2015 LTMS BIOP with Addendum.pdf

ii

Table of Contents

1.0 INTRODUCTION

1.1 Background

1.2 Consultation History

1.2.1 LTMS Actions Following the Issuance of the September 18, 1998 Biological Opinion

1.3 Proposed Action

1.3.1 Administration of the Program

1.3.2. Dredging Activities

1.3.3 Disposal

1.3.4 Avoidance, Minimization and Mitigation Measures

1.4 Action Area

2.0 ENDANGERED SPECIES ACT:

BIOLOGICAL OPINION AND INCIDENTAL TAKE STATEMENT

2.1 Analytical Framework

2.1.1 Jeopardy Analysis

2.1.2 Adverse Modification Analysis

2.1.3 Use of Best Available Scientific and Commercial Information

2.2 Status of the Species and Critical Habitat

2.2.1 Species Description, Life History, and Status

2.2.2 Factors Responsible for Steelhead, Chinook Salmon, and Green Sturgeon Stock Declines

2.3 Environmental Baseline

2.3.1 Action Area Overview

2.3.2 Status of Species and Critical Habitat in Action Area

2.3.3 Factors Affecting the Species Environment in the Action Area

2.3.4 Previous Section 7 Consultations and Section 10 Permits in the Action Area

2.4 Effects of the Action

2.4.1 Exposure to Dredge and Disposal Sites

2.4.2 Effects of Dredging and Disposal on Listed Fish

2.4.3 Effects on Designated Critical Habitat

2.4.4 Effects of Beneficial Re-use for Wetland Restoration

2.5 Cumulative Effects

2.6 Integration and Synthesis

2.7 Conclusion

2.8 Incidental Take Statement

2.8.1 Amount or Extent of Take

2.8.2 Effect of the Take

2.8.3 Reasonable and Prudent Measures

2.8.4 Terms and Conditions

2.9 Conservation Recommendations

2.10 Reinitiation Notice

3.0 DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW ...80

3.1 Utility

iii

3.2 Integrity

3.3 Objectivity

4.0 REFERENCES

iv

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 CSLC California State Lands Commission Corps U.S. Army Corps of Engineers CV Central Valley cy cubic yards cy/yr cubic yards per year dB decibel DDT dichlorodiphenyltrichloroethane DPS distinct population segment DWR Department of Water Resources DQA Data Quality Act EFH essential fish habitat EIS Environmental Impact Statement ESA Endangered Species Act ESU evolutionary significant unit FEIR Final Environmental Impact Report FMP Fishery Management Plan FRH Feather River Hatchery ft foot FWS United States Fish and Wildlife Service GCID Glenn Colusa Irrigation District ITS incidental take statement MHHW mean higher high water MISP Marine Invasive Species Program MLLW mean lower low water mm millimeter MSA Magnuson-Stevens Fishery Conservation and Management Act MOTCO Military Ocean Terminal NMFS National Marine Fisheries Service NTU nephlometric turbidity units PCE primary constituent element RBDD Red Bluff Diversion Dam SFBRWQCB San Francisco Bay Regional Water Quality Control Board TL total length TMDL Total Maximum Daily Load USFWS United States Fish and Wildlife Service

1.0 INTRODUCTION

1.1 Background

In response to growing concerns over direct, indirect, and cumulative effects of dredging and dredged material disposal activities on the aquatic environment of the San Francisco Bay/Estuary, Federal and state agencies joined with navigation interests, fishing groups, environmental organizations, and other interested parties to develop the Long Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region (LTMS Program). The San Francisco Bay LTMS Program is a cooperative effort of the U.S. Army Corps of Engineers (Corps), U.S. Environmental Protection Agency (EPA), the San Francisco Bay Regional Water Quality Control Board (Water Board), San Francisco Bay Conservation and Development Commission (BCDC), and State Water Resources Control Board (SWRCB) (herein after referred to as LTMS agencies).

In 1998, the LTMS agencies completed the Final Policy Environmental Impact Statement/Programmatic Environmental Impact Report (Programmatic EIS/EIR), selecting the new long-term plan for reducing disposal within San Francisco Bay over time, and increasing recycling of dredged material for "beneficial uses" including habitat restoration, levee maintenance, and construction fill. The San Francisco Bay LTMS is designed to develop technically feasible, economically prudent, and environmentally acceptable long-term solutions to the disposal of dredged material over a fifty year period. It specifically addresses maintenance dredging, and is not intended to address new dredging or sand mining. The primary goals of the LTMS includes managing dredging and disposal in an economically and environmentally sound manner, maximizing the use of dredged material for beneficial reuse, and developing a coordinated permit application review process for dredging and disposal projects.

During the development of the LTMS Program, the LTMS agencies worked with the California Department of Fish and Wildlife (CDFW, previously referred to as California Department of Fish and Game), the U.S. Fish and Wildlife Service (USFWS), and NOAA’s National Marine Fisheries Service (NMFS) to develop measures to avoid and minimize the potential impacts of dredging and disposal projects. One of the primary tools used to avoid and minimize the potential adverse effects of dredging and in-bay disposal was environmental work windows.

Environmental work windows are established periods within the calendar year that avoid or minimize overlap with the presence of a target species or a sensitive life stage of a target species.

For certain species listed under the Endangered Species Act of 1973, as amended (ESA), and some non-listed species of special concern, environmental work windows were incorporated into the LTMS Program. During environmental work window periods, dredging and disposal activities are restricted in specific areas to protect listed species and species of special concern.

As early as 2001, the Corps, EPA, and NMFS began to discuss difficulties associated with the environmental work windows. Both the Corps’ dredging program for federal navigation channels as well as small dredging projects by industry, municipalities, and private businesses were having problems accomplishing all their maintenance dredging projects within the established work windows. Frequent requests to work outside the LTMS windows were submitted to NMFS for review and there became a need to develop mitigation actions for dredge projects that must work outside the established windows.

In June 2006, NMFS listed the southern distinct population segment (DPS) of North American green sturgeon as a threatened species under the ESA and in March 2009, the State of California listed longfin smelt (Spirinchus thaleichthys) as a threatened species under the California Endangered Species Act (CESA).

