B08.01 20140512 Yuba 2014 Daguerre BiOp and Cover Letter Signed.pdf

Michael J. Farrell Colonel, U.S. Army Commander U.S. Army Engineer District, Sacramento 1325 J Street Sacramento, California 95814-2922

Dear Colonel Farrell:

UNITED STATES DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

NATIONAL MARINE FISHERIES SERVICE

West Coast Region 650 Capitol Mall, Suite 5-1 00 Sacramento, California 9581 4-4 700

MAY 1 2 2014 In response refer to:

WCR-2013-1

This document transmits NOAA's National Marine Fisheries Service's (NMFS) biological opinion (Enclosure) for the U.S. Army Corps ofEngineers' (Corps) operation and maintenance ofDaguerre Point Dam on the Yuba River. The biological opinion reviews the effects of the action on federally listed threatened Central Valley spring-run Chinook salmon (Oncorhynchus tshawytscha), threatened California Central Valley steelhead (0. myldss), the threatened Southern distinct population segment of green sturgeon (Acipenser medirostris), and their designated critical habitat in accordance with section 7(a)(2) of the Endangered Species Act (ESA) of 1973, as amended (16 U.S.C. 1531 et seq.).

On August 13, 2013, the U.S. District Court, Eastern District of California, ordered NMFS to file a new biological opinion by May 12, 2014. Your request for reinitiation of formal consultation, which included the final biological assessment, was received on October 22, 2013.

The proposed action is the Corps' continued operation and maintenance ofDaguerre Point Dam on the lower Yuba River. Operation and maintenance at Daguerre Point Dam includes operation of the fish ladders (flow gates, baffle boards, debris removal), sediment management, flashboard management, a river stage gage, a contract for operation of fish counting system in the fish ladders and a contract for the installation of flashboards on the dam.

The attached document is NMFS' final biological opinion on the Corps' operation and maintenance of existing fish passage facilities at Daguerre Point Dam on the Lower Yuba River, in accordance with section 7 of the ESA. The Corps requested ESA consultation in two separate BAs submitted to NMFS on October 22, 2013:

(1) U.S. Army Corps of Engineers Ongoing Operation and Maintenance ofEnglebright Dam and Reservoir on the Yuba River; and

(2) U.S. Army Corps of Engineers Authorized Operation and Maintenance of Existing Fish Passage Facilities at Daguerre Point Dam on the Lower Yuba River.

It is NMFS understanding that the October 22, 2013, submittal was limited to the Corps' discretionary activities. Effects of the Corps discretionary activities associated with operation and maintenance of Englebright Dam and Englebright Reservoir are addressed in a separate consultation.

The attached final biological opinion supersedes the February 29, 2012, NMFS biological opinion on operations of Englebright Dam/Englebright Lake and Daguerre Point Dam on the Yuba River, California. The attached final biological opinion is based on: (1) the biological assessment provided by the Corps on October 22, 2013; (2) key information included in the 2007 Lower Yuba River Fisheries Agreement (Yuba Accord), and 2014 Final Recovery Plan for the Evolutionarily Significant Units of Sacramento River Winter-Run Chinook Salmon and Central Valley Spring-Run Chinook Salmon, and the Distinct Population Segment of Central Valley Steelhead, published by NMFS (2014), and the Yuba Accord Monitoring and Evaluation Program draft interim report (RMT 2013); and (3) scientific literature and reports. A complete administrative record of this consultation is on file at the NMFS, California Central Valley Office.

Based on the best available scientific and commercial information, including our review of the biological assessment, this biological opinion concludes that implementation of the proposed action is not likely to jeopardize the above species or adversely modify designated critical habitat. NMFS has included Reasonable and Prudent Measures and discretionary terms and conditions that will minimize incidental take associated with the proposed action.

If you have any questions regarding this correspondence please contact Mr. Gary Sprague in our California Central Valley Area Office, 650 Capitol Mall, Suite 5-100, Sacramento, California 95814. Mr. Sprague may be reached by telephone at (916) 930-3615 or by Fax at (916) 930- 3629.

Sincerely, /Jlafo~~ ~illiam W. Stelle, Jr.

Regional Administrator

Enclosure cc: Randy P. Olsen Chief, Operations and Readiness Branch U.S. Army Corps of Engineers, Sacramento District 1325 J Street Sacramento, CA 95814

Doug Grothe Park Manager Harry L. Englebright Lake U.S. Army Corps of Engineers P.O. Box 6 Smartsville, CA 95977-0006

Lisa H. Clay Senior Assistant District Counsel

U.S. Army Corps of Engineers, Sacramento District 1325 J Street Sacramento, CA 95814

Copy to File: ARN 151422SWR2013SA00280

ACTION AGENCY:

ACTION:

CONSULTATION

CONDUCTED BY:

COVERED SPECIES:

CRITICAL HABITAT:

FILE NUMBER:

PCTS TRACKING

DATE ISSUED:

Enclosure 1

BIOLOGICAL OPINION

U.S. Army Corps of Engineers

Operation and Maintenance of Daguerre Point Dam and Fish Ladders

National Marine Fisheries Service, West Coast Region

Threatened Central Valley spring-run Chinook salmon evolutionarily significant unit (ESU), threatened California Central Valley steelhead distinct population segment (DPS), and threatened Southern DPS of North American green sturgeon

