadically significant.” // // 55

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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 82. 80.

(2)

Dr. Benn ett’s Work. (a) Impact of VAMP on Po pulat ion Dynamics.

Dr. Ben nett’s unpub lished research

“demonst rated that the number of larv ae tha t survived to the fall is related to when they hatch in the spr ing.... [and] th at larvae th at hatched during the VAMP .. . protecti ve period[] were the ones that survived t o the fall in the pe riod that he examined.” 81. The BiOp concluded: Based on Bennett’s u npublished analysis, reduced spring expor ts resulting from VAMP have sel ectively enh anced the survival of delta sm elt larvae s pawned in the Central Delta th at emerge du ring VAMP by reducing their entrainment. Initial ot olith studies by Benne tt’s lab sug gest that these springspawned fish dominat e subsequent recruitment to adult life stages . By contrast, delta smelt sp awned prior to and after the VAMP have bee n poorly-rep resented in the adult stock in recent years. The da ta suggests that the differentia l fate of early, middle and late cohorts aff ects sizes of delta smelt in fall becaus e the later cohorts have a shorte r growing se ason. The se findings suggest that direct entrainment of larvae and juve nile d elta s melt duri ng the spring are rele vant to popu lation dynamics. BiOp at 170 (emphasi s added). Nothing in the rec ord 4/7/ 10 Tr. 93.

suggests this conclu sion was unreasonable. (b) Big Mama Hypot hesis.

Federal Defendants a nd Defendant Intervenors

also sug gest that Dr . Bennett’s work provided “ev idence” 56

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to suppo rt the “big mama” hypothesis that Project operatio ns may affec t delta smelt abundance by en training the most fecund indi viduals in the population, th ereby creating a dispropor tionate impact on the reproductive potentia l and growth rate of the population. 83. However, the BiOp do es not suggest Bennett’s

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

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been pro ved. (3) 84. Consider ation of Lif e Stage and Geograph ic Dis tribut ion.

The BiOp considers t he life stage of delta smelt

and wher e the popula tion is located in the estuar y, to help ass ess en trainment risk. Dr. Grimaldo expla ined:

[I]n the fall [and] winter, we have very low entrainm ent risk. Bu t once the first flush events h appen, begin ning sometime in mid December , Delta smel t often migrate upstream. So they’re vulnerable a t this part of th e life stage. After they m igrate upstream, they stage for a li ttle bit. An d they’re vulnerable to entrainm ent during t he staging period. And then after th e staging pe riod, they spawn. And their progeny are vulnerab le to entrainment at this period. So there ’s vulnerabi lity to different life stages a s -- and, in general, as they become distribu ted closer t o the central and south Delta ce ntral and so uth Delta, their entrainment risk goe s up. 4/7/10 T r. 50- 51. The RPA takes into account these

spatial and li fe sta ge fa ctors by breaking actions int o differen t components over different periods of ti me. at 64-65 . 85. Mr. Feyr er and Dr. G rimaldo testified that the Id.

export p umps affect the geographic distribution o f delta smelt, a nd that prev entin g th e fish from coming n ear the pumps re duces the ri sk of entraining those fish. Tr. 180; 4/7/10 Tr. 64. 4/2/10

Larval and juvenile delt a smelt,

in parti cular, are “ neutrally buoyant” and thus f ollow the flow in the Delt a in a manner similar to part icles. 58

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4/7/10 T r. 54- 55.

Particle-tracking modeling sho ws that

many of the particle s are “lost” to the pumps whe n export-i nflow ratios are increased. Id. at 59-60.

Kimmerer and Nobriga (2008), relied on in the BiO p, asserts that these s tudies “suggest a direc t link between the posi tion of the smelt population as determine d by outflow and losses a s determined by export flow” and “may be enoug h to recomme nd strong protective measures for Delta sm elt in sprin g (March-May) of low ou tflow years when the y are highly vulnerable to export losses.” at 60-62 . Id .

Non-export factors influence entrainment too,

“such as river inflo ws, the position of X2 and wh ere the fish are distributed .” Id. However, as Mr . Feyr er

testifie d, “essentia lly the closer [the fish] are , the more vul nerable [the y] will be” to the effects of entrainm ent. 6 Id.

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 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 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 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 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 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 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 exp os ur e to t he se s ou rce s of m or ta l ity . I d. a t 18 3.

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7

c. 86.

Life Cyc le Analysis.

Studies cited in the BiOp failed to demonstrate

that wat er exports a ffect the delta smelt populat ion growth r ate. Kimmer er (2008), for example, noted a “l ack

of evide nce for popu lation-level effects” o f the water projects and stated that “no effect of export flo w on subseque nt midwater trawl is evident.” AR 018878 , Be nnett

018855; MWD Ex. 600 at 53; MWD Ex. 600 at 28.

(2005) f ound that “i t is unlikely that losses of young fish to the export f acilities consistently reflec t a direct i mpact on rec ruitment success later in the year.” AR 01700 4; MWD Ex. 6 07; SLDMWA Ex. 240. 87. All expe rts agree th at applic ation of a lif e-

cycle mo del 7 is accep ted method for evaluating the effects of an action upon a population’s growth r ate. a. The Delt a Smelt Acti on Evaluation Team

recogniz ed that such a model should be developed and utilized . b. MWD Ex. 6 33 at 5, 9, 10, 11. Dr. Deri so testified that a population

growth r ate analysis is the method by which fishe ries biologis ts normally evaluate the impact of a stre ssor on a popula tion. c. 4/6/1 0 Tr. 38:11-18. Dr. Hilb orn similarl y testified that life-

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 ., 4/2 T r. 2 55 ; 4/ 6 Tr . 41.

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cycle mo dels are the accepted method in population dynamics to evaluate anthropogenic effects on the probabil ity of growt h or decline of a species. Tr. 154: 16-24. 4 /5/10

Dr. Hilborn testified that develo pment of

such a m odel is “sta ndard operating procedure” fo r fisherie s management agencies to evaluate human impact s on fish species. d. 4/ 5/10 Tr. 155:20-25.

FWS’s ex pert, Dr. Ne wman, stated in his

declarat ion that he “agreed with the utility of l ife history models for a ssessing population level eff ects of SWP/CVP operations.” e. Fed. Go v’t Smelt Ex. 17 at ¶8.

Dr. Newm an said he w ould have developed a 4/5/10 Tr. 107:21 -108:5.

life-cyc le mod el for the BiOp.

Dr. Newm an stated th e methodology employed in the BiOp was “qui te a differe nt way of doing things” from the statisti cal analysis he was “familiar with” and “comfort able with.” f. 4/5/10 Tr. 107:21-108:5.

Federal Defendants’ expert, Mr. Feyrer,

testifie d that, once developed, a life-cycle model wou ld be the b est availabl e science to evaluate the pop ulationlevel im pacts of the water projects on the delta smelt . 4/2/10 T r. 253:4-10. g. Accordin g to Mr. Fey rer, use of a life-cycle

modeling methodology in the BiOp would have reduc ed the 61

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uncertai nty in the R PAs. 88.

4/2/10 Tr. 258:22-259:8 .

How long it would ha ve taken FWS to develop an

appropri ate li fe cyc le model is a matter of consi derable debate. a. Life-cyc le modeling is an analytical

techniqu e that has b een known and available to sc ientists for year s. 4/5/10 T r. 109:19-110:3. Numerous textboo ks

and refe rence articl es explain how to devel op a lifecycle mo del, which a re a standard tool used by fi sheries scientis ts to evalua te population-lev el impacts. Tr. 254: 23-255 :14. 4/2/10

Basic growth rate models such as the

Ricker m odel and the Beverton-Holt mo del were develope d in the 1 950s. b. 4/6/10 Tr. 41:22-42:4; 49:16 -22. Dr. Deri so testified that sufficient data

existed at the time of the creation of the BiOp t o enable FWS to p erform a qua ntitative life-cycle modeling analysis . c. 4/6/10 Tr . 46:16-47:16. Dr. Deri so testified that a basic

quantita tive life-cycle m odeling analysis c ould b e performe d in less th an an hour, while a more comp licated modeling effort coul d be completed in a few weeks . 4/6/10 T r. 43:2-7. d. Mr. Feyr er testified that FWS could have

complete d a life-cycle mo deling analy sis within 1 8 62

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months.

4/2/10 Tr. 263:15-24. e. In a 200 5 research a rticle Dr. Bennett

employed a life-cycle model to evaluate a n umber of impacts on the delta smelt. f. 4/2/10 Tr. 46:16-47: 16.

Dr. Hilb orn testifie d that a life-cycle

modeling effor t could have been performed for the delt a smelt wi thin a matte r of months. 4/5/10 Tr. 175: 5-21.

He furth er testified that even an incomplete life -cycle modeling analysis, s uch as the one found in Benne tt (2005), would be sup erior to simply relying on professi onal or expe rt opinion withou t use of any such model. 4/5/10 Tr. 2 12:23-213 :6. How ever, Dr. Hi lborn

admitted that when h e and Dr. Maunder actually en deavored to build a quantitat ive population dynamics model for delta sm elt over 18 months ago, they abandoned that particul ar modeling effort as too complicated and timeconsumin g. g. Id . at 217-18. Dr. Punt stated “[i] t is surprising that a

populati on dynamics model was not developed for d elta smelt fo r the BiOp.. .. The model developed by Ben nett could ha ve bee n exte nded to more fully account fo r the biology of delta sme lt and fitted to data to asse ss the populati on-lev el effects of impact of the project .” 4/6/10 T r. 44:16-21; Doc. 633, Ex. A, at 3. 63

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89.

Yet, a quantitative population dynamics mo del

for delt a smelt is “ not something that you go to the store an d just buy [ like] a piece of equipment,” but rather w ould consist of a large amount of formula s. 4/2/10 T r. 254; 4/5/ 10 Tr. 48 (Dr. Newman concurr ing that “there’s not off-the-shelf software to buil d such models”) . Dr. Newma n testified that previous eff orts to

build su ch models in which he has been involved h ave taken tw o to three y ears, 4/5/10 Tr. 50, and have involved numerous pe ople because you need experti se in biology, statistics, and modeling. Id. at 131. Mr.

Feyrer s tated that “ the construction of a full bl own high quality life cycle m odel is no simple task.” 255, 258 . 90. Mr. Fey rer also poi nted out the importance of 4/2 /10 Tr.

construc ting an appr opriate and well-calibrated model: “even fo r individual s with the amazing skills of [Drs. Maunder, Deriso and Hilborn], it still takes a lo t of time to develop thos e to where you have the confi dence in them so that you can actually apply them in a sit uation where, y ou know, the re's obviously a lot at stake here. You don' t want to ap ply something prematurely wit hout really u nderstanding how well it works.” Id. at 258.

