A01.12__SOW_Supplement_NMFS_Sac16-8L_BO_ _Ltr_May_2106.pdf

Ms. Alicia Kirchner Chief, Planning Division Department of the Army United States Army Corps of Engineers Sacramento District 1325 J Street Sacramento, California 95814-2922

UNITED STATES DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

NATIONAL MARINE FISHERIES SERVICE

West Coast Region 650 Capitol Mall , Suite 5-100 Sacramento, California 95814-4700

MAY 1 8 2016 Refer to NMFS No: WCR-2016-4550

Re: Endangered Species Act Section 7(a)(2) Biological Opinion reinitiation for the Sacramento River Bank Protection Project at river mile 16.8L

Dear Ms. Kirchner:

Thank you for your letter of February 25, 2016, requesting reinitiation of consultation with NOAA's National Marine Fisheries Service (NMFS) pursuant to section 7 of the Endangered Species Act of 1973 (ESA) (16 U.S.C. 1531 et seq.) for the Sacramento River Bank Protection Project (SRBPP) on the Sacramento River near Isleton, California. The purpose of your request is to modify the Sacramento River mile 16.8L (SAC 16.8L) project, originally included in NFMS ' 2008 amended programmatic biological opinion (BO) for Phase II of the Sacramento River Bank Protection Project. This project has been modified to incorporate recommendations by the US Fish and Wildlife Service and to ensure compliance with the U.S. Army Corps of Engineers policy defining vegetation on levees. Enclosed is a new BO, which supersedes the former analysis of SAC 16.8L levee repair project. No other changes have been made to the original BO, which is still in effect.

Based on the best available scientific and commercial information, the enclosed BO concludes that the SAC 16.8 levee repair project is not likely to jeopardize the continued existence of the federally listed threatened Central Valley (CV) spring-run Chinook salmon evolutionarily significant unit (ESU) (Oncorhynchus tshawytscha), endangered Sacramento River winter-run Chinook salmon ESU (0. tshawytscha), threatened California CV steelhead distinct population segment (DPS) (0. mykiss), or the threatened Southern DPS (sDPS) of North American green sturgeon (Acipenser medirostris) and is not likely to destroy or adversely modify their designated critical habitats. For the above species, NMFS has included an incidental take statement with reasonable and prudent measures and non-discretionary terms and conditions that are necessary and appropriate to avoid, minimize, or monitor incidental take oflisted species associated with the project.

Please contact Taney Moore in the NMFS California Central Valley Area Office at 916-930- 3605, or at Tancy.Moore@noaa.gov, if you have any questions concerning this section 7 consultation, or if you require additional information.

Sincerely, ~ iam W. Stelle, Jr.

Regional Administrator

Enclosure

CC: CHRON File: ARN 151422-WCR2014-SA00133 Division- File copy

Mr. Michael Fong, Enviromnental Planning Section, U.S. Army Corps of Engineers, Sacramento District, 1325 J Street, Sacramento, California 95814

UNITED STATES DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

NATIONAL MARINE FISHERIES SERVICE

West Coast Region 650 Capitol Mall, Suite 5-100 Sacramento, California 95814-4700

Endangered Species Act (ESA) Section 7(a)(2) Biological Opinion Reinitiation

Sacramento River Bank Protection Project River Mile 16.8 NMFS Consultation Number: ARN 151422-WCR2014-SA00133

Action Agency: U.S. Army Corps of Engineers (Corps)

Af£ d S dNMFS' D ecte ;pec1es an etermmatlons:

Is Action Likely Is Action Likely Is Action Likely

ESA-Listed Species Status to Adversely To Jeopardize To Destroy or Affect Species the Species? Adversely or Critical Modify Critical Habitat?* Habitat?

CV spring-run Chinook salmonESU Threatened Yes No No ( Oncorhynchus tshawytscha)

Sacramento River winter-run Chinook salmon ESU Endangered Yes No No

(0. tshawytscha)

California CV steelhead DPS (0. mykiss) Threatened Yes No No

Southern DPS ofNorth American green sturgeon Threatened Yes No No (Acipenser medirostris)

Consultation Conducted By: National Marine Fisheries Service, West Coast Region

Issued By:

~ illiam W. Stelle, Jr.

Regional Administrator

Date: MAY 1 8 2016

1. INTRODUCTION

This Introduction section provides information relevant to the other sections of this document and is incorporated by reference into Sections 2 and 3 below.

1.1 Background

NOAA’s National Marine Fisheries Service (NMFS) prepared the biological opinion (BO) and incidental take statement portions of this document in accordance with section 7(b) of the Endangered Species Act (ESA) of 1973, as amended (16 USC 1531 et seq.), and implementing regulations at 50 CFR 402.

NMFS completed pre-dissemination review of this document using standards for utility, integrity, and objectivity in compliance with applicable guidelines issued under the Data Quality Act (section 515 of the Treasury and General Government Appropriations Act for Fiscal Year 2001, Public Law 106-554). The document will be available through NMFS’ Public Consultation Tracking System (pcts.nmfs.noaa.gov/pcts-web/homepage.pcts). A complete record of this consultation is on file at NMFS’ California Central Valley Area Office in Sacramento, California.

1.2 Consultation History

On November 2, 2007, NMFS received a formal consultation request from the U.S. Army Corps of Engineers (USACE) for Phase II of the Sacramento River Bank Protection Project (SRBPP).