Central Valley spring-run Chinook salmon ESU, California Central Valley steelhead DPS, and Southern DPS of North American green sturgeon

151422SVV1t2013SA00280

WCR-2013-1

i

Contents

(I) INTRODUCTION AND BACKGROUND

(A) Environmental Setting Englebright Dam........................................................................................................... 1 (1) Daguerre Point Dam ..................................................................................................... 2 (2) Upper Yuba River ......................................................................................................... 2 (3)

(II) CONSULTATION HISTORY

(A) 2002 Consultation with the Corps on Operations of Englebright Dam and Daguerre Point Dam on the Yuba River, California

(B) 2007 Consultation with the Corps on Operations of Englebright and Daguerre Point Dams on the Yuba River, California

(C) U. S. District Court, Eastern District of California, 2010 Ruling and 2011/2012 NMFS Consultation with the Corps on Continued Operation and Maintenance of Englebright Dam and Reservoir, Daguerre Point Dam, and Recreational Facilities On and Around Englebright Reservoir

(D) 2012 Consultation with the Corps on the Continued Operation and Maintenance of Englebright Dam and Reservoir, Daguerre Point Dam, and Recreational Facilities On and Around Englebright Reservoir on the Yuba River, California

(E) Current Consultation

(F) 2012 Biological Opinion

(III) BACKGROUND

(A) Section 7 Setting

(B) ESA Recovery Planning

California Central Valley Salmonid Recovery Planning ............................................ 10 (1)

(C) Lower Yuba River Fisheries Agreement

(D) Hydropower Licensing and Water Deliveries

(E) VAKI Riverwatcher Fish Counter

(IV) PROPOSED ACTION (Description of the Proposed Action)

(A) Proposed Action Components

Operation and Maintenance of the Fish Passage Facilities at Daguerre Point Dam .. 13 (1) Staff Gage Maintenance ............................................................................................. 19 (2) Administration of a License Issued to CDFW for VAKI Riverwatcher Operations at (3)

Daguerre Point Dam ii

Administration of a License Issued to Cordua Irrigation District for Flashboard (4) Installation, Removal and Maintenance at Daguerre Point Dam

Protective Conservation Measures ............................................................................. 21 (5) Corps’ Voluntary Conservation Program ................................................................... 23 (6)

(B) Interrelated Actions

(C) Interdependent Actions

(V) DESCRIPTION OF ACTION AREA

(VI) ANALYTICAL FRAMEWORK

(VII) STATUS OF THE SPECIES AND CRITICAL HABITAT

(A) CV spring-run Chinook Salmon Species Listing History ............................................................................................... 27 (1) Critical Habitat Designation and Primary Constituent Elements for CV Spring-run (2)

Chinook Salmon Historical Abundance and Distribution ...................................................................... 31 (3) Species Life History ................................................................................................... 32 (4) Factors Affecting the Species and Critical Habitat .................................................... 38 (5) Description of Viable Salmonid Population (VSP) Parameters ................................. 63 (6)

(B) CCV Steelhead Species Listing History ............................................................................................... 74 (1) Critical Habitat Designation ....................................................................................... 74 (2) Historical Distribution and Abundance ...................................................................... 77 (3) Species Life History ................................................................................................... 78 (4) Factors Affecting the Species and Critical Habitat .................................................... 83 (5) Description of Viable Salmonid Population (VSP) Parameters ............................... 100 (6)

(C) Green Sturgeon Species Listing History ............................................................................................. 113 (1) Critical Habitat Designation ..................................................................................... 113 (2) Historical Abundance and Distribution .................................................................... 121 (3) Species Life History ................................................................................................. 123 (4) Factors Affecting the Species and Critical Habitat .................................................. 131 (5) Viability Factors for Southern DPS green sturgeon ................................................. 138 (6)

(VIII) ENVIRONMENTAL BASELINE

(A) Background

Environmental Setting .............................................................................................. 143 (1) Summary of Past and Ongoing Fisheries Studies on the Lower Yuba River ........... 146 (2) iii

Physical Habitat ........................................................................................................ 146 (3) Flows ........................................................................................................................ 166 (4) Global Climate Change ............................................................................................ 176 (5) BiOp for the Central Valley Project/State Water Project ......................................... 177 (6)

(B) Physical Features Daguerre Point Dam ................................................................................................. 179 (1) Diversions in the Vicinity of Daguerre Point Dam .................................................. 188 (2) Waterway 13 and the Yuba Goldfields Fish Barrier Project .................................... 202 (3) Barriers Upstream of the Action Area (including Englebright Dam) ...................... 206 (4) Deer Creek ................................................................................................................ 208 (5)

(C) CV Spring-run Chinook Samon ESU CV Spring-run Chinook Salmon Historical Abundance and Distribution ............... 209 (1) CV Spring-run Chinook Salmon General Life History and Habitat Requirements . 211 (2) Spring-run Chinook Salmon Adult Immigration and Holding ................................. 212 (3) CV Spring-run Chinook Salmon Limiting Factors, Threats and Stressors .............. 222 (4) Viability of CV Spring-run Chinook Salmon ........................................................... 242 (5)