Dr. Deri so, in contr ast, applied a generic “textb ook” 64

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version of a life hi story model in the analysis h e presente d to the Cou rt, without modifying it to a pply specific ally to delt a smelt biology and character istics. 4/6/10 T r. 42. Sign ificant disagreement exists a mong

competen t experts as to what constitutes a reliab le quantita tive populat ion dynamics model for delta smelt . 91. Federal Defendants w ere aware of the value of a At a March 8, 2007 meeti ng regardin g

life-cyc le mod el.

the OCAP ESA Re-consultation, attended by a numbe r of FWS employee s, the impor tance of using a life cycle m odel was recogniz ed and the p rogress to date was inquired into. 4/7/10 T r. 183:9-188:4; S WC Ex. 960. Likewise, during

the Delt a Smelt Acti on Evaluation Team meeting on August 8, 2008, the Team re cognized that population mode ls for delta sm elt already had been developed, and that it wa s possible to use thos e models as a starting point for quantita tive analyse s with appropriate assumption s added as bound s to the ana lysis. 92. 4/7/10 Tr. 188:9-190:22.

Neverthe less, it is undisputed that, despite

over thr ee yea rs of controversy regarding t he spe cies, no quantita tive life cy cle model adapted to the delt a smelt was avai lable to or used by FWS at th e time the B iOp was issued. A quantitat ive population dynamics model for

delta sm elt does not currently exist, although there a re 65

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several efforts unde rway to develop one. 4/5/10 T r. 44.

4/2/10 Tr. 189;

Rese archers from a number of

universi ties, includ ing Drs. Wim Kimmerer, Bill B ennett, Kenny Ro se and Steve Monismith, have been working on developi ng such a mo del for a number of yea rs. 189-90; 4/5/10 Tr. 46. Id. at

Dr. Mark Maunder has also been

working on such a mo del for delta smelt since at least March 20 08, with the assistance of Dr. Hilborn an d Dr. Deriso. Id. a t 258; 4/5/10 Tr. 47. Dr. Newman, who h as

previous ly developed three quantitative life hist ory models, is currently working with the National Ce nter for Ecologic al Analysis and Synthesis (“NCEAS”) to de velop one for delta smelt, an effort that has been unde rway since Oc tober 2007. 93. 4/5/10 Tr. 44-46.

No party who partici pated in the preparation of

the BA o r commented on the public review drafts o f the BiOp sub mitted a qua ntitative life cycle model or the results of such an a nalysis using a life cycle mo del for delta sm elt to FWS d uring the consultation. 16-18. 94. It is no table that F WS did make use of the 4/5/ 10 Tr.

relative ly simple an d limited life-cycle model describ ed by Dr. B ennett in hi s 2005 paper. 4/2/10 Tr. 256 -57. It

utilized that existi ng model by conducting the effects 66

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analysis in the BiOp according to a similar conce ptual life-cyc le mod el. Id. at 258 . The agency then c onducted

analyses on specific components of those life sta ges that would be affected by the proposed Project operati ons. Id. Dr. Hilbo rn asserts that FWS erred by not us ing t he

Bennett model to jus tify the export limitations i n the RPA, 4/5 /10 Tr. 241, but the Bennett 2005 paper a nd Dr. Bennett himself caut ioned that the life-cyc le mod el it presente d is “premat ure for management purposes.” 18, 115, 240-4 1. 95. In sum, although all agree that a quantitative Id. at

life-cyc le mod el would help FWS evaluate im pacts on de lta smelt, F WS had not d eveloped an appropriate model , and no such mod el was avail able for FWS’s use (or otherw ise presente d to FWS) pr ior to the issuance of the Bi Op. d. 96. Incident al Take Stat ement.

Plaintif fs inc luded propo sed findings of fa ct

concerni ng FWS’s for mulation of the Incidental Ta ke Statemen t (“ITS”). However, at the evidentiary h earing,

Plaintif fs aba ndoned their request to enjoin implemen tation of th e ITS. 4/7/10 Tr. 243-44

(“Plaint iffs do not seek modification of the inci dental take lim it at this t ime. Even though the current low ITS

limits a re not suppo rted by the data and applicat ion of 67

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quantita tive populat ion dynamics analysis, that v ery conserva tive limit, Your Honor, plaintiffs believ e will serve as a back stop that will provide an additio nal level of assurance t o the Court that during the c omponent two peri od, which en ds in June, the surviva l of the sm elt will not be jeopardi zed by project operations.”). e. 97. Critical Habitat.

Federal Defendants a nd Defendant Intervenors

maintain , in the alt ernative, that negative OMR f lows adversel y modify cri tical habitat and Component 2 can be upheld b ecause it ad dresses this adverse modifica tion. 4/7/10 T r. 272:8-273:3; 4 /6/10 Tr. 93:2-6; 4/5/10 Tr. 225:18-2 26:22. 98. However, the specifi c quantitative criteria

establis hed for RPA Component 2 are not derived f rom or justifie d by a ny independent analysis of adverse modifica tion of delt a smelt critical habitat. 344-68. 99. Discussi on of habita t in the justific ations for Bi Op at

RPA Comp onents 2 def ines habitat solely in terms of entrainm ent risk. B iOp at 34 4-368. The on ly

quantita tive analysi s of entrainment risk is foun d in Figures B-13 a nd B-14 of the BiOp. B iOp at 348, 350.

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f.

Indirect Harm.

100. Federal Defendants c laim that Component 2 also protects against ind irect harm. However, the

quantita tive analysi s used to derive the flow levels does not ment ion indirect harm as a basis for the flow restrict ions imposed . g. The Role of RPA Comp onent 2 in Avoiding Jeopardy to the Spec ies and Adverse Modifica tion of Crit ical Habitat.

101. All of t he experts q ualified in delta smelt biology concurred th at enjoining parts or all of Componen t 2 would ca use jeopardy or adverse impac ts to delta sm elt and desi gnated critical habitat. 102. Dr. Grim aldo explain ed that entrainment risk is particul arly h igh from March to May because delta smelt larvae a nd juveniles are most likely to behave li ke neutrall y buoyant pa rticles during this time peri od. 4/7/10 T r. 68. 103. Ms. Goud e testified that the Projects exert a direct e ntrainment effect on delta sm elt, a s well as indirect impacts upo n the species’ food supply, r isk of predatio n, and expos ure to contaminants and other stressor s, and affec t critical habitat by changin g the amount a nd location of habitat in winter, spring and fall. I d. at 150-51. In her opinion, enjo ining Actio n 3 69

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of the R PA would res ult in irreparable harm to th e delta smelt du e to very lo w abundance levels and the ri sk of a “huge” e ntrainment e vent causing “catastrophic ev ents.” Id. at 169-70. 104. However, none of these experts offered any quantita tive or qual itative analysis, apart from that discusse d above, whi ch utilized raw salvage data, to specific ally justify the imposition of a -5,000 c fs ceiling on negative OMR flows . h. Alternat ive Proposal to Limit negative OMR Flow to -5,600 cfs.

105. Plaintif fs suggest i mposition of a -5,600 ceiling on OMR flows . This is based entirely on Dr.

Deriso’s analysis of population-index ed sal vage rates versus n egative OMR flows. Although Dr. Deriso’s

analysis corre cts for the fundamental error of re lying on raw salv age figures, given the large number of va riables not accounted for in Dr. Deriso’s analysis, it is unclear whether the -5 ,600 break- point he suggests is any more or less app ropriate as a ceiling than th e -5,0 00 fig ure utilized in the BiOp . 106. Mr. Feyr er opined th at operating the Project pumps to meet OMR fl ows no less negative than -5,600 cfs, the alte rnative OMR ceiling proposed by Plaintiff s, during t he spring wo uld not avoid jeopardy to the delta 70

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smelt or adverse mod ification of its critical hab itat. 4/2/10 T r. 208. 107. Regardle ss of the ap propriate upper limit for negative OMR flows, RPA Component 2 defines a ran ge of OMR flow s within whi ch the Projects may operate d uring designat ed time peri ods. This range of flows “pr ovides

flexibil ity in [] wa ter operations [and] the abil ity to be prote ctive when t heir conditions are not favor able -or when entrainment risk increases.... So it max imizes

protecti on for the s pecies while providing flexib ility for wate r operations .” 4/7/10 Tr. 66-67. According to

Dr. Grim aldo, operat ing to a “unitary” flow, as recommen ded by Plain tiffs, “removes your flexibil ity from managing that risk”: So there may be time s when the fish become distribu ted in the s outh Delta or the central Delta. And perhaps a lot of them, like we saw in April 2002 and Ap ril 2003 were large number of the l arvae were i n the central and south Delta. If you were at a fixed number, that your risk wou ld be high a nd you would have substant ial losses, which were demonstrated in Kimmerer 2008 during that time period. Id. at 67. 108. Both the BiOp and su bsequent peer reviews have acknowle dged that th e specific OMR flow triggers and the implemen tation of th e OMR -flo w related requirements of the RPA “need[] to b e accompanied by careful moni toring, 71

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adaptive management and additional analyses that permit regular review and a djustment of strategies as kn owledge improves .” 4/2/10 T r. 195; BiOp at 279 (“[t]he speci fic

flow req uirements, a ction triggers and monitoring stations prescribed in the RPA will be continuous ly monitore d and evalua ted consistent with the adapt ive process. As new inf ormation becomes available, t hese

action t riggers may be modified without necessarily requirin g re-c onsultation on the overall proposed action.” ). 109. Althoug h the record shows that FWS’s -5,00 0 OMR ceiling is not based on the best available scienc e, the record d oes not cont ain sufficient information to conclude that the imposition of Plaintiff’s suggested -5,600 O MR ceiling w ould be sufficien tly pr otective of the smel t, particula rly in light of the fact that Plaintif fs do not pr opose any flexibility in the manageme nt regime th at would permit greater restr ictions if a large sal vage event was approaching or ongoing. 110. Providi ng flexibili ty to permit adaptive manageme nt for delta smelt is justified. D. Irrepara ble Harm. 111. The reco rd evidence has established a variety of adverse impacts to h umans and the human environme nt from 72

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reduced CVP and SWP deliveries, including irretri evable resource losses (per manent crops, fallowed lands, destruct ion of famil y and entity farming business es); social d isruption an d dislocation; as well as environm ental harms caused by, among other things , increase d groundwate r consumption and overdraft, and possible air quality reduction. (1) Water Su pply Impacts .

112. Any lost pumping cap acity directly attributable to the 2 008 Smelt Bi Op will contribute to and exa cerbate the curr ently catast rophic situation faced by Pla intiffs, whose fa rms, busines ses, water service areas, and impacted cities and counties, are dependent, some exclusiv ely, upon CV P and/or SWP water deliveries . 113. Every ac re-foo t of p umping fo regone during critical time period s is an acre-foot that does not re ach the San Luis Reservo ir where it can be stored for future delivery to users du ring times of peak demand in the water ye ar. 114. It is un disputed tha t, in the three water y ears prior to the 2009-2010 wa ter year, Californ ia has experien ced three co nsecutive years of drought conditio ns. at 18. Gov’t S almon Ex. 5 at (internal) Exh ibit 1

This influen ces the amount of run-off for ecast ed 73

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for 2010 and is indi cative of why reservoir storages w ere at a low state enter ing the 2009-2010 water year. Tr. 208: 7-15. 4/1 /10

Hydro logic conditions are no t within th e

control of the parti es and have materially contri buted to water se rvice reduct ions to contractors. 115. It is al so undispute d that other, non-project factors, such as tid es, wind events, storm surges , San Joaquin River flows, Contra Costa Water District operatio ns, and dive rsions by in-Delta wate r users eff ect how Recl amation must operate the project to meet flow targets. See id. at 202:12-204:1.

