Attachment_6_-_NMFS_Biological_Opinion_11_19_2014_MOTCO_Piers_2.pdf

iii

TABLE OF CONTENTS

List of Acronyms

1. INTRODUCTION

1.1 Background

1.2 Consultation History

1.3 Proposed Action

1.4 Action Area

2. ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND INCIDENTAL

TAKE STATEMENT

2.1 Analytical Approach

2.2 Rangewide Status of the Species and Critical Habitat

2.3 Environmental Baseline

2.4 Effects of the Action on Species and Designated Critical Habitat

2.5 Cumulative Effects

2.6 Integration and Synthesis

2.7 Conclusion

2.8 Incidental Take Statement

2.9 Conservation Recommendations

2.10 Reinitiation Notice

3. MAGNUSEN-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT

ESSENTIAL FISH HABITAT CONSULTATION

3.1 Essential Fish Habitat Affected by the Project

3.2 Adverse Effects on Essential Fish Habitat

3.3 Essential Fish Habitat Conservation Recommendations

3.4 Statutory Response Requirement

3.5 Supplemental Consultation

4. DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION

REVIEW

4.1 Utility

4.2 Integrity

4.3 Objectivity

5. REFERENCES

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LIST OF ACRONYMS

BA Biological Assessment

BCDC Bay Conservation and Development Commission

BMP best management practices

BOR Bureau of Reclamation

BRT Biological Review Team

CCC Central California Coast

CDFW California Department of Fish and Wildlife

Corps U.S. Army Corps of Engineers cSEL cumulative sound exposure level cy cubic yards dB decibel

DDT dichlorodiphenyltrichloroethane

DMMO Dredge Material and Management Office

DOA Department of Army

DPS distinct population segment

DWR Department of Water Resources

EFH essential fish habitat

EIS Environmental Impact Statement

ESA Endangered Species Act

ESU evolutionary significant unit

FHWG Fisheries Hydroacoustic Working Group

FMP Fishery Management Plan

FRH Feather River Hatchery ft foot

FWS United States Fish and Wildlife Service

GCID Glenn Colusa Irrigation District

HDPE high-density polyethylene

ITS incidental take statement

MEC munitions and explosives of concern

MHHW mean higher high water

MLLW mean lower low water mm millimeter

MOTCO Military Ocean Terminal Concord

MSA Magnuson-Stevens Fishery Conservation and Management Act

NMFS National Marine Fisheries Service

NTU nephlometric turbidity units

PAHs polycyclic aromatic hydrocarbons

PCBs polychlorinated biphenyls

PCE primary constituent element

RBDD Red Bluff Diversion Dam

RMS root mean squared

SAP sediment analysis plan

SAV submerged aquatic vegetation

SFBRWQCB San Francisco Bay Regional Water Quality Control Board v

SPL sound pressure levels

TL total length

TTS temporary threshold shift

UXO unexploded ordnance

VSP viable salmonid population

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 this 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 the NMFS North-Central Coast Office in Santa Rosa, California.

1.2 Consultation History

On September 27, 2010, NMFS received a letter from the Department of the Army (DOA) requesting informal consultation pursuant to section 7 of the Endangered Species Act for the Pier

2 Replacement Project at Military Ocean Terminal Concord (MOTCO) Project, in the City of

Concord, Contra Costa County, California.

On November 4, 2010, an interagency meeting was held to discuss the draft project design and description. Following the interagency meeting, NMFS informed DOA by letter dated

November 15, 2010, that NMFS did not have all the information required to complete an assessment of the project’s potential impacts. A second interagency meeting was held February

25, 2011, to further discuss the draft project description. By electronic mail message (email) to

NMFS on August 22, 2011, DOA withdrew their request for consultation pursuant to section 7 of the Endangered Species Act for the Pier 2 Replacement Project at MOTCO.

The DOA sent NMFS a letter dated September 26, 2011, requesting technical assistance on the

MOTCO Piers 2 and 3 Project. NMFS provided information regarding threatened and endangered species in the action area and applicable best management practices for the project via a letter dated October 18, 2011. On January 23, 2012, the DOA sent a letter to NMFS which provided an updated draft project description and requested NMFS provide an updated species list. NMFS responded by letter dated February 29, 2012, stating that the information provided in

NMFS’ letter of October 18, 2011, remained current.

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

NMFS participated in a site visit on August 20, 2013, to assess site conditions and applicable best management practices. DOA provided NMFS the draft Environmental Impact Statement

(EIS) for the project in November 2013.