(D) CCV steelhead DPS Steelhead General Life History and Habitat Requirements ...................................... 256 (1) Steelhead Limiting Factors, Threats and Stressors ................................................... 263 (2) Viability of the CCV Steelhead ................................................................................ 269 (3) Future Needs ............................................................................................................. 283 (4)

(E) Southern DPS of Green Sturgeon Historical Distribution and Abundance .................................................................... 283 (1) Green Sturgeon General Life History and Habitat Requirements ............................ 284 (2) Summary of the Current Viability of the Southern DPS of Green Sturgeon ........... 289 (3)

(IX) EFFECTS OF THE PROPOSED ACTION

(A) Operation and Maintenance of Fish Passage Facilities

Exposure ................................................................................................................... 296 (1) Response ................................................................................................................... 296 (2) Critical Habitat ......................................................................................................... 297 (3)

(B) Fishway Debris Removal Exposure ................................................................................................................... 297 (1) Response ................................................................................................................... 297 (2) Critical Habitat ......................................................................................................... 298 (3)

(C) Sediment management iv

Exposure ................................................................................................................... 298 (1) Response ................................................................................................................... 299 (2) Critical Habitat ......................................................................................................... 300 (3)

(D) Staff Gage Maintenance Exposure ................................................................................................................... 300 (1) Response ................................................................................................................... 300 (2) Critical Habitat ......................................................................................................... 300 (3)

(E) VAKI Riverwatcher Exposure ................................................................................................................... 300 (1) Response ................................................................................................................... 301 (2) Critical Habitat ......................................................................................................... 301 (3)

(F) Dam Flashboard Management Exposure ................................................................................................................... 301 (1) Exposure ................................................................................................................... 302 (2) Response ................................................................................................................... 302 (3) Critical Habitat ......................................................................................................... 303 (4)

(G) Gravel Augmentation Exposure ................................................................................................................... 303 (1) Response ................................................................................................................... 304 (2) Critical Habitat ......................................................................................................... 304 (3)

(H) Woody Instream Material Management Program Exposure ................................................................................................................... 304 (1) Response ................................................................................................................... 304 (2) Critical Habitat ......................................................................................................... 305 (3)

(X) CUMULATIVE EFFECTS

(A) Yuba Goldfields Sand and Gravel Mining Operations

Teichert Aggregates .................................................................................................. 305 (1) Western Aggregates .................................................................................................. 306 (2) Baldwin Contracting Company and Springer Family Trust Hallwood Aggregate (3)

Facility

(B) Wheatland Project

(C) Agricultural Practices

(D) Browns Valley Irrigation District Agricultural Return Flow Recapturing Project

(E) Trust for Public Lands

(F) Increased Urbanization and Human Population Growth v

(XI) INTEGRATION AND SYNTHESIS OF EFFECTS

(A) Impacts on Species

CV Spring-Run Chinook Salmon ESU .................................................................... 311 (1) California Central Valley Steelhead DPS ................................................................. 314 (2) Green Sturgeon Southern Population DPS ............................................................... 316 (3)

(B) Impacts on Critical Habitat

(XII) CONCLUSIONS

(XIII) INCIDENTAL TAKE STATEMENT

(A) Amount or Extent of Take

(B) Effect of the Take

(C) Reasonable and Prudent Measure

(D) Terms and Conditions

(XIV) CONSERVATION RECOMMENDATIONS

(XV) REINITIATION NOTICE

(XVI) DATA QUALITY ACT DOCUMENTATION AND PRE- DISSEMINATION

REVIEW

(XVII) REFERENCES CITED

(I) INTRODUCTION AND BACKGROUND

(A) Environmental Setting

The proposed action is located on the Yuba River in Yuba and Nevada counties, California. The Yuba River watershed is historical habitat for the threatened Central Valley (CV) spring-run Chinook salmon (Oncorhynchus tshawytscha) evolutionarily significant unit (ESU), threatened California Central Valley (CCV) steelhead (O. mykiss) distinct population segment (DPS), and the threatened Southern DPS of North American green sturgeon (green sturgeon) (Acipenser medirostris). Within the Yuba River watershed, Englebright Dam defines the present upstream extent of CV spring-run Chinook salmon and CCV steelhead. Daguerre Point Dam defines the present upstream extent of green sturgeon. The sympatric Central Valley fall/late fall-run Chinook salmon (O. tshawytscha) is an unlisted salmon ESU that occupies the lower Yuba River and is significantly more abundant that the threatened species.

The Yuba River watershed has a history of hydraulic mining, which resulted in geographic changes that continue to affect the Yuba River today. The upper watershed has multiple dams and facilities that store water for delivery and energy generation. Downstream of Englebright Dam is a narrow gorge (called the Narrows), followed by an extensive area of placer mining debris called the Yuba Gold Fields.

Englebright Dam (1)

Englebright Dam is at river mile 24.1 on the Yuba River. The dam was constructed in 1941 to retain hydraulic mining debris. It is 260 feet high and stores 70,000 acre-feet of water. The area downstream of Englebright Dam is referred to as the lower Yuba River, and the area upstream is referred to as the upper Yuba River. The U. S. Army Corps of Engineers (Corps) administers the operation and maintenance of Englebright Dam.