116. The proj ects are sub ject to export reductions required to protect species listed under the Cali fornia Endanger ed Species A ct, including longfin smelt, delta smelt, w inter- run Chinook salmon, and spring-run Chinook salmon, which subjec t the water project operators to controls under state law that are similar, and, i n some cases, i dentical to those contained in the 2008 S melt BiOp and the Nationa l Marine Fisheries Service’s (“NFMS”) June 4, 2009 Biologi cal Opinion (“2009 Salmonid B iOp”) concerni ng various E SA-listed anadromous and ocea nic species. See id. at Tr. 212:4-213:8. In t he abs ence of

the BiOp s’ RPAs, tho se protections are argued to have likely l imited expor t pumping to levels below tho se 74

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allowabl e unde r State Water Resources Contr ol Boa rd Decision 1641 (“D-1641”), whi ch also limits Project pumping at certain t imes of the year. See, e.g., SWC Ex.

938 (DWR ’s 3/30/10 a llocation announcement consid ered several “SWP operati onal constraints” including “ the incident al take perm it for longfin smelt”). 117. Plaintif fs’ estimate s of water losses do not account for or other wise offset losses attributab le to proposed remedies in the consolidated Delta Smelt and Salmon c ases. See 4/7/10 Tr. 17:10-20:14.

118. The quan tity of expo rtabl e wa ter has been reduced by the imple mentation of the Salmonid and Smelt BiOp’s R PAs. Id. From J anuary 20 through March 24,

2010, Mr . Erlewine t estified that potential and a ctual exports were diminis hed by 522,561 acre fee t (“AF ”), o f which a 433,000 AF l oss was attributable to the S WP and a 89,000 A F loss was a ttributable to the CVP. 185:16-1 9; SWC Demon strative Ex. 903. 119. DWR made its initial water supply allocation announce ment o n November 30, 2009, allocating 5% of Table A contra cted amounts for SWP water contractors. Tr. 240: 16-22; SWC Ex. 923, Ex. B. 4/6/10 4/6/ 10 Tr.

As of March 3 0, 2010, 4/6/10 On

DWR incr eased the SW P allocation for 2010 to 20%. Tr. 189: 15-17; SWC Ex. 938; 4/1/10 Tr. 249:22-25. 75

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April 23 , 2010, DWR again increased its allocatio n of SWP deliveri es to 30%. See Doc. 323-2 (DWR Pre ss Release) .

120. Reclamat ion announce d its initial allocation of CVP wate r on Februar y 26, 2010. (Third M illiga n Decl.) at ¶11. Fed. Gov’t Salmo n Ex. 5 Under the 90% exceedance

forecast , Reclamatio n allocated CVP agricultural users 5% of their contract am ounts, and CVP municipal and industri al (“M&I”) c ontractors 55% of their contr act amounts. Id. at ¶12. Under the 50% exceedance foreca st,

north-of -Delta agric ultural and M&I contractors w ere allocate d 100% of th eir contract amounts, while s outh- ofDelta ag ricultural c ontractors were allocated 30% and M&I contract ors 75%. Id.

121. CVP wate r users face d similar reducti ons to their in dividual all ocations. Farmers on the wes t side

of the S an Joaquin V alley have received reduced C VP water supply a llocations i n the 2007-2008, 2008-2009, a nd 20 092010 wat er years, an d face similar reductions in 20102011. S LDMWA Ex. 153 at ¶3; SLDMWA E x. 154 at ¶4; SLD MWA In 2 007-2008, Reclamation allocated to In 2008-2009, that For t he 2009-

Ex. 156 at ¶4.

Westland s 40% of its contract supply. allocati on was 10%.

SLDMWA Ex. 155 at ¶8.

2010 wat er year, Wes tlands was advised the initial allocati on was zero percent. 76 SLDMWA Ex. 155 at ¶ 9.

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122. On March 16, 2010, R eclamation raised the allocati on for south-of-Delta agricultural users to 25 % under a 90% forecast and 30% under a 50% forecast . 4/1/10 T r. 210:14-22; Fed . Gov’t Salm on Exh . 13. 123. These in cremental in creases do not alter the fact tha t water deli veries will likely increase f urther if the t wo RPAs are enjoined. 4/1/10 Tr. 213:14- 20

(acknowl edging that deliveries would increase by 5% - 10% if the R PAs we re enjoined). 124. The quan tity of wate r lost through pumping reductio ns translate s directly into water losses for urban an d agricultur al water users. In the SWP s ervice

area, on e acre-foot of water serves about five to seven people f or one year. 4/6/10 Tr. 186:25-187 :1-3. An S WP

loss of 433,000 AF, if available to urban users, would have sup plied approx imately 2.6 million people fo r one year. 4 /6/10 Tr. 18 7:8-11. Seventy-five to eighty-fi ve

percent of SWP suppl y is provided for urban uses, with the rema inder provid ed to agricultural users. 187:15-1 7. 4/ 6/10 Tr.

The Metr opolitan Water District of So uthern

Californ ia alone ser ves approximately 20 million urban users. 125. Water lo ss for agric ultural users results in reductio n in t he num ber o f acres that may b e sustained 77

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with act ual water su pply.

Water duty is the amou nt of

water th at a crop ne eds per acre for a growing se ason. 4/6/10 T r. 187:21-22. DW R information indi cates that for

the SWP service area , the water duty is approxima tely three AF per acre. 4/6/10 Tr. 187:22-25. If 433,000 AF

were wit hheld from a lmond crops, for example, alm ond producti on would be reduced by approximately 140, 000 acres. 4/6/10 Tr. 1 88:1- 4.

126. Reduced CVP and SWP water supply allocations have inc reased the c ost of supplemental water. F armers

have bee n forced to purchase supplemental water a t drastica lly increase d cost. SLDMWA Ex. 154 at ¶7 ; SLDMWA Since 2007 , the

Ex. 155 at ¶17; SLDM WA Ex. 156 at ¶6.

cost of securing sup plemental water has mor e than tripled. SLDMWA Ex. 156 at ¶6; SLDMWA Ex. 154 at ¶7. As

of Janua ry 2010, the cost for buying replacement water for tran sfer in a dr y year is at least $300 per a cre foot, pl us transport ation costs. SLDMWA Ex. 157 at ¶12.

127. Increase d water allo cations may lessen this increase d cost, and will mitigate anticipated har ms from reduced water alloca tions. Farmers anticipate th at

increase d water allo cations would mitigate antici pated damage t o crops in p roportion to the amount of wa ter received and prevent further layoffs of farm empl oyees. 78

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SLDMWA E x. 156 at ¶1 0. 128. In 2009, the Federal Defendants accounted for actions taken under the Delta smelt biological op inion as (b)(2) a ctions, purs uant to section 3406(b)(2) of the CVPIA. 4/1/10 Tr. 2 13:24-214 :2. Federal Defendants h ave

indicate d their inte nt to follow the same account ing procedur e for federa l export reductions related t o both BiOps in 2010, to th e extent that (b)(2) assets a re availabl e at the tim e the act ion is taken. 7. (2) Other Re source Impac ts Caused or Exacerbated by the 2008 Smelt BiOp RPA Actions. Id. at 214:3-

129. Plaintif fs attribute a number of other human impacts to reduction s in the water supply. There is

consider able dispute among the parties rega rding the extent t o which the 2008 Smelt BiOp RPA is respon sible for thes e other impa cts. It is undisputed that t he RPA

is, at t he very leas t, exacerbating the following impacts. (1) Permanen t Crops.

130. Reductio ns in the qu antity of water supply deliveri es have resu lted in changes to farming pr actices, includin g an increas ed reliance on permanent crop s. SLDMWA E x. 154 at ¶6 ; SLDMWA Ex. 155 at ¶¶ 18, 22 ; SLDMWA 79

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Ex. 157 at ¶11. 131. Permanen t crops plac e farmers at greater ri sk than row crops, as f armers cannot cut back on the water to perma nent crops w ithout destroying them. SLDM WA Ex.

154 at ¶ 6; SLDMWA Ex . 155 at ¶¶ 18, 22; SLDMWA Ex . 157 at ¶11. (2) Fallowed Lands.

132. Because of reduced w ater forecasts and uncertai nty regardin g future water supply, farmer s have fallowed hundreds an d thousands of acres of field s. SLDMWA E x. 155 at ¶1 0; SLDMWA Ex. 153 at ¶3; SLDM WA Ex. 156 at ¶ 5. 133. Fallowed lands and r educed water supply have caused t he loss of thousa nds of acres of cr ops. Todd

Allen, a third-generation farmer in Fresno County, was able to salvage and harvest only 40 acres of a wh eat crop out of a total arabl e 616 acres on his farm in 20 09. SLDMWA E x. 153 at ¶3 . 134. For ever y 1,000 AF of water lost by the San Luis Plaintif fs’ member a gencies, approximately 400 ac res of land may remain out of production. ¶13. 135. Fallowin g fields als o negatively impacts the air quality of the San J oaquin Valley by increasing dust a nd 80 SLDMWA Ex. 15 7 at

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particul ate matter.

SLDMWA Ex. 155 at ¶20.

Redu ced air

quality in turn impa irs major transportation rout es through the valley. (3) SLDMWA Ex. 155 at ¶20.

Lack of Access to Cr edit.

136. The more unreliable the water supply, the more difficul t it is for farmers to secure necessary f inancing for thei r farming op erations. SLDMWA Ex. 153 at ¶4;

SLDMWA E x. 154 at ¶1 3; SLDMWA Ex. 155 at ¶26; SLD MWA Ex. 156 at ¶ 7; SLDMWA Ex . 157 at ¶15. In some cases, lenders

deny loa n applicatio ns becaus e of a lack of reliable water su pply. SLDMW A Ex. 153 at ¶4; SLDMWA Ex. 1 54 at

¶13; SLD MWA Ex. 155 at ¶26; SLDMWA Ex. 156 at ¶7; SLDMWA Ex. 157 at ¶15. In others, lenders’ concerns abo ut

availabi lity to land s irrigated by federally-supplied water ha s requ ired farmers to make a 50% down pay ment to secure a ny loans. (4) S LDMWA Ex. 156 at ¶7. Social D isruption an d Dislocation.

137. It is un disputed tha t farm employees and their families have faced devastating losses due to red uctions in the a vailab le water supply. The impact on the farm

economy from the com bination of a three-yea r drou ght a nd diversio n limitation s relating to the delta smelt has already been severe. SLDMWA Ex. 157 at ¶14.