1.2 Consultation History

On February 18, 1998, the EPA initiated consultation with NMFS pursuant to section 7 of the ESA for the proposed adoption of the LTMS Program. The LTMS Program proposed to avoid and minimize adverse effects to listed anadromous salmonids by restricting dredging and the associated disposal of dredge materials to periods when the likelihood of listed anadromous salmonids presence in San Francisco Bay was low (i.e., environmental work windows).

Appendix J of the LTMS Programmatic Environmental Impact Statement/Environmental Impact Report (EIS/EIR) presents the environmental work windows by species and location. NMFS, the Corps and EPA agreed during consultation that all dredge projects would adhere to these work windows. If a project was unable to restrict dredging or disposal to the environmental work window for listed anadromous salmonids, the Corps would conduct a separate, project-specific, section 7 consultation with NMFS.

A draft biological opinion/conference opinion and incidental take statement was provided by NMFS to EPA on August 19, 1998. Comments were provided by EPA and on September 18, 1998, NMFS issued a biological and conference opinion to EPA that addressed potential impacts to listed and proposed salmonids and to their designated critical habitat. The biological opinion concluded that dredging activities conducted in accordance with the 50-year LTMS Program would not likely jeopardize the continued existence of the following anadromous salmonid species: (1) endangered winter-run Chinook salmon; (2) threatened Central California Coast coho salmon; (3) threatened Central California Coast steelhead; (4) threatened California Central Valley steelhead; (5) proposed-threatened Central Valley fall/late-fall run Chinook salmon; (6) proposed-threatened Southern Oregon/California Coastal fall-run Chinook salmon; and (7) proposed-endangered Central Valley spring-run Chinook salmon.

By letter dated January 16, 1999, to NMFS, EPA clarified the following points regarding the LTMS Program addressed in the 1998 consultation with NMFS: (1) only dredging and disposal for navigational projects are included; (2) NMFS participation in the Dredge Materials Management Office does not require entering the interagency Memorandum of Understanding;

(3) correction of a typographical error regarding the biological opinion and Table J-2 of the LTMS Final EIS/EIR; and (4) the Corps shall be included as a consulting agency under the LTMS Program’s biological opinion.

By letter dated August 13, 2004, to NMFS, EPA and the Corps requested two modifications to the environmental work windows for the LTMS Program: (1) South San Francisco Bay work window would be from June 1 to November 30; and (2) Napa River, Petaluma River, and Sonoma Creek work windows would be from July 1 to October 31. NMFS informed EPA and the Corps that these environmental work windows were generally consistent with the September 19, 1998 biological opinion and incidental take statement.

During the latter half of 2004, NMFS actively solicited information regarding the status of North American green sturgeon (Acipenser medirostris) for the purpose of updating the NMFS’ 2002 risk assessment for this species. The NMFS Biological Review Team (BRT) completed an updated status review in February 2005 and it was submitted to NMFS Regional Offices for further consideration. On April 6, 2005, NMFS published a proposed rule to list the southern DPS of North American green sturgeon as a threatened species (70 FR 17386). On April 4, 2006, NMFS published the final rule listing the southern DPS of green sturgeon as a threatened species (71 FR 17757).

By letter dated November 29, 2006, NMFS requested the Corps and EPA provide information regarding the following topics: (1) characteristics of maintenance dredge sites; (2) characteristics of San Francisco Bay Region areas that are not being dredged; (3) in-bay disposal sites; (4) potential entrainment risk of listed species by large suction dredges; (5) natural and anthropogenic contaminants in dredged sediment; and (6) activity of large vessels that transit San Francisco Bay. On February 13, 2007, the Corps provided the requested information, less the information regarding large vessel activity. In April 2007, the Corps provided the vessel traffic data to NMFS.

On May 24, 2007 a conference call with representatives from NMFS and Corps discussed environmental work windows and measures for the protection of green sturgeon. The group reviewed the results of acoustic tag detections of sturgeon in the vicinity of the Richmond Harbor.

On January 28, 2008 the Corps provided NMFS an analysis regarding green sturgeon movements in relation to Corps dredging projects. The analysis utilized the results of acoustic tag detections of green sturgeon and concluded that the species spend 77 percent of their time in shallow water and are not likely to be present at the deeper in-bay aquatic disposal sites.

On November 20, 2008, NMFS, EPA and the Corps meet in San Francisco to discuss the effects of LTMS dredging projects on green sturgeon.

EPA submitted draft project description of the current LTMS Program to NMFS in June 2009.

On February 24, 2010, representatives of NMFS, Corps and EPA met to discuss the measures under development for the programmatic consultation for Essential Fish Habitat (EFH) pursuant to the Magnuson Stevens Fishery Conservation and Management Act (MSA), and the relationship to the reinitiated ESA consultation for listed species. In February 2010, the Corps provided detailed information to NMFS regarding the location and volume of dredging performed in federal navigation channels which occurred outside of the environmental work windows.

A meeting was held on March 26, 2010 with representatives of NMFS, Corps, EPA and BCDC to discuss environmental work windows, monitoring, research and green sturgeon. In particular, NMFS requested information from the Corps regarding the monitoring of water quality at dredging and disposal sites. Discussions on these topics continued by conference call on March 29, 2010, at a April 13, 2010 meeting, and at a April 27, 2010 meeting.

During 2011 and 2012, the Corps worked with CDFW staff to develop measures to avoid and reduce impacts to State-listed longfin smelt. NMFS participated in several conferences calls regarding this topic to gain a better understanding of the fisheries issues associated with the Corps’ dredging equipment and collaborate on measures to reduce impacts associated with dredging. NMFS and CDFW coordination also ensured measures to avoid and reduce impacts to longfin smelt did not inadvertently cause harm to listed salmonids or green sturgeon.

On March 29, 2012, NMFS attended the LTMS Program 12-year review meeting with representatives from Corps, EPA, Water Board, BCDC, and various dredging stakeholder groups. The meeting provided a summary of the first 12 years of implementation of the LTMS Program.