By letter dated October 28, 2013, to NMFS, the DOA requested formal consultation for the

Modernization and Repair of Piers 2 and 3 Project at MOTCO. The DOA determined the project has the potential to adversely affect the threatened Southern distinct population segment (DPS) of North American green sturgeon (Acipenser medirostris), threatened Central Valley steelhead

(Oncorhynchus mykiss), threatened Central Valley spring-run Chinook salmon (O. tshawytscha), endangered Sacramento River winter-run Chinook salmon (O. tshawytscha), and designated critical habitat. Additionally, it was determined that the project may adversely affect Essential

Fish Habitat (EFH) for various federally managed fish species within the Pacific Coast

Groundfish, Pacific Coast Salmon, and Coastal Pelagic Species FMPs. A Biological Assessment

(BA) and an EFH Assessment accompanied DOA’s October 28, 2013, letter.

An interagency teleconference with representatives from DOA, NMFS and U.S. Fish and

Wildlife Service (FWS) was held on December 4, 2013, to discuss information required for initiation of consultation. Following this teleconference, NMFS reviewed the project’s draft EIS, the BA and EFH Assessment, and other information garnered in meetings and teleconferences with DOA representatives. Via email on December 17, 2013, NMFS requested DOA provide additional information regarding dredging methodologies and avoidance and minimization measures for submerged aquatic vegetation (SAV) in the action area. By letter received January

16, 2014, the DOA provided updated information in the form of a revised BA, and a Natural

Resource Assessment.

Via email message to DOA on February 28, 2014, NMFS requested information regarding the project’s dredging component, including a sediment analysis plan (SAP) and mitigation plans for unavoidable impacts. A teleconference was held between NMFS and the DOA on March 14, 2014, to discuss the section 7 consultation process and the extent of potential impacts to listed fish. It was agreed during the call that the consultation would be formal due to the potential for adverse effects to NMFS-listed fish species. Regarding dredging, the DOA agreed to produce a

SAP and collaborate with NMFS to develop mitigation plans during the consultation process.

By letter dated March 18, 2014, the DOA requested that NMFS begin drafting a biological opinion while awaiting the information regarding dredging and associated sediment analyses.

NMFS responded to DOA via letter dated April 4, 2014, specifying the information required by

NMFS to complete consultation and stated that NMFS will use all of the information provided thus far to begin development of a biological opinion for this project. A teleconference with representatives from DOA, NMFS and FWS was held on April 20, 2014, to discuss the lacking information and best methods to proceed.

DOA provided to NMFS a preliminary sediment sampling and analysis report in May of 2014, and presented the project’s final report in August of 2014. DOA performed chemical analyses and acute toxicity bioassays of Bay sediments from the project area to determine the chemical constituents of the sediments that may be resuspended during project construction and knockdown dredging. Chemical analyses were performed for metals, dioxins/furans, total residual petroleum hydrocarbons, sulfides, ammonia, organochlorine pesticides, phenols, phthalates, polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), tributyltin, and pyrethroids.

Beginning on April 23, 2014, biweekly teleconferences between the DOA, their contractor

Cardno TEC, NMFS, FWS and the U.S. Army Corps of Engineers (Corps) were initiated and these teleconferences extended through August 2014. The teleconferences were used to exchange information regarding the project and its schedule.

NMFS transmitted by letter dated October 17, 2014, to DOA a draft biological opinion and EFH conservation recommendations for the MOTCO Piers 2 and 3 Modernization Project. Comments on this draft were provided by DOA to NMFS via letter dated October 28, 2014.

By letter dated October 27, 2014, to the San Francisco District Corps, the San Francisco Bay

Regional Water Quality Control Board (SFBRWQCB), and the San Francisco Bay Conservation and Development Commission (BCDC), DOA requested authorization to drill six in-water borings in the action area to obtain geotechnical information about the site and provide information to inform the construction of the Pier 2. Via email on November 3, 2014, to DOA, NMFS suggested that this geotechnical site investigation activity by DOA be included in the consultation on the Piers 2 and 3 Modernization Project. DOA concurred and via email on

November 4, 2014 requested NMFS use the activity description presented in DOA’s October 27, 2014, letter to the Corps, SFBRWQCB and BCDC.

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). At Pier 2, the DOA proposes to demolish part of the pier, partially reconstruct structural elements, replace damaged piles, and replace pier-side infrastructure and supporting facilities. At Pier 3, DOA proposes to repair damaged piles. The project will also involve redistribution of 750 cubic yards (cy) of sediment immediately north of Pier 2. MOTCO is located in the City of Concord, along the southern shore of Suisun Bay (Figure 1). The goal of the proposed project is to modernize and repair

Piers 2 and 3 to meet the current and future mission requirements at MOTCO, which is principally loading and unloading of ammunition from vessels. The project is scheduled to begin construction in July of 2015. There are no interdependent or interrelated actions associated with the proposed action.