138. Lost wat er supply ha s decreased the number of 81

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producti ve agricultu ral acres, which has resulted in reductio ns in employ ee hours, salaries, and posit ions, devastat ing farm emp loyees and their families. Ex. 154 at ¶11; SLDM WA Ex. 156 at ¶8. 139. The remo val of 250,0 00 acres from pro ductio n translat es to a loss of approximately 4,200 perma nent agricult ural worker positions. SLDMWA Ex. 155 at ¶19. S LDMWA

Water sh ortages also cause jobs to be lost in agricult ure-re lated businesses, such as packing sheds, processi ng plants, a nd other related servic es. Id. The

projecte d agricultur e-rel ated wage loss for the S an Joaquin Valley stand s at $1.6 billion. Id.

140. Dr. Mich ael, Defenda nt Intervenors’ economist with exp ertise in re gional and environmental econ omics, counters that “[a]lthough water impacts hav e affected parts of the west si de, there is no evidence that reduced water de liveries hav e had a severe effect on farm or nonfarm emp loyment in t he Central Valley as a whole. ” Exh. 100 6 (Michael D ecl.) ¶10. Instead, it is a D- I

combinat ion of facto rs, including the three-year droug ht, the glob al economic recession, the foreclosure cr isis, and the collapse of the real estate market and construc tion industr y, not RPA Component 3, that are mainly d riving crop and job losses, food bank nee ds, a nd 82

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credit p roblems in t he Central Valley.

Id. at ¶¶ 6-10 .

Dr. Mich ael estimate s that ESA-related pump ing restrict ions have re sulted in the loss of less th an 2,000 jobs. S ee id. at ¶4.

141. Unemploy ment has led to hunger on the west side of the S an Joaquin V alley. SLDMWA Ex. 158 at ¶8. The

Communit y Food Bank, serving Fresno, Madera and K ings Counties , estimates 435,000 people in its service area do not have a reliable source of food. ¶4. SLDMWA Ex. 1 58 at

The Chief Execu tive Offi cer of the Community Food

Bank, Da na Wilkie, b elieves that hunger in the communit ies served b y the Food Bank in the wester n San Joaquin Valley will continue to increase in 2010 because of ongoi ng water sho rtages. SLDMWA Ex. 158 at ¶5 . Ms.

Wilkie u nderst ands that at least 42,000 people served by the Food Bank in Oct ober 2009 were employed by fa rmrelated businesses b efore losing their jobs. 158 at ¶ 8. (5) Groundwa ter Consumpt ion and Overdraft. SLD MWA Ex.

142. Reductio ns in the av ailable water supply have caused w ater users t o increase groundwater pumpin g in attempts to make up the difference between irriga tion need and allocated w ater supplies. SLDMWA Ex. 15 5 at ¶¶

4, 7; SL DMWA Ex. 157 at ¶10; 4/6/10 Tr. 216:6-7. 83

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143. However, groundwater is not always availabl e, and cann ot be used i n all areas or for all crops. Ex. 155 at ¶11. SLDMWA

Inc reased groundwater pumping re duces

the qual ity of water applied to the soil by incre asing soil sal inity. SLDM WA Id. at ¶15. Not all fields and Id. at ¶¶ 11 ,

crops can be i rrigated with groundwater. 15.

144. Increase d reliance o n and overuse of groundwater has caus ed groundwat er overdraft, which occurs wh en pumping exceeds the safe yield of an aquifer. ¶12. Id. at

Ov erdraft caus es increased land subsidence and

potentia l damage to CVP conveyance facilities, id. at ¶¶ 12-13, althoug h it is not clear that any subsidence of Project facilities h as occurred as a result of th e implemen tation of th e 2008 Smelt BiOp RPA Actions , as the only rep orted incide nt of subsidence at a S WP conveyan ce facility predates cu rrent implementation, 4/7/10 Tr. 16:1-13. 145. Increase d groundwate r pumping also increases demand f or energy. SLDMWA Ex. 155 at ¶16. Due t o the

falling water table, wells require increase d amou nts o f energy. Id. Westlands estimates that pumping of

groundwa ter in 2009 required approximately 425,00 0,000 kWh. Id . Adverse e nvironmental impacts are asso ciated 84

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with suc h increased demand for and use of energy. 146. Increase d groundwate r pumping has depleted groundwa ter reserves .

Id.

Groundwater reserves that were at

2 millio n AF in the beginning of 2007 are now les s than 900,000 AF. 4/6/10 Tr. 216:21-24. Within MWD’s servi ce

area, st orage levels are at 1.3 million AF, about half of normal s torage level s. (6) 4/6/10 Tr. 217:4-8.

Related, Recent Impa cts on Naval Air Station Lemoore.

147. Captain James Knapp testified as a fact witness on behal f of Naval A ir Station Lemoore, which is located approxim ately 30 miles south of Fresn o, eig ht miles we st of the t own of Lemoo re, California. 14. 4/7/10 Tr. 2 08:12-

Its daytime pop ulation is approximately 14,0 00

people, includ ing residents, who are sailors and dependen t families. Id. at 2 08:15-21.

148. The air station’s lo cation was selected at a time whe n the Navy w as transitioning from propell erdriven a ircraft to j et aircraft, the latter being incompat ible with ur ban environments such as the Naval Air Stat ion Alameda in the San Francisco Bay Area . at 211:1 7-212: 21. T he ai r station’s 18,000 acres of Id .

agricult ure-co mpatible land and neighboring land under permanen t agricultur al easements help to ensure t here will be no urban bui ld-out to interfere with the Navy’s 85

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operatio ns.

I d. at 211:17-212:21, 213:2-19.

From its

location , the instal lation supports aircraft carr ier activiti es along the Pacific Coast. Id.

149. Active a gricultural operations on the air station’ s 18,000 acr es and in the surrounding are as also serve “t o control bi rd and animal strike hazards, gras s fires, r odent activi ty, dust, and the release of Coccidio idomycosis ( Valley Fever) spores carried by dust.” SLDMWA Ex. 3 90 at p. 3. These risks are

interrel ated; for ex ample, fallowed fields attrac t rodents and predator y birds. 4/7/10 Tr. at 213:10-25.

An incre ased bird pr esence increases the chances of bird strikes by naval air craft. Id. at 214:1-6.

150. Ongoing agricultural activities are v itally importan t to the Nav y’s ability to safely train a nd support flight operations at Naval Air Stat ion Le moore . 4/7/10 T r. at 214:7- 24; S LDMWA EX. 390 at p . 2. 151. Lemoore Naval Air St ation’s principal source of municipa l, industria l, and agricultural water is Westland s Water Dist rict. 4/7/10 Tr. 208:24-209:2.

152. The past water year began with a zero percent water al location whi ch increased to a ten percent allocati on, resultin g in 6,000 acres of fallow fi elds. SLDMWA E x. 390 at p. 3. Pilots training at low a ltitude 86

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witnesse d an increas e in bird activity, wit h one aircr aft sufferin g thousands of dollars in damage as a res ult of a bird str ike. 43. Id.

Captain Knapp testif ied that Naval Air Station

Lemoore had requeste d and received emergency supp lemental water al locations fr om Reclamation for these propertie s. Id. at 2 10, 21 7-18; SLDMWA Ex. 391. 44. This pos t-reco rd evi dence is received for t he limited purpose of s howing the action agency’s ab ility to respond to condition s that pose imminent harm to the human en vironment. (3) Harm to Species.

45. To the extent such infor mation is in the r ecord, the pote ntial harms to the species of enjoining C omponent 2 (Actio n 3) a re dis cusse d above. VI. CONCLUSI ONS OF LAW 1. A. Jurisdic tion. 1. Jurisdic tion over cl aims brought unde r NEPA

exists u nder 28 U.S. C. § 1331 (Federal Question) and the Administ rative Proce dure Act (“APA”), 5 U.S.C. § 702 et seq. Ju risdiction o ver the ESA claims exists und er the

ESA citi zen-su it provision, 16 U.S.C. § 1540(g)(1)(A). Personal jurisdiction over all the pa rties exists by virtue o f their part icipation in the lawsuit as 87

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Plaintif fs, Defendan ts, and Intervenors. B. Likeliho od of Succes s on the Merits: NEPA Claims. 2. claim. 3. Plaintif fs have alre ady succeeded on their NEPA See Do c. 399. NEPA ins ures that fe deral agencies “make

informed decisions a nd ‘contemplate the environme ntal impacts of [their] a ctions.’” Ocean Mammal Inst. v.

Gates, 5 46 F. Supp. 2d 960, 971 (D. Hi. 200 8) (qu oting Idaho Sp orting Cong. v. Thomas, 137 F .3d 1146, 1149 (9 th Cir. 199 8). 4. “NEPA em phasizes the importance of coherent and

comprehe nsive up-front en vironmental analys is to insure informed decision-making to the end that th e agen cy wi ll not act on incomplet e information, only to regret its decision after it is too late to correct.” Ctr. for

Biologic al Diversity v. U.S. Forest Serv., 349 F.3d 11 57, 1166 (9t h Cir. 2003) . 5. Federal Defendants’ violations of NEPA prevented

the requ ired reasona ble evaluation, analysis, “ha rd look at,” and disclosure of the harms of implementing the 2008 Smelt Bi Op RPA Actio ns to human health and safety , the human en vironment, a nd other environments not inh abited by the d elta smelt. 6. Harms th at have been caused by RPA water supply 88

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reductio ns include b ut are not limite d to: destruction of permanen t crops; fal lowed lands; increased ground water consumpt ion; land su bsidence; reduction of air qu ality; destruct ion of famil y and entity farming business es; and social d isruption an d dislocation, such as increa sed property crime and i ntra- family crimes of violenc e, adverse effects on s chools, and increased unemplo yment leading to hunger an d homelessness. 7. Where a federal agen cy takes action in violation High Sierra

of NEPA, “that actio n will be set asi de.”

Hikers A ss’n v. Blac kwell, 390 F.3d 630, 640 (9th Cir. 2004). 8. However, a court may not issue an injunction

under NE PA that woul d cause a violation of other statutor y requiremen ts, such as those found in se ction 7 of the E SA. S ee United States v. Oakland Cannabis

Buyers’ Coop., 532 U.S. 483, 497 (2001) (“A district court ca nnot, for ex ample, override Congress’ pol icy choice, articulated in a statute, as to what beha vior should b e prohibited .”). Nor should an injunctio n issue

under NE PA when enjo ining government action would result in more harm to the environment than denying inju nctive relief. Save Our Ec osystems v. Clarke, 747 F.2d 1240,

1250 (9t h Cir. 1984) ; Am. Motorcyclis t Ass’ n v. Watt, 714 89

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F.2d 962 , 966 (9th C ir. 1983) (holding publ ic int erest does not favor grant ing an injunction where “gove rnment action a llegedly in violation of NEPA might actua lly jeopardi ze natural r esources”); Alpin e Lake s Prot. Soc ’y v. Schla pfer, 518 F.2d 1089, 1090 (9th Cir. 1975) (denying injun ctive relief in NEPA case where more har m could oc cur to fores t from disease if injunction was granted) . C. Likeliho od of Succes s on the Merits: ESA Claims. (1) 9. Legal St andards.