Representatives of NMFS, Corps, EPA, BCDC, and the Water Board met on October 16, 2012, to update the LTMS project description and evaluate the program’s environmental work windows. This group continued work in 2012 to simplify the work window requirements and develop mitigation for dredging projects that must work outside the environmental work windows.

In February 2013, the Regional Water Board and the Corps announced their intent to prepare a joint Environmental Assessment and Environmental Impact Report for the operation and maintenance of federal navigation channels in San Francisco Bay, consistent with the LTMS Program (Federal Navigation Channels EA/EIR). NMFS, EPA, and the Corps agreed that the reinitiated LTMS consultation with NMFS should be coordinated with this environmental review process to ensure consistency in the measures adopted to protect the state-listed longfin smelt.

Coordination between representatives with NMFS, Corps, EPA, BCDC, CDFW, and the Regional Water Board continued in 2013 regarding the project schedule, modification of the LTMS environmental work windows, and fisheries measures for the Federal Navigation Channels EA/EIR.

From December 2013 through March 2014, representatives from the Corps, NMFS, EPA, BCDC, and the Water Board drafted a proposal that would allow for some dredging to occur outside the environmental work windows provided certain measures and mitigation actions are taken. This proposal was presented to the San Francisco Bay dredging stakeholder community at a LTMS Management Committee meeting on April 30, 2014. The proposal was generally well received by stakeholders and the LTMS agencies were encouraged to adopt this plan.

Stakeholder comments were solicited and the final plan for updating the LTMS Program with these measures was submitted to NMFS by joint letter from EPA, dated October 8, 2014, and Corps, dated October 14, 2014. For purposes of the reinitiated section 7 consultation with NMFS, the October 2014 letter and plan constituted the final project description for the updated LTMS Program.

Via email message dated November 17, 2014, EPA provided to NMFS a clarification regarding the term “clamshell” in the final project description. The term “clamshell dredge” was used under the “Best Practices” section of paragraph 2(a) of the October 2014 project description.

EPA requested “mechanical” be used in place of “clamshell” because there are some dredgers that use an excavator or other mechanical equipment that are not considered a “clamshell” dredge.

1.2.1 LTMS Actions Following the Issuance of the September 18, 1998 Biological Opinion

Following the issuance of the NMFS biological opinion in 1998, the LTMS agencies developed specific guidance for implementing the strategy selected in the program’s Policy Environmental Impact Statement/Programmatic Environmental Impact Report and this program guidance was presented in the 2001 LTMS Management Plan (Management Plan). The LTMS is a 50-year plan that covers all federal and non-federal operations and maintenance dredging and dredged material placement in the region. To allow time for planning, budgeting, and creating alternatives to in-Bay disposal, the Management Plan established a 12-year transition period for achieving the reduced in-Bay disposal goal of 1.25 million cubic yards (plus 250,000 cubic yards contingency) annually. The transition period’s disposal volume limits were voluntary as long as in-Bay goals were met overall. The 12-year transition period was completed in 2012 and the LTMS agencies issued a 12-Year Review Report in August 2012 (LTMS 2012).

1.2.1.1. Dredged Material Management Office

The Management Plan also formalized the Dredged Material Management Office (DMMO) for the purpose of providing a coordinated review of dredging and dredged material disposal project proposals. The DMMO is a joint program with representation from the Corps, EPA, BCDC, and Regional Water Board, and State Lands Commission. NMFS, California Department of Fish and Wildlife, and U.S. Fish and Wildlife Service are encouraged to participate at DMMO meetings as commenting resource agencies. Since implementation of the LTMS, the DMMO serves as a single point-of-entry into the state and federal regulatory process for dredge project applicants.

The DMMO does not issue permits; rather it makes consensus-based recommendations to the member agencies on the completeness of permit applications, adequacy of sediment sampling and analysis plans (SAP), and suitability of sediments for proposed disposal locations.

1.2.1.2 LTMS Studies and Literature Reviews

To improve the scientific understanding of listed fish species in San Francisco Bay and the potential impacts to these species from dredging, the LTMS Program has funded a number of studies, intended to help address the basis of some of the existing work windows with an eye toward whether they could be modified to allow dredging for longer periods in some locations.

The LTMS environmental work window Science Framework was developed, with input from NMFS and the other resource agencies, to identify agency concerns and potential studies that may be able to address those concerns. The LTMS Program went on to undertake a number of the identified studies, including both literature reviews and laboratory and field studies. The completed and draft studies that perform by and in conjunction with the LTMS Program in San Francisco Bay are listed in Table 1. Since 2011-12, funding has been nearly eliminated and consequently additional scientific studies have been put on hold.

Table 1. LTMS-Associated Scientific Studies, Literature Reviews and Symposia

Completed Studies and Report Sediment Framework for Assessment of Potential Effects of Dredging on Sensitive Fish Species in San Francisco Bay.

August 2004 Spatial Characterization of Suspended Sediment Plumes During Dredging Operations Through Acoustic Monitoring (Oakland Outer Harbor). January 2004.

Suspended Sediment Plumes Associated with Mechanical Dredging at the Port of Oakland, California. 25th Annual WEDA Conference, 2005.

Characterization of Suspended Sediment Plumes Associated with Knockdown Operations at Redwood City, California. October 2005.

Anadromous Salmonids Young Salmonid Out-Migration Through San Francisco Bay with Special Focus on their Presence at the San Francisco Waterfront. May 2011.

Inter-annual variation of reach specific migratory success for Sacramento River hatchery yearling late-fall run Chinook Salmon (Oncorhynchus tshawytshca) and steelhead trout (Oncorhynchus mykiss). May 2012.

Juvenile Salmonid Outmigration and Distribution in the San Francisco Estuary: 2006-2008 Interim Draft Report.

January 2010.

Longfin Smelt LTMS Longfin Smelt Literature Review and Study Plan. August 2011.

Entrainment of Smelt in San Francisco Bay by Hydraulic Dredges: Rates, Effects, and Mitigation. October 2013.

