A.01.13_EFHDredgeProgrammatic_07_14_2010_final.pdf

MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT

ESSENTIAL FISH HABITAT CONSULTATION

ACTION AGENCIES: United States Army Corps of Engineers, South Pacific Division, San Francisco District (USACE)

United States Environmental Protection Agency, Region IX

(USEPA)

ACTION: Operations and maintenance dredging in the San Francisco Bay area and associated dredged material placement

CONDUCTED BY: National Marine Fisheries Service, Southwest Region

TRACKING NUMBER: 2009/06769

DATE ISSUED: JULY 13, 2010

Table of Contents

I. STATUTORY AND REGULATORY INFORMATION

II. BACKGROUND AND CONSULTATION HISTORY

III. PROPOSED ACTION

A. Overview of Programmatic Consultation B. Actions

1. Dredging

2. Knockdown

3. Disposal

C. LTMS Environmental Protection Measures

IV. ACTION AREA

A. Geographic scope B. Habitat types

1. Soft bottom habitat

2. Wetland habitat

3. Eelgrass habitat

V. EFFECTS OF THE ACTION

A. Level of Effect

1. Low

2. Medium

3. High

B. Types of Effects

1. Direct removal/burial of organisms

2. Turbidity/siltation

3. Contaminant release

4. Release of oxygen consuming substances

5. Entrainment

6. Noise

7. Adjacent habitat

8. Invasive species

9. Alteration to hydrodynamic regimes and physical habitat

C. Effect by action

1. Dredging

2. Knockdown

3. Disposal

D. Effects Analysis

1. Soft bottom habitat (prey loss)

2. Wetland habitat (prey and refugia loss)

3. Eelgrass habitat (refugia loss)

4. Contaminants effects analysis

5. Other effects

6. Area outside San Francisco Bay

VI. EFH CONSERVATION RECOMMENDATIONS

A. Soft bottom habitat permanent disturbance (prey loss) B. Eelgrass indirect effects (refugia loss) i ii

C. Eelgrass direct effects (refugia loss) D. Turbidity E. Contaminants F. Invasives G. Other Submerged Aquatic Vegetation H. Reporting requirements

VII. STATUTORY RESPONSE REQUIREMENT

VIII. SUPPLEMENTAL CONSULTATION

IX. LITERATURE CITED

Appendix 1. Contaminant Analysis Appendix 2. Eelgrass Indirect Effects Flowchart Appendix 3. Light Monitoring Protocol Appendix 4. Southern California Eelgrass Mitigation Policy Appendix 5. EFH Dredge Programmatic Report Form Appendix 6. Comments provided by USACE and USEPA on draft consultation Appendix 7. NMFS Responses

I. STATUTORY AND REGULATORY INFORMATION

The Magnuson-Stevens Fishery Conservation and Management Act (MSA), as amended by the Sustainable Fisheries Act of 1996, establishes a national program to manage and conserve the fisheries of the United States through the development of federal Fishery Management Plans (FMPs), and federal regulation of domestic fisheries under those FMPs, within the 200-mile U.S.

Exclusive Economic Zone (“EEZ”). 16 U.S.C. §1801 et seq. To ensure habitat considerations receive increased attention for the conservation and management of fishery resources, the amended MSA required each existing, and any new, FMP to “describe and identify essential fish habitat for the fishery based on the guidelines established by the Secretary under section 1855(b)(1)(A) of this title, minimize to the extent practicable adverse effects on such habitat caused by fishing, and identify other actions to encourage the conservation and enhancement of such habitat.” 16 U.S.C. §1853(a)(7). Essential Fish Habitat (EFH) is defined in the MSA as “those waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity” 16 U.S.C. §1802(10). The components of this definition are interpreted at 50 C.F.R.

§600.10 as follows: “Waters” include aquatic areas and their associated physical, chemical, and biological properties that are used by fish and may include aquatic areas historically used by fish where appropriate; “substrate” includes sediment, hard bottom, structures underlying the waters, and associated biological communities; “necessary” means the habitat required to support a sustainable fishery and the managed species’ contribution to a healthy ecosystem; and “spawning, breeding, feeding, or growth to maturity” covers a species’ full life cycle.

Pursuant to the MSA, each federal agency is mandated to consult with NMFS (as delegated by the Secretary of Commerce) with respect to any action authorized, funded, or undertaken, or proposed to be, by such agency that may adversely affect any EFH under this Act. 16 U.S.C.