The Admi nistrative P rocedure Act (“APA”) requires

Plaintif fs to show t hat FWS’s action was “a rbitrary, capricio us, an abuse of discretion, or otherwise not in accordan ce with law. ” a. 10. 5 U.S.C. § 706(2)(A).

Record R eview.

A court reviews a bi ological opinion “based upon

the evid ence contain ed in the administrative record.” Arizona Cattle Growe rs’ Ass’n v. FWS, 273 F .3d 12 29, 1 245 (9th Cir . 2001). Ju dicial review under the APA m ust

focus on the adminis trative record already in exi stence, not some new record made initially in a reviewing court. Parties may not use “post -dec ision information as a ne w rational ization eith er for sustaining or attackin g the agency’s decision.” Ass’n of Pac. Fi sherie s v. EPA, 615 90

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F.2d 794 , 811- 12 (9th Cir. 1980). 11. Exceptio ns to admini strative record review for

technica l info rmation or expert explanation make such evidence admissible only for limited purposes, an d those exceptio ns are narro wly construed and applied. Lands

Council v. Powell, 395 F. 3d 1019, 1030 (9th Cir. 2005). 12. Here, th e Court has considered expert testi mony

only for explanation of technical terms and compl ex subject matter beyon d the Court’s knowledge; to understa nd the agenc y’s explanations, or lack the reof, underlyi ng the RPA; and to determine if any bad f aith existed. b. 13. Deferenc e to Agency Exper tise.

The Cour t must defer to the agency on matters

within t he agency’s expertise, unless the agency complete ly failed to address some factor, conside ration of which was essenti al to making an informed deci sion. Nat’l Wi ldlife Fed’n v. NMFS, 422 F.3 d 782, 798 ( 9th Cir. 2005). The court “m ay not substitute its judgmen t for

that of the agency c oncerning the wisdom or prude nce of the agen cy’s action. ” River Runners for Wilderne ss v.

Martin, 593 F.3d 106 4, 1070 (9th Cir. 2009). In condu cting an APA revi ew, the court must determin e whether th e agency’s decision is “founded on a ration al connection between the facts fo und and the choices made ... and whether 91

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[the age ncy] has com mitted a clear error of judgment .” Ariz. Cattle Growers’ Ass’n v. U.S. Fish & W ildlife, 273 F.3d 122 9, 1243 (9th C ir. 2001). “The [agency ’s] action ... need be only a reason able, not th e best or most reasonable, decision .” Nat’l Wildlife Fed. v. Burford, 871 F.2d 849 , 855 (9th C ir. 1989).

Although deferential , judicial review under the

APA “is designed to ensure that the agency consid ered all of the r elevant fact ors and that its decision con tained no clear error of ju dgment.” Arizona v. Thomas, 824 F.2d

745, 748 (9th Cir. 1 987) (internal citations omitted). “The def erence accor ded an agency’s scientific or technica l expertise is not unlimited.” Bro wer v. Evan s,

257 F.3d 1058, 1067 (9th Cir. 2001) (internal cit ations omitted) . Deference is not owed when “the agency has

complete ly failed to address some fac tor consider ation of which wa s essential to making an informed decisio n.” (interna l citations and quotations omitted). [An agen cy’s decisio n is] arbitrary and capricio us if it has relied on factors which Congress has not int ended it to consider, entirely failed to c onsider an important aspect of the p roblem, offe red an explanation for its decision that runs c ounter to the evidence before t he agency, o r is so implausible that it could no t be ascribe d to a difference in view or the prod uct of agenc y expertise. Motor Ve hicle Mfrs. Ass’n of U.S. v. State Farm M ut. Auto. In s. Co., 463 U.S. 29, 43 (1983); see also Citiz ens to Prese rve Overton Park, Inc. v. Volpe, 401 U.S. 402, 92 Id.

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416 (197 1) (“A revie wing court may overturn an ag ency’s action a s arbitrary and c apricious if the a gency failed to consi der relevant factors, failed to base its decision on those factors, an d/or made a clear error of judgment .”). c. 15. General Obligations Under the ESA.

ESA Sect ion 7(a)(2) prohibits agency action that

is “like ly to jeopar dize the continued existence” of any endanger ed or threat ened species or “result in th e destruct ion or adver se modification” of its criti cal habitat. 16. 16 U.S.C. § 1536(a)(2). To “jeop ardize the c ontinued existence of” means

“to enga ge in an act ion that reasonably would be expected , directly o r indirectly, to reduce appre ciably the like lihood of bo th the survival and recovery of a listed s pecies in th e wild by reducing the reprod uction, numbers, or distribu tion of that species.” 50 C.F.R. §

402.02; see also Nat ’l Wildlife Fed’n v. NMFS, 524 F.3d 917 (9th Cir. 2008) (“NWF v. NMFS II”) (rej ecting agen cy interpre tation of 50 C.F.R. § 402.02 that in effe ct limited jeopardy ana lysis to survival and did not realisti cally evalua te recove ry, thereby avoiding an interpre tation that reads the provision “and reco very” entirely out of the text). An action is “jeopard izing” 93

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if it ke eps recovery “far out of reach,” even if the species is able to c ling to survival. 17. Id. at 931 .

“[A]n a gency may no t take action that will tip

a specie s from a sta te of precarious survival int o a state of likely exti nction. Likewise, even where

baseline conditions already jeopardize a species, an agency m ay not take action that deepens the jeopa rdy by causing additional h arm.” 18. Id. at 930 .

To satis fy this obli gation, the federal agency

undertak ing the acti on (the “action agency”) must prepare a “biolo gical assess ment” that evaluates the acti on’s potentia l impacts on species and species’ h abitat . U.S.C. § 1536(c); 50 C.F.R. § 402.12(a). 19. If the p roposed acti on “is likely to adversely 16

affect” a threatened or endangered species or adv ersely modify i ts designate d critical habitat, the actio n agency must eng age in “form al consul tation” with FWS to obtai n its biol ogical opini on as to the impacts of the p roposed action o n the listed species. 16 U.S.C. § 1536(a)(2), Onc e the

(b)(3); see also 50 C.F.R. § 402.14(a), (g) .

consulta tion process has been completed, FWS must give the acti on age ncy a written biological opinion “setting forth [F WS’s] opinio n, and a summary of the infor mation on which the opinion is based, detailing how the agency 94

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action a ffects the s pecies or its critical habita t.”

16

U.S.C. § 1536(b)(3)( A); see a lso 50 C.F.R. § 402.14(h) . 20. If FWS d etermines th at jeopardy or destruction

or adver se modificat ion of critical habitat is li kely, FWS “sha ll suggest t hose reasonable and prudent alternat ives which [ it] believes would not violat e subsecti on (a)(2) of this section and can b e taken by the Federal agency or ap plicant in implementing the a gency action.” 16 U.S.C. § 153 6(b) (3)(A). “Following the

issuance of a ‘jeopa rdy’ opinion, the agency must either terminat e the action , implement the proposed alte rnati ve, or seek an exemption from the Cabinet-level Endangered Species Committee pu rsuant to 16 U.S.C. § 1536(e) .” National Ass’n of Ho me Builders v. Defenders of W ildlife, 551 U.S. 644, 652 (2 008). d. 21. Best Ava ilable Scien ce.

Under th e ESA, an ag ency’s actions mu st be based

on “the best scienti fic and commercial data avail able.” 16 U.S.C . § 1536(a)( 2); 50 C.F.R. § 402.14(g)(8) (“In formulat ing its Biol ogical Opinion, any reasonabl e and prudent alternatives , and any reasonable and prud ent measures , the Servic e will use the best scientifi c and commerci al data avai lable.”). “The obvious purpo se of

the [bes t available science requirement] is to en sure 95

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that the ESA not be implemented haphazardly, on t he basis of specu lation or su rmise.” 154, 176 (1997). Bennett v. Spear, 520 U.S.

A failure by the agency to util ize the See

best ava ilable scien ce is arbitrary and capriciou s. Gutierre z II, 606 F. Supp. 2d at 1144. 22.

A decisi on about jeo pardy must be made based on

the best science ava ilable at the tim e of the dec ision; the agen cy cannot wa it for or promise future stud ies. See Ctr. for B iological Diversity v. Rumsfeld, 198 F. Supp. 2d 1139, 1156 (D. Ariz. 2002). 23. The “bes t available science” mandate of the ESA

sets a b asic standard that “prohibits the [ agency] fro m disregar ding availab le scientific evidence that i s in some way better than the evidence [it] relies on. ” Am.

Wildland s v. Kemptho rne, 530 F.3d 991, 998 (D.C. Cir. 2008) (c itation omit ted). 24. What con stitutes the “best” available scien ce

implicat es core agen cy judgment and expertise to which Congress requires th e courts to defer; a court sh ould be especial ly wary of o verturning such a determinati on on review. Baltimore G as & Elec. Co. v. Natural Res .

Defense Council, 462 U.S. 87, 103 (1983) (a court must be “at its most deferen tial” when an agency is “maki ng predicti ons within i ts area of special expertise, at the 96

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frontier s of science ”).

As explained by the en b anc

panel of the Ninth C ircuit in Lands C ouncil, 537 F.3d at 993, cou rts may not “impose on the agency their o wn notion o f which proc edures are best or most likel y to further some vague, undefined public good.” Id. In

particul ar, an agenc y’s “scientific methodology i s owed substant ial deferenc e.” Gifford Pinc hot Task For ce v.

U.S. Fis h & Wildlife Serv., 3 78 F.3d 1059, 1066 (9th C ir. 2004). 25. This def erence exten ds to the use and As

interpre tation of st atistical methodologies.

explaine d by the D.C . Circuit in Appalachia n Power Co. v. EPA, 135 F.3d 791 (D .C. Cir. 1998), i n reviewing a challeng e to a decis ion of the Environmental Prot ection Agency ( “EPA”) under the “arbitrary and capriciou s” standard of review: Statisti cal analysis is perhaps the prime example of those are as of technical wildern ess into whi ch judicial expeditions are best limited to ascer taining the lay of the land. Although computer models are “a useful and often essentia l tool for p erforming the Herculean labors C ongress impo sed on EPA in the Clean Air Act,” [c itation] the ir scientific nature does not easi ly lend itse lf to judicial review. Our consider ation of EPA ’s use of a regression analysis in this cas e must therefore comport with the deference t raditionally given to an agency w hen reviewin g a scientific analysis within i ts area of e xpertise without abdicating our duty to ensure t hat the application of this model wa s not arbitr ary. Id. at 802. 97

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26.

