ENV Attachment 2 for reference.pdf

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

UNITED STATES DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administ ration

NATIONAL MARI NE FISHERIES SERVICE

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

'~N 3 201'i Refer to NMFS No: WCR-2016-4548

Re: Endangered Species Act Section 7(a)(2) Biological Opinion, and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response for the Sacramento and Stockton Deep Water Ship Channels Maintenance Dredging and Bank Protection Project

Dear Ms. Kirchner:

Thank you for your letter of July 17, 2014, requesting reinitiation of fonnal 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 proposed Sacramento and Stockton Deep Water Ship Channels Maintenance Dredging and Bank Protection Project (project) in Sacramento, Solano, Contra Costa, Yolo, and San Joaquin Counties, California. The U.S. Army Corps of Engineers (Corps) has determined that the project may adversely affect the endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha), threatened Central Valley spring-run Chinook salmon (0. tshawytscha), threatened California Central Valley steelhead (0. mykiss), threatened Southern distinct population segment of the North American green sturgeon (Acipenser medirostris ), and their respective designated critical habitats. Your July 17, 2014, request for reinitiation of formal consultation was received in our office on July 18, 2014. Formal consultation was reinitiated on April 6, 2015.

This biological opinion is based on information provided in the July 2014 Biological Assessment (BA), information supplemental to the BA provided subsequently through e-mail correspondence, and discussions held at meetings and through telephone conversations between representatives of NMFS and the Corps. A complete administrative record of this consultation is on file at the NMFS California Central Valley Office located in Sacramento, California.

Based on the best available scientific and commercial information, this biological opinion concludes that the Sacramento and Stockton Deep Water Ship Channels Maintenance Dredging and Bank Protection project, as proposed by the Corps, is not likely to jeopardize the continued existence of the listed species listed above, nor likely to adversely modify any of their respective designated critical habitats. 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 associated with the proposed project.

This letter also transmits NMFS' Essential Fish Habitat conservation recommendations for Pacific salmon (0. tshawytscha) , starry flounder (Platichthys stellatus), and northern anchovy (Engraulis mordax) as required by the Magnuson-Stevens Fishery Conservation and Management Act (MSA) as amended (16 U.S.C. 1801 et seq.) . This document concludes that the proposed project will adversely affect the EFH of Pacific salmon, starry flounder, and northern anchovy in the action area and adopts certain terms and conditions of the incidental take statement and the ESA conservation recommendations of the biological opinion as the EFH conservation recommendations.

Section 305(b)(4)(B) of the MSA requires the Corps to submit a detailed written response to NMFS within 30 days of receipt of these conservation recommendations, and 10 days in advance of any action, that includes a description of the measures adopted by the Corps for avoiding, minimizing, or mitigating the impact of the activity on EFH (50 CFR 600.920 (j)). In the case of a response that is inconsistent with our recommendations, the Corps must explain its reasons for not following the recommendations, including scientific justification for any disagreements with NMFS over the anticipated effects of the proposed action and the measures needed to avoid, minimize, or mitigate such effects. If unable to complete a final response within 30 days, the Corps should provide an interim written response within 30 days before submitting its final response.

Please contact Douglas Hampton in the California Central Valley Office located in Sacramento, California by telephone at 916-930-3610 or by email at Douglas.Hampton@NOAA.gov if you have any questions concerning this section 7 consultation, or if you require additional information.

Sincerely, ;L1cJu~ ~iam W. Stelle, Jr.

Regional Administrator

Enclosure cc: Division Chon File: ARN# l51422-WCR2015-SA00150

UNITED STATES DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administ ration

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 and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Consultation

Sacramento and Stockton Deep Water Ship Channels Maintenance Dredging and Bank Protection Project

NMFS Consultation Number: 151422-WCR2015-SA00150

Action Agency: U.S. Army Corps of Engineers

Affi d S ecte >pec1es an d NMFS' D etermmations:

BSA-Listed Species Status Is Action Is Action Is Action Is Action Likely

Likely to Likely To Likely To To Destroy or Adversely Adversely Jeopardize the Adversely Affect the Affect Critical Species? Modify Critical Species? Habitat? Habitat?

California Central Valley Threatened Yes Yes No No Steelhead ( Oncorhynchus mykiss) Southern Distinct Threatened Yes Yes No No Population Segment of North American Green Sturgeon (Acipenser medirostris) Sacramento River Winter- Endangered Yes Yes No No run Chinook Salmon

(0. tshawytscha) Central Valley Spring-run Threatened Yes Yes No No Chinook Salmon

(0. tshawytscha)

Fishery Management Plan That Does Action Have an Are EFH Conservation Describes EFH in the Project Area Adverse Effect on EFH? Recommendations Provided?

Pacific Salmon Yes Yes Pacific Groundfish Yes Yes Coastal Pelagic Species Yes Yes

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

Issued By: J..d.a&'z.. _~ ~illiam W. Stelle, Jr.

Regional Administrator

Date:

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

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

50 CFR 402.

We also completed an essential fish habitat (EFH) consultation on the proposed action, in accordance with section 305(b)(2) of the Magnuson-Stevens Fishery Conservation and Management Act (MSA) (16 U.S.C. 1801 et seq.) and implementing regulations at 50 CFR 600.

We 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 (https://pcts.nmfs.noaa.gov/pcts-web/homepage.pcts). A complete record of this consultation is on file at California Central Valley Area Office in Sacramento, California.

1.2 Consultation History

On February 5, 2013, the U.S. Army Corps of Engineers (Corps) met with NMFS to discuss the development of a biological assessment (BA) to support a pending request for consultation under the ESA.

On July 16, 2013, the Corps met with NMFS to further discuss the development of a BA to address the effects of the proposed project.

On March 25, 2014, the Corps and NMFS held an additional meeting to further coordinate on the development of a BA for the proposed project.

On July 18, 2014, the Corps delivered the BA along with a letter to NMFS requesting re-initiation of the 10-year programmatic consultation addressing the effects of maintenance dredging of the Sacramento and Stockton deep water shipping channels.

On February 17, 2015, the Corps and NMFS participated in a teleconference call to discuss the updated status of the BA and consultation.

On March 26, 2015, the Corps delivered a revised BA to NMFS describing the effects of the action.

https://pcts.nmfs.noaa.gov/pcts-web/homepage.pcts

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).

The Corps proposes to continue to perform routine maintenance dredging and bank protection on the Sacramento and Stockton Deep Water Ship Channels (DWSC) under Indefinite Delivery/Indefinite Quantity (IDIQ) contracts yearly during the 10 dredging seasons from 2016 through 2025. The proposed project includes work performed by using a hydraulic cutterhead dredge (also known as a pipeline dredge) for dredging and a clamshell crane for rock placement.

The dredged material would be deposited at previously authorized Dredged Material Placement Sites (DMPS). Dredge slurry would be routed to the DMPS via pipelines. DMPS would be diked in order to allow dredge slurry to settle and consolidate. Decant water would then be discharged back into the Sacramento or Stockton DWSC from whichever DMPS is servicing the area being dredged as determined during annual coordination. Dredged spoils would be allowed to dry in the DMPS. Bank protection rock may be placed at any site that previously contained bank protection work, and where there is a need for additional rock due to bank erosion following specific work windows to minimize impacts.

1.3.1 Dredging

Prior to each proposed dredging season, the Corps will coordinate with NMFS, providing documentation of the exact reaches of the Sacramento and Stockton DWSC to be dredged, the schedule for that dredging season, and identifying which DMPS would be used. If there are changes to DMPS boundaries, location, or function, separate documentation will be provided for NMFS approval. A maintenance dredging work window is proposed to follow a yearly schedule from August 1 to October 31 for the Sacramento DWSC and from August 1 to November 30 for the Stockton DWSC during the 10-year span from 2016 through 2025. All sites will be dredged to maintain the current allowable depth: the downstream portion of the channel will be maintained at a depth of 30 feet below mean lower low water (MLLW), and the upstream portion of the channel will be maintained at a depth of 35 feet MLLW. An allowable over depth of 1 to 2 feet is also anticipated for all sites. These depths maintain safe conditions for ships using the channels while not increasing the quantity or size of commercial navigation traffic. All dredging will be performed using a hydraulic cutterhead suction dredge and all dredged material and dredge slurry will be deposited at a previously authorized DMPS via pipelines. DMPS will be diked and dredge slurry will be allowed to settle and consolidate. Depending on the size of the DMPS and the amount of material being dredged, the decant water could be released from the DMPS into the river. Effluent discharge from all DMPS are done only with prior approval from the Central Valley Regional Water Quality Control Board (CVRWQCB) through the 401 Water Quality Certification.

The quantity of material to be dredged each dredging season will not exceed 500,000 cubic yards. The dredge is expected to operate 24 hours a day, 7 days a week within the identified work windows. When the dredge is positioned in a location where shoaling is to be removed, the dredge is anchored by alternately planting one of two spuds, or vertical poles, into the bottom sediment, and rotating itself around whichever of the two spuds is planted by pulling on swing anchors, alternately raising and planting the spud as the dredge “walks” forward. The hydraulic pipeline dredge is equipped with a rotating cutterhead (excavator) surrounding the intake of the suction line. Excavated solids and a large volume of the surrounding water are passed through the dredge centrifugal pump to the discharge pipeline as slurry, which typically has a solids content of 10 to 20 percent by weight.

Dredging activities will be limited to depths greater than 25 feet, and the cutterhead will be kept within 3 feet of the channel bottom while drawing in water. The cutterhead is mounted on a ladder that is free to pivot in the vertical plane and is rotated down to various depths. The ladder will be mounted on a floating dredge that swings left and right while proceeding along the channel. The dredge can be self-propelled or transported to the area by a tugboat. Typically, the dredge is tended by two tenders that pick up and place the swing anchors as the dredge progresses and can also move the dredge short distances. There are also two outboard engine-powered skiffs that transport crews and conduct the water sampling upstream and downstream of the dredge.

The discharge pipeline will run from the dredge in the channel, across the bank, and onto the relevant DMPS. At all DMPS, a nominal area of the outboard levee will be temporarily disturbed during positioning of the slurry pipe. To minimize disturbance, a survey will be taken of the area immediately prior to pipe placement, and upon completion of the dredging operation any disturbed banks will be restored to pre-project conditions. Annual coordination within the 10 dredging seasons will include consideration of appropriate pipe placement in order to avoid or minimize adverse effects to any listed species or designated critical habitats.

The pipeline is made of durable plastic and will either float or sink depending on the specific gravity of the material it contains. The top of the pipeline will float approximately 2 inches above the water surface when filled with water or air, and would rest on the channel bottom when containing dredged material and water. The dredge contractor will determine the best route for the pipeline (per the disposal plan) in conjunction with a qualified biologist in order to avoid or minimize adverse effects to any listed species or their designated critical habitats. The pipeline will be marked by buoys and/or high visibility paint to warn boaters of its presence.

Additional safety measures may include signs, flaggers, and/or other measures as required.

1.3.2 Dredged Material Placement Sites

A total of 11 different landward areas are used as DMPSs in conjunction with the planned annual maintenance dredging. Five of these DMPS will service the Sacramento DWSC and six will service the Stockton DWSC. The majority of these areas have been utilized over multiple years and do not provide suitable habitat for riparian species. A brief description of each of the DMPS follows.

1.3.2.1 Sacramento DWSC Dredged Material Placement Sites

1. Grand Island, S-14

This DMPS is located on the southern tip of Grand Island at the confluence of the Sacramento River, Steamboat Slough, and the Sacramento DWSC in Sacramento County.

These are shallow ponds adjacent to the Sacramento / Steamboat Slough. Water is available throughout the year from the river, runoff, and seepage. Regular channel maintenance consists of dredging the ponds. Approximately half of this DMPS is useable, while the remainder is heavily wooded. This DMPS has not been used as a DMPS since 2000.

2. Rio Vista, S-16

This DMPS is located on the west bank of the Sacramento River just south of the City of Rio Vista in Solano County. The site is a seasonal wetland, but dredged material will be placed in non-wetland areas of the site. The water that carries the material drains into the wetland areas and eventually recedes via culvert into the river. This site has been used as a DMPS in 2000, 2006, 2008, 2010, 2011, and 2013.

3. Decker Island, S-19

This DMPS is located on the central western portion of Decker Island in the vicinity of a commercial sand mining operation in Solano County. The great majority of the area consists of sand spoils partially vegetated with common herbaceous species. A portion of the site contains a seasonal wetland and holding pond, but dredged material will be placed in non-wetland areas of this site. Water that carries the dredged material drains into the wetland areas and eventually recedes via culvert into the river. This site has been used as a DMPS in 2000-2003 and 2006-2008.

4. Augusto Pit, S-20

This DMPS is a small, flat parcel on Sherman Island in Sacramento County. Water on the site may pond within areas excavated in uplands creating seasonal wetlands, but as such these areas are not considered jurisdictional waters of the United States. This site has been used as a DMPS in 2001, 2002, and 2005.

5. S-31

This DMPS is located along the western bank of the Sacramento DWSC between the channel and the Yolo Bypass in Yolo County. The lower slope of the ship channel is vegetated by a mosaic of emergent vegetation at the water’s edge, with grasses, scattered willows and blackberry bushes higher on the bank away from the water. The berm area is the portion of the site that will be used for the placement of dredged material. The majority of the berm area is vegetated with grasses and is grazed by cattle and goats. The remaining portions of the berm between the channel and the levee are vegetated with oak woodlands and mixed riparian vegetation. A toe drain and the Yolo Bypass border the west side of the levee. Overstory vegetation includes very few large trees along either the toe drain or channel, good cover on the east bank of the toe drain, and thick riparian vegetation on the west bank. There is not much observable aquatic vegetation in the channel, but there is some along the bank and there is a thin row of riparian vegetation along the west bank of the toe drain. This site has been used as a DMPS in 2000, 2001, 2003, 2005, 2007-2011, and 2013.

1.3.2.2 Stockton DWSC Dredged Material Placement Sites

1. Roberts Island I

This 250-acre site is located on Roberts Island, northwest of the West Complex, Port of Stockton, and adjacent to House Road in San Joaquin County. This site is bermed and has a matrix of bare sand and short herbaceous vegetation. The landing allowance is 300 feet and the Port of Stockton maintains the site. This site has been used as a DMPS in 2000, 2003, and 2006-2012.

2. Roberts Island II

This 220-acre site is located on Roberts Island, between the outlet of Black Slough and the Windmill Cove marina in San Joaquin County. The site is bermed and primarily consists of clay soils with little vegetation. The landing allowance is 600 feet and the site is maintained by the Port of Stockton. This site has been used as a DMPS in 2000, 2001, 2003-2005, and 2009-2011.

3. Bradford Island

This 110-acre site is located on the southwestern portion of Bradford Island, at the confluence of the San Joaquin and False rivers in Contra Costa County. The site is bermed and is currently irrigated pastureland. There are drainage ditches that transect a portion of the site and there is evidence of subsidence. There is some ponded water on site which will be avoided during dredged material placement. The water that carries the dredged material may drain into the ponded areas and eventually recede via a culvert into the river. The landing allowance is 500 feet and the site is maintained by the Port of Stockton and Reclamation District (RD) 2059. This site has been used as a DMPS in 2000, 2003, 2006, and 2010.

4. McCormick Pit

This 26-acre site is located on Sherman Island, east of the Antioch Bridge along the Stockton DWSC in Sacramento County. The site is bermed and contains sand material from past maintenance dredging. There is an emerging freshwater marsh located on a portion of this site as a result of past placement of dredged materials. The marsh contains wetland vegetation that includes a tule reed and cattail mix, along with a mixture of medium aged willows and tall herbaceous cover. Dredged material will be placed in non-wetland areas of this site. The water that carries the dredged material drains through the wetland areas into an agricultural drainage canal on Sherman Island which is pumped back to the river by RD 341. This site contains underlying peat and has a landing allowance of 3,700 feet. The site is maintained by the California Department of Water Resources (DWR) and RD 341. This site has been used as a DMPS in 2002, 2008-2011, and 2013.

5. Scour Pond

This 125-acre site is located on Sherman Island, west of the Antioch Bridge in Sacramento County. Some areas on this site are already bermed, while others will receive berms prior to use as a DMPS. The existing berm is located outside the marsh fringe around Scour Pond and is currently pastureland. A 200-foot buffer will be maintained around Scour Pond, and no decant water or dredged materials will be placed or allowed to drain into the Scour Pond portion of the site. This site contains underlying peat and has a landing allowance of 900 feet. The site is maintained by DWR and RD

341. This site has been used as a DMPS in 2007-2011, and 2013.

6. Antioch Dunes

The Antioch Dunes National Wildlife Refuge is an approximately 55-acre refuge managed by the U.S. Fish and Wildlife Service (FWS) that consists of two parcels separated by a Georgia-Pacific Gypsum Plant and a Pacific Gas and Electric utility easement. The refuge was founded in 1980 and is located along the shoreline of the San Joaquin River in Antioch, California in Sacramento County. The western parcel, the 41-acre Stamm Unit, is the only unit proposed to receive dredged material from this project.

The site is surrounded by industry including a gypsum plant, a former shipyard, and a former wastewater treatment facility, which now functions as a municipal landfill. As part of the Comprehensive Conservation Plan (CCP) for the Antioch Dunes National Wildlife Refuge, dune restoration is one of the primary objectives for habitat restoration.

Beginning in 1991, the FWS has imported sand to the refuge in order to create additional habitat. The CCP calls for identifying potential sources of clean sand, specifically from the Stockton DWSC, and importing the sand for habitat restoration. This site has been used as a DMPS in 2013.

1.3.3 Bank Protection

Suitable rock protection will be placed at eroded sites. Where scour, wash, settlement, or failure of a portion of the original stone protection has been noted, or where inspection indicates that such damage may result during the next flood or high water period, the scour or wash will be filled with earth free from brush, roots, sod, or other unsuitable material and additional stone will be placed upon the earth fill. This maintenance bank protection will bring the rock protection to its original section, using rock fill, embankment, filter, and quarry rock. The rock used will, as much as possible, be similar to the kind and gradation as originally used and described in the 1980 and 1986 Environmental Impact Statement documents.

Along reaches of the Sacramento and Stockton DWSC where filter material was originally placed or where it may be required, maintenance repair of rock protection will include the placement of a properly graded filter layer under the rock protection. In the event an inspection reveals that due to scour, settlement, or other causes, rock protection on the bank is required beyond the limits of the original construction or in reaches of the bank not originally provided with such protection, the Corps will provide additional sloping of the bank and placement of rock protection, as needed, to protect completed works.

Activities in shallow water habitats will be avoided to the fullest extent possible. However, proposed maintenance bank stabilization work may involve some shallow water areas. This maintenance bank protection work is located along both banks of the manmade portion of the Sacramento DWSC at various locations. Rock may be placed at any site that previously contained bank protection work, and where there is a need for additional rock due to bank erosion. On the Stockton DWSC, the maintenance bank protection work is located along the right and left banks, between approximately river mile (RM) 4.0 and 42.0. Authorized sites are those within 1,000 feet from the centerline of the Stockton DWSC. Rock may be placed at any site that previously contained bank protection work, and where there is a need for additional rock due to bank erosion.

A maintenance bank protection work window is proposed to follow a yearly schedule from June 15 to November 30 during each year of the 10-year period from 2016 through 2025 in order to minimize the exposure of listed species to the temporary effects associated with work performed either in the water or in close proximity to the shoreline.

1.3.4 Proposed Conservation Measures

The following conservation measures have been proposed by the Corps:

1. All decant water will be monitored for Central Valley Regional Water Quality Control Board (CVRWQCB) constituents of concern and physical parameters. Management practices will include placing flash boards at the spillway of DMPSs to increase the retention time, using interior dikes within the DMPSs to increase the hydraulic efficiency of the DMPSs, and varying the dredge production rates. Decant water will only be discharged to the river if it meets all of the water quality standards stated in the CVRWQCB Waste Discharge Requirements General Order. If the water does not meet those standards, then it will be retained on the relevant DMPS until further analyses reveal such compliance. The effluent will not exceed water quality objectives or criteria for any constituent that is on the Clean Water Act section 303(d) list.

2. The effects to water quality will further be minimized by not allowing the release of oils, grease, waxes, or other materials that could form a visible film or coating on the water surface or on the stream bottom or creating a nuisance or adversely affecting beneficial uses. Any spills of hazardous materials will be cleaned up immediately and reported in compliance reports.

3. The dredge will not be operated when the cutterhead is off the river bottom. The cutterhead will be buried in the sediment of the river bed during maintenance dredging activities or raised no more than 3 feet off the river bottom when the pumps are operating.

4. Suction will not be employed as the dredge head is deployed and retrieved through the water column until the cutterhead is on the bottom. The suction head will be maintained at a constant elevation near the channel bed when dredging to reduce the field of influence where fish might become entrained into the dredge pipe.

5. Additional hydraulic dredging practices included in the conservation measures include reducing the rotation speed of the cutterhead which minimizes the amount of substrate material sidecast or resuspended into the overlaying water column and reducing the speed of the arm swing which ensures that the cutterhead is not moving faster than its ability to pump the dredged material, and that all of the removed material is pulled into the orifice of the dredge intake pipe.

6. The contractor will be responsible for providing erosion and sediment control measures in accordance with Federal, State, and local laws and regulations to ensure compliance with water quality standards. This will be accomplished by implementing temporary and permanent erosion and sediment control best management practices. These may include, but are not limited to, use of vegetation cover, stream bank stabilization, slope stabilization, silt fences, construction of terraces, interceptor channels, sediment traps, inlet and outfall protection, diversion channels, and sedimentation basins. Any temporary measures will be removed after the area has been stabilized.

7. A Corps representative will be identified as the point of contact for any contractor who might incidentally take a listed salmonid species or sturgeon, or find dead, injured, or entrapped listed sturgeon or salmonids. This point of contact will be identified to all construction employees during an orientation regarding the potential effects of the proposed project on listed steelhead, sturgeon, and Chinook salmon species. The orientation will be conducted by a qualified fisheries biologist and cover specific information on measures to prevent injury to listed fish and what to do if any are found in the project area.

8. NMFS will be notified immediately if a salmon, steelhead, or sturgeon is found dead or injured. Follow-up written notification within 72 hours will include the date, time, and location of the dead or injured specimen, a photograph, cause of injury or death, and name and agency affiliation of the individual who found the specimen.

9. The Corps, through the dredging contractors, will coordinate with NMFS on any plans to mitigate for the loss of riparian habitat with no net loss of quantity or quality.

10. Dredging at depths of less than 25 feet will be avoided at all times.

11. The point at which the dredge material pipeline crosses the levee and discharges into the DMPS will be the position at which the pipeline is securely fixed to the levee so that the pipeline will not drag along the levee.

12. Overflow or bypass from the dredge into the channel will not be allowed.

13. The use of a drag beam or similar piece of equipment to knock down high spots or ridges in the channel bottom will be prohibited.

14. The Corps will participate in a joint onsite inspection with NMFS upon the completion of maintenance dredging and bank protection activities in order to review project effects to essential fish habitat.

1.3.5 Interrelated and Interdependent Actions

“Interrelated actions” are those that are part of a larger action and depend on the larger action for their justification. “Interdependent actions” are those that have no independent utility apart from the action under consideration (50 CFR 402.02). No interrelated or interdependent activities have been identified for this project. Although the proposed project will maintain both the Sacramento and Stockton DWSC as commercial shipping lanes, no increase in the number of commercial vessel transits per day or vessel size is anticipated in the Sacramento and Stockton DWSC for the foreseeable future, and shipping impacts are therefore considered only as part of the environmental baseline.

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 for the purposes of this opinion includes portions of both the Sacramento and Stockton DWSC in the Delta where water levels are influenced by tributary inflows and tidal action. The action area is situated across portions of Contra Costa, Sacramento, San Joaquin, Solano, and Yolo counties, as described in further detail below.

In the Sacramento River, the action area includes the Sacramento DWSC from Collinsville to the City of West Sacramento, including portions of Suisun Bay, Montezuma Slough, Horseshoe Bend, Three Mile Slough, Steamboat Slough, Cache Slough, Miner Slough, Prospect Slough, Babel Slough, and the Port of West Sacramento. The Sacramento DWSC varies in width from 200 to 400 feet before it terminates at the Port of West Sacramento turning basin which is triangularly shaped, 3,100 feet long, and 1,800 feet wide at its widest point.

In the San Joaquin River, the action area includes the Stockton DWSC from the upstream end of New York Slough to the City of Stockton, including portions of Suisun Bay, Sacramento River, Montezuma Slough, New York Slough, Middle Slough, Broad Slough, Cabin Slough, Mayberry Slough, Dutch Slough, Gallagher Slough, False River, Three Mile Slough, Fisherman’s Cut, Seven Mile Slough, Mokelumne River, Potato Slough, Old River, Little Connection Slough, Whiskey Slough, Disappointment Slough, Turner Cut, Fourteen Mile Slough, Buckley Cove, Burns Cutoff, Calaveras River, Smith Canal, and the Port of Stockton. The Stockton DWSC varies in width from 200 to 600 feet before it terminates at the Port of Stockton turning basin, which is 970 feet wide.

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 biological opinion 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 biological opinion 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:

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

• Describe the environmental baseline in the action area.

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).

• Analyze the effects of the proposed action on both species and their habitat using an “exposure-response-risk” approach.

• Describe any cumulative effects in the action area.

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

• Reach jeopardy and adverse modification conclusions.

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

2.2 Rangewide Status of the Species and Critical Habitat

This opinion 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 opinion 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 that help to form that conservation value.

The designations of critical habitat for each species uses the term primary constituent element (PCE) or essential features. The new critical habitat regulations (81 FR 7414) replace this term with physical or biological features (PBFs). The shift in terminology does not change the approach used in conducting a “destructive or adverse modification” analysis, which is the same regardless of whether the original designation identified PCE, physical or biological features, or essential features. In this opinion, we use the term PBF to mean PCE or essential feature, as appropriate for the specific critical habitat.

2.2.1 Sacramento River winter-run Chinook salmon Evolutionarily Significant Unit (ESU)

• First listed as threatened (August 4,1989, 54 FR 32085), reclassified as endangered (January 4, 1994, 59 FR 440), reaffirmed as endangered (June 28, 2005, 70 FR 37160 and August 15, 2011, 76 FR 50447)

• Designated critical habitat (June 16, 1993, 58 FR 33212)

A. Species Listing and Critical Habitat History

The Sacramento River winter-run Chinook salmon (winter-run, Oncorhynchus tshawytscha) ESU, currently listed as endangered, was listed as a threatened species under emergency provisions of the ESA on August 4, 1989 (54 FR 32085), and formally listed as a threatened species in November 1990 (55 FR 46515). On January 4, 1994, NMFS re-classified winter-run as an endangered species (59 FR 440). NMFS concluded that winter-run in the Sacramento River warranted listing as an endangered species due to several factors, including: (1) the continued decline and increased variability of run sizes since its first listing as a threatened species in 1989; (2) the expectation of weak returns in future years as the result of two small year classes (1991 and 1993); and (3) continued threats to the “take” of winter-run (August 15, 2011, 76 FR 50447).

On June 28, 2005, NMFS concluded that the winter-run ESU was “in danger of extinction” due to risks to the ESU’s diversity and spatial structure and, therefore, continues to warrant listing as an endangered species under the ESA (70 FR 37160). In August 2011, NMFS completed a 5-year status review of five Pacific salmon ESUs, including the winter-run ESU, and determined that the species’ status should again remain as “endangered” (August 15, 2011, 76 FR 50447).

The 2011 review concluded that although the listing remained unchanged since the 2005 review, the status of the population had declined over the past 5 years (2005–2010).

The winter-run ESU currently consists of only one population that is confined to the upper Sacramento River (spawning below Shasta and Keswick dams) in California’s Central Valley.

In addition, an artificial propagation program at the Livingston Stone National Fish Hatchery (LSNFH) produces winter-run that are considered to be part of this ESU (June 28, 2005, 70 FR 37160). Most components of the winter-run life history (e.g., spawning, incubation, freshwater rearing) have been compromised by the habitat blockage in the upper Sacramento River. All historical spawning and rearing habitats have been blocked since the construction of Shasta Dam in 1943. Remaining spawning and rearing areas are completely dependent on cold water releases from Shasta Dam in order to sustain the remnant population.

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.

B. Critical Habitat: Essential Features for Sacramento River Winter-run Chinook Salmon

Critical habitat for winter-run is defined as specific areas (listed below) that contain the physical and biological features 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 near shore 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 physical and biological habitat features that are considered to be essential for the conservation of winter-run (June 16, 1993, 58 FR 33212):

1. Adult Migration Corridors

Adult migration corridors are defined as “providing access from the Pacific Ocean to appropriate spawning areas”, providing 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 2013a). 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. Spawning Habitat

Spawning habitat is defined as “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 below 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

Adequate River flows are defined as providing “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 Game2 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

2 The agency changed its name in 2013 to California Department of Fish and Wildlife.

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

Optimum water temperatures for successful spawning, egg incubation, and fry development range from 6–10°C (42.8–50°F). 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 biological opinion on the long-term operations of the Central Valley Project and State Water Project (CVP/SWP, NMFS 2009a). 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 location of 56°F daily average temperature to make the best use of the cold water available based on water temperature modeling, current spawning distribution, and Reclamation’s other operational commitments including those to water contractors, D-1641 regulations and criteria, and projected end of September storage volume. 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, heavy metals and persistent organochlorine pesticides continue to be found in watersheds throughout the Central Valley. 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, 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 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

Riparian and floodplain habitat is defined as providing “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…