Demolition of Pier 2 and Two Buildings

MOTCO’s Pier 2 consists of a 211,065 square-foot pile-supported creosote-treated timber structure with dilapidated wooden decks and piles. The current pier consists of two decks – a main deck and a platform deck. In 2002, portions of the pier were upgraded and concrete piles were added. Approximately 159,000 square feet of Pier 2 is proposed to be demolished. The

DOA proposes to retain the remaining 52,065 square-foot area of Pier 2 and perform modifications to modernize the structure. Demolition will include the removal of 1,300 cy of concrete slab, 1,895 cy of asphalt, and 200 tons of reinforcing steel. Demolition will also include removal of 4,514 creosote-treated timber piles ranging from 12 to 16 inches in diameter and 55

Figure 1. Location of MOTCO, Suisun Bay, California.

to 75 feet long, 136 18-inch concrete apron piles approximately 70 feet long, and 118 16-inch concrete piles approximately 70 feet long. The creosote-treated timber piles will be either removed completely or will be cut two feet below the mudline. The platform and dilapidated structures of Pier 2 will be removed using barges and excavators. Piles will be removed with a vibratory hammer or direct pull with a crane; any broken piles will be cut two feet below the mudline.

In addition to Pier 2, the DOA proposes to remove approximately 6,358 square feet of buildings, located on the southern edge of Pier 2 (Building A-21) and on the shore (Building 160).

Building A-21 is a 5,782 square foot structure used as an office and battery charging area.

Building 160 is a 576 square foot building used as a steam plant. The buildings will be inspected for any toxic materials and all toxic materials will be removed prior to demolition. The structures will be demolished and processed for recycling, salvage, or landfill disposal.

The work staging areas will include areas on shore and the Barge Pier located west of Pier 2.

Demolition of the pier will be conducted from the water using barge-mounted excavators or cranes. A small tug boat will be used to bring the barges from the stockpile area (shore) to the work site. Floating booms and tarps will be used to catch debris, and trucks will be used to transport materials off site to an authorized upland disposal site. Building demolition will be conducted with a land-based excavator. Demolition of Pier 2 and the two buildings is scheduled to begin in May 2016.

In order to perform demolition activities safely, there will be a clearance of any unexploded ordnance (UXO) or munitions and explosives of concern (MEC). This will begin prior to pile removal and will take approximately six weeks. The work will be conducted by up to eight divers who remove any UXO or MEC encountered during the six week investigation. There would also be one tender per diver, a stand-by diver, and a dive supervisor along with other

UXO specialists for a total of up to 40 on-site personnel supporting dive operations. A qualified

MEC dive team would also be on hand to support construction activities in the event suspected

MEC is encountered after work begins. MEC diving operations would only occur during daylight hours.

Modernization and Repair of Pier 2

The completed project at Pier 2 will consist of modernization of the remaining 52,065 square feet of the existing Pier 2 and the construction of approximately 127,000 square feet of new pier structure. Upon completion, the new Pier 2 will have a single level, 1,000 foot-long by 95 foot-wide working area for container handling, loading, and offloading (total Main Platform square footage of 95,000). The new construction at the pier will result in the rotation of the terminus to place the west end 48 feet further offshore and into deeper water.

Modernization of the existing portion of Pier 2 and construction of the new portion of Pier 2 requires the installation of 1,001 piles. Piles will consist of 876 24-inch octagonal pre-stressed concrete piles and 125 16-inch and/or 18-inch square concrete piles (square concrete piles will be reused from existing Pier 2). Piles will be driven by a Delmag Pile Hammer D62-22 or equivalent and sound will be attenuated with a cushion block. Pile driving will be done at a rate of one pile every 2 hours (i.e., 4 - 5 piles a day) and will take approximately 52 weeks to complete installation of all 1,001 piles. DOA estimates the installation of 4-5 piles per day will require a total of 1,000 impact hammer strikes. All pile driving will occur during daylight hours.

After the piles are driven, a reinforced steel molding will be built and then the concrete will be poured. This will be done at a rate of 24 feet every 2 days and will progress along the 95-foot wide deck for the entire 1,000-foot length of the pier. A derrick barge will be used as support during construction and concrete will be pumped from trucks on land. Construction will proceed from west to east. Construction for modernization of Pier 2 is expected to begin immediately following demolition activities in 2016 and will extend until May of 2018.

Prior to the commencement of construction at Pier 2, a geotechnical site investigation will occur to determine the bearing characteristics of the site soils and underlying strata. This activity will require the drilling of six in-water borings. The borings will be up to 9 inches in diameter and located within 50 feet of Pier 2. The borings will be conducted from the vessel Quin Delta and preformed with a skid mounted mobile B80 drill and an automatic 140-pound hammer to drive the samples. Borings will be drilled to a maximum depth of 80 feet below the mudline and will occur within -15 ft to -35 ft mean lower low water (MLLW). Bore holes will be backfilled with bentonite. Drilling mud and boring waste will be disposed of following all applicable regulations. The six in-water borings associated with the geotechnical site investigation work are expected to take one week to complete.

White Road Infrastructure Improvements

Onshore improvements associated with modernization of Pier 2 include repairs to White Road and expansion of Lot T-10. Road work will require 0.9 acres of the existing road to be repaired.