More gen erally, “[w] hen specialists express

conflict ing views, a n agency must have discretion to rely on the r easona ble opinions of its own qualified experts even if, as an origi nal matter, a court might fin d contrary views more persuasive.” Lan ds Council, 537 F.3d

at 1000 (quoting Marsh v. Oregon Natural Re s. Cou ncil, 490 U.S. 360, 378 (1 989)). 27. Mere unc ertainty, or the fact that evidence may

be “weak ,” is not fa tal to an agency decision. Greenpea ce Action v. Franklin, 14 F.3d 1324 , 1337 (9th Cir. 199 2) (upholdin g biological opinion, despite uncertai nty about th e effectiveness of management measures , beca use decision was based on a reasonable evaluati on of all av ailable data); Nat’l Wildlife Fed' n v. Babbi tt, 12 8 F. S upp. 2d 1274, 1300 (E.D . Cal. 2000 ) (holding that the “m ost reasonable” reading of th e best scientif ic data avai lable standard is that it “permits the [FWS ] to take ac tion based on imperfect data, so long as the d ata is the b est available”). 28. The defe rence afford ed under the best available For example, Tucson

science standard is not unlimited.

Herpetol ogical Socie ty v. Salazar, 566 F.3d 870, 879 ( 9th Cir. 200 9), held tha t an agency may not rely on “ambiguo us studies a s evidence” to support findin gs made 98

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under th e ESA.

Beca use the studies did not lead to the

conclusi on reached b y FWS, the Ninth Circuit held that these st udies provided in adequate support i n the administ rative recor d for the determination made by FWS. Id.; see also Rock Creek Alliance v. U.S. F ish & Wildl ife Service, 390 F. Supp . 2d 993 (D. Mont. 2005) (rej ecting FWS’s re liance on a disputed scientific report, w hich explicit ly stated it s analysis was not applicable to the small po pulations ad dressed in the challenged opi nion); Greenpea ce v. NMFS, 80 F. Supp. 2d 1137, 11 49-50 (W.D. Wash. 20 00) (where a gency totally failed to devel op any projecti ons regardin g population viability, it co uld n ot use as a n excuse the fact that relevant data had not been analyzed ). 29. The pres umption of a gency expertise may be

rebutted if the agen cy’s decisions, although base d on scientif ic expertise , are not reasoned. F. Supp. 2d at 1147. Greenpeace, 80

Agencies cannot disregard a vailable

scientif ic evidence better than the evidence on w hich it relies. Kern County Farm Bureau v. Allen, 450 F.3d 10 72,

1080 (9t h Cir. 2006) ; S.W . Ct r. for Biological Di versity v. Babbi tt, 21 5 F.3d 58, 60 (D.C. Cir . 2000 ). 30. Courts r outinely per form substantive reviews of

record e vidence to e valuate the agency's treatmen t of 99

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best ava ilable scien ce.

The judicial review proc ess is See, e. g., Kern County, 450

not one of blind acc eptance.

F.3d 107 2 (thoroughl y reviewing three post-comment studies and FWS’s tr eatment of those studies to d etermine whether they “provid e[d] the sole, essential supp ort for” or “mer ely suppleme nted” the data used to suppor t a

listing decision); Home Builders Ass’n of N . Cal. v. U .S. Fish and Wildlife Se rv., 529 F. Supp. 2d 1110, 1120 (N .D. Cal. 200 7) (examinin g substance of challenge to F WS’s determin ation that c ertain data should be disrega rded); Trout Un limited v. L ohn, 645 F. Supp. 2d 929 (D. Or. 2007) (f inding best available science standard had been violated after thoro ugh examination of rationale for NMFS’s d ecision to w ithdraw its proposal to list Oregon Coast Co ho salmon); Ocean a, Inc. v. Evans, 384 F. Supp . 2d 203, 217-18 (D.D.C. 2005) (carefully considering scientif ic underpinn ings of challenge to Service’ s use of a partic ular model, including post decision evide nce presente d by an expe rt, to help the court underst and a complex model, apply ing one of several record rev iew exceptio ns articulat ed in Esc h v. Yeutter, 876 F.2d 97 6, 991 (D.C . Cir. 1989) , which are similar to those articula ted by the N inth Circuit). 31. Courts a re not requi red to defer to an agency 100

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conclusi on that runs counter to that of other age ncies or individu als with spe cialized expertise in a parti cular technica l area. See, e.g ., Am. Turnb oat Ass’n v.

Baldrige , 738 F.2d 1 013, 1016-17 (9th Cir. 1984) (NMFS ’s decision under the M arine Mammal Protection Act w as not supporte d by substan tial evidence because agency ignored data tha t was product of “many years’ effort by traine d research personnel”) ; Sie rra Club v. U.S. Army Co rps of Eng’rs, 701 F.2d 101 1, 1030 (2d Cir. 1983) (“court may properly be skeptica l as to whether an EIS’s conc lusions have a s ubstantial b asis in fact if the responsib le agency h as apparentl y ignored the conflicting vie ws of other ag encies havin g pertinent experience[]”) (i nternal citation s omitted). A court should “reject concl usory

assertio ns of agency ‘expertise’ where the agency spurns unrebutt ed expert op inions wi thout itself offering a credible alternative explanation.” N. Spot ted Ow l v.

Hodel, 7 16 F. Supp. 479, 483 (W.D. Wash. 19 88) (c iting Am. Turn boat Ass’n, 738 F .2d at 1016). 32. In Conner v. Burford, 848 F.2d 1441, 1453-54

(9th Cir . 1988), the agency attempted to de fend its biologic al opinions by arguing that there was a l ack of sufficie nt informati on. In rejecting this defens e, the

court he ld that “inc omplete information ... does not 101

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

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

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34.

When det ermining the “effects of the action,”

the agen cy first mus t evaluate the status of the species or criti cal habitat, which will involve “consider ation of the pres ent environm ent” in which the species or habitat exists a s well as “t he environment th at will exist when the acti on is comple ted, in terms of the totality of factors affecting th e species or critical habitat .” Fed. Reg . 19,926, 19 ,932 (June 3, 1986). 51

This ev aluation

is to se rve as the “ baseline” for determining the effe cts of the a ction on the species or critical habitat. However, all of thes e elements are to be evaluate d together as the “eff ects of the action.” 35. If addit ional data w ould provide a better Id.

informat ion base fro m which to formul ate a biological opinion, the consult ing agency (FWS or NMFS) may request an exten sion of form al consultation and that the action agency o btain additi onal data to determine how or to what extent t he action ma y affect listed species or cr itical habitat. 50 C.F.R. § 402.14(f); FWS and NMFS, En dangered

Species Consultation Handbook (March 1998) at 4-6. 8 36. The Nint h Circuit di rects the consulting agency

to consi der the effe cts of its actions “within th e context of other exi sting human activities that impact
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: 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 .
8

103

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the list ed species.”

NWF v. NMFS II, 524 F .3d at 930.

“[T]he p roper baseli ne analysis is not the propor tional share of responsibil ity the federal agency bears for the decline in the speci es, but what jeopardy might r esult from the agency’s propose d actions in the p resent and future h uman and nat ural contexts.” Id. The relevant

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

baseline analysis is that the BiOp improperly conclude d 104

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that “CV P and SWP op erations exacerbate the effec ts of other fa ctors, such as food or predation on the d elta smelt.” See D oc. 667, Pltf’s Proposed Conclusions of Law
9

## 316-1 8.

Plaintiffs argue “FWS sim ply determined that

these fa ctors are attributable to CVP and SWP operations” and ther efore “based the effects analysis of the 2008 BiOp upo n an unreaso ned premise.” Conclusi on of Law # 343. 38. Plaintif fs are corre ct that the general Id. at Proposed

assertio n that Proje ct operations exa cerbate the effects of these other stres sors is unsupported by the re cord. However, the inclusi on of this unsupported assert ion does not inva lidate the B iOp’s baseline analysis. 140-189. the BiOp . BiOp at

FWS does discuss “other stressors” at length in See , e.g., id. at 182-88, 198, 2 01-2.

Specific ally, FWS co nsidered the effects of “pred ation, contamin ants, introd uced species..., habitat suitabili ty, food sup ply, aquatic macrophytes, and microcystis .” at 202, 277.
9

Id.

The CVP and SWP are not ident ified as th e

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 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 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 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 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 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 of th e pe nd in g mo ti on fo r pr el im in a ry in ju nc ti on .

105

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sole sou rce of the d elta smelt’s problems.

Rathe r, FWS

expressl y recognizes that the long-term decline of the species “was very st rongly affected by ecosystem changes caused b y non- indigenous species invasions and other factors. ...” Id. at 189. The BiOp repeate dly

acknowle dges that th ere is “no single primary dri ver of delta sm elt populati on dynamics,” id. at 202, but rath er that the re are “mult iple factors” and that “not a ll are directly influenced by operations of the CVP/SWP. ” at 328. 39. It is un disputed tha t uncertainty surrounding Id .

the meas urement of t he other stressors makes it d ifficult (if not impossible) to separate those effects fro m the effects of joint Pro ject operations. Even if it were

possible to separate the quantitative effec t of the ot her stressor s, which are part of the environmental ba seline, the ESA does not req uire that FWS qua ntify and/or parc el out the “proportiona l share” of harms among the b aseline and the proposed act ion. See Pacific Coast Fed’n of

Fisherme n's Ass'ns v . U.S. Bureau of Reclamation, 426 F.3d 108 2, 1093 (9th Cir. 2005); see also P acific Coas t Fed’n of Fishermen's Ass'ns v. U.S. Bureau of Reclamat ion, 2 26 Fed . App x. 715, 718 (9th C ir. 2007) (rejecti ng water use rs’ argument that agenc y acti on mu st 106

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be the “ historical c ause” of the jeopardy to salm on). 40. FWS’s tr eatment of t he “other stressors” in the

BiOp did not violate the ESA’s baseline analysis requirem ents because the ESA does not demand a quantita tive separat ion of project st ressors from nonproject stressors. See NWF v . NMFS II, 524 F.3d at 930.

(“[T]he proper basel ine analysis is not the propo rtional share of responsibil ity the federal agency bears for the decline in the speci es, but what jeopardy might r esult from the agenc y’s proposed actions in the present and future h uman and nat ural contexts.”). FWS was re quired

to and d id describe the present and future federa l, state, a nd private a ctions in the action area, wh ich include the “other s tressors”. Whether it sufficiently

justifie d whether je opardy might result from the agency’s proposed actions vie wed in this context is a sepa rate question . 41. It is in equitable to put the entire burden of However, this

the stre ssors on the water supply.

decision goes beyond science to implicate the Exe cutiv e’s (Departm ent of Inter ior) allocation of resources. A

court la cks authorit y to interfere with such a po licy choice b y a coordina te branch of government.

107

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a.

Discreti onary v. Non-Discretionary.

Plaintif fs complain that the BiOp does not

distingu ish between discretionary and non-discret ionar y actions. Home Build ers, 551 U.S. 644, held that ESA §

7’s cons ultation req uirements do not apply to non discreti onary action s. Where an agency is required by

law to p erform an ac tion, it lacks th e power to insure that the action will not jeopardize the species. 667. 43. However, Home Builde rs sa ys n othing about Id. at

whether, once sectio n 7 consultation is triggered , the jeopardy analysis sh ould segregate di scretionary and nondiscreti onary action s, relegating the non-discret ionar y actions to the envir onmental baseline. Hom e Buil ders

fundamen tally concer ns whether the section 7 cons ultation obligati on attaches to a particular agency action at all. See Home Builders, 551 U. S. at 679-80 (“duty does not attach t o actions... that an agency i s required by statute to undertake ....”) (emphasis added). b. Reclamat ion’s Treatm ent of the Coordinated Operatio ns Agreement .