In response, NMFS issued a Programmatic BO for this project on July 02, 2008.

On May 7, 2007, NMFS received a formal consultation request from the USACE for 13 levee erosion sites on the Sacramento River. The request included the draft Environmental Assessment, a Biological Assessment, and a SAM analysis for all sites. On July 30, 2008, NMFS issued an addendum to the programmatic BO for Phase II of the SRBPP to include these 13 projects.

On February 25, 2016, the USACE sent a request for reinitiation of consultation for the amended programmatic BO for Phase II of SRBPP. The request was made as a result of changes to the original project description of one of the 13 levee repair sites (Sacramento River Mile 16.8).

NMFS initiated consultation on March 23, 2016. A complete administrative record is on file at the NMFS Central Valley Area Office in Sacramento, California.

1.3 Proposed Action

“Action” means all activities or programs of any kind authorized, funded, or carried out, in whole or in part, by Federal agencies (50 CFR 402.02).

On July 30, 2008, the National Marine Fisheries Service (NMFS) provided the USACE with a BO for the construction of 13 levee repair projects, which concluded that the 13 levee erosion repairs, including SAC 16.8L, was not likely to jeopardize the following species and their critical habitat: Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha), Central Valley spring-run Chinook salmon (O. tshawytscha), Central Valley steelhead (O. mykiss), and sDPS green sturgeon (Acipenser medirostris). The USACE proposes to make changes to the Sacramento River Mile 16.8 levee repair project that may impact these species, and thus has requested reinititation of consultation with NMFS. The purpose of this BO is to analyze the potential effects of the modified project on endangered species and their designated critical habitat within the project’s area of effect (action area). Updates were made to the design of the proposed levee erosion repair at SAC 16.8L to ensure compliance USACE’s Engineering Technical Letter 1110-2-583 (ETL), which limits the type and amount of vegetation on levees.

The project will also be modified to incorporate additional design considerations recommended by US Fish and Wildlife Service (USFWS). Recent guidance from USFWS suggests that ideal spawning habitat for the Delta smelt should maximize shallow water habitat and minimize Instream Woody Material (IWM) and aquatic vegetation.

In 2016, the USACE and the Central Valley Flood Protection Board (CVFPB) propose to implement bank protection measures at Sacramento River RM 16.8L. The proposed repair site is located just downriver of the City of Isleton in Sacramento County, California and has been identified as one of the most critical erosion sites in the SRBPP project area due to the poor past performance of the levee, immediate proximity of the erosion to HWY 160 (a significant transportation route), and close proximity to the City of Isleton (a large population center). The site length for RM 16.8L is 690 linear feet. Site preparation activities at RM 16.8L, including clearing, grubbing, and site shaping will occur on the landside with access from the levee road.

In-water construction will occur between August 1 and November 30. The proposed designs include:

(1) Placement of 9,850 cubic yards of quarry stone;

(2) Placement of 3,900 cubic yards of soil-filled quarry stone;

(3) Placement of 680 cubic yards of sand;

(4) Slope of 2:1 and 6:1 outside of wetland bench area;

(5) Slope of 10:1 within the wetland bench area;

USACE conducted a risk based investigation into the potential to protect in place existing vegetation that does not pose a threat to levee integrity. Due to the highly degraded condition of the existing levee, limited real estate, and near vertical eroded bank of much of the waterside levee slopes, only 6 existing trees will be protected in place. The remainder will be removed during construction as they either increase risk of levee failure due to seepage or erosion or will be physically buried by the new project. The removed trees include 3 interior live oaks, 1 coast oak, 2 willows, 2 sycamores, 1 fruit tree, and 2 dead trees. Some isolated trimming may also be necessary due to safety concerns during construction. The USACE plans to mitigate for these impacts by planting a mixed palette of willow pole cuttings between the levee prism toe and riparian bench using the following species: Goodding's black willow (Salix gooddingii), red willow (Salix laevigata), yellow willow (Salix lasiandra), and arroyo willow (Salix lasiolepis).

The willow cuttings would be installed in rows of 3 at 3 feet apart perpendicular to the levee with a 10 foot spacing between the rows, and would be irrigated and maintained for a period of three years to aid survival. The cuttings would be installed to a depth of 4 feet with 2 feet extending above the surface using a 'stinger' hole drilling attachment or by hand. Similar levee planting projects by the USACE and the California Department of Water Resources (DWR) within the immediate river area have produced survival levels of 60% to 80% using the previously mentioned spacing patterns. Because the willows will be planted in the ETL 1110-2-583’s vegetation free zone, the USACE will apply for a variance in order to get permission to complete the plantings as described above. The USACE also plans to mitigate for the temporal impacts of the SAC 16.8L repair project by purchasing credits from an approved mitigation bank at a 1:1 ratio. The purchase of credits at a mitigation bank would occur concurrently with implementation of the proposed levee erosion repair at SAC 16.8L.

1.4 Action Area

“Action area” means all areas to be affected directly or indirectly by the Federal action and not merely the immediate area involved in the action (50 CFR 402.02). The action area is not the same as the project boundary area because the action area must delineate all areas where federally-listed populations of salmon, steelhead, and green sturgeon may be affected by the implementation of the proposed action. The action area for the proposed action analyzed in amended programmatic BO for Phase II of the SRBPP extends from Sacramento RM 177.8 downstream to Sacramento RM 0, and includes Feather RM 28.5, American RM 2.8, Cache Slough RM 21.8, and Steamboat Slough RM 16.6, downstream to the Sacramento River. This represents the full geographic extent of the 13 sites described in the amended programmatic BO for Phase II of the SRBPP and the effects that are associated with these projects. The action area for this repair at SAC 16.8L is within this broader action area.