Repair will involve removing and replacing 8,500 linear feet of asphalt. White Road repairs will occur after Pier 2 construction is completed. Lot T-10, which is located behind White Road, will be expanded by 39,500 square feet to make room for large handling containers. A new electrical substation will be built next to Lot T-10 and this work is slated to begin in September 2016 and to culminate in September 2017. Repairs to White Road and expansion of Lot T-10 are expected to have no effect on listed anadromous fish, designated critical habitat, nor EFH due to the upland location of these activities and there are best management practices (BMPs) that will prevent any discharge of toxic materials into Suisun Bay. For example, BMPs include proper storage and handling of fuels and other contaminants, an accidental spill plan, and a storm water management plan that prevent the runoff and discharge of pollutants from these activities into the aquatic environment. Thus, these activities are not discussed further in this biological opinion.

Pier 3 Repairs

MOTCO Pier 3 is a timber structure with a 15-foot concrete apron extension on the water side of the pier, a concrete approach trestle on the east side, concrete rail girders on the water and land side, and electrical support structures on the shore side. Pier 3 will be repaired to support port operations while Pier 2 is being constructed. Repairs consist of wrapping existing piles with high-density polyethylene (HDPE) jackets.

As described above for Pier 2 demolition, divers will investigate for the presence of UXO and/or

MEC. If any UXO or MEC are present, divers will remove the item prior to project activities.

After UXO and MEC clearance, approximately 1,753 existing timber pilings on Pier 3 will be cleaned via hydrojetting or hand tools and any rotted portions will be removed. Following cleaning, timber piles will be wrapped with HDPE jackets to protect the piles from infestation by marine borers. HDPE jackets will be installed by divers and the jackets will extend approximately two feet above the highest tide level and two feet below the mudline. Pier 3 repairs are scheduled to begin in July of 2015 and will take approximately 31 weeks to complete.

“Knockdown” Dredging

The DOA proposes to redistribute an accumulation of sediment immediately north of Pier 2 to improve vessel access. Although DOA describes this activity as dredging, the material will not be removed from Suisun Bay because the proposal is to redistribute 750 cy yards of sediment with a bed level device. The bed-leveler consists of a large customized plow or box beam suspended from a work barge. Over a period of approximately one week following Pier 2 construction, the bed-leveler will operate within a 1.55 acre-area to redistribute bottom sediments and create a water depth of -32 feet MLLW. Since Pier 2 construction is scheduled for completion in May 2018, and proposed dredging work will be performed between August 1 and

November 30, this knockdown activity is expected to occur over a 7-day period between August

1, 2018, and November 30, 2018.

Monitoring

The DOA has developed a Turbidity Monitoring Plan to be implemented during construction work at Piers 2 and 3. Turbidity will be monitored with a Nephelometer within 100 yards of construction activities. Turbidity measurements will be taken twice a day, with one measurement being taken during construction activities. Turbidity levels are not to increase by greater than 1.0 Nephelometric Turbidity Unit (NTU) when natural turbidity is between 0 and 5

NTU, by 20% where natural turbidity is between 5 and 50 NTU, by 10.0 NTU when natural turbidity is between 50 and 100 NTU, and by 10% when natural turbidity is greater than 100

NTU. If turbidity exceeds the above standards, work will cease and avoidance and/or minimization measures will be implemented.

To assess sound levels during pile driving, hydroacoustic monitoring will take place at the commencement of installation of each pile type (16-, 18- and 24-inch piles). The monitoring will measure sound pressure during the installation of 10 to 17 24-inch piles and 12 to 13 16-and

18-inch piles. DOA proposes to develop the specific details of the hydroacoustic monitoring plan with the Pier 2 design contractor and the plan will be submitted to NMFS and FWS for review and approval prior to pile driving activities. The monitoring plan is to ensure sounds levels do not reach above the levels anticipated in the BA.

Mitigation Actions

DOA proposes to assess potential impacts to submerged aquatic vegetation (SAV) in the project area by conducting pre- and post-construction surveys of SAV. If the impacts to SAV are larger than the reduction in Pier 2 square footage (approximately 28,211 square feet), mitigation will be performed. Mitigation actions would be on-site at MOTCO and in the form of removal of existing piles, removal of overwater structure, or active restoration. Active restoration involves the seeding or transplanting of SAV. The amount, location, schedule, and other details of the mitigation actions will be based on the amount of SAV actually impacted by project construction. Pre- and post- construction survey methods are described in a SAV Monitoring

Plan developed by DOA. It is anticipated that the maximum amount of SAV mitigation would be 5.48 acres, 0.02 acre of pile removal and 5.46 acres of overwater structure removal or a combination of removal and active restoration. Pile removal will be performed with a vibratory hammer or direct pull with a crane during the period between June 1 and November 30. Any broken piles will be cut two feet below the mudline. Overwater structure removal may be performed at any time of year. Active restoration will occur between June 1 and November 30.