§1855(b)(2). The MSA further mandates that where NMFS receives information from a Fishery Management Council or federal or state agency or determines from other sources that an action authorized, funded, or undertaken, or proposed to be, by any federal or state agency would adversely effect any EFH identified under this Act, NMFS has an obligation to recommend to such agency measures that can be taken by such agency to conserve EFH. 16 U.S.C.

§1855(4)(A). The term “adverse effect” is interpreted at 50 C.F.R. §600.810(a) as any impact that reduces quality and/or quantity of EFH and may include direct or indirect physical, chemical, or biological alterations of the waters or substrate and loss of, or injury to, benthic organisms, prey species and their habitat, and other ecosystem components, if such modifications reduce quantity and/or quality of EFH. In addition, adverse effects to EFH may result from actions occurring within EFH or outside EFH and may include site-specific or habitat-wide impacts, including individual, cumulative, or synergistic consequences of actions.

If NMFS determines that an action would adversely affect EFH and subsequently recommends measures to conserve such habitat, the MSA proscribes that the federal action agency that receives the EFH Conservation Recommendation must provide a detailed response in writing to NMFS within 30 days after receiving EFH Conservation Recommendations. The response must include a description of measures proposed by the agency for avoiding, mitigating, or offsetting the impact of the activity on EFH. In the case of a response that is inconsistent with NMFS EFH Conservation Recommendations, the federal agency must explain its reasons for not following the recommendations. 16 U.S.C. §1855(b)(4)(B).

II. BACKGROUND AND CONSULTATION HISTORY

The Long Term Management Strategy (LTMS) for the Placement of Dredged Material in the San Francisco Bay was organized in 1990 to evaluate and address the potential direct, indirect and cumulative effect of dredging and aquatic disposal of dredged material in the San Francisco Bay.

The LTMS agencies include USACE, USEPA, San Francisco Bay Conservation and Development Commission (BCDC), and San Francisco Bay Regional Water Quality Control Board. The LTMS agencies issued a final Environmental Impact Statement (EIS)/Programmatic Environmental Impact Report (EIR) in 1998 with its recommended program to reduce in-Bay disposal and increase beneficial reuse of dredged material, and signed the Record of Decision in 1999. 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. The LTMS EIS/EIR and subsequent Management Plan did not explicitly include EFH consultation. Coordination with NMFS regarding EFH consultation began in 2004, with an official request for consultation on July 21, 2009. Because of the LTMS agency partnership and at the request of the USEPA and USACE this programmatic consultation has included the state agencies.

2004 – 2007 USACE, USEPA, and NMFS began discussions for Programmatic EFH consultation.

November 2007 USACE provided NMFS with Draft EFH Assessment February 4, 2008 NMFS submitted comments on Draft EFH Assessment to USACE, USEPA, and BCDC including requests for additional information.

Additional information requests included:

Specific reports referenced in the document Electronic data files presented in the document Data missing from tables in the document

February 19, 2008 USEPA provided NMFS with three of the requested reports.

February 23, 2009 NMFS requested status update from USACE on EFH Assessment based on comments provided and restated additional information request from 2008 not yet received.

July 21, 2009 USACE and USEPA issued request for Programmatic EFH consultation for operations and maintenance dredging activities in San Francisco Bay and associated placement of dredged material.

August 2009 NMFS requested additional information:

Electronic data files presented in the document Data missing from tables in the document

November 2009 - USACE and NMFS coordinated to fill data gaps needed for January 2010 analysis of action effects on EFH.

February - NMFS, USACE, USEPA, and BCDC met to discuss results of analyses May 2010 and potential mitigation options.

May 1, 2010 NMFS provided a first draft of this document to USACE and USEPA for preliminary review.

May 21, 2010 USACE and USEPA comments received by NMFS (Appendix 6).

June 14, 2010 NMFS requested additional information from USACE and USEPA based on comments received.

June 17, 2010 Discussion regarding contaminant analysis and associated recommendations between USEPA and NMFS staff.

June 22, 2010 Additional information provided by USACE and USEPA.

July 13, 2010 Programmatic consultation concluded.