The same reasoning a pplies to Plaintiffs’ related argument that Federa l Defendants acted unlawfully by attribut ing to the p roject the effects of “mandat ory” complian ce with the Coordinated Operations Agreem ent 108

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(“COA”).

Even assum ing, arguendo, th at any mandatory

obligati on exists un der the COA, a proposition that is question able given t he open-ended wor ding of the COA and language in the CVPI A subjecting project operatio ns to the ESA, Home Builde rs do es n ot require the agenc y to segregat e discretion ary from non-discretion ary activit ies during a n ESA § 7 consultation. 10 Moreover, this argument See

was not presented in Plaintiffs’ opening brief.

Alaska C tr. for Envt . v. U.S. Forest Serv., 189 F .3d 8 51, 858 n. 4 (9th Cir. 1 999) (arguments not raised in opening brief ar e waived). c. 44. Comparis on of CalSim Data aga inst Dayflow Data.

Plaintif fs also argu e that FWS’s analysis is

flawed b ecause FWS c ompared CalSim data to Dayflo w Data. As discu ssed in the Findings of Fact, although Mr. Miller presents some substa ntive criticisms of the way t he BiOp utilized CalSi m runs and compared those run s to other types of data, these specific concerns were not raised before t he agency pr ior to the issuance of the Bi Op. FWS

had legi timate concerns, shared by other scientists, w ith the excl usive relian ce on CalSim data. Finally, Mr.

Miller c oncedes that even if the approach he reco mmends
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 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.
10

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had been taken, the same fundamental result would have obtained : upstream . project o perations shift the position of X2 The magni tude of this shift is relevan t to the

justific ation for and design of Component 3, which takes effect i n September, but that need not be resolve d at this tim e. (3) 45. Effects Analysis Cha llenges (Food Web). Plaintif fs’ original motion attacked the BiOp’s

analysis regarding P. forbesi , a food item for de lta smelt du ring the sum mer and fall seasons. 21-26. Doc. 4 47 at

Plaint iffs appear to have abandoned this

argument , as it was not discussed during the evid entiary hearing or in their proposed Findings of Fact or Conclusi ons of Law. (4) Challeng es to Component 2. a. 46. Use of R aw Salvage N umbers.

The evid ence describ ed in the Findings of Fact

establis hes that FWS ’s use of gross salvage numbe rs to justify the quantita tive pumping restrictions in RPA Componen t 2 did not utilize the best available sc ience. 47. There wa s agreement among all the experts that

the best available, scientifically accepted metho dology is to us e normalized salvage data to analyze the effect of OMR f lows on the delta smelt population. 110 Norm alized

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salvage data was ava ilable to FWS, bu t FWS failed to incorpor ate any anal ysis of normalized salvage da ta into its quan titative jus tification for the specific f low prescrip tions impose d by RPA Component 2. To exa cerbate

this fai lure, FWS di d not explain why it did not. 48. FWS’s di sregard for an available scie ntific

methodol ogy that was “in some way better than the evidence [the agency ] relied on” was a violation of th e “best av ailable scie nce” standard of the ESA. County, 450 F.3d at 1080. 49. Addition ally, by ent irely failing to explain its Kern

use of g ross salvage numbers despite internal dis cussions indicati ng an awaren ess of the problem and critic ism from the Inde pendent Peer Review, FWS “has entirely fa iled to articula te a satisfa ctory explanation for its conclusi ons.” 50. Gutierrez II, 606 F. Supp. 2 d at 1 183.

Plaintif fs have show n a likelihood of success on

the meri ts of their claim that the use of gross s alvage numbers in Figures B-13 and B -14 of t he BiOp was a violatio n of the ESA , and was arbitra ry, capricio us, and an abuse of discreti on. 51. However, Plaintiffs have not demonstrated that

Dr. Deri so’s alterna tive -5,6 00 cfs flow limit is any more val id than the -5,000 cfs limit impose d by RPA 111

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Componen t 2.

The condition of the delta smelt continu es

to be no n-viab le and prec arious, with a lik ely risk of extincti on if protec tions are not afforded. Plai ntiffs

must pro duce evidenc e that shows otherwise to jus tify a flow res triction tha t permits negative OMR flows to exceed - 5,000 cfs. b. 52. studies. Failure to Use a Qua ntitative Life Cycle Model.

The agen cy is not re quired to generate new For exampl e, in Sou thwest Center for Biologi cal

Diversit y v. Babbitt, 215 F.3d 58, 60-61 (D .C. Cir. 2000), t he district court found the availab le evi dence regardin g FWS’s deci sion not to list the Queen Ch arlotte goshawk “inconclusiv e” and held that the agency w as obligate d to find be tter data on the species’ abu ndance. The D.C. Circuit rev ersed, emphasizing that, alth ough “the dis trict court’s vie w has a superficia l appe al .. . this sup erficial app eal cannot circumvent the sta tute’s clear wo rding: The secretary must make his decis ion as

to wheth er to list a species as threatened or end angered ‘solely on the basis of the best scientific and commercial dat a available to him....’ 16 U.S.C. § 1533(b)( 1)(A).” 53. Id. at 61.

The use of a quantit ative life cycle model is FWS made a

the pref erred scient ific methodology. 112

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consciou s choice not to use expertise available w ithin the agen cy to develop one, nor did it explain why it did not. Ho wever, a com pleted life-cycle model was not

availabl e for FWS’s use prior to the issuance of the BiOp, an d the Court does not have the authority t o require the agency t o create one. (5) 54. Critical Habitat. As requi red by the E SA, if FWS finds that the

proposed agency acti on will result in “jeopardy o r adverse modification [of critical habitat] ... th e Secretar y shall sugg est those reasonable and prud ent alternat ives which [ it] believes would not violate [Section 7(a)(2)] an d can be taken by the Federal agency or appli cant in impl ementing the agency action.” U.S.C. § 1536(b)(3)( A). 16

Avoiding adverse modific ation of

critical habitat is an indepe ndent statutory basis for the prom ulgation of an RPA. 55. The BiOp sets forth extensive findings regarding

the adve rse effects of export pumping on the crit ical habitat of the delta smelt. See BiOp at 19 0-202, 239- 78.

For inst ance, the Bi Op found that the export pump s “alter the hydr ologic condi tions wit hin spawning habitat througho ut the spawn ing period for delta smelt by impactin g various ab iotic factors including the 113

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distribu tions of tur bidity, food, and contaminant s,” and further adversely mo dify spawning habitat by “contrib ut[ing] to u pstream movement of the LSZ [low salinity zone],” whi ch in turn “reduc[es] the amo unt and quality of spawning habitat available to delta sm elt.” Id. at 239-40. 56. In light of such fin dings, the BiOp concluded

that the operations of the CVP and SWP “are likel y to adversel y modify del ta smelt critical habitat” be cause “[t]he p ast and pres ent operations of the CVP/SWP have degraded [delta smel t] habitat elements (particul arly PCEs 2-4 [“primary c onstituent elements” – water, wate r flow, an d salinity]) to the extent th at their cooccurren ce at the ap propriate places and times is insuffic ient to supp ort successful delta smelt recruitm ent at level s that will provide for the s pecies’ conserva tion.” 57. Id. at 278.

Plaintif fs have not challenged the BiOp’s

findings on adverse modification of critical habi tat in this mot ion. Plaint iffs’ experts Dr. Deriso and Dr.

Hilborn stated that their criticisms of the BiOp’ s OMR flow res trictions di d not apply to critical habit at. 4/5/10 T r. 226; 4/6/ 10 Tr. 93. Rather, Pla intiff s arg ue

that the only stated rationale for the specific f low 114

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prescrip tions impose d by Component 2 is to avoid jeopardy , and that C omponent 2 does not itself in dicate that it is necessary to prevent adverse modificat ion. See Pls.’ Repl y (Doc. 491 ) at 1 n.1. 58. Federal Defendants r espond that “[t]h is arg ument

elevates form over s ubstance and needlessly compartm entalizes po rtions of the BiOp that are d esigned to work together as part of the same document.” 666, Pro posed Conclu sion of Law #187. 59. As a gen eral matter, Federal Defendan ts are Doc.

correct that the BiO p’s critical habitat modifica tion finding operates as an independent justification for imposing flow restri ctions on the projects. Howe ver, the

BiOp jus tifies the specific flow prescripti ons im posed by Componen t 2 with a q uantitative analysis that say s nothing whatsoever a bout critical habitat. Rathe r, an

improper analysis of raw salvage data is utilized to generate a series of “break points,” including a -5,000 cfs ceil ing on negat ive OMR flows. There is no a nalysis

of criti cal habitat that independently justifies this specific flow prescr iption, as opposed to the cei ling of -5,600 p roposed by P laintiffs, or any other level. // // 115

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(6) 60.

Reclamat ion’s ESA Re sponsibility. The ESA regulations require the action agency to

“determi ne whether a nd in what manner to proceed with the action i n light of i ts section 7 obligations and the Service’ s biological opinion.” 50 C.F.R. § 402.1 5(a).

Prior to accepting a nd im plem enting the 2008 Smel t BiOp RPA, Rec lamation had an independent obligation un der ESA section 7(a)(2) to e nsure that it “use[d] the bes t scientif ic and comme rcial data available.” 61. Reclamat ion, as the federal action agency, “may

not rely solely on a FWS biological opinion to es tablish conclusi vely its com pliance with its substantive obligati ons under se ction 7(a)(2).” Pyramid Lake Paiu te

Tribe of Indians v. U.S. Dept. of the Navy, 898 F .2d 1410, 14 15 (9th Cir. 1990). “[T]he action agency must

not blin dly adopt th e conclusions of the consulta nt agency.” City of Ta coma v. Fed. Energy Reg ulatory

Comm’n, 460 F.3d 53, 76 (D.C. Cir. 20 06). 62. Reclam ation did no t ens ure that the RPA u tilize d Rather, it uncritica lly

the best available s cience.

accepted the RPA and did not independently identi fy an d analyze alternative RPA Actions that minimized je opardy to human s and the hu man environment while protect ing threaten ed species. 116

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D.

Balancin g of the Har ms. (1) 63. Balancin g of the Har ms in ESA Cases. The Supr eme Court he ld in TVA v. Hill, 437 U.S.

153, 194 (1978), tha t Congress struck the balance in favor of affording e ndangered species the highest of prioriti es. In adop ting the ESA, Congress intend ed to

“halt an d reverse th e trend toward species’ extin ction , whatever the cost.” Id. at 1 84 (emphasis added). TVA v.

Hill con tinues to be viable.