Englebright Dam has no fish ladders. Salmon, steelhead, and sturgeon have been blocked from accessing the upper Yuba River and watershed since 1941. Since 1963 flow releases from Englebright Reservoir have been generally governed by guidelines outlined within the Federal Energy Regulatory Commission (FERC) licenses, commonly referred to as “FERC minimum flows.” Since 2008 the Lower Yuba River Accord has governed the minimum flows. The Lower Yuba River Accord is an agreement that addresses water issues downstream of Englebright Dam.

The majority of the time releases from the Englebright Reservoir into the lower Yuba River are made through two hydroelectric power facilities, one of which (Narrows II) is located just downstream of the base of the dam and the other (Narrows I), is located approximately 0.2 mile downstream. Water releases from the reservoir are administered by the Yuba County Water Agency (YCWA) and Pacific Gas and Electric Company (PG&E) for hydroelectric power generation, irrigation and maintenance of the downstream riverine ecosystem.

Daguerre Point Dam (2)

Daguerre Point Dam is 12.6 miles downstream of Englebright Dam. Daguerre Point Dam is 24 feet high and was built in 1910 to retain hydraulic mining debris. The dam is not operated for flood control because of the uniform flow over the crest of the dam (ogee crest/ogee spillway), and the entire reservoir behind the dam has been filled with hydraulic mining debris and sediments. Daguerre Point Dam has two fish ladders, designed for adult salmonids. Green sturgeon are unable to ascend the fish ladders. There are three conjunctive-use irrigation diversions from the Daguerre Point Dam pool, and the three diversions have a combined capacity of 1,085 cubic-feet-per-second (cfs).

Upper Yuba River (3)

There are major, human-made fish passage barriers upstream of Englebright Dam. By one count there are over 90 dams and diversions in the Yuba River watershed. A significant amount of water is annually diverted out of the watershed.

(II) CONSULTATION HISTORY

(A) 2002 Consultation with the Corps on Operations of Englebright Dam and Daguerre Point

Dam on the Yuba River, California

On March 27, 2002, NOAA’s National Marine Fisheries Service (NMFS) issued a biological opinion (BiOp) which analyzed the effects of the Corps’ operations of Englebright and Daguerre Point Dams on the Yuba River in Yuba and Nevada Counties, California, on threatened CV spring-run Chinook salmon and threatened CCV steelhead. The BiOp covered a five-year period, and concluded that the proposed action was not likely to jeopardize the continued existence of the CV spring-run Chinook salmon ESU or CCV steelhead DPS, and was not likely to destroy or adversely modify designated critical habitat for these species over that time period.

The 2002 BiOp expired on March 27, 2007.

In December 2006, the South Yuba River Citizens League (SYRCL) and Friends of the River, filed suit in U.S. District Court against both the Corps and NMFS under the Administrative Procedures Act. The suit was amended on March 12, 2007, after a required 60-day notice period, to include complaints under the ESA. The plaintiffs alleged that NMFS unlawfully issued an inadequate BiOp and failed to reinitiate consultation with the Corps. The suit further alleged that the Corps had failed to comply with the requirements of the BiOp, including improving the effectiveness and reliability of the existing fish ladders at Daguerre Point Dam, developing a plan to remove sediment from the ladders and egress at Daguerre Point Dam, and augmenting spawning gravels in reaches downstream of Englebright Dam.

(B) 2007 Consultation with the Corps on Operations of Englebright and Daguerre Point Dams on the Yuba River, California

On March 23, 2007, the Corps delivered to NMFS’ Sacramento Area Office, an initiation package including a cover letter requesting the initiation of formal consultation under section 7 of the Endangered Species Act (ESA) for the proposed action along with a biological assessment (BA) and Essential Fish Habitat assessment for the proposed action. Included in the Corps’ March 23, 2007, cover letter was a request for the extension of the timeframe covered by the 2002 BiOP in order to maintain coverage for the proposed action until a new consultation could be completed and a new long-term BiOp issued.

On April 27, 2007, NMFS issued a preliminary BiOp, which analyzed the effects of continuation of operation of the proposed action for a period of one year. On November 21, 2007, NMFS adopted the preliminary BiOp as the final BiOp for the proposed action, which analyzed the effects of long-term continuation of operation of the proposed action into the foreseeable future (NMFS 2007). Both of these BiOps concluded that the proposed action would not jeopardize CV spring-run Chinook salmon, CCV steelhead, or green sturgeon, or destroy or adversely modify designated CVspring-run Chinook salmon and CCV steelhead critical habitat.

(C) U. S. District Court, Eastern District of California, 2010 Ruling and 2011/2012 NMFS

Consultation with the Corps on Continued Operation and Maintenance of Englebright Dam and Reservoir, Daguerre Point Dam, and Recreational Facilities On and Around Englebright Reservoir

On July 8, 2010, a Federal judge determined that the existing NMFS BiOp on the operation of Englebright and Daguerre Point dams was inadequate. NMFS was directed to provide a more explicit analysis of effects to the species and to include analysis of the effects of hatcheries, the San Francisco Bay Delta, overall salmonid viability, poaching, and global warming on the species. NMFS was also asked to explain how the species will be able to tolerate cumulative effects such as the Wheatland project (a new water-delivery project).

On October 17, 2011, the Corps provided NMFS with a draft BA on the proposed action. On December 2, 2011, NMFS notified the Corps that the draft BA was insufficient to initiate section 7 consultation pursuant to section 402.14(c) Initiation of formal consultation . On January 27, 2012, the Corps initiated formal consultation on the proposed action and submitted the final BA and references to NMFS. On February 29, 2012, NMFS issued a BiOp.