The proposed action is located at Sacramento RM 16.8L, near the City of Isleton in Sacramento County, California. For projects with in-water construction activities, such as installation of riprap, the downstream extent of the action area is defined by the distance of potential turbidity and sediment deposition. For the proposed project, turbidity impacts are expected to occur up to 100 feet from the shoreline, and 1,000 feet downstream of any in-water construction activities.

The levee repair itself will be approximately 700 feet in length.

2. ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND

INCIDENTAL TAKE STATEMENT

The ESA establishes a national program for conserving threatened and endangered species of fish, wildlife, plants, and the habitat upon which they depend. As required by section 7(a)(2) of the ESA, Federal agencies must ensure that their actions are not likely to jeopardize the continued existence of endangered or threatened species, or adversely modify or destroy their designated critical habitat. Per the requirements of the ESA, Federal action agencies consult with NMFS and section 7(b)(3) requires that, at the conclusion of consultation, NMFS provides an opinion stating how the agency’s actions would affect listed species and their critical habitat.

If incidental take is expected, section 7(b)(4) requires NMFS to provide an incidental take statement (ITS) that specifies the impact of any incidental taking and includes non-discretionary reasonable and prudent measures and terms and conditions to minimize such impacts.

2.1 Analytical Approach

This BO includes both a jeopardy analysis and an adverse modification analysis.

The jeopardy analysis relies upon the regulatory definition of “to jeopardize the continued existence of a listed species,” which is “to engage in an action that would be expected, directly or indirectly, to reduce appreciably the likelihood of both the survival and recovery of a listed species in the wild by reducing the reproduction, numbers, or distribution of that species” (50 CFR 402.02). Therefore, the jeopardy analysis considers both survival and recovery of the species.

The adverse modification analysis considers the impacts of the Federal action on the conservation value of designated critical habitat. This BO does not rely on the regulatory definition of "destruction or adverse modification" of critical habitat at 50 CFR 402.02. Instead, we have relied upon the statutory provisions of the ESA to complete the following analysis with respect to critical habitat.1

We use the following approach to determine whether a proposed action is likely to jeopardize listed species or destroy or adversely modify critical habitat:

1. Identify the rangewide status of the species and critical habitat likely to be adversely affected by the proposed action.

2. Describe the environmental baseline in the action area.

3. Analyze the effects of the proposed action on both species and their habitat using an

“exposure-response-risk” approach.

4. Describe any cumulative effects in the action area.

5. Integrate and synthesize the above factors to assess the risk that the proposed action poses to species and critical habitat.

6. Reach jeopardy and adverse modification conclusions.

7. If necessary, define a reasonable and prudent alternative to the proposed action.

2.1.1 Use of Analytical Surrogates

The effects of the SAC 16.8L levee repair are primarily analyzed using Standard Assessment Methodology (SAM). The USACE provided the background data, assumptions, analyses, and assessment of habitat compensation requirements for the federally protected fish species relevant to this consultation.

The SAM was designed to address a number of limitations associated with previous habitat assessment approaches and provide a tool to systematically evaluate the impacts and compensation requirements of bank protection projects based on the needs of listed fish species.

It is a computational modeling and tracking tool that evaluates bank protection alternatives by taking into account several key factors affecting threatened and endangered fish species. By

1 Memorandum from William T. Hogarth to Regional Administrators, Office of Protected Resources, NMFS (Application of the “Destruction or Adverse Modification” Standard Under Section 7(a)(2) of the Endangered Species Act) (November 7, 2005).

identifying and then quantifying the response of focal species to changing habitat conditions over time, project managers, biologists and design engineers can make changes to project design to avoid, minimize, or provide on- or off-site compensatory mitigation for impacts to habitat parameters that influence the growth and survival of target fish species by life stage and season.

The model is used to assess species responses as a result of changes to habitat conditions, either by direct quantification of bank stabilization design parameters (e.g., bank slope, substrate). The preferred hierarchy of mitigation in all cases is avoid, minimize, compensate onsite and compensate off-site. In the case of most levee projects, most or all of these mitigation strategies are applied due to their large size, challenges associated with completely avoiding and minimizing impacts to species and habitat, temporal delays in habitat function of onsite compensatory mitigation, and limitations associated with being able to provide full compensation at project sites, which warrants the need for some form of off-site compensation.

In 2003, the USACE established a program to carry out “a process to review, improve, and validate analytical tools and models for USACE Civil Works business programs”. Reviews are conducted to ensure that planning models used by the USACE are technically and theoretically sound, computationally accurate, and in compliance with the USACE planning policy. As such, all existing and new planning models developed by the USACE are required to be certified through the appropriate Planning Center of Expertise and Headquarters in accordance with USACE rules and procedures.

The assumptions, model variables, and modeling approaches used in the SAM have been developed to be adapted and validated through knowledge gained from monitoring and experimentation within the SRBPP while retaining the original overall assessment method and framework. The first update to the SAM included the addition of sDPS green sturgeon as well as a number of modifications to modeled-species responses based upon updated literature reviews and recent monitoring efforts at completed bank protection sites (Stillwater Sciences 2009;

USACE 2009).