Longfin Smelt Monitoring During Dredging of the Pinole Shoal Channel in San Pablo Bay, California in June 2010. July 2010.

2011 Longfin Smelt Monitoring During Dredging By the USACE Hopper Dredge Essayons In the San Francisco Bay Area. December 2011.

Herring A Review of Scientific Information on the Effects of Suspended Sediments on Pacific herring (Clupea pallasi) Reproductive Success. April 2005.

White Paper: Potential Impacts of Dredging on Pacific Herring in San Francisco Bay. March 2005.

Impacts of Suspended Sediments on Fertilization, Embryonic Development, and Early Larval Life Stages of the Pacific herring, Clupea pallasi. April 2009 Impacts of Suspended Sediments on Fertilization, Embryonic Development and Early Larval Life Stages of the Pacific Herring, Clupea pallasi. July 2008.

Methylmercury Mercury Concentrations Bordering The Hamilton Army Air Field Remediation Site: September, 2001. October 2002.

Mercury Concentrations Bordering The Hamilton Army Air Field Remediation Site: February. 2003. September 2003.

Pre-Construction Biogeochemical analysis of mercury in Wetlands Bordering the Hamilton Army Airfield Wetlands Restoration Site. September 2005.

Mercury Cycle Studies Associated with the Hamilton Wetland Restoration Project. May 2006.

Pre-Construction Biogeochemical analysis of mercury in Wetlands Bordering the Hamilton Army Airfield (HAAF) Wetlands Restoration Site. Part 2. September 2007.

Pre-Construction Biogeochemical analysis of mercury in Wetlands Bordering the Hamilton Army Airfield (HAAF) Wetlands Restoration Site. Part 3. December 2009.

Comparison of DGT Sentinels and Bioassays for Long-term Mercury TMDL Monitoring under San Francisco Bay Field Conditions. December 2009.

LTMS Symposia on Methylmercury in Dredging Operations and Dredged Sediment Reuse (January 2010) Miscellaneous Least Tern Literature Review and Study Plan Development. February 2012.

Tools for Assessing and Monitoring Fish Behavior Caused by Dredging Activities. June 2011.

Literature Review (for studies conducted prior to 2008): Fish Behavior in Response to Dredging & Dredged Material Placement Activities. August 2009.

Supplement to the “Framework for Assessment of Potential Effects of Dredging on Sensitive fish Species in San Francisco Bay”. 2013.

Effects of Short-term Water Quality Impacts Due to Dredging and Disposal on Sensitive Fish Species in San Francisco Bay. September 2008.

LTMS Science Symposium 2007, 2008 and 2010 LTMS Symposium on Green Sturgeon, Longfin Smelt and Dredging Operations in the San Francisco Bay (December 2009) Dredging 201: The Permit Process and Beyond Workshop

Draft Reports Juvenile Salmonid Outmigration: Interim Draft Report 2008-2009 Juvenile Salmonid Outmigration & Green Sturgeon: Distribution Draft Annual Report 2009, 2010 & 2011 Juvenile Salmonid Outmigration and Distribution in the San Francisco Estuary: Draft Annual Report. September Draft San Francisco Bay Juvenile Salmonid distribution and Tracking Project: Data Report. 14 August 2007.

Potential Impacts of Re-suspended sediments associated with Dredging and Dredged material placement of fishes in San Francisco Bay, California – Literature review and identification of Data Gaps. July 2010.

Draft - Bibliography of Scientific Literature on Pacific Herring (Clupea pallasi), with Additional Selected References for Baltic Herring (Clupea harengus). August 2004.

1.3 Proposed Action

The Corps and EPA propose to continue implementation of the LTMS dredging as described below with the addition of several conservation and mitigation measures described in section

1.3.4 below. This reinitiation of consultation on the LTMS Program and this biological opinion applies to operations and maintenance dredging within San Francisco, San Pablo and Suisun Bays, as well as areas immediately outside the Golden Gate at San Francisco Bar and Ocean Beach, conducted by the Corps, other federal agencies, and non-federal entities. Corps and EPA authorities for these actions are as follows.

Non-Corps dredging and disposal of dredged material in the San Francisco Bay Region requires a Department of Army permit pursuant to Section 404 of the Clean Water Act (CWA), Section 103 of the Marine Protection, Research, and Sanctuaries Act (MPRSA), and Section 10 of the Rivers and Harbor Act of 1899. For Corps’ conducted dredging projects, the Corps does not issue itself a CWA section 404 permit, but the CWA’s Section 404(b)(1) Guidelines and other substantive requirements of the CWA and other environmental laws do apply. EPA provides oversight to the Corps CWA permit program, and has additional authorities pursuant to the Marine Protection, Resources, and Sanctuaries Act (MPRSA). Section 102 of the MPRSA authorizes EPA to establish criteria for evaluating all dredged material proposed for ocean dumping. These criteria are published separately in the Ocean Dumping Regulations at 40 C.F.R. pt. 220-228. Section 102 also authorizes EPA to designate permanent ocean-dredged material disposal sites in accordance with specific site selection criteria designed to minimize the adverse effects of ocean disposal of dredged material.

Under the LTMS Program, dredging is performed at 11 federal navigation channels (Table 2 and Figure 1) and approximately 100 maintenance dredging sites associated with ports, marinas, and homeowners associations (Table 3 and Figure 1). There are seven in-water disposal locations that are currently in use: Ocean Disposal (SF-DODS); San Francisco Bar (SF-8); Carquinez Strait (SF-9); San Pablo Bay (SF-10); Alcatraz (SF-11); Suisun Bay (SF-16); and Ocean Beach Demonstration Site (SF-17) (Figure 1).