(D) 2012 Consultation with the Corps on the Continued Operation and Maintenance of

Englebright Dam and Reservoir, Daguerre Point Dam, and Recreational Facilities On and Around Englebright Reservoir on the Yuba River, California

In response to the July 2010 remand of the 2007 BiOp, the Corps provided NMFS with a draft BA on the proposed action on October 17, 2011. On December 2, 2011, NMFS notified the Corps that the draft BA was insufficient. On January 27, 2012, the Corps initiated formal consultation on the proposed action and submitted the final BA and references to NMFS. NMFS provided a draft of the BiOp to the Corps and its applicants on February 27, 2012. Comments were provided to NMFS on February 28, 2012. NMFS provided the final BiOp to the Corps on February 29, 2012, in accordance with the deadline set by the U.S. District Court.

The February 29, 2012, BiOp concluded that the operation and maintenance of these two dams as proposed by the Corps would likely jeopardize the continued existence of CV spring-run Chinook salmon, CCV steelhead, and the Southern distinct population segment of green sturgeon, and result in the adverse modification of their critical habitat. The 2012 BiOp includes a reasonable and prudent alternative (RPA) that modifies the proposed action to avoid jeopardizing the species and adversely modifying their critical habitat.

NMFS received many comments on the 2012 BiOp. The comments were of both a technical and legal nature. NMFS met with the Corps and stakeholders to discuss issues associated with the BiOp. Over 900 written comments were submitted to NMFS. Written comments were received from the Corps (letter dated July 3, 2012), Yuba County Water Agency (letter dated June 29, 2012), Pacific Gas and Electric (letter dated July 12, 2012), Nevada Irrigation District (letter dated July 11, 2012), and from the Brophy Water District - Dry Creek Mutual Water Company – Hallwood Irrigation Company – South Yuba Water District – Wheatland Water District (letter dated September 24, 2012).

In response to the comments NMFS held a number of meetings with the Corps and its attorneys to address legal issues, and held a series of meetings with the Corps and key stakeholders to address the technical issues in the BiOp.

(E) Current Consultation

On February 26, 2013, the Corps sent a letter to NMFS requesting reinitiation of formal consultation “for ongoing activities at Englebright and Daguerre Point Dams, and for operation of the fish ladders at Daguerre Point Dam.” On April 11, 2013, NMFS provided a written response to the Corps identifying the necessary information for reinitiation of formal consultation under section 7 of the Endangered Species Act. As set forth in 50 CFR §402.16, reinitiation of formal consultation is appropriate where discretionary Federal agency involvement or control over an action has been retained (or is authorized by law) and if: (1) the amount or extent of taking specified in any incidental take statement is exceeded, (2) new information reveals effects of the agency action that may affect listed species or critical habitat in a manner or to an extent not previously considered, (3) the agency action is subsequently modified in a manner that causes an effect to the listed species that was not considered in the BiOp, or (4) a new species is listed or critical habitat is designated that may be affected by the action. In this case, the Corps has determined that reinitiation of consultation is necessary in order for the Corps to provide NMFS with additional information and clarification on subjects that include the following:

(1) To more accurately and specifically define the scope of the Corps’ authorities and discretion, for purposes both of appropriately defining the proposed action and ensuring that any RPA measures are within the scope of the Corps’ legal authority and jurisdiction. See 50 C.F.R. § 402.02,

(2) To more clearly define the scope of the proposed action area, and the determination of which other activities are interrelated and interdependent with the proposed action,

(3) To provide additional information regarding the nature of the Corps’ proposed activities at Englebright and Daguerre Point Dams, and

(4) To provide the most recent scientific and technical information regarding the listed species and the effects of the proposed action on them.

As described in CFR 402.14(c), formal consultation is initiated through a request that must include the following six pieces of information:

(1) Include a description of the proposed action to be covered. The Corps should describe with specificity the character of their involvement with existing structures associated with the proposed action, the boundaries of discretion, and the extent of the discretion that the Corps is proposing to exercise. This includes describing areas of non-discretion, where the scope of the Corps’ discretion is specifically constrained.

(2) Include a description of the specific area that may be affected by the proposed action.

(3) Included a description of any listed species or critical habitat that may be affected by the proposed action.

(4) Include a description of the manner in which the action may affect any listed species or critical habitat, and an analysis of any direct, indirect, or cumulative effects.

(a) Direct Effects: Effects to listed species of designated critical habitat that occur during implementation of the project,

(b) Indirect Effects: Effects to listed species that occur later in time or offsite, but are reasonably certain to occur, and

(c) Cumulative Effects: For purposes of the ESA, cumulative effects are defined as the effects of future State or private activities, not involving Federal activities, that are reasonably certain to occur within an action area of the Federal action subject to consultation (50 CFR 402.02).

Future Federal actions are not included here because they require separate consultation pursuant to section 7 of the ESA.

(5) Include relevant reports, including any environmental impact statements, environmental assessments, BAs or other analysis prepared regarding the proposal.

(6) Include any other relevant studies or other information available on the action, the affected listed species, or critical habitat.