In late 2010, the certification process for the SAM was initiated by the USACE, Sacramento District in coordination with the Ecosystem Planning Center of Expertise. The process entailed charging a panel of six experts to review the SAM, along with the SAM (version 3.0). The Review Panel was composed of a plan formulation expert, fisheries biologist, aquatic ecologist, geomorphologist/geologist, population biologist/modeling expert, and software programmer.

A major advantage of the SAM is that it integrates species life history and seasonal flow-related variability in habitat quality and availability to generate species responses to project actions over time. The SAM systematically evaluates the response of each life stage to habitat features affected by bank protection projects.

The SAM quantifies habitat values in terms of a weighted species response index (WRI) that is calculated by combining habitat quality (i.e., fish response indices) with quantity (i.e., bank length or wetted area) for each season, target year, and relevant species/life stage. The fish response indices are derived from hypothesized relationships between key habitat attributes (described below) and the species and life stage responses. Species response indices vary from 0 to 1, with 0 representing unsuitable conditions and 1 representing optimal conditions for survival, growth, and/or reproduction. For a given site and scenario (i.e., with or without project), the SAM uses these relationships to determine the response of individual species and life stages to the measured or predicted values of each habitat attribute for each season and target year, and then multiplies these values together to generate an overall species response index.

This index is then multiplied by the linear feet or area of shoreline to which it applies to generate a weighted species response index expressed in feet or square feet. The species WRI provides a common metric that can be used to quantify habitat values over time, compare project conditions to existing conditions, and evaluate the effectiveness of onsite and off-site compensation actions.

The WRI represent an index of a species growth and survival based on a 30-day exposure to post project conditions over the life of the project. As such, negative SAM values can be used as a surrogate to quantify harm to a target fish species by life stage and season. Also, although SAM values represent an index of harm to a species, since the values are expressed as “weighted bankline feet” or “weighted area”, these values can be used to help quantify compensatory conservation actions such as habitat restoration, and are used for that purpose in this BO.

The Effects Analysis section of this BO analyzes the Sacramento River 16.8L levee repair project.

2.2 Rangewide Status of the Species and Critical Habitat

This BO examines the status of each species that would be adversely affected by the proposed action. The status is determined by the level of extinction risk that the listed species face, based on parameters considered in documents such as recovery plans, status reviews, and listing decisions. This informs the description of the species’ likelihood of both survival and recovery.

The species status section also helps to inform the description of the species’ current “reproduction, numbers, or distribution” as described in 50 CFR 402.02. The BO also examines the condition of critical habitat throughout the designated area, evaluates the conservation value of the various watersheds and coastal and marine environments that make up the designated area, and discusses the current function of the essential physical and biological features (PBFs) that help to form that conservation value. One factor affecting the rangewide status of CV spring-run Chinook salmon, CCV steelhead, and the sDPS green sturgeon, and aquatic habitat at large is climate change.

The descriptions of the status of species and conditions of the designated critical habitats in this BO are a synopsis of the detailed information available on NMFS’ West Coast Regional website.

The following federally listed species ESUs or DPSs and designated critical habitat occur in the action area and may be affected by the proposed action.

Sacramento River winter-run Chinook salmon ESU (Oncorhynchus tshawytscha) Listed as endangered (70 FR 37160, June 28, 2005)

Sacramento River winter-run Chinook salmon designated critical habitat (58 FR 33212, June 16, 1993) http://www.westcoast.fisheries.noaa.gov/protected_species/salmon_steelhead/sal mon_and_steelhead_listings/chinook/sacramento_river_winter_run/sacramento_ri ver_winter_run_chinook.html http://www.westcoast.fisheries.noaa.gov/protected_species/salmon_steelhead/salmon_and_steelhead_listings/chinook/sacramento_river_winter_run/sacramento_river_winter_run_chinook.html http://www.westcoast.fisheries.noaa.gov/protected_species/salmon_steelhead/salmon_and_steelhead_listings/chinook/sacramento_river_winter_run/sacramento_river_winter_run_chinook.html http://www.westcoast.fisheries.noaa.gov/protected_species/salmon_steelhead/salmon_and_steelhead_listings/chinook/sacramento_river_winter_run/sacramento_river_winter_run_chinook.html

CV spring-run Chinook salmon ESU (O. tshawytscha)

Listed as threatened (70 FR 37160, June 28, 2005)

CV spring-run Chinook salmon designated critical habitat (70 FR 52488, September 2, 2005) mon_and_steelhead_listings/chinook/central_valley_spring_run/central_valley_sp ring_run_chinook.html

CCV steelhead DPS (O. mykiss)

Listed as threatened (71 FR 834, January 5, 2006)

CCV steelhead designated critical habitat (70 FR 52488, September 2, 2005) mon_and_steelhead_listings/steelhead/california_central_valley/california_central _valley_steelhead.html

Southern DPS of North American green sturgeon (Acipenser medirostris)

Listed as threatened (71 FR 17757, April 7, 2006)

Southern DPS of North American green sturgeon designated critical habitat (74 FR 52300, October 9, 2009) http://www.westcoast.fisheries.noaa.gov/protected_species/green_sturgeon/green _sturgeon_pg.html