If active restoration is warranted, a restoration design plan will be developed in concert with

NMFS.

Measures to Protect Listed Fish

Cushion blocks made of wood or a composite material will be used to reduce elevated sound levels during impact pile driving.

To the extent feasible, a vibratory hammer would be used to drive the concrete piles to reduce underwater sound from impact pile driving.

If timber pile breakage occurs (world War II-era piles may be more vulnerable), the stub will be removed utilizing a hydraulic shear and crane or other equipment in attempts to cleanly pull out the stub. If the stub cannot be removed, it will be cut two feet below the mudline.

A floating surface boom will be placed around the work area to ensure that debris that falls in the water will be captured and promptly removed. The upper part of the boom will consist of sorbent material to capture floating hydrocarbons that may be associated with creosote piles.

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 proposed project is located in the City of Concord, Contra Costa County, California, in and along the southern shore of Suisun Bay. Suisun Bay is in the upper portion of the San Francisco estuary and receives freshwater inflow from the Sacramento-San Joaquin Delta, which creates a brackish-transition zone. The project action area is approximately 96 acres in Suisun Bay (Figure 2). This area includes Piers 2 and 3 and the shoreline at the project site. The portion of Suisun Bay that will be affected by elevated sound levels during pile driving extends 117 meters from Pier 2 and includes an area of approximately 90 acres (Figure 3). Turbidity and other construction disturbance at Pier 2 are anticipated to be entirely within this 90-acre area. At Pier 3, the action area includes an additional 6 acres which encompasses a 100-foot zone surrounding the pier that may be affected by turbidity and other construction disturbance at Pier 3. The action area is primarily located along the channel edge of Suisun Bay and is comprised of mud-laden sediments with high organic matter (Thompson et al. 2007). Portions of Suisun Bay support a rich benthic community comprised of a myriad of invertebrates including bivalves, polychaetes, cumaceans, isopods, etc. (Thompson et al. 2007).

Figure 2. Action area for Piers 2 and 3 Project at MOTCO in Concord, California.

Figure 3. Area of elevated sound levels during pile driving. Green line is approximately 117-meter radius from the piles.

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.

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.

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).

For listed salmon and steelhead, NMFS has developed specific guidance for analyzing the status of listed species’ component populations in a “viable salmonid populations” (VSP) paper

(McElhany et al. 2000). The VSP approach considers four population viability parameters (i.e., abundance, productivity, spatial structure, and diversity) as part of the overall review of a species status. In describing the range-wide status of listed species, NMFS relies on viability assessments and criteria in technical recovery team documents and recovery plans, where available, that describe how VSP criteria are applied to specific populations, major population groups, and species. For critical habitat, NMFS determines the range-wide status of critical habitat by examining the condition of its physical or biological features (also called “primary constituent elements” or PCEs) - which were identified when critical habitat was designated.

Species and critical habitat status are discussed in Section 2.2 of this biological opinion.

To conduct the assessment, NMFS examined an extensive amount of information from a variety of sources. Detailed background information on the biology and status of the listed species and critical habitat has been published in a number of documents including peer reviewed scientific journals, primary reference materials, and governmental and non-governmental reports.

Additional information regarding the effects of the project’s actions on the listed species in question, their anticipated response to these actions, and the environmental consequences of the actions as a whole was formulated from the aforementioned resources, and the following:

Addendum to the Revised Final Biological Assessment, prepared by Cardno TEC and received August 2014.

Revised Final Biological Assessment for Potential Effects on NMFS-Listed Species and

Critical Habitat from the Modernization and Repair of Piers 2 and 3 at Military Ocean

Terminal Concord, CA, prepared by Cardno TEC and dated January 2014;

Essential Fish Habitat Assessment for the Modernization and Repair of Piers 2 and 3 at

Military Ocean Terminal Concord, CA, prepared by Cardno TEC and dated October

2013;

Final Natural Resources Survey Report for the Modernization and Repair of Piers 2 and 3 at Military Ocean Terminal Concord, CA, dated September 2013;

Draft Environmental Impact Statement (EIS) (with Appendices) for the Modernization and Repair of Piers 2 and 3 at Military Ocean Terminal Concord, CA, prepared by HT

Harvey and Associated and dated November 2013.

Information was also provided in email messages and telephone conversations between

September 2010 and June 2014. For information that has been taken directly from published, citable documents, those citations have been referenced in the text and listed at the end of this document.

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.

2.2.1 Species Description, Life History, and Status

This biological opinion analyzes the effects of the federal action on the threatened CCC steelhead, threatened CV steelhead, threatened Central Valley spring-run Chinook salmon, endangered Sacramento River winter-run Chinook salmon, and the Southern DPS of North

American green sturgeon. This opinion also analyzes the effects of the federal action on designated critical habitat for Sacramento River winter-run Chinook salmon and the Southern

DPS of green sturgeon.