A primary goal of the LTMS Program is to reduce the amount of in-Bay disposal. Specifically, the plan aims for a minimum of 40 percent of all dredged material to be beneficially reused (e.g., for enhancing or creating aquatic habitat, maintaining levees, etc.), up to 40 percent of material to be discharged offshore at the EPA-designated San Francisco Deep Ocean Disposal Site (SF- DODS) when beneficial reuse is not feasible, and no more than 20 percent of dredged material to be discharged in Bay (referred to as the “40-40-20 Plan”). The long-term goal of the LTMS Program is to limit in-bay disposal volumes to a maximum of 1.25 million cubic yards per Year (plus 250,000 cubic yards contingency).

Figure 1. LTMS Dredging and Disposal Locations

Notes:

* For areas not dredged since 2000, the last dredging event is reported.

1 Range of volume dredged per fiscal year since 2000 (USACE, 2014). For areas not dredged since 2000, the last dredging event is reported.

2 Median volume dredged per fiscal year since 2000. For areas not dredged since 2000, the last dredging event is reported.

3 Due to the lower frequency at which these channels are dredged, future dredge volumes could be greater.

4 Due to the deepening of Oakland Harbor completed in 2010, future dredge volumes could be greater.

CY = cubic yards, MWRP = Montezuma Wetlands Restoration Project, Solano County

Table 2. Corps Dredging of Federal Navigation Channels in SF Bay Region 2000-2014 Source: Federal Navigation Channels draft EA/EIR, December 2014.

Channel

Dredge Type

Typical Dredging Frequency (years)

Range of Volume Dredged per

Episode (CY)1

Median Volume Dredged Per

Episode (CY)2

Placement Site

Richmond – Inner Harbor Outer Harbor

Clamshell-Bucket 1 11,000 – 631,000 390,000 SF-DODS, Upland24,870 Hopper 1 78,000 – 318,000 190,000 SF-11

San Francisco Harbor – Main Ship Channel Hopper 1 78,000 – 613,000 306,000 SF-8, SF-17 Napa River Channel* Cutterhead-Pipeline 6-10 140,0003 140,0003 Upland (Sponsor Provided) Petaluma River Channel (and Across the Flats*) Cutterhead-Pipeline

(River Channel) Clamshell-Bucket (Across the Flats)

4-7 150,0003 150,0003 Upland (Sponsor Provided) for the River Channel SF-10 for Across the Flats

San Rafael Creek Channel Clamshell-Bucket 4-7 78,000 – 87,0003 83,0003 SF-11 Pinole Shoal Hopper 1 80,000 – 487,000 146,000 SF-10 Suisun Bay Channel and New York Slough Hopper 1 21,000 – 423,000 159,000 SF-16 Oakland Inner and Outer Harbor Clamshell-Bucket 1 122,000 – 1,055,0004 330,000 SF-DODS, MWRP San Leandro Marina (Jack D. Maltester Channel) Cutterhead-Pipeline 4-6 121,000 – 187,0003 154,0003 Upland (Sponsor Provided) Redwood City Harbor Clamshell-Bucket

(Harbor Channels) Hopper (San Bruno Channel)

1-2 10,000 – 560,000 179,000 SF-11

Table 3. San Francisco Bay Region non-Corps dredge project sites. Latitudes and longitudes are provided for reference only and do not represent spatial extent of sites.

Name Latitude Longitude Aeolian Yacht Club 37° 45.003' N 122° 14.079' W Alameda Point Channel 37° 46.441' N 122° 18.907' W Arques Shipyard and Marina 37° 52.064' N 122° 29.769' W Ballena Isla Marina 37° 45.978' N 122° 17.109' W Ballena Isla Townhomes 37° 46.149' N 122° 17.240' W Bel Marin Keys Community Services District 38° 5.686' N 122° 29.445' W Bellevue Channel (Belvedere Cove) 37° 52.337' N 122° 27.575' W Belvedere Land Company 37° 52.363' N 122° 27.584' W Benicia Marina 38° 2.597' N 122° 9.444' W Benicia Port Terminal (Amport) 38° 2.488' N 122° 8.087' W Berkeley Marina 37° 52.122' N 122° 18.972' W Black Point Boat Launch Ramp 38° 6.880' N 122° 30.356' W BP, Richmond Terminal 37° 54.439' N 122° 21.817' W Brickyard Cove Homeowners Association 37° 54.497' N 122° 22.799' W Brisbane Marina at Sierra Point 37° 40.462' N 122° 22.797' W C&H Sugar Company 38° 3.494' N 122° 13.083' W CA Maritime Academy 38° 3.976' N 122° 13.835' W Cass Marina Turney Boat Ramp 37° 51.615’N 122° 29.116’W Castrol North American Consumer's Berth 37° 55.342' N 122° 22.367' W Chevron Rod and Gun 37° 57.617' N 122° 24.658' W Chevron, Richmond Long Wharf 37° 55.492' N 122° 24.766' W City of Emeryville Marina 37° 50.430' N 122° 18.750' W City of Napa, JFK Boat Ramp 38°15.929’N 122°17'.04’W City of Suisun Pierce Island Boat Ramp 38° 13.980' N 122° 2.249' W City of Sunnydale Boat Ramp 37° 26.131' N 122° 1.622' W Clipper Yacht Harbor 37° 51.858' N 122° 29.543' W Coast Guard Station, Golden Gate 37° 49.968' N 122° 28.633' W Coast Guard Station, Yerba Buena Island 37° 48.685' N 122° 21.637' W Coast Guard, Alameda Station 37° 46.780' N 122° 14.963' W Conoco Philips, Richmond 37° 54.754' N 122° 21.875' W Conoco Philips, Rodeo Terminal 38° 3.421' N 122° 15.711' W Corinthian Yacht Club 37° 52.359' N 122° 27.406' W Corona Del Mar Homeowners Association 37° 45.832' N 122° 13.513' W Coyote Point Marina 37° 35.339' N 122° 19.012' W Emery Access Chanel 37° 50.563' N 122° 18.867' W Emery Cove Marina 37° 50.312' N 122° 18.628' W Exploratorium 37° 48.160' N 122° 23.902' W Foster City Lagoon 37° 32.647' N 122° 15.829' W Galilee Harbor 37° 51.759' N 122° 29.329' W Gallinas Creek 38° 1.023' N 122° 30.472' W Glen Cove Marina 38° 4.023' N 122° 12.790' W Greenbrae Marina Neighborhood 37° 56.540' N 122° 30.627' W Hanson Aggregates 37° 45.799' N 122° 13.439' W Harbor Bay Ferry Channel 37° 44.143' N 122° 15.479' W High Tide Boat Sales 37° 58.080' N 122° 30.718' W Jackson Property 37° 45.862' N 122° 13.526' W