2.2.1 Sacramento River Winter-run Chinook Salmon

Summary of Sacramento River Winter-run Chinook Salmon ESU Viability

There are several criteria (only one is required) that would qualify the winter-run ESU at moderate risk of extinction, and since there is still only one population that spawns downstream of Keswick Dam, that population would be at high risk of extinction in the long-term according the criteria in Lindley et al. (2007). Recent trends in those criteria are: (1) continued low abundance; (2) a negative growth rate over 6 years (2006–2012), which is two complete generations; (3) a significant rate of decline since 2006; and (4) increased risk of catastrophe from oil spills, wildfires, or extended drought (climate change). The most recent 5-year status review (NMFS 2011a) on winter-run concluded that the ESU had increased to a high risk of extinction. In summary, the most recent biological information suggests that the extinction risk for the winter-run ESU has increased from moderate risk to high risk of extinction since 2005, and that several listing factors have contributed to the recent decline, including drought and poor ocean conditions (NMFS 2011a).

http://www.westcoast.fisheries.noaa.gov/protected_species/salmon_steelhead/salmon_and_steelhead_listings/chinook/central_valley_spring_run/central_valley_spring_run_chinook.html http://www.westcoast.fisheries.noaa.gov/protected_species/salmon_steelhead/salmon_and_steelhead_listings/chinook/central_valley_spring_run/central_valley_spring_run_chinook.html http://www.westcoast.fisheries.noaa.gov/protected_species/salmon_steelhead/salmon_and_steelhead_listings/chinook/central_valley_spring_run/central_valley_spring_run_chinook.html http://www.westcoast.fisheries.noaa.gov/protected_species/green_sturgeon/green_sturgeon_pg.html http://www.westcoast.fisheries.noaa.gov/protected_species/green_sturgeon/green_sturgeon_pg.html

Critical Habitat: Physical and Biological Features for Sacramento River Winter-run Chinook Salmon

NMFS designated critical habitat for winter-run Chinook salmon on June 16, 1993 (58 FR 33212). Critical habitat was delineated as the Sacramento River from Keswick Dam at river mile (RM) 302 to Chipps Island, RM 0, at the westward margin of the Sacramento-San Joaquin Delta (Delta), including Kimball Island, Winter Island, and Brown’s Island; all waters from Chipps Island westward to the Carquinez Bridge, including Honker Bay, Grizzly Bay, Suisun Bay, and the Carquinez Strait; all waters of San Pablo Bay westward of the Carquinez Bridge, and all waters of San Francisco Bay north of the San Francisco-Oakland Bay Bridge from San Pablo Bay to the Golden Gate Bridge. In the Sacramento River, critical habitat includes the river water, river bottom, and the adjacent riparian zone.

Critical habitat for winter-run is defined as specific areas (listed below) that contain the PBFs considered essential to the conservation of the species. This designation includes the river water, river bottom (including those areas and associated gravel used by winter-run as spawning substrate), and adjacent riparian zone used by fry and juveniles for rearing (June 16, 1993, 58 FR 33212). NMFS limits “adjacent riparian zones” to only those areas above a stream bank that provide cover and shade to the nearshore aquatic areas. Although the bypasses (e.g., Yolo, Sutter, and Colusa) are not currently designated critical habitat for winter-run, NMFS recognizes that they may be utilized when inundated with Sacramento River flood flows and are important rearing habitats for juvenile winter-run. Also, juvenile winter-run may use tributaries of the Sacramento River for non-natal rearing. Critical habitat also includes the estuarine water column and essential foraging habitat and food resources used by winter-run as part of their juvenile outmigration or adult spawning migration.

The following is the status of the PBFs that are considered to be essential for the conservation of winter-run (June 16, 1993, 58 FR 33212):

1. Access from the Pacific Ocean to Appropriate Spawning Areas

Adult migration corridors should provide satisfactory water quality, water quantity, water temperature, water velocity, cover, shelter and safe passage conditions in order for adults to reach spawning areas. Adult winter-run generally migrate to spawning areas during the winter and spring. At that time of year, the migration route is accessible to the appropriate spawning grounds on the upper 60 miles of the Sacramento River, however much of this migratory habitat is degraded and they must pass through a fish ladder at the Anderson-Cottonwood Irrigation Dam (ACID). In addition, the many flood bypasses are known to strand adults in agricultural drains due to inadequate screening (Vincik and Johnson 2013). Since the primary migration corridors are essential for connecting early rearing habitat with the ocean, even the degraded reaches are considered to have a high intrinsic conservation value to the species.

2. The Availability of Clean Gravel for Spawning Substrate

Suitable spawning habitat for winter-run exists in the upper 60 miles of the Sacramento River between Keswick Dam and Red Bluff Diversion Dam (RBDD). However, the majority of spawning habitat currently being used occurs in the first 10 miles downstream of Keswick Dam.

The available spawning habit is completely outside the historical range utilized by winter-run upstream of Keswick Dam. Because Shasta and Keswick dams block gravel recruitment, the U.S. Bureau of Reclamation (Reclamation) annually injects spawning gravel into various areas of the upper Sacramento River. With the supplemented gravel injections, the upper Sacramento River reach continues to support a small naturally-spawning winter-run Chinook salmon population. Even in degraded reaches, spawning habitat has a high conservation value as its function directly affects the spawning success and reproductive potential of listed salmonids.