III. PROPOSED ACTION

A. Overview of Programmatic Consultation

This programmatic consultation applies to operations and maintenance dredging and dredged material placement/disposal projects within the defined geographic area (see section IV.A below) conducted by USACE (federally-authorized dredging projects) or by non-federal entities which USACE and USEPA review for authorization under section 10 of the Rivers and Harbors Act of 1899 (33 USC §403), section 404 of the Clean Water Act (33 USC §1344), and/or section 103 of the Marine Protection Research and Sanctuaries Act (33 USC §1401).

There are 7 in-water disposal sites and 123 maintenance dredging projects (15 generally maintained by USACE and 108 non-USACE) proposed for inclusion in this programmatic consultation (Table 1). Up to 10 additional non-federal maintenance dredging projects that have been previously authorized but are not explicitly named in Table 1 (referenced as “dummy” projects) may be covered by this programmatic consultation (see section V.D.1 for explanation of dummy projects). Some projects in Table 1 may not be covered if project-specific EFH Conservation Recommendations (i.e., those recommendations related to eelgrass and contaminant levels, see section VII below) are not accepted.

Program 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. Maintenance dredging of new or deepened areas following completion of initial work may be considered part of this consultation pending NMFS approval.

The time of coverage by this programmatic consultation matches the remaining duration of the LTMS Program. Originally a 50 year program, the LTMS has been in effect for 11 years, resulting in a 39 year lifetime for the current consultation. This programmatic consultation will cover the actions specified below until June, 2049. The USACE, USEPA, and NMFS will meet on the LTMS six year review cycle, or as needed, for the following purposes: (1) to evaluate and discuss the continued effectiveness of the programmatic consultation, (2) to ensure that activities authorized by the programmatic consultation continue to minimize adverse effects to EFH, and

(3) to update procedures and project criteria, if necessary. The most recent LTMS six year review occurred in 2006, with the next review scheduled for 2012. An assessment of this programmatic consultation will occur in conjunction with the 2012 LTMS review, with subsequent assessments in 2018, 2024, 2030, 2036, 2042, and 2049.

At any time, NMFS may revoke or revise this programmatic consultation if it is determined that it is not being implemented as intended or if new information becomes available indicating a significant discrepancy in either the effects analysis or effectiveness of EFH Conservation Recommendations.

B. Actions

Below is a list of the actions currently employed for the purpose of maintaining previously dredged areas in San Francisco Bay:

1. Dredging The dredging process 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.

a. 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.

i. 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 barge for deposit. Several diverse bucket configurations are available to be specifically tailored to the various sediment types.

ii. 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).

iii. 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.

b. Hydraulic dredging: Hydraulic dredges remove bottom sediments by suction force and those sediments are transported in the liquid slurry form for transport to a dredge disposal site.

i. Cutterhead: Cutterhead dredges are equipped with a rotating cutter apparatus surrounding the intake end of a suction pipe. The revolving cutterhead helps to break up bottom sediments and facilitates the pumping of the sediment up through the pipe.

ii. Suction/Hopper: Suction or 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 the vessel moves directly to the disposal site where dredged material is disposed through large doors at the bottom of the dredge.

2. 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.

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, offshore, and nearshore unconfined locations, and upland disposal locations.

a. In-Bay: In-Bay disposal sites are open water locations within the San Francisco Bay action area (as defined in section IV below) but limited to the estuarine waters inside the Golden Gate Bridge. There are currently four in-Bay sites approved for disposal, including SF-9 and SF-10 in San Pablo Bay, SF-11 in the Central Bay, and SF-16 in Suisun Bay.

b. Offshore: Offshore disposal sites are open water locations within the San Francisco Bay action area (as defined in section IV below) located in the ocean waters outside of the Golden Gate Bridge, far from shore in deep water. There is currently one offshore, deep water site approved for placement of dredge material. SF-DODS (Deep Ocean Disposal Site) is located approximately 49 nautical miles offshore from the Golden Gate Bridge, encompassing an area of 4160 acres, at depths ranging from 2500 to 3000 meters.

c. Nearshore: Nearshore disposal sites are open water locations within the San Francisco Bay action area (as defined in Section IV below), located in the ocean waters outside the Golden Gate Bridge, but within 10 nautical miles of the Golden Gate Bridge. Currently there are two nearshore sites designated for placement of dredged material; these include SF-8 and SF-17 (under consideration) both located south of the Main Ship Channel.

d. Upland: Upland disposal includes any disposal site not located in the open waters of the San Francisco Bay action area (as defined in section IV below), and may include diked former baylands, wetlands surrounding the margins of the San Francisco Bay estuary, confined disposal facilities, rehandling facilities, levees requiring maintenance, sanitary landfills, construction sites, or sites suitable for habitat development (restoration, enhancement). Both mechanical and hydraulic equipment may be used to transport dredged material to an upland disposal site.