Johnson Property 37° 52.405' N 122° 27.644' W Kappas Marina – Richardson Bay Marina 37° 52.580' N 122° 30.262' W Kiewit Pacific Company 38° 5.477' N 122° 15.294' W Larkspur Landing Ferry Terminal 37° 56.744' N 122° 30.551' W Larkspur Marina 37° 56.417' N 122° 31.391' W Larkspur Sea Scout Base 37° 56.587' N 122° 30.699' W Levin-Richmond Terminal Corporation 37° 55.269' N 122° 22.017' W Loch Lomond Marina – Marina Village 37° 58.343' N 122° 28.867' W Lowrie Yacht Harbor 37° 58.037' N 122° 30.469' W Mare Island Shipyard 38° 5.796' N 122° 15.869' W Marin Rowing Association 37° 56.557' N 122° 31.026' W Marin Yacht Club 37° 58.315' N 122° 29.922' W Marina Bay Yacht Harbor 37° 54.804' N 122° 20.960' W Marina Plaza Harbor 37° 52.008' N 122° 29.706' W Marina Vista Canal and Homeowners Assoc. 37° 58.385' N 122° 29.754' W Martinez Marina 38° 1.629' N 122° 8.230' W Martinez Shore Terminal 38° 2.748' N 122° 6.082' W Montezuma Harbor 38° 11.229' N 121° 58.230' W Napa Valley Marina 38° 13.245' N 122° 18.783' W Oakland Yacht Club 37° 47.021' N 122° 15.818' W Oyster Cove Marina 37° 39.821' N 122° 22.709' W Oyster Point Marina 37° 39.820' N 122° 22.682' W Paradise Cay Homeowners Assoc. 37° 54.825' N 122° 28.659' W Paradise Cay Yacht Club 37° 54.930' N 122° 28.590' W Petaluma Marina 38° 13.797' N 122° 36.811' W Petaluma River Turning Basin 38° 14.106' N 122° 38.262' W Pittsburg Marina 38° 2.143' N 121° 52.950' W Plains Marketing (Martinez Shore Terminal) 38° 2.612' N 122° 6.142' W Point San Pablo Yacht Club 37° 57.818' N 122° 25.103' W Port of Oakland 37° 48.646' N 122° 19.715' W Port of Redwood City 37° 30.808' N 122° 12.576' W Port of Richmond 37° 54.729' N 122° 21.876' W Port of San Francisco 37° 48.022' N 122° 23.770' W Port Sonoma Marina 38° 7.060' N 122° 29.949' W Redwood City Marina 37° 30.421' N 122° 12.727' W Redwood City Harbor 37° 30.292' N 122° 12.420' W Redwood Shores Lagoon 37° 32.315' N 122° 14.691' W Richmond Yacht Club 37° 54.510' N 122° 23.015' W RMC Lonestar Cement Marina Terminal 37° 30.850' N 122° 12.522' W Ron Valantine Boat Dock 37° 46.160' N 122° 17.255' W Ryer Island Boat Harbor (Veneco) 38° 4.467' N 122° 0.713' W San Francisco Dry Dock 37° 45.801' N 122° 22.984' W San Francisco Marina (Golden Gate & St. Francis Yacht Clubs) 37° 48.410' N 122° 26.661' W San Francisco Yacht Club 37° 52.308' N 122° 27.735' W San Leandro Marina 37° 41.820' N 122° 11.485' W San Rafael Creek, Residential Berths (Canal) 37° 58.068' N 122° 30.680' W San Rafael Rock Quarry 37° 59.302' N 122° 26.838' W San Rafael Yacht Harbor 37° 58.134' N 122° 31.062' W Sausalito Marina Properties 37° 51.603' N 122° 29.044' W Sausalito Yacht Club/Harbor 37° 51.581' N 122° 28.877' W

Schnitzer Steel 37° 47.628' N 122° 17.538' W Schoonmaker Point Marina 37° 51.859' N 122° 29.479' W Shamrock Materials 38° 13.515' N 122° 36.478' W Shell Terminal 38° 2.002' N 122° 7.380' W South Beach Yacht club 37° 46.804' N 122° 23.158' W Strawberry Recreation District 37° 53.311' N 122° 30.001' W Suisun City Marina 38° 14.056' N 122° 2.247' W Time Oil Terminal 37° 55.079' N 122° 21.856' W Timmers Landing 37° 54.554' N 122° 28.481' W Tosco Refinery 37° 54.926' N 122° 21.900' W US Army Reserve Center, Mare Island 38° 5.277' N 122° 15.468' W USCG Integrated Support Command, Alameda 37° 46.753' N 122° 14.943' W USCG Station Golden Gate 37° 49.996' N 122° 28.581' W USCG Station Vallejo/Mare Island 38° 6.751’ N 122° 16.265’ W USCG Station Yerba Buena Island 37° 48.568' N 122° 21.677' W USS Posco 38° 1.915' N 121° 52.250' W Valero Refinery Co. - Benicia Crude Dock 38° 2.676' N 122° 7.741' W Vallejo Ferry Terminal 38° 5.982' N 122° 15.808' W Vallejo Marina 38° 6.424' N 122° 16.096' W Vallejo Yacht Club 38° 6.283' N 122° 16.063' W WesPac Energy Pittsburg 38° 2.542’ N 121°53.565’ W WETA Central Bay Ferry Maintenance Facility 37°46'16.48"N 122°17'57.29"W WETA Harbor Bay Terminal 37°44.182’ N 122°15.423’ W WETA Vallejo Baylink Ferry Terminal 38° 6.001' N 122° 15.789' W

Program administration and activities are described in detail below, with certain limitations and restrictions. Specifically, this programmatic consultation will not cover the following: (1) any new or previously unauthorized dredging; (2) any deepening of areas below currently authorized depths plus allowable overdepth; (3) dredging for power plant maintenance; and (4) dredging for levee maintenance. The reinitiated consultation and this biological opinion consider the effects of the remaining duration of the LTMS Program. Originally a 50-year program, the LTMS has been in effect for 15 years, resulting in a 35-year remaining lifetime for the program.

