San Luis & Delta-Mendota Water Auth. v. Locke, 1:09-CV-01053 OWW DLB

• Decision Date: 20 September 2011
• Docket Number: 1:09-CV-01520 OWW SMS,1:09-CV-01373 OWW DLB,1:09-CV-01580 OWW DLB,1:09-CV-01053 OWW DLB,1:09-CV-01625 OWW SMS,1:09-CV-01090 OWW DLB
• Court: U.S. District Court — Eastern District of California
• Parties: SAN LUIS & DELTA-MENDOTA WATER AUTHORITY; WESTLANDS WATER DISTRICT v. GARY F. LOCKE, as Secretary of the United States Department of Commerce; et al. (1:09-cv-01053-OWW-DLB) STOCKTON EAST WATER DISTRICT, et al. v. NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, et al. (1:09-cv-01090-OWW-DLB) STATE WATER CONTRACTORS v. GARY F. LOCKE, et al. (1:09-cv-01378-OWW-SMS) KERN COUNTY WATER AGENCY, et al. v. UNITED STATES DEPARTMENT OF COMMERCE, et al. (1:09-cv-01520-OWW-SMS) OAKDALE IRRIGATION DISTRICT, et al. v. UNITED STATES DEPARTMENT OF COMMERCE, et al. (1:09-cv-01580-OWW-DLB) THE METROPOLITAN WATER DISTRICT OF SOUTHERN CALIFORNIA v. NATIONAL MARINE FISHERIES SERVICE, et al. (1:09-cv-01625-OWW-SMS)

SAN LUIS & DELTA-MENDOTA WATER AUTHORITY; WESTLANDS WATER DISTRICT
v.
GARY F. LOCKE, as Secretary of the United States Department of Commerce; et al. (1:09-cv-01053-OWW-DLB)
STOCKTON EAST WATER DISTRICT, et al.
v.
NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, et al. (1:09-cv-01090-OWW-DLB)
STATE WATER CONTRACTORS
v.
GARY F. LOCKE, et al. (1:09-cv-01378-OWW-SMS)
KERN COUNTY WATER AGENCY, et al.
v.
UNITED STATES DEPARTMENT OF COMMERCE, et al. (1:09-cv-01520-OWW-SMS)
OAKDALE IRRIGATION DISTRICT, et al.
v.
UNITED STATES DEPARTMENT OF COMMERCE, et al. (1:09-cv-01580-OWW-DLB)
THE METROPOLITAN WATER DISTRICT OF SOUTHERN CALIFORNIA
v.
NATIONAL MARINE FISHERIES SERVICE, et al. (1:09-cv-01625-OWW-SMS)

1:09-CV-01053 OWW DLB
1:09-CV-01090 OWW DLB
1:09-CV-01373 OWW DLB
1:09-CV-01520 OWW SMS
1:09-CV-01580 OWW DLB
1:09-CV-01625 OWW SMS

UNITED STATES DISTRICT COURT FOR THE EASTERN DISTRICT OF CALIFORNIA

Dated: September 20, 2011

THE CONSOLIDATED SALMONID CASES

MEMORANDUM DECISION RE CROSS MOTIONS FOR SUMMARY JUDGMENT (DOCS. 430, 435, 446, 474, 477)
TABLE OF CONTENTS

I. INTRODUCTION.................................................4

II. BACKGROUND..................................................6

A. The Listed Species......................................6

1. Sacramento River Winter-Run Chinook Salmon.........6

2. Spring Run Chinook.................................8

3. Central Valley Steelhead...........................9

4. Green Sturgeon....................................11

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5. Southern Resident Killer Whale....................12

B. The 2009 Salmonid BiOp and RPA.........................12

III. STANDARD OF DECISION......................................15

IV. BASIC LEGAL FRAMEWORK......................................16

A. Review under the APA...................................16

1. Record Review.....................................16

2. Deference to Agency Expertise.....................17

B. General Obligations Under the ESA......................19

1. Best Available Science............................21

2. Best Available Science Standards and the Application of Analytical/Statistical Methodologies.....................................27

V. EXPORT PLAINTIFFS' & DWR'S CLAIMS...........................29

A. Alleged Clear Scientific Errors Pertaining to Delta Operations.............................................29

1. Challenged Statistical Methodologies..............30

2. Failure to Perform a Population-Level Quantitative Analysis.............................46

B. Baseline Analysis Challenges...........................65

1. Failure to Distinguish Between Discretionary and Nondiscretionary Actions..........................65

2. Treatment of Available Data on Ocean Harvest and Ocean Conditions..................................77

C. Effects Analysis Challenges............................87

1. Use of a 100-Year Timeframe.......................87

2. Winter-Run Viability Analysis.....................92

3. Orca Analysis....................................100

4. Interior Delta Mortality as an Indirect Effect. ..104

D. Critical Habitat Analysis.............................113

1. There Is No Requirement that NMFS Identify a Numerical Threshold for Adverse Modification.....113

2. Significance of Impacts to Critical Habitat......115

E. Use of Surrogates.....................................128

F. Challenges to the Reasonable and Prudent Alternative. .132

1. RPA Action IV.2.1................................132

2. RPA Action IV. 2. 3................................161

3. Action IV. 3......................................180

G. Compliance with 50 C.F.R. § 402.02....................184

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1. Consistency with Purposes of the Action..........189

2. Consistency with the Action Agency's Legal Authority and Jurisdiction.......................194

3. Economic and Technical Feasibility...............199

4. Avoidance Jeopardy and/or Adverse Modification. ..204

5. DWR's Feasibility Challenges to Action IV.4.2. ...204

VI. STANISLAUS RIVER PLAINTIFFS' CLAIMS.......................215

A. Relevant Factual Background...........................215

1. The New Melones Project..........................215

2. The Stanislaus River Plaintiffs..................216

3. The Status of Steelhead in the Stanislaus River. .216

B. Inclusion of the New Melones Unit in the Proposed Action Subject to Consultation........................220

C. Effects Analysis Challenges...........................223

1. New Melones Operations v. Baseline Effects. ......223

2. Challenge to Critical Habitat Adverse Modification Finding.............................228

D. Stanislaus River RPA Challenges.......................234

1. Challenge to the Assumptions Used to Model New Melones Project Operations.......................234

2. Do Actions III.1.2, III.1.3, and IV.1.2 Improperly Require Reclamation to Infringe Upon OID and SSJID's Prior Right to Stanislaus River Water in violation of 50 C.F.R. § 402.02?........236

3. Use of the San Joaquin River Temperature Model. ..243

4. Exceptions Built into Action III.1.2.............252

5. Does the Record Support the Finding that Action III.1.3 Will Avoid Jeopardy to or Adverse Modification of CV Steelhead or Critical Habitat? 254

6. DFG Salmon Population Model......................259

7. SR Plaintiffs' "Impermissible Major Changes" Argument.........................................260

8. Challenges to the BiOp's Feasibility Analyses? ...261

9. Are Actions III.1.3, III.2.2 Consistent with the Purposes of the Project?.........................264

10. Waste and Unreasonable Use of Water (California Constitution Article X, Section 2)...............265

VII. RECLAMATION'S LIABILITY UNDER THE ESA....................267

VIII. CONCLUSION..............................................270

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I. INTRODUCTION

These consolidated cases arise out of continuing efforts to protect several species listed under the Endangered Species Act ("ESA"), namely the endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) ("winter-run"), threatened Central Valley spring-run Chinook salmon (O. tshawytscha) ("spring-run"), threatened Central Valley steelhead (O. mykiss) ("CV steelhead"), threatened Southern Distinct Population Segment ("DPS") of North American green sturgeon (Acipenser medirostris), and endangered Southern Resident killer whales (Orcinus orca) (collectively, "Listed Species"); and associated impacts to the water supply for more than half the State of California.

Plaintiffs, San Luis & Delta Mendota Water Authority and Westlands Water District; State Water Contractors ("SWC"); Kern County Water Agency and Coalition for a Sustainable Delta; and Metropolitan Water District of Southern California ("MWD" or "Metropolitan") (collectively "Export Plaintiffs") move for summary judgment on their claims that the United States National Marine Fisheries Service's ("NMFS") June 4, 2009 Biological Opinion, addressing the impacts of the coordinated operations of the federal Central Valley Project ("CVP") and State Water Project ("SWP") (collectively the "Project") on the Listed Species ("2009 Salmonid BiOp" or "BiOp") and its Reasonable and Prudent Alternative ("RPA"), violates the ESA and the

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Administrative Procedure Act ("APA"). Doc. 430.¹ Plaintiffs Stockton East Water District, Oakdale Irrigation District, and South San Joaquin Irrigation District ("Stanislaus River Plaintiffs" or "SR Plaintiffs") filed a separate motion for summary judgment, raising unique challenges to the BiOp. Doc. 435. Plaintiff-in-Intervention, the California Department of Water Resources ("DWR") filed a separate motion for summary judgment on narrower grounds. Doc. 446.

Federal Defendants, the United States Department of Commerce ("DOC"), the National Oceanic and Atmospheric Administration ("NOAA"), the agency within DOC of which NMFS is a part, NMFS, the United States Department of the Interior ("DOI"), and its sub-agency the United States Bureau of Reclamation ("Reclamation"), oppose and cross move for summary judgment on all remaining claims, Doc. 477, as do Defendant-Intervenors California Trout, Friends Of The River, Natural Resources Defense Council, Northern California Council of the Federation of Fly Fishers, Pacific Coast Federation of Fishermen's Associations/Institute for Fisheries Resources, Sacramento River Preservation Trust, San Francisco Baykeeper, The Bay Institute, and the Winnemem Wintu Tribe, Doc. 474. All parties filed replies. Docs. 487, 492, 513, 515. These cross motions, which included over 700 pages of briefing and thousands of pages of supporting declarations and exhibits, came on for hearing on December 16 and 17, 2010.

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II. BACKGROUND

A. ...