3. Adequate River Flows for Successful Spawning, Incubation of Eggs, Fry Development and Emergence, and Downstream Transport of Juveniles

An April 5, 1960, Memorandum of Agreement between Reclamation and the California Department of Fish and Wildlife (CDFW) originally established flow objectives in the Sacramento River for the protection and preservation of fish and wildlife resources. In addition, Reclamation complies with the 1990 flow releases required in State Water Resource Control Board (SWRCB) Water Rights Order (WRO) 90-05 for the protection of Chinook salmon. This order includes a minimum flow release of 3,250 cubic feet per second (cfs) from Keswick Dam downstream to RBDD from September through February during all water year types, except critically dry.

4. Water Temperatures at 5.8–14.1°C (42.5–57.5°F) for Successful Spawning, Egg Incubation, and Fry Development

Summer flow releases from Shasta Reservoir for agriculture and other consumptive uses drive operations of Shasta and Keswick dam water releases during the period of winter-run migration, spawning, egg incubation, fry development, and emergence. This pattern, the opposite of the pre-dam hydrograph, benefits winter-run by providing cold water for miles downstream during the hottest part of the year. The extent to which winter-run habitat needs are met depends on Reclamation’s other operational commitments, including those to water contractors, Delta requirements pursuant to State Water Rights Decision 1641 (D-1641), and Shasta Reservoir end of September storage levels required in the NMFS 2009 BO (NMFS 2009) on the long-term operations of the CV Project and State Water Project (CVP/SWP). WRO 90-05 and 91-1 require Reclamation to operate Shasta, Keswick, and Spring Creek Powerhouse to meet a daily average water temperature of 13.3°C (56°F) at RBDD. They also provide the exception that the water temperature compliance point (TCP) may be modified when the objective cannot be met at RBDD. Based on these requirements, Reclamation models monthly forecasts and determines how far downstream 13.3°C (56°F) can be maintained throughout the winter-run spawning, egg incubation, and fry development stages.

In every year since WRO 90-05 and 91-1 were issued, operation plans have included modifying the TCP to make the best use of the cold water available based on water temperature modeling and current spawning distribution. Once a TCP has been identified and established in May, it generally does not change, and therefore, water temperatures are typically adequate through the summer for successful winter-run egg incubation and fry development for those redds constructed upstream of the TCP (except for in some critically dry and drought years). However, by continually moving the TCP upstream, the value of that habitat is degraded by reducing the spawning area in size and imprinting upon the next generation to return further upstream.

5. Habitat and Adequate Prey Free of Contaminants

Water quality conditions have improved since the 1980s due to stricter standards and Environmental Protection Agency (EPA) Superfund site cleanups (see Iron Mountain Mine remediation under Factors). No longer are there fish kills in the Sacramento River caused by the heavy metals (e.g., lead, zinc and copper) found in the Spring Creek runoff. However, legacy contaminants such as mercury (and methyl mercury), polychlorinated biphenyls (PCB), heavy metals and persistent organochlorine pesticides continue to be found in watersheds throughout the CV. In 2010, the EPA, listed the Sacramento River as impaired under the Clean Water Act, section 303(d), due to high levels of pesticides, herbicides, and heavy metals (http://www.waterboards.ca.gov/water_issues/programs/tmdl/2010state_ir_reports/category5_rep ort.shtml). Although most of these contaminants are at low concentrations in the food chain, they continue to work their way into the base of the food web, particularly when sediments are disturbed and previously entombed compounds are released into the water column.

Adequate prey for juvenile salmon to survive and grow consists of abundant aquatic and terrestrial invertebrates that make up the majority of their diet before entering the ocean.

Exposure to these contaminated food sources such as invertebrates may create delayed sublethal effects that reduce fitness and survival (Laetz et al. 2009). Contaminants are typically associated with areas of urban development, agriculture, or other anthropogenic activities (e.g., mercury contamination as a result of gold mining or processing). Areas with low human impacts frequently have low contaminant burdens, and therefore lower levels of potentially harmful toxicants in the aquatic system. Freshwater rearing habitat has a high intrinsic conservation value even if the current conditions are significantly degraded from their natural state.

6. Riparian and Floodplain Habitat that Provides for Successful Juvenile Development and Survival

The channelized, leveed, and riprapped river reaches and sloughs that are common in the Sacramento River system typically have low habitat complexity, low abundance of food organisms, and offer little protection from predators. Juvenile life stages of salmonids are dependent on the natural functioning of this habitat for successful survival and recruitment.

Ideal habitat contains natural cover, such as riparian canopy structure, submerged and overhanging large woody material (LWM), aquatic vegetation, large rocks and boulders, side channels, and undercut banks which augment juvenile and adult mobility, survival, and food supply. Riparian recruitment is prevented from becoming established due to the reversed hydrology (i.e., high summer time flows and low winter flows prevent tree seedlings from http://www.waterboards.ca.gov/water_issues/programs/tmdl/2010state_ir_reports/category5_report.shtml http://www.waterboards.ca.gov/water_issues/programs/tmdl/2010state_ir_reports/category5_report.shtml establishing). However, there are some complex, productive habitats within historical floodplains [e.g., Sacramento River reaches with setback levees (i.e., primarily located upstream of the City of Colusa)] and flood bypasses (i.e., fish in Yolo and Sutter bypasses experience rapid growth and higher survival due to abundant food resources) seasonally available that remain in the system. Nevertheless, the current condition of degraded riparian habitat along the mainstem Sacramento River restricts juvenile growth and survival (Michel 2010; Michel et al.