2.2.1.1 Steelhead General Life History

Steelhead are anadromous forms of O. mykiss, spending some time in both freshwater and saltwater. Unlike Pacific salmon, steelhead are iteroparous, or capable of spawning more than once before death (Busby et al. 1996). Although one-time spawners are the great majority, Shapovalov and Taft (1954) reported that repeat spawners are relatively numerous (17.2 percent) in California streams. Steelhead young usually rear in freshwater for 1 to 3 years before migrating to the ocean as smolts, but rearing periods of up to 7 years have been reported.

Migration to the ocean usually occurs in the spring. Steelhead may remain in the ocean for 1 to 5 years (2 to 3 years is most common) before returning to their natal streams to spawn (Busby et

al. 1996). The distribution of steelhead in the ocean is not well known. Interannual variations in climate, abundance of key prey items (i.e., squid), and density dependent interactions with other salmonid species are key drivers of steelhead distribution and productivity in the marine environment (Atcheson et al. 2012a and 2012b). Recent information indicates that steelhead originating from Central California use a cool, stable, thermal habitat window (ranging between

8-14 degrees Celsius [C°]) in the marine environment (Hayes et al. 2012). This thermal regime is typically characteristic of conditions in northern waters above the 40th parallel to the southern boundary of the Bering Sea (Hayes et al. 2012). Adult steelhead typically migrate from the ocean to freshwater between December and April, peaking in January and February (Fukushima and Lesh 1998).

Juvenile steelhead migrate as smolts to the ocean from January through May, with peak migration occurring in April and May (Fukushima and Lesh 1998). Barnhart (1986) reported that peak smolt migration occurs in March and April, and steelhead smolts in California typically range in size from 140 to 210 millimeter (mm) (fork length). Steelhead of this size can withstand higher salinities than smaller fish (McCormick 1994). Steelhead smolts in most river systems must pass through estuaries prior to seawater entry. It is believed that the majority of juvenile steelhead transiting through the Bay migrate within deeper areas of dredged ship channels opposed to the surrounding shallows. In San Francisco Bay, juvenile steelhead are known to use the deeper channels through San Pablo Bay (Klimley et al. 2010).

2.2.1.2 Status of CCC steelhead DPS

Historically, approximately 70 populations2 of steelhead existed in the CCC steelhead DPS

(Spence et al. 2008, Spence et al. 2012). Many of these populations (about 37) were independent, or potentially independent, meaning they had a high likelihood of surviving for 100 years absent anthropogenic impacts (Bjorkstedt et al. 2005). The remaining populations were dependent upon immigration from nearby CCC steelhead DPS populations to ensure their viability (McElhaney et al. 2000; Bjorkstedt et al. 2005).

While historical and present data on abundance are limited, CCC steelhead numbers are substantially reduced from historical levels. A total of 94,000 adult steelhead were estimated to spawn in the rivers of this DPS in the mid-1960s, including 50,000 fish in the Russian River - the largest population within the DPS (Busby et al. 1996). Near the end of the 20th century the population of wild CCC steelhead was estimated to be between 1,700- 7,000 fish (McEwan

2001). Recent estimates for the Russian River population are unavailable since monitoring data is limited. Abundance estimates for smaller coastal streams in the DPS indicate low population levels that are slowly declining, with recent estimates (2011/2012) for several streams (Redwood

[Marin County], Waddell, San Vicente, Soquel, and Aptos creeks) of individual run sizes of 50 fish or less (Nature Conservancy 2013). Some loss of genetic diversity has been documented and attributed to previous among-basin transfers of stock and local hatchery production in interior populations in the Russian River (Bjorkstedt et al. 2005). Similar losses in genetic diversity in the Napa River may have resulted from out-of-basin and out-of-DPS releases of steelhead in the Napa River basin in the 1970s and ‘80s. These transfers included fish from the

South Fork Eel River, San Lorenzo River, Mad River, Russian River, and the Sacramento River.

In San Francisco Bay streams, reduced population sizes and fragmentation of habitat has likely also led to loss of genetic diversity in these populations. For more detailed information on trends in CCC steelhead abundance, see: Busby et al. 1996, NMFS 1997, Good et al. 2005, Spence et

al. 2008.

CCC steelhead have experienced serious declines in abundance and long-term population trends suggest a negative growth rate. This indicates the DPS may not be viable in the long term. DPS populations that historically provided enough steelhead immigrants to support dependent populations may no longer be able to do so, placing dependent populations at increased risk of extirpation. However, because CCC steelhead remain present in most streams throughout the

DPS, roughly approximating the known historical range, CCC steelhead likely possess a resilience that is likely to slow their decline relative to other salmonid DPSs or Evolutionary

Significant Units (ESU) in worse condition. In 2005, a status review concluded that steelhead in the CCC steelhead DPS remain “likely to become endangered in the foreseeable future” (Good et

al. 2005). On January 5, 2006, NMFS issued a final determination that the CCC steelhead DPS is a threatened species, as previously listed (71 FR 834). A more recent viability assessment of

CCC steelhead concluded that populations in watersheds that drain to San Francisco Bay are highly unlikely to be viable, and that the limited information available did not indicate that any

2 Population as defined by Bjorkstedt et al. 2005 and McElhaney et al. 2000 as, in brief summary, a group of fish of the same species that spawns in a particular locality at a particular season and does not interbreed substantially with fish from any other group. Such fish groups may include more than one stream. These authors use this definition as a starting point from which they define four types of populations (not all of which are mentioned here).

other CCC steelhead populations could be demonstrated to be viable3 (Spence et al. 2008).