C. LTMS Environmental Protection Measures

Below is a list of the environmental protection measures implemented by the LTMS agencies to avoid or minimize adverse effects to EFH:

1. Reducing in-Bay disposal: Over the life of the San Francisco Bay LTMS, proposed 80 percent reductions in the volume of dredged material disposed of in the Bay will be achieved through the elimination of unnecessary dredging activities, and by maximizing reuse of dredged sediments. To date, in-Bay disposal has been reduced from 6.0 million cubic yards per year pre- 1990 to less than 2.0 million cubic yards per year in 2009. The current level of annual in-Bay disposal is 1.64 million cubic yards.

2. Beneficial reuse of dredged material (habitat restoration): Dredged sediments that are determined to be suitable for reuse are used maximally to benefit the environment. The majority of beneficial reuse has been for restoring wetland ecosystems around San Francisco Bay (Table 2). Sediments are also being used to renourish eroded areas of coastline at Ocean Beach.

3. Dredged Material Management Office (DMMO) regulation on quality of sediments disposed in-Bay: Material to be dredged must be tested to determine wether it is suitable for the proposed disposal or reuse site.

Funding of scientific studies to improve knowledge about potential impacts of dredging and dredged material placement: To date, the San Francisco Bay LTMS has provided over $7 million in funding to support studies to investigate effects of dredging and dredge disposal on sensitive fish species, mercury contamination at wetland reuse sites, assessments of sediment resuspension associated with dredging activities and effect of turbidity on sensitive fish species.

Information on how dredging has been modified or fish habitat has been protected as a result of these LTMS-funded studies has not been compiled for the purpose of this programmatic consultation.

The environmental protection measures described here and in the consultation initiation package as parts of the proposed action reduce or avoid adverse effects to EFH. The NMFS regards these environmental protection measures as integral components of the proposed action and expects that all proposed activities will be completed consistent with those measures. Any deviation from these environmental protection measures will be beyond the scope of this consultation and may require supplemental consultation to determine what effect the modified action is likely to have on EFH.

IV. ACTION AREA

The proposed activities occur within areas identified as EFH for various life stages of fish species managed with the following Fishery Management Plans (FMP) under the MSA:

Pacific Groundfish FMP – various rockfish, sole and sharks Pacific Salmon FMP – Chinook salmon Coastal Pelagic FMP – northern anchovy, Pacific sardine, mackerel, squid

In addition, some activities will occur within areas designated as Habitat Areas of Particular Concern (HAPC) for various federally managed fish species within the Pacific Groundfish FMP.

HAPC are described in the regulations as subsets of EFH that are rare, particularly susceptible to human-induced degradation, especially ecologically important, or located in an environmentally stressed area. Designated HAPC are not afforded any additional regulatory protection under MSA; however, federal projects with potential adverse impacts to HAPC are more carefully scrutinized during the consultation process. As defined in the Pacific Groundfish FMP San Francisco Bay is designated as estuary HAPC. Submerged aquatic vegetation (SAV), such as eelgrass and widgeon grass, which occurs within the project footprint, is also designated as HAPC.

A. Geographic scope

The action area spans 11 counties, including Marin, Sonoma, Napa, Solano, Sacramento, San Joaquin, Contra Costa, Alameda, Santa Clara, San Mateo, and San Francisco Counties. The geographic scope of potential impacts included in this consultation comprises the estuarine waters of the San Francisco Bay region and portions of the Sacramento-San Joaquin Delta (Delta) west of Sherman Island. It also includes the wetlands and shallow intertidal areas that form a margin around the estuary and the tidal portion of its tributaries. Outside of the Golden Gate bridge, the action area includes ocean waters that encompass the San Francisco Main Ship Channel, the San Francisco Deep Ocean Disposal Site (SF-DODs), the San Francisco Bar Disposal Site (SF-8), the Ocean Beach near shore dredged material beneficial reuse site (SF-17), and the waters that are used by vessels en route to these sites. It does not include the mountainous or inland areas far removed from navigable waters. The action area defines the region where navigational dredging covered by the San Francisco Bay LTMS program may occur, where dredged material disposal and beneficial use sites are located and where additional disposal or beneficial use sites may be feasible. See Figure 1 for detailed representation of the action area and the geographic scope covered by this programmatic.