2012).

7. Access Downstream so that Juveniles can Migrate from the Spawning Grounds to San Francisco Bay and the Pacific Ocean

Freshwater emigration corridors should be free of migratory obstructions, with water quantity and quality conditions that enhance migratory movements. Migratory corridors are downstream of the Keswick Dam spawning areas and include the mainstem of the Sacramento River to the Delta, as well as non-natal rearing areas near the confluence of some tributary streams.

Migratory habitat condition is strongly affected by the presence of barriers, which can include dams (i.e., hydropower, flood control, and irrigation flashboard dams), unscreened or poorly screened diversions, degraded water quality, or behavioral impediments to migration. For successful survival and recruitment of salmonids, freshwater migration corridors must function sufficiently to provide adequate passage. Unscreened diversions that entrain juvenile salmonids are prevalent throughout the mainstem Sacramento River and in the Delta. Predators such as striped bass (Morone saxatilis) and Sacramento pikeminnow (Ptychocheilus grandis) tend to concentrate immediately downstream of diversions, resulting in increased mortality of juvenile Chinook salmon.

Water pumping at the CVP/SWP export facilities in the South Delta at times causes the flow in the river to move back upstream (reverse flow), further disrupting the emigration of juvenile winter-run by attracting and diverting them to the interior Delta, where they are exposed to increased rates of predation, other stressors in the Delta, and entrainment at pumping stations.

NMFS’ BO on the long-term operations of the CVP/SWP (NMFS 2009) sets limits to the strength of reverse flows in the Old and Middle Rivers, thereby keeping salmon away from areas of highest mortality. Regardless of the condition, the remaining estuarine areas are of high conservation value because they provide factors which function as rearing habitat and as an area of transition to the ocean environment.

2.2.2 Central Valley Spring-run Chinook salmon

Summary of CV Spring-run Chinook salmon DPS Viability

Since the independent populations in Butte, Deer and Mill creeks are the best trend indicators for ESU viability, we can evaluate risk of extinction based on Viable Salmonid Population (VSP) parameters in these watersheds. Lindley et al. (2007) indicated that the spring-run Chinook salmon populations in the Central Valley had a low risk of extinction in Butte and Deer creeks, according to their population viability analysis (PVA) model and other population viability criteria (i.e., population size, population decline, catastrophic events, and hatchery influence, which correlate with VSP parameters abundance, productivity, spatial structure, and diversity).

The Mill Creek population of spring-run Chinook salmon was at moderate extinction risk according to the PVA model, but appeared to satisfy the other viability criteria for low-risk status. However, the CV spring-run Chinook salmon ESU failed to meet the “representation and redundancy rule” since there are only demonstrably viable populations in one diversity group (northern Sierra Nevada) out of the three diversity groups that historically contained them, or out of the four diversity groups as described in the NMFS Central Valley Salmon and Steelhead Recovery Plan. Over the long term, these three remaining populations are considered to be vulnerable to catastrophic events, such as volcanic eruptions from Mount Lassen or large forest fires due to the close proximity of their headwaters to each other. Drought is also considered to pose a significant threat to the viability of the spring-run Chinook salmon populations in these three watersheds due to their close proximity to each other. One large event could eliminate all three populations.

In the 2011 status review of the CV spring-run Chinook salmon ESU, the authors concluded that the ESU status had likely deteriorated on balance since the 2005 status review and the Lindley et

al. (2007) assessment, with two of the three extant independent populations (Deer and Mill creeks) of spring-run Chinook salmon slipping from low or moderate extinction risk to high extinction risk. Additionally, Butte Creek remained at low risk, although it was on the verge of moving towards high risk, due to the rate of population decline. In contrast, spring-run Chinook salmon in Battle and Clear creeks had increased in abundance since 1998, reaching levels of abundance that place these populations at moderate extinction risk. Both of these populations have likely increased at least in part due to extensive habitat restoration. The Southwest Fisheries Science Center concluded in their viability report (Williams et al. 2011) that the status of CV spring-run Chinook salmon ESU has probably deteriorated since the 2005 status review and that its extinction risk has increased. The degradation in status of the three formerly low- or moderate-risk independent populations is cause for concern.

Critical Habitat: Physical and Biological Features for CV Spring-Run Chinook Salmon

Critical habitat was designated for CV spring-run Chinook salmon on September 2, 2005 (70 FR 52488). Critical habitat for CV spring-run Chinook salmon includes stream reaches of the Feather, Yuba and American rivers, Big Chico, Butte, Deer, Mill, Battle, Antelope, and Clear creeks, the Sacramento River, as well as portions of the northern Delta. Critical habitat includes the stream channels in the designated stream reaches and the lateral extent as defined by the ordinary high-water line (OHWL). In areas where the OHWL has not been defined, the lateral extent will be defined by the bankfull elevation (defined as the level at which water begins to leave the channel and move into the floodplain; it is reached at a discharge that generally has a recurrence interval of one to two years on the annual flood series) (Bain and Stevenson 1999; 70 FR 52488). Critical habitat for CV spring-run Chinook salmon is defined as specific areas that contain the PBFs essential to the conservation of the species. Following are the inland habitat types used as PBFs for CV spring-run Chinook salmon.

1. Spawning Habitat

Freshwater spawning sites are those with water quantity and quality conditions and substrate supporting spawning, incubation, and larval development. Most spawning habitat in the CV for Chinook salmon is located in areas directly downstream of dams containing suitable environmental conditions for spawning and incubation. Spawning habitat for CV spring-run Chinook salmon occurs on the mainstem Sacramento River between RBDD and Keswick Dam and in tributaries such as Mill, Deer, and Butte creeks; as well as the Feather and Yuba rivers, Big Chico, Battle, Antelope, and Clear creeks. However, little spawning activity has been recorded in recent years on the Sacramento River mainstem for spring-run Chinook salmon.

Even in degraded reaches, spawning habitat has a high conservation value as its function directly affects the spawning success and reproductive potential of listed salmonids.

2. Freshwater Rearing Habitat

Freshwater rearing sites are those with water quantity and floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and mobility; water quality and forage supporting juvenile salmonid development; and natural cover such as shade, submerged and overhanging LWM, log jams and beaver dams, aquatic vegetation, large rocks and boulders, side channels, and undercut banks. Both spawning areas and migratory corridors comprise rearing habitat for juveniles, which feed and grow before and during their outmigration. Non-natal, intermittent tributaries also may be used for juvenile rearing. Rearing habitat condition is strongly affected by habitat complexity, food supply, and the presence of predators of juvenile salmonids. Some complex, productive habitats with floodplains remain in the system (e.g., the lower Cosumnes River, Sacramento River reaches with setback levees [i.e., primarily located upstream of the City of Colusa]) and flood bypasses (i.e., Yolo and Sutter bypasses). However, the channelized, leveed, and riprapped river reaches and sloughs that are common in the Sacramento-San Joaquin system typically have low habitat complexity, low abundance of food organisms, and offer little protection from piscivorous fish and birds. Freshwater rearing habitat also has a high intrinsic conservation value even if the current conditions are significantly degraded from their natural state. Juvenile life stages of salmonids are dependent on the function of this habitat for successful survival and recruitment.

3. Freshwater Migration Corridors

Ideal freshwater migration corridors are free of migratory obstructions, with water quantity and quality conditions that enhance migratory movements. They contain natural cover such as riparian canopy structure, submerged and overhanging large woody objects, aquatic vegetation, large rocksand boulders, side channels, and undercut banks which augment juvenile and adult mobility, survival, and food supply. Migratory corridors are downstream of the spawning areas and include the lower mainstems of the Sacramento and San Joaquin rivers and the Delta. These corridors allow the upstream passage of adults and the downstream emigration of juveniles.

Migratory habitat condition is strongly affected by the presence of barriers, which can include dams (i.e., hydropower, flood control, and irrigation flashboard dams), unscreened or poorly screened diversions, degraded water quality, or behavioral impediments to migration. For successful survival and recruitment of salmonids, freshwater migration corridors must function sufficiently to provide adequate passage. For adults, upstream passage through the Delta and much of the Sacramento River is not a problem, yet a number of challenges exist on many tributary streams. For juveniles, unscreened or inadequately screened water diversions throughout their migration corridors and a scarcity of complex in-river cover have degraded this PBF. However, since the primary migration corridors are used by numerous populations and are essential for connecting early rearing habitat with the ocean, even the degraded reaches are considered to have a high intrinsic conservation value to the species.

4. Estuarine Areas

Estuarine areas free of migratory obstructions with water quality, water quantity, and salinity conditions supporting juvenile and adult physiological transitions between fresh and salt water are included as a PBF. Natural cover such as submerged and overhanging LWM, aquatic vegetation, and side channels are suitable for juvenile and adult foraging.

The remaining estuarine habitat for these species is severely degraded by altered hydrologic regimes, poor water quality, reductions in habitat complexity, and competition for food and space with exotic species. Regardless of the condition, the remaining estuarine areas are of high conservation value because they provide factors which function to provide predator avoidance, as rearing habitat and as an area of transition to the ocean environment.

2.2.3 California Central Valley steelhead

Summary of CCV Steelhead DPS Viability

All indications are that natural CCV steelhead have continued to decrease in abundance over the past 25 years (Good et al. 2005; NMFS 2011a). The long-term trend remains negative.

Hatchery production and returns are dominant over natural fish. Continued decline in the ratio between naturally produced juvenile steelhead to hatchery juvenile steelhead in fish monitoring efforts indicates that the wild population abundance is declining. Hatchery releases (100 percent adipose fin clipped fish since 1998) have remained relatively constant over the past decade, yet the proportion of adipose fin-clipped hatchery smolts to unclipped naturally produced smolts has steadily increased over the past several years.

Although there have been recent restoration efforts in the San Joaquin River tributaries, CCV steelhead populations in the San Joaquin Basin continue to show a decline, an overall low abundance, and fluctuating return rates. Lindley et al. (2007) developed viability criteria for CV salmonids. Using data through 2005, Lindley et al. (2007) found that data were insufficient to determine the status of any of the naturally-spawning populations of CCV steelhead, except for those spawning in rivers adjacent to hatcheries, which were likely to be at high risk of extinction due to extensive spawning of hatchery-origin fish in natural areas.

The widespread distribution of wild steelhead in the CV provides the spatial distribution necessary for the DPS to survive and avoid localized catastrophes.