Monitoring data from the last ten years of adult CCC steelhead returns in Lagunitas and Scott creeks show steep declines in adults in 2008/2009. In 2011/2012 population levels began to increase, but still remained lower than levels observed over the past ten years (Nature

Conservancy 2013). The most recent status update found that the status of the CCC steelhead

DPS remains “likely to become endangered in the foreseeable future” (Williams et al. 2011), as new and additional information available since Good et al. (2005), does not appear to suggest a change in extinction risk. On December 7, 2011, NMFS chose to maintain the threatened status of the CCC steelhead (76 FR 76386).

2.2.1.3 Status of the CV Steelhead DPS

Central Valley steelhead historically were well-distributed throughout the Sacramento and San

Joaquin rivers (Busby et al. 1996). Although it appears Central Valley steelhead remain widely distributed in Sacramento River tributaries, the vast majority of historical spawning areas are currently above impassable dams. At present, all Central Valley steelhead are considered winter-run steelhead (McEwan and Jackson 1996), although there are indications that summer steelhead were present in the Sacramento River system prior to the commencement of large-scale dam construction in the 1940s (IEP Steelhead Project Work Team 1999). McEwan and Jackson

(1996) reported that wild steelhead stocks appear to be mostly confined to upper Sacramento

River tributaries such as Antelope, Deer, and Mill creeks and the Yuba River. However, naturally spawning populations are also known to occur in Butte Creek, and the upper

Sacramento mainstem, Feather, American, Mokelumne, and Stanislaus rivers (CALFED 2000).

It is possible that other small populations of naturally spawning steelhead exist in Central Valley streams, but are undetected due to lack of sufficient monitoring and research programs; increases in fisheries monitoring efforts led to the discovery of steelhead populations in streams such as

Auburn Ravine and Dry Creek (IEP Steelhead Project Work Team 1999).

Small self-sustaining populations of CV steelhead exist in the Stanislaus, Mokelumne, Calaveras, and other tributaries of the San Joaquin River (McEwan 2001). On the Stanislaus River, steelhead smolts have been captured in rotary screw traps at Caswell State Park and Oakdale each year since 1995 (Demko et al. 2000). Incidental catches and observations of steelhead juveniles also have occurred on the Tuolumne and Merced Rivers during fall-run Chinook salmon monitoring activities, indicating that steelhead are widespread, if not abundant, throughout accessible streams and rivers in the Central Valley (Good et al. 2005).

Steelhead counts at the Red Bluff Diversion Dam (RBDD) have declined from an average annual count of 11,187 adults for the ten-year period beginning in 1967, to an average annual count of

2,202 adults in the 1990's (McEwan and Jackson 1996). Estimates of the adult steelhead population composition in the Sacramento River (natural origin versus hatchery origin) have also changed over this time period; through most of the 1950’s, Hallock et al. (1961) estimated that

88 percent of returning adults were of natural origin, and this estimate declined to 10-30 percent in the 1990’s (McEwan and Jackson 1996). Furthermore, the California Fish and Wildlife Plan estimated a total run size of about 40,000 adults for the entire Central Valley, including San

Francisco Bay, in the early 1960s (CDFG 1965). In 1991-92, this run was probably less than

3 Viable populations have a high probability of long-term persistence (> 100 years).

10,000 fish based on dam counts, hatchery returns and past spawning surveys (McEwan and

Jackson 1996).

The status of Central Valley steelhead appears to have worsened since the 2005 status review

(Good et al. 2005), when the Biological Review Team (BRT) concluded that the DPS was in danger of extinction. New information available since Good et al. (2005) indicates an increased extinction risk (Williams et al. 2011). Steelhead have been extirpated from most of their historical range in this region. Habitat concerns in this DPS focus on the widespread degradation, destruction, and blockage of freshwater habitat within the region, and water allocation problems. Widespread hatchery production of introduced steelhead within this DPS also raises concerns about the potential ecological interactions between introduced and native stocks. Because the Central Valley steelhead population has been fragmented into smaller isolated tributaries without any large source population, and the remaining habitat continues to be degraded by water diversions, the population remains at an elevated risk for future population declines. Based on this information, NMFS chose to maintain the threatened listing for this species (76 FR 76386), but recommends reviewing Central Valley steelhead status again in 2-3 years, (instead of the normal 5 years) if species numbers do not improve (NMFS 2011a).