In order to meet the requirements of CFR 402.14(c), to initiate formal consultation; and 50 CFR 402.14(d), to provide the best scientific and commercial data available; NMFS recommended that the Corps develop an updated BA to evaluate the potential effects of the action on listed species and designated critical habitat, pursuant to 50 CFR 402.12. NMFS identified that consultation will begin once NMFS has received a final BA that includes a proposed project description and addresses all of the information necessary to evaluate the effects of the action on listed species and critical habitat.

(F) 2012 Biological Opinion

On November 6, 2012, the Yuba County Water Agency submitted a 60 day notice of intent to sue the Corps and NMFS, pursuant to section 11(g) of the Endangered Species Act. The intent to sue was based on alleged violations of the Endangered Species Act and its implementing regulations. In a letter dated November 13, 2012, the South Yuba River Citizens League submitted a 60 day notice of intent to sue the Corps for allegedly not implementing reasonable and prudent alternative actions and allegedly unauthorized take of species listed under the Federal Endangered Species Act.

At the request of the Corps, on November 27, 2012, NMFS modified the schedule for implementation of the reasonable and prudent alternative in the February 29, 2012 BiOp. The schedule modifications were based on new information about the Corps authorities and ability to meet the schedules in the BiOp.

On January 11, 2013, the South Yuba River Citizens League filed for relief under the Administrative Procedure Act regarding the extensions of time given to the Corps by NMFS.

The South Yuba River Citizens League requested an injunction and order for NMFS to rescind its November 27, 2012, letter. On January 28, 2013, the South Yuba River Citizens League and Friends of the River filed an amended complaint for declaratory and injunctive relief against NMFS and the Corps. The amended complaint requested the same relief as the January 11, 2013, filing and requested the Court to find the Corps in violation of the Endangered Species Act.

(III) BACKGROUND

(A) Section 7 Setting

The Corps’ authorized operations and maintenance (O&M) and planning activities associated with the proposed action includes making minor modifications to the fish ladders at Daguerre Point Dam. The Corps’ O&M of the fish ladders at Daguerre Point Dam does not include major ladder reconfigurations or reconstruction. According to the Corps Regulation (No. 1165-2-119) titled “Modifications to Completed Projects” (Corps 1982), such activities would require additional Congressional authorization and appropriation of necessary funding. Consequently, the proposed action is comprised of O&M of the existing fish passage facilities at Daguerre Point Dam, and specified conservation measures.

The Corps has identified the following authorities as governing their discretion and the proposed action (Corps 2013b):

(1) The California Debris Act (Ch 183, §1, 27 Stat. 507,

(2) The Rivers and Harbors Act of 1935, Public Law No. 409,

(3) Flood Control Act of 1970, Section 216,

(4) National Dam Inspection Act of 1972,

(5) Water Resources Development Act 1986, Section 906(b), Section 1106, and

Section 1135,

(6) Water Resources Development Act 1996, Section 206,

(7) National Dam Safety Program Act of 1996 (Public Law 92-367),

(8) Public Law 109-460, and

(9) Engineer Regulation 1105-1-100, Appendix G, paragraph 13(c).

The Chief of Engineers has authority to modify projects without further authorization from Congress within strictly defined limits, i.e., as long as the scope of the project, including the function and purpose of the project, and the area served by the project, is not materially changed. This understanding, set forth in detail in a 1951 report by the Chief of Engineers, was approved in the report of a special subcommittee to the House Public Works Committee in 1952, Report on the Civil Functions Program of the Corps of Engineers, United States Army to the House Committee on Public Works, 82d Congress, 2d Session 1 (1952) (Corps 2013b).

The Corps requested ESA consultation in two separate BAs submitted to NMFS on October 22, 2013:

(1) U.S. Army Corps of Engineers Ongoing Operation and Maintenance of

Englebright Dam and Reservoir on the Yuba River (Corps 2013a), and

(2) U.S. Army Corps of Engineers Authorized Operation and Maintenance of

Existing Fish Passage Facilities at Daguerre Point Dam on the Lower Yuba River (Corps 2013b).

Previous ESA consultations have been conducted addressing various Corps projects and their activities on the Yuba River (see Consultation History above). Those consultations encompassed activities at both Englebright Dam and Daguerre Point Dam (projects). However, the October 22, 2013, submittal was limited to the Corps’ discretionary activities associated with Englebright Dam and reservoir and a separate BA was submitted at the same time for the Corps’ discretionary activities associated with Daguerre Point Dam. The Corps evaluated these projects separately in two BAs because “each dam has a separate authorization and appropriation, and because the actions at Englebright and Daguerre are wholly separate and are not dependent upon each other to operate.”

The Corps limited their proposed action in the Daguerre Point Dam BA to discretionary actions, and determined that the proposed action may affect and is likely to adversely affect CV spring-run Chinook salmon, and CCV steelhead. The Corps determined that adverse effects to CV spring-run Chinook salmon critical habitat, and CCV steelhead critical habitat are discountable and/or insignificant. For the southern DPS of green sturgeon the Corps determined that the proposed action may affect, but is not likely to adversely affect green sturgeon and its critical habitat. Discretionary actions for which the Corps determined the effects were: “may affect, but is not likely to adversely affect”, or “may affect and is likely to adversely affect”, or “discountable, or insignificant”, were carried forward in the Corps request for consultation.

Actions for which the Corps determined there would be no effects, and actions for which the Corps determined they have no discretion were not carried forward and are not subject to this consultation.

In the Daguerre Point Dam BA (Corps 2013b) the Corps deconstructed their Yuba River activities into five categories as follows:

(1) Future Corps Actions Requiring Separate ESA Consultation,

(2) Non-Discretionary Actions,

(3) Discretionary Actions with No Effects to Listed Species or Critical Habitat,

(4) Englebright Dam and Reservoir, and

(5) O&M of Existing Fish Passage Facilities at Daguerre Point Dam.

Future Corps Actions Requiring Separate ESA Consultation: The Corps has identified that ESA issues related to the outgrants associated with the two hydropower facilities adjacent to Englebright Dam will be addressed through the Federal Energy Regulatory Commission. This will occur through the ESA consultations for the hydropower relicensing processes. The anticipated dates for new outgrants are 2016 and 2023. At this time the specifics associated with the Federal Power Act licenses for the hydropower facilities and for the specifics to be included in the new outgrants have not been determined.

Non-Discretionary Actions: The Corps has determined that a number of actions associated with Daguerre Point Dam and Englebright Dam that are non-discretionary. These include security and safety inspections. The Corps has provided information the about their authority, and which actions over which they have discretion. The ESA regulations state “Section 7 and the requirements of this part apply to all actions in which there is discretionary Federal involvement or control.” (50 CFR Ch. IV, section 402.03 Applicability). Therefore, the Corps has not proposed these actions for consultation, and they are not covered by this BiOp and take statement.

Discretionary Actions with No Effects to Listed Species or Critical Habitat: The Corps has identified a number of actions associated with Englebright Dam and Englebright Reservoir as having no effects on listed species or designated critical habitat. These actions include:

• Ongoing Maintenance of Recreational Facilities;

o Maintenance Facilities Upkeep, o Roads and Parking Area Maintenance, o Sign and Waterway Marker Maintenance, o Maintenance of Recreation Area Buildings, o Wastewater Monitoring Plan Implementation, o Campground Repairs and Renovations, o Campground Fire Break Clearing, o Park Office Facility Upkeep, o Grounds Maintenance, and o Narrows Day Use Facility Improvements.

• Continued Administration of Maintenance Service Contracts; and o Janitorial Service and Garbage Pickup, and o Water Quality Testing.

• Continued Administration of Outgrants.

o Easement for Use of Power Generation Facilities to YCWA and PGE, o Power Transmission Line Easement to PG&E for Narrows I, and o Road Right of Way Easement to YCWA for Narrows II.

For the first two categories of actions (Ongoing Maintenance of Recreation Facilities, and Continued Administration of Maintenance Service Contracts), all of the activities are upstream of Englebright Dam. Currently, no ESA listed anadromous fish species are present upstream of Englebright Dam, nor is there any designated critical habitat upstream of Englebright Dam. The upstream extent of critical habitat on the Yuba River for salmonids is Englebright Dam, and for green sturgeon it is Daguerre Point Dam. For the first two subcategories, no effects from these Corps actions are expected to persist downstream of Englebright Dam. The Corps has determined that these actions would have no effect on ESA listed anadromous fish species or designated critical habitat.

For the action subcategory of “Continued Administration of Outgrants” the Corps has identified that the actions are “The administration of ongoing outgrants consists of monitoring for compliance of the terms and conditions of the outgrant.” These outgrants include: 1) road right of way permits and easements, 2) a telephone line license, 3) power transmission line easements, and 4) the concessionaire lease at the Englebright Lake marina. The Corps has identified that only actions associated with these outgrants are the annual compliance inspection. The Corps has identified that “These inspections constitute administrative actions and not activities that have the potential to affect listed species or their critical habitats in the lower Yuba River.”

While future Corps actions to enforce compliance with outgrants conditions do have the potential to affect ESA listed anadromous fish species and/or designated critical habitat downstream of Englebright Dam, the specifics of those future actions cannot be determined at this time, and the timing and extent of those actions is undetermined at this time. Therefore it is not possible to include the potential effects of undetermined actions on ESA listed anadromous fish species in this consultation or to concur with an effects determination.

Operations and Maintenance of Existing Fish Passage Facilities at Daguerre Point Dam:

The remaining proposed actions that “may affect” listed species are the subject of this consultation and are described in detail in the Corps’ BA (Corps 2013b) and are summarized as follows:

• Operation and maintenance of the fish passage facilities at Daguerre Point Dam,

• Maintenance of the staff gage at Daguerre Point Dam,

• Administration of a right-of-way (license) issued to CDFW for VAKI

Riverwatcher operations at Daguerre Point Dam,

• Administration of a right-of-way (license) issued to Cordua Irrigation District for flashboard installation, removal and maintenance at Daguerre Point Dam,

• Protective Conservation Measures (annual funding availability and ongoing implementation is reasonably certain to occur based on past operations),

• Implementation of the Daguerre Point Dam Fish Passage Sediment Management Plan,

• Administration of a long-term Flashboard Management Plan at Daguerre Point Dam,

• Implementation of a Debris Monitoring and Maintenance Plan at Daguerre Point Dam,

• Voluntary Conservation Measures for Habitat Enhancement Purposes (planned for implementation, but less certain and subject to funding availability).

o Gravel Injection in the Englebright Dam Reach of the lower Yuba River, and o Large Woody Material Management Program

(B) ESA Recovery Planning

California Central Valley Salmonid Recovery Planning (1)

In 2009, NMFS released a draft recovery plan for CV salmon and CCV steelhead that specifically addresses the recovery goals and needs for CV spring-run Chinook salmon and CCV steelhead (NMFS, 2009). The draft plan states that reintroducing CV spring-run Chinook salmon and CCV steelhead populations into the upper Yuba River basin above Englebright Dam would contribute to the recovery of both species by increasing their abundance, improving their spatial structure and diversity, and reducing their overall extinction risk. There are several reasons why reintroducing these species into the upper Yuba River basin is likely to be successful and promote their recovery. First, both species historically occurred in the upper basin (Lindley et al., 2004, Yoshiyama et al., 1996) and studies suggest that multiple areas in the upper basin could support both species (DWR, 2007, Stillwater Sciences, 2012). Second, available evidence suggests that a significant portion of the summer holding habitat in the upper basin is expected to remain thermally suitable for both species throughout the 21st century, despite increased warming from global climate change (Lindley et al., 2007). Third, the upper Yuba River watershed is separated by a considerable distance from the small number of watersheds that support extant CV spring-run Chinook salmon (e.g., Deer Creek, Mill Creek, and Butte Creek) and establishing a population in this upper watershed would reduce the risks to CV spring-run Chinook salmon from catastrophic events such as a volcanic eruption at Mt. Lassen or major wildfires. Fourth, the Yuba River watershed has an ample supply of water to support both species with one of the highest annual discharges (~2,300,000 acre-feet/year) in the Central Valley (Lindley et al., 2004).

The Final Central Valley Chinook Salmon and Steelhead Recovery Plan will be published in the spring of 2014. The final plan identifies the reintroduction of CV spring-run Chinook salmon and CCV steelhead into the upper Yuba River as a number 1 action priority.

(C) Lower Yuba River Fisheries Agreement

The 2007 Lower Yuba River Fisheries Agreement (Yuba Accord) established flows in the lower Yuba River until the 2016 expiration of YCWA’s hydropower license for the Yuba River Hydroelectric Development Project. Minimum instream flow schedules for the lower Yuba River were developed through negotiations between YCWA, California Department of Fish and Game (CDFG), South Yuba River Citizens League, Friends of the River, Trout Unlimited, and the Bay Institute. The U. S. Fish and Wildlife Service (USFWS) and NMFS participated in the discussions, but did not sign the Yuba Accord. The USFWS and NMFS participate in the River Management Team processes, with the signatories.

(D) Hydropower Licensing and Water Deliveries

Several major hydroelectric power and water delivery projects are in the Yuba River watershed and influence operation and flows at Englebright Dam and flows at Daguerre Point Dam. These are the (1) Yuba River Development Project (FERC Project No. 2246), (2) Narrows I Project (FERC License No. 1403), (3) the Yuba-Bear Project (FERC Project No. 2266), (4) Drum- Spaulding Project (FERC Project No. 2310), Hallwood-Cordua diversion at Daguerre Point Dam (Corps License No. DACW03-01-592), and (5) South Yuba/Brophy diversion at Daguerre Point Dam (expired Corps License No. DACW05-3-85-537). The Corps licenses are only for access.

(E) VAKI Riverwatcher Fish Counter

A VAKI Riverwatcher infrared and photogrammetric system is installed in the fish ladders at Daguerre Point Dam. The Corps licenses the California Department of Fish and Wildlife to operate the VAKI Riverwatcher.

(IV) PROPOSED ACTION (Description of the Proposed Action)

The ESA section 7 regulations define “action” as: “…all activities or programs of any kind authorized, funded, or carried out, in whole or in part, by Federal agencies in the United States or upon the high seas. Examples include, but are not limited to: …(d) actions directly or indirectly causing modifications to the land, water, or air” (50 CFR 402.02).

As described above, the Corps requested ESA consultation through two separate BAs submitted to NMFS on October 22, 2013:

(1) U.S. Army Corps of Engineers Ongoing Operation and Maintenance of

Englebright Dam and Reservoir on the Yuba River (Corps 2013a).

(2) U.S. Army Corps of Engineers Authorized Operation and Maintenance of Existing Fish Passage Facilities at Daguerre Point Dam on the Lower Yuba River (Corps 2013b).

The proposed action, that is the subject of this consultation, is described in the U.S. Army Corps of Engineers’ Ongoing Operation and Maintenance of Daguerre Point Dam on the Yuba River BA (Corps 2013b). In the BA, the Corps limited its proposed action to discretionary activities.

The description of the proposed action provided below comes primarily from the BA.

The Corps has identified the following authorities as governing their descretion with respect to the proposed action (Corps 2013b):

(1) The California Debris Act (Ch 183, §1, 27 Stat. 507,

(2) The Rivers and Harbors Act of 1935, Public Law No. 409,

(3) Flood Control Act of 1970, Section 216,

(4) National Dam Inspection Act of 1972,

(5) Water Resources Development Act 1986, Section 906(b), Section 1106, and

Section 1135,

(6) Water Resources Development Act 1996, Section 206,

(7) National Dam Safety Program Act of 1996 (Public Law 92-367),

(8) Public Law…