See Hom e Builders, 551 U.S.

at 669-7 1; see also Oakland Cannabis Buyers’ Co-op., 532 U.S. 496 -97; A moco Prod. Co. v. Village of Gambell, 480 U.S. 531 , 543 n.9 (1 987). 64. Winter d oes not modi fy or discuss the TVA v. Alth ough Winter altered the Ninth

Hill sta ndard. 11

Circuit’ s general pr eliminary injunctive relief s tandard by makin g that stand ard more rigorous, Winter did not address, nor c hange, the approach to the ba lancing of economic hardships w here endangered s pecies and their critical habitat are jeopardized. See Biodiversity Le gal

Found. v . Badgley, 309 F. 3d 1166, 1169 (9th Cir. 2002) (Congres s removed th e courts’ traditional equitable discreti on to balanc e parties’ competing interest s in ESA injuncti on proceedin gs); Nat’l Wildlife Fed’n v.

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 dec is io n di d no t ad dr ess a ny E SA c l aim s.

11

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Burlingt on N. R.R., Inc., 23 F.3d 1508, 1510-11 (9th Cir. 1994)(sa me). 65. Prior de cisions invo lving the coordinated

projects ’ operations found that TVA v . Hill and relate d Ninth Ci rcuit author ities foreclose the district court’s traditio nal discreti on to balance economic equiti es under the ESA. There is n o such bar in NEPA injunction

proceedi ngs. 66. Plaintif fs have adva nced a hu man welfare

exceptio n and conten d that unlike any of the prio r cases, this cas e juxtaposes species’ survival against hu man welfare, requiring a balancing of the BiOp’s thre ats of harm to humans, heal th, safety, and protection of affected communities. No case, including TVA v. Hill,

which co ncerned the competing economic interest i n the operatio n of a hydro-electric project and p rohibited federal courts from balancing the loss of funds s pent on that pro ject against the loss of an endangered sp ecies, expressl y addresses whether the ESA precludes bal ancing of harms to humans a nd the human environment unde r the circumst ances presen ted here. 67. This c ase in volves both harm to threatene d Con gress

species and to human s and their environment.

has not nor do es TVA v. Hill elevate species prot ection 118

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over the health and safety of humans. (2) 68. Balancin g the Harms under NEPA. Although it is undis puted that all harms may be

consider ed in evalua ting a claim for injunctive r elief under NE PA, an injunction should not issue if enjoining such gov ernment acti on would result in more harm to the environm ent than den ying injunctive relief. Ecosyste ms, 74 7 F.2d at 1 250. E. The Publ ic Interest. 69. In adopt ing the ESA, Congress explicitly fo und Save Our

that all threatened and endangered species “are o f esthetic , ecological , educational, historical, recreati onal, and sc ientific value to the Nation and its people.” 16 U.S.C. § 1531(a)(3). The ESA advanc es a

Congress ional policy to “halt and reverse the trend toward s pecies extin ction, whatever the cost.” Hill, 43 7 U.S. at 184. 70. The publ ic policy un derlying NEPA favors TVA v.

protecti ng the balan ce between humans and the environm ent. See 42 U.S. C. § 4321 (declari ng a national

policy t o “enc ourage productive and enjoyable har mony between man and his environment; to promote effor ts which will pre vent or elim inate damage to the environme nt and biospher e and stimul ate the health and welfare of man; 119

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[and] to enrich the understanding of the ecologic al systems and natural resources important to the Nation.. ..”). 71. If both these object ives can be realized by

astute m anagement, i t is the government’s obligat ion to do so. 72. It is in the publi c int erest that relief be

granted to Pla intiffs, who represent a subs tantia l populati on of water users in California, to enhan ce the water su pply to redu ce the adverse harms of destr uction of perma nent crops; fallowed lands; increased gro undwater consumpt ion; reducin g groundwater supplies; land subsiden ce; reductio n of air quality; destruction of family a nd entity fa rming businesses; and social disrupti on and dislo cation, such as increased pro perty crimes a nd intra-family c rimes of violence, adverse effects on schools, and increased unemploym ent leading to hunger a nd homelessn ess. This must be done witho ut

jeopardi zing the spe cies and their critical habit at. VII. CONCLUSI ON 1. 1. Plaintif fs have succ eeded on the merits of their

NEPA cla im. a. NEPA req uires that t he respon sible agency

take a h ard look at the environmental consequence s of its 120

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actions, Robertson v . Methow Valley Citizen’s Cou nsel, 490 U.S. 332, 350 (1 989), obligating federal agen cies to prepare an environme ntal impact statement (“EIS”) for all “major f ederal actions significantly affecting the quality of the human environment.” 4332(2)( C). b. Federal Defendants a re required to evaluate 42 U.S.C. §

the impa ct of the co ordinated operations of the C VP and SWP, whi ch constitut es major federal action. The

evidence overwhelmin gly establishes significant detrimen tal effects visited on the quality of the human environm ent by imple mentation of the BiOp’s RPA A ctions, which im pose substan tial restrictions on the wate r supply to Calif ornia to pro tect the delta smelt. c. Where re quired, an EIS discloses

environm ental effects of a proposed action and considers alternat ive courses of action. Id. Here, Federal

Defendan ts completel y abdicated their responsibil ity to consider alternative remedies in formulating RPA Actions that wou ld not only protect the species, but woul d also minimize the adverse impact on humans and the hum an environm ent. d. In consi dering RPA a lternatives, the record

shows th e burden of other causes is allocated to the 121

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water su pply, withou t the required an alysis whether alternat ives, less h armful to humans and the huma n environm ent, exist. Although this allocation of

resource s ultimately is the prerogative of the ag ency, NEPA nev ertheless re quires a hard look. 2. Plaintif fs have also shown a likeliho od of Althou gh the

success on the merit s of their ESA claim.

premise underlying C omponent 2 -- that the species may be jeopardi zed by incre ased negative flows occasione d by export p umping -- has rec ord support, FWS h as failed to adequate ly justify b y generally recog nized scientific principl es the preci se flow prescriptions imposed by Componen t 2. The ex act restrictions imposed, whi ch are

inflicti ng material harm to humans and the human environm ent, are not supported by the record, mak ing it impossib le to determ ine whether RPA Component 2 overly protecti ve. Judicia l deference is not owed to ar bitrary,

capricio us, and scie ntifically unreasonable agenc y action. 3. It is hi ghly signifi cant that the co-operat or of

the Proj ects, DWR, with access to scientifi c comp etenc e in the f ields of fis h biology and ecology, and pr oject operatio ns, does not oppose the motion for a prel iminary injuncti on. 122

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4.

Under th e balance of hardships analysis,

Defendan ts’ contenti on that the ESA, under TVA v. Hill , preclude s equitable weighing of Plaintiffs’ inter ests is not supp orted by tha t case, as evidence of harm t o the human en vironment in the form of social dislocati on, unemploy ment, and ot her threats to human welfare were not present in Hil l. 5. They are in this case.

Defendan ts argue tha t jeopardy to the species

cannot b e avoided wi thout continuing substantial reductio n of pumping , with resultant reduction of water supply t o Plaintiffs , representing over 20,000,00 0 persons, affec ted communities, and the agricultural industry in Northern , Central, and Southern Calif ornia. 6. Congre ss created public exp ectations in the

Amended Reclamation Act by instructing Reclamatio n to contract for water s ervice to hundreds of public- entity water se rvice provid ers that supply water to mill ions of people a nd thousands of acres of productive agric ultural land. T he agencies have not fully discharged the ir

responsi bility to ef fectively allocate Project wa ter resource s. Federal Defendants have acted a rbitra rily and

capricio usly in form ulating Component 2 of the RP A, wh ich lacks fa ctual and sc ientific justification, while effectiv ely ignoring the irreparable harm that pumping 123

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restrict ions have in flicted and will inflict on humans and the human enviro nment. 7. The sp ecies and its cri tica l habitats are The specie s has

entitled to protecti on under the ESA. been and will be pro tected.

That is the law.

Nonethel ess, FWS and Reclamation, as the consulti ng and action a gencies, must tak e the hard look un der NE PA at the seve re consequen ces visited upon Plaintiffs, the water su pply of Cali fornia, the agricultural indu stry, and the residents an d communities impacted by the water supply l imitations i mposed by the Component 2. F ederal

Defendan ts have fail ed to comprehensi vely a nd competen tly evaluate whether RPA alternatives can be prescrib ed that will be mutually pro tective of all the statutory purposes of the P rojects. 8. This i s a case of first imp ression. The stakes

are high , the harms to the affected human c ommuni ties great, a nd the injur ies unacceptable if they can be mitigate d. NEPA. FWS and Reclamation have not complied with

T his prevente d in- depth analysis of the po tential

RPA Acti ons through a properly focused study to identi fy and sele ct alternati ve remedial measures that min imize jeopardy to affected humans and their communities , as well as protecting t he threatened species. 124 No pa rty has

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suggeste d that human s and their environment are l ess deservin g of protect ion than the species. Until

Defendan t Agencies h ave complied with the law, so me injuncti ve relief pe nding NEPA compliance may be appropri ate, so long as it will not further jeopa rdize the spec ies or their habitat. 9. Injunc tive relief also may be warra nted u nder the

ESA, bec ause, althou gh the general premises under lying Componen t 2 find some support in the record , the preci se flow pre scriptions i mposed on coordinated project operatio ns are not s upported by the best availabl e science and are not explained as the law requires . 10. Injunc tive r elief canno t be imposed witho ut

current evidence of the status of the species to assure that alt ered operati ons will not deepen jeopardy to the affected species or otherwise violate other laws. The

evidence has not suf ficiently focused on re medies to provide a confidence level that Plaintiffs’ propo sed remedy o f a flat -5,600 cfs ceiling o n negative O MR flows will not jeopardize the continued existence of th e species and/or adver sely modify its critical habi tat. 11. Legal and eq uitabl e gro unds for injunctiv e

relief h ave otherwis e been established by a prepo nderance of the e vidence. 125

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12.

RPA componen t 2 su ffers fro m a lack of

populati on scaling i n violation of the requiremen t FWS use the best availab le science. There is no reli able

lifecycl e model, whi ch best available science cal ls for, even if the Court ca nnot require the agency to de velop one. Co ntinuing evi dence of the extreme risk to the

continue d existence of the Delta smelt population has been pre sented by De fendants. Absent a showing b y

Plaintif fs that Delt a smelt are not within immine nt risk of entra inment by Pr oject pumping facilities and/ or not within h ydraulic inf luence of the pumps in the da nger area of the Central and South Delta, the -5,000 c fs fl ow restrict ion cannot b e enjoined. 13. A telephonic confe rence to discuss whether

Plaintif fs have evid ence that imminence of harm t o Delta smelt do es not exist to justify injunction of pum ping restrict ions shall be held May 28, 2010 in Courtr oom 3 at 10:00 a. m.

SO ORDER ED Dated: M ay 27, 2010 /s/ O liver W. Wanger Oliver W. Wang er United States Distri ct Ju dge

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