2.2.1.4 CV Spring-run and Sacramento River Winter-run Chinook Salmon General Life

History

Chinook salmon return to freshwater to spawn when they are 3 to 8 years old (Healy 1991).

Runs are designated on the basis of adult migration timing; however, distinct runs also differ in the degree of maturation at the time of river entry, thermal regime and flow characteristics of their spawning site, and actual time of spawning (Myers et al. 1998). Both winter-run and spring-run Chinook salmon tend to enter freshwater as immature fish, migrate far upriver, and delay spawning for weeks or months. For comparison, fall-run Chinook salmon enter freshwater at an advanced stage of maturity, move rapidly to their spawning areas on the mainstem or lower tributaries of rivers, and spawn within a few days or weeks of freshwater entry (Healey 1991).

Adult endangered Sacramento River winter-run Chinook salmon enter San Francisco Bay from

November through June (Hallock and Fisher 1985), and delay spawning until late spring and early summer. Adult threatened Central Valley spring-run Chinook salmon enter the

Sacramento-San Joaquin Delta (Delta) beginning in January and enter natal streams from March to July (Myers et al. 1998). Central Valley spring-run Chinook salmon adults hold in freshwater over summer and spawn in the fall. Central Valley spring-run Chinook salmon juveniles typically spend a year or more in freshwater before migrating toward the ocean. Adequate instream flows and cool water temperatures are more critical for the survival of Central Valley spring-run Chinook salmon due to over-summering by adults and/or juveniles.

Sacramento River winter-run Chinook salmon spawn primarily from mid-April to mid-August, peaking in May and June, in the Sacramento River reach between Keswick Dam and the Red

Bluff Diversion Dam. Central Valley spring-run Chinook salmon typically spawn between

September and October depending on water temperatures. Chinook salmon generally spawn in waters with moderate gradient and gravel and cobble substrates. Eggs are deposited within the gravel where incubation, hatching, and subsequent emergence take place. The upper preferred water temperature for spawning adult Chinook salmon is 55oF (Chambers 1956) to 57 oF (Reiser and Bjornn 1979). The length of time required for eggs to develop and hatch is dependent on water temperature, and is quite variable.

Sacramento River winter-run Chinook salmon fry begin to emerge from the gravel in late June to early July and continue through October (Fisher 1994). Juvenile winter-run Chinook salmon spend 4 to 7 months in freshwater prior to migrating to the ocean as smolts. Central Valley spring-run Chinook salmon fry emerge from November to March and spend about 3 to 15 months in freshwater prior to migrating towards the ocean (Keljson et al. 1981). Post-emergent fry seek out shallow, nearshore areas with slow current and good cover, and begin feeding on small terrestrial and aquatic insects and crustaceans. Chinook fry and parr may spend time rearing within riverine and/or estuarine habitats including natal tributaries, the Sacramento River, non-natal tributaries to the Sacramento River, and the Delta.

Within estuarine habitat, juvenile rearing Chinook salmon movements are generally dictated by tidal cycles, following the rising tide into shallow water habitats from the deeper main channels, and returning to the main channels when the tide recedes (Levy and Northcote 1982; Levings

1982; Healey 1991). Juvenile chinook migrate through San Francisco Bay in the deeper channels (Hearn et al. 2013). Juvenile Chinook salmon forage in shallow areas with protective cover, such as intertidal and subtidal mudflats, marshes, channels and sloughs (McDonald 1960;

Dunford 1975). As juvenile Chinook salmon increase in length, they tend to school in the surface waters of the main and secondary channels and sloughs, following the tides into shallow water habitats to feed (Allen and Hassler 1986). Keljson et al. (1981) reported that juvenile

Chinook salmon demonstrated a diel migration pattern, orienting themselves to nearshore cover and structure during the day, but moving into more open, offshore waters at night. The fish also distributed themselves vertically in relation to ambient light. Juvenile Sacramento River winter-run Chinook salmon migrate to the sea after only rearing in freshwater for 4 to 7 months, and occur in the Delta from October through early May (CDFG 1998). Most Central Valley spring-run Chinook salmon smolts are present in the Delta from mid-March through mid-May depending on flow conditions (CDFG 2000).

2.2.1.5 Status of the CV Spring-run Chinook Salmon

Historically, the predominant salmon run in the Central Valley was the spring-run Chinook salmon. Extensive construction of dams throughout the Sacramento-San Joaquin basin has reduced the Central Valley spring-run Chinook salmon run to only a small portion of its historical distribution. The Central Valley drainage as a whole is estimated to have supported

Central Valley spring-run Chinook salmon runs as large as 600,000 fish between the late 1880s and 1940s (CDFG 1998). The ESU has been reduced to only three naturally-spawning populations that are free of hatchery influence from an estimated…