No interrelated and interdependent activities have been identified for this project. Although the proposed LTMS Program will help maintain existing maritime facilities including marinas, docks, wharfs, ports and navigation channels, future implementation of the program will not increase in the number of vessel transits per day, vessel size, or other maritime activities in the action area for the foreseeable future because the LTMS Program does not include any additional dredging for new or expanded maritime facilities. Therefore, the impacts of shipping and other maritime activities are considered as part of the environmental baseline.

1.3.1 Administration of the Program

The DMMO will continue to provide a coordinated review of dredging and dredged material disposal project proposals1. The DMMO does not issue permits; rather it makes consensus-based recommendations to the member agencies on the completeness of permit applications, adequacy of sediment sampling and analysis plans (SAP), and suitability of sediments for proposed disposal locations.

The DMMO meets twice monthly to exchange technical information about dredging projects.

Meetings are open to the public. The Corps serves as the “host” agency for the DMMO and provides logistical support for meetings. The Corps also maintains DMMO files and maintains the DMMO website, containing information on the DMMO and dredging-related issues. Dredge permit applicants must submit to the DMMO a SAP to confirm the suitability of sediment proposed to be dredged for unconfined aquatic placement in-Bay or at San Francisco Deep Ocean Disposal Site (SF-DODS), or upland/beneficial reuse placement. However, an applicant may alternatively submit a written request for a “Tier I” exclusion from the testing requirements based on factors such as previous testing history and physical characteristics of the material proposed for dredging. The LTMS Program permitting agencies (i.e., Regional Water Board, EPA, Corps, and BCDC) have delegated to the DMMO ultimate discretion over the required content and adequacy of the SAP. Sediment testing and analysis must be implemented as approved in the SAP and the results presented to the DMMO. Based on the results of sediment testing, the DMMO is responsible for ensuring all material dredged is physically, chemically, and biologically suitable for its disposal/placement site.

When some material is not suitable for the proposed disposal or placement site, the DMMO works with permittees to identify an appropriate alternative placement or disposal site. In cases where an alternative site is unavailable or perceived as too costly to use, permittees often choose not to immediately dredge that portion of the project. In addition to addressing sediment quality, the DMMO works closely with permittees to ensure dredging and disposal is performed within the relevant environmental work windows and other permit requirements. Annual reports prepared by the DMMO summarize the dredging and disposal activities of the previous year, and this information is used by the LTMS agencies for periodic review of the program.

In response to Conservation Measures developed during the 2011 NMFS-Corps consultation pursuant to the essential fish habitat (EFH) provisions of the Magnuson-Stevens Fishery Conservation and Management Act (MSA), the DMMO improved its procedures and requirements for sediment testing at dredge projects conducted in San Francisco Bay.

Specifically, the new procedures include more systematic and predictable requirements for bioaccumulation testing and “residual” (post-dredge sediment surface) sampling and characterization. The program improvements also tie the sediment testing to San Francisco

1 The DMMO is a joint program with representation from the Corps, EPA, BCDC, and Regional Water Board, and State Lands Commission. NMFS, California Department of Fish and Wildlife, and U.S. Fish and Wildlife Service are encouraged to participate at DMMO meetings as commenting resource agencies (see consultation history section of this opinion).

Bay’s existing Total Maximum Daily Load (TMDL) for mercury and PCB’s, and the Regional Monitoring Program for San Francisco Bay. The Regional Monitoring Program is part of a region-wide program aimed at identifying chemical thresholds for sediment management. The LTMS agencies consider the DMMO and the sediment testing requirements to be ongoing projects that will continue to adapt as scientific understanding improves, testing methods advance, and resources permit.

1.3.2. Dredging Activities

Dredging involves the removal or excavation of bottom sediments from the aquatic environment in order to create or maintain waterways deep enough to support navigation, including access channels, turning basins, ports, and marinas. Dredging methods can be divided into two broad categories, mechanical and hydraulic (Gren 1976), differentiated primarily by the volume of water furnished with the dredged material. Mechanical dredges are commonly used for smaller, localized sites, and include clamshell, bucket, and excavator dredges. Hydraulic dredges remove and transport sediments by suction and pumping, which mixes large volumes of water with the sediment to form a slurry that is piped or barged to a disposal area. The most common hydraulic dredges include the cutterhead and the hopper dredge. Below is a list of the actions currently employed for the purpose of maintaining previously dredged areas in the San Francisco Bay Region.

1.3.2.1 Mechanical Dredging

Mechanical dredges remove bottom sediments by direct application of mechanical force to dislodge sediments, scooping the sediments from the bottom and placing them into a barge or scow for transport to a dredge disposal or reuse site. Mechanical dredging is typically used at the larger port and wharf facilities. Buckets on mechanical dredges typically range in size from 1 to 25 cubic yards.

Clamshell: A clamshell dredge employs a vertical loading grabber connected to wire rope which is lowered in the open position into the sediment, closed around the sediment load, and raised above the water surface where the sediment is deposited on a barge. Several diverse bucket configurations are available to be specifically tailored to the various sediment types.

Environmental bucket: An environmental bucket is similar to a conventional clamshell dredge;

however the environmental bucket generally has features that include some combination of covers, exterior pulleys, and sealed joints, intended to reduce the amount of sediments that can spill or flow out of the bucket during dredging activities (Wang et al. 2002).

Excavator: Excavator dredging involves a backhoe excavator mounted to a barge. The excavator bucket is lowered to the seafloor where it scoops up sediment, brings the sediment up through the water column in the open bucket, where it is deposited on the barge.

1.3.2.2 Hydraulic Dredging

Hydraulic dredges remove bottom sediments by suction force and those sediments are transported in the liquid slurry form for storage or transport to a disposal site. The Corps frequently operates one of two government-owned hopper dredges Essayons and the Yaquina, in San Francisco Bay for maintenance of Federal navigation channels. Small scale suction dredge are commonly used for marina projects and under-pier clearing. The intakes of some hydraulic dredges are equipped with a rotating cutter apparatus (i.e., cutterhead) to help break up bottom sediments and facilitate the pumping of the sediment up through the pipe.

Suction/Hopper: Hopper dredges are ships with both a suction pipe for dredging and a large hull for holding and transporting the dredged material. Hopper dredges are equipped with a drag arm, long suction pipes with drag heads attached to the end. During active dredging, the drag arm is slowly dragged across the seafloor using the forward motion of the vessel. The sediment and water slurry is drawn up through the drag head and drag arm by on-board pumps and deposited within the hopper bin. Once full, dredging ceases and hopper dredges move directly to the disposal site where dredged material is disposed through large doors at the bottom of the dredge. Although the Essayons and the Yaquina are not currently equipped as such, some hopper dredges have the ability to offload material via pipeline and pumps directly to an upland or beneficial reuse site. The intake pipe on the Essayons is 28 inches in diameter and the intake pipe on the Yaquina is 20 inches.

Suction: Suction dredges without a “hopper” cannot store the dredged material on-board and typically transport dredged materials in a slurry via pipeline for disposal at an upland or beneficial reuse location. As with hopper dredges, suction dredges are equipped with a drag arm and this arm moves across the seafloor to collect sediments. The most common small barge-mounted suction dredge used in San Francisco Bay is equipped with an 8- to 12-inch diameter intake.

1.3.2.3 Knockdown

Knockdowns employ an I-beam or other similar equipment to redistribute shoaled sediment into deeper areas within the dredging site. These are generally used for smoothing the bottom following conventional mechanical or hydraulic dredging, and for managing localized mounds without the need to mobilize a full dredging episode. Typically knockdowns are used to alleviate shoaling in marinas, ports, and in some navigational channels.

1.3.3 Disposal

During the dredging process the sediment removed from the seafloor must be transported to and disposed of at an alternate location. Dredged material may be deposited in several different location types, including in-bay, nearshore and offshore locations, and upland disposal locations.

1.3.3.1 In-Bay Aquatic Disposal

In-bay disposal sites are open water locations within the estuarine waters of San Francisco Bay and inside the Golden Gate. There are currently four in-bay sites approved for disposal:

Carquinez Strait (SF-9); San Pablo Bay (SF-10); Alcatraz (SF-11); and Suisun Bay (SF-16) (Figure 1).

1.3.3.2 Nearshore Aquatic Disposal

Nearshore disposal sites are open water locations in ocean waters outside the Golden Gate, but within 10 nautical miles of the Golden Gate Bridge. Currently there are two nearshore sites designated for placement of dredged material: San Francisco Bar Channel (SF-8) and Ocean Beach Demonstration Site (SF-17), both located south of the Main Ship Channel (Figure 1).

1.3.3.3 Ocean Disposal

Offshore disposal sites are deep open water locations in ocean waters outside of the Golden Gate Bridge. There is currently only one offshore disposal site. The San Francisco Deep Ocean Disposal Site (SF-DODS) is located approximately 49 nautical miles outside the Golden Gate (Figure 1).

1.3.3.4 Upland Disposal/Beneficial Reuse

Upland disposal includes any disposal site not located in the open waters of the San Francisco Bay estuary or ocean waters. Upland disposal may include a sanitary landfill or a beneficial reuse site. Beneficial use is the use of dredged material for human or environmental purposes and are intended to provide benefits beyond that of simple disposal. Beneficial reuse sites include placement at diked former bayland areas under conversion to wetlands, shoreline stabilization and erosion control, levees requiring maintenance, beach nourishment, construction sites, or capping of contaminated sediments. Both mechanical and hydraulic equipment may be used to transport dredged material to an upland disposal or beneficial reuse site.

Beneficial reuse sites for dredged material utilized by the LTMS Program to date include Montezuma Wetlands, Port of Oakland Middle Harbor Enhancement Area, Inner Bair Island, Hamilton Wetland Restoration Site, Sonoma Baylands, Winter Island and several remediation project sites. Upland/beneficial reuse sites are typically confined disposal in diked nearshore areas so that dredged materials do not come in direct contact with aquatic environs. Beneficial reuse sites currently available in 2015 to accept dredged material are limited to Montezuma Wetlands, Winter Island, and Cullinan Ranch; however, several additional sites are anticipated to be developed over the remaining term of the LTMS Program.

1.3.4 Avoidance, Minimization and Mitigation Measures

The October 2014 LTMS Program consultation update provided to NMFS by the Corps and EPA proposes the following measures to avoid, minimize and mitigate the impacts of dredging and disposal in the San Francisco Bay Region. Corps conducted or funded dredging of federal navigation channels will be performed in compliance with these measures. Non-federal dredge projects authorized by the Corps’ Regulatory Branch will include these measures as permit conditions.

1.3.4.1 Environmental Work Windows

1. For NMFS-listed salmon, steelhead and green sturgeon in San Francisco Bay (inshore of the Point Lobos-Point Bonita line), San Pablo Bay, and Suisun Bay, the work window is June 1 through November 30. Routine dredging and disposal operations conducted pursuant to the LTMS program during this time frame do not need further coordination with NMFS.

2. No dredging (mechanical or hydraulic) will be permitted from December 1 through May 31 upstream or within 1000 feet bayward of the mouths of Larkspur/Corte Madera Creek, Napa River Channel/Mare Island Strait (including Vallejo), Petaluma River, and Novato Creek without individual consultation.

3. For all other locations, a proponent may plan a project that performs work outside the work window (e.g., from December 1 through May 31) if the project mitigates for potential impacts by placing the dredged sediment at a beneficial reuse site that NMFS…