B. Habitat types

For the purposes of this programmatic consultation, habitats within the geographic scope of the proposed project are categorized and described as follows:

1. Soft bottom habitat Soft bottom substrates are the most common substrate types in San Francisco Bay. They are characterized by a lack of large stable surfaces for plant and animal attachment. Exposure to wave and current action, temperature, salinity, and light penetration determine the composition and distribution of organisms within the sediments (USGS 1998). Two types of soft bottom substrate comprise the majority of the Bay bottom where dredging and disposal activities occur:

sand and fine grain sediment.

a Sand benthic habitat: Bottom sediments that contain greater than 80% sand (particles

0.062 to 2.0 mm in diameter) are considered sand benthic habitat for the purposes of this document. Sand habitat is more dynamic than fine grain habitat due to greater movements of larger grain sediment by wave and current action. This reduces the amount of productivity and invertebrate species diversity in this habitat type, making it less valuable as foraging habitat for fish. However, sand substrate does provide benthic habitat for fish to reproduce, rear, and grow (NMFS 2007).

b Fine grain benthic habitat: Fine grain sediments include mud, silts, and clay (particles

0.001 to 0.062 mm in diameter). Bottom sediments that contain less than 80% sand are considered fine grain benthic habitat for the purposes of this document. Fine grain sediment is considered good foraging habitat for fish because, when undisturbed, it provides a substrate for invertebrate epifauna and infauna, upon which fish prey. Fine grain benthic habitat also provides substrate for fish to reproduce, rear, and grow (NMFS 2007).

2. Wetland habitat There are numerous definitions for the term “wetland” with 19 recently identified by the San Francisco Estuary Institute (SFEI 2009). At the federal level both the US Fish and Wildlife Service (USFWS) and the Army Corps of Engineers (USACE) have specified unique definitions.

The USFWS definition includes the following language:

Wetlands are lands transitional between terrestrial and aquatic systems where the water table is usually at or near the surface or the land is covered by shallow water. For purposes of this classification, wetlands must have one or more of the following three attributes: (1) at least periodically, the land supports hydrophytes, (2) the substrate is predominantly undrained hydric soil; and (3) the substrate is non-soil and is saturated with water or covered by shallow water at some time during the growing season of each year.

The USACE defines wetlands as follows:

The term "wetlands" means those areas that are inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances do support, a prevalence of vegetation typically adapted for life in saturated soil conditions.

Wetlands generally include swamps, marshes, bogs, and similar areas.

The USACE has established identification and delineation procedures for wetlands, specifically the USACE 1987 Wetland Manual and subsequent regional supplements (USACE 2010).

According to the USACE definition and delineation methodology, areas that are not dominated by hydrophytes but that provide wetland beneficial uses and ecological services, such as tidal flats, are not necessarily identified as wetlands. However, tidal flats are known to provide productive shallow water habitat for epibenthic fishes (Sogard and Able 1991).

While all areas of a properly functioning wetland benefit fish in some way, there are specific components that are directly considered fish habitat. For the purposes this document, the following wetland components are considered fish habitat: tidal marsh, tidal flats, and tidal sloughs. Given the varying definitions for the term “wetland”, these wetland components that are important for fish survival, reproduction, and growth to maturity will be collectively referred to as “marsh complex” in subsequent sections.

Tidal marshes, which include brackish and salt marshes, are vegetated wetlands subject to tidal action that occur throughout much of the Bay extending from approximately Mean Sea level to the maximum height of the tides. Established tidal marshes provide an essential and complex habitat for many species of fish, other aquatic organisms and wildlife. Tidal marshes provide foraging habitat and refugia for fish (Boesch and Turner 1984). In the early 1800s, tidal marshes covered some 190,000 acres on the fringes of the Bay. Tidal marsh bordering the Bay now totals approximately 40,000 acres, a loss of approximately 80 percent of the Bay's historic tidal marshes.

Tidal flats occur from the elevation of the lowest tides to approximately Mean Sea Level and include mudflats, sandflats and shellflats. Mudflats comprise the largest area of tidal flat areas and support an extensive community of invertebrate aquatic organisms, such as diatoms, worms and shellfish, as well as fish that feed during higher tides, and plants such as algae and eelgrass.

Of the 50,000 acres of tidal flats that historically occurred around the margins of the Bay, approximately 30,000 acres remain, a reduction of approximately 40 percent (Goals Project 1999).

Sloughs/channels are the primary paths of moving water through wetlands, providing fish access to productive foraging habitat. Sloughs are subtidal, allowing fish permanent access and offering a haven between tidal inundations of salt marshes. Slough habitat is used for more than just transit to productive wetlands as demonstrated by observations of greater species diversity in sloughs than in associated shallow tidal creeks (Desmond et al. 2000). Sloughs occur throughout the San Francisco Bay for example, Montezuma and Suisun Sloughs in Suisun Bay, branches off the lower portions of the Napa and Petaluma Rivers in the North Bay, branches off Corte Madera

Creek in the Central Bay, and Redwood, Alviso, and Guadalupe Sloughs in the South Bay.

3. Eelgrass habitat Eelgrass (Zostera marina) is a flowering vascular plant that grows both subtidally and intertidally in estuaries and in shallow coastal areas. Studies have shown that seagrasses, including eelgrass, are among the areas of highest primary productivity in the world (Herke and Rogers 1993, Hoss and Thayer 1993). In San Francisco Bay, eelgrass beds are considered to be a valuable shallow-water habitat, providing shelter, feeding, or breeding habitat for many species of invertebrates, fishes, and some waterfowl. Eelgrass beds supply organic material to nearshore environments, and their root systems stabilize area sediments. Intermittent eelgrass surveys suggest eelgrass abundance has varied greatly in San Francisco Bay in the last several decades.

In the late 1920s, eelgrass was reported as an abundant species along the shores of San Francisco Bay (Setchell 1929). In 1987 a survey of the Bay found only 128 hectares of eelgrass, with much of the existing habitat exhibiting conditions of environmental stress (Wyllie-Echeverria and Rutten 1989, Wyllie-Echeverria 1990). In 2003 hydro acoustic surveys documented 1165.7 hectares of eelgrass, covering approximately 1 percent of San Francisco Bay (Merkel & Associates 2004).

As discussed above, eelgrass is designated as EFH for various federally-managed fish species within the Pacific Groundfish and Pacific Salmon Fisheries Management Plans (FMP) (PFMC 2008 and PFMC 1999). Eelgrass is also designated HAPC for various species within the Pacific Groundfish FMP. Eelgrass is also considered a special aquatic site under the 404 (b)(1) guidelines of the Clean Water Act (40 CFR Part 230.43). Under these guidelines, special aquatic sites are subject to greater protection than other waters of the United States, because of their significant contribution to the overall environment.

Other native submerged aquatic vegetation, such as widgeon grass (Ruppia) or sago pondweed (Stuckenia or Potamogeton) occurs within San Francisco Bay. While less is known about these species than is known about eelgrass, they likely provide primary productivity and organic material to nearshore environments and may provide shelter for invertebrates and fishes. Native submerged aquatic vegetation is designated as EFH for various federally-managed fish species within the Pacific Groundfish and Pacific Salmon FMPs and is designated HAPC for various species within the pacific Groundfish FMP (PFMC 2008 and PFMC 1999).

V. EFFECTS OF THE ACTION

A. Level of Effect

As described in Section I above, the term “adverse effect” is interpreted at 50 C.F.R. §600.810(a) as any impact that reduces quality and/or quantity of EFH. Impacts to marine habitats from dredging related activities can be placed into three categories: (1) permanent loss; (2) degradation; and (3) periodic disturbance. Generally, activities that lead to a permanent loss of habitat reduce the quantity of habitat, whereas habitat degradation and periodic disturbances result in a loss of habitat quality. The primary differences between the three categories are that recovery of habitat function can not occur from permanent loss, recovery may or may not occur from degradation, and recovery is possible from periodic disturbances (Deegan & Buchsbaum 2005).

These three categories are interpreted as a low, medium or high level of effect in the current analysis, as described below:

1. Low A low level of effect arises from an action that is short term, infrequent, and small in area, and does not affect sensitive habitat types (i.e., eelgrass). The effect is considered a periodic disturbance. While low level effects should be avoided or minimized when possible, compensation is generally not required.

2. Medium A medium level of effect arises when an action occurs for a long time but in a small area or conversely when an action occurs for a short time but over a large area. A medium level of effect may also arise from an action that occurs for a moderate time over a medium area, or negatively affects sensitve habitat types (i.e., eelgrass). The effect is usually considered degradation of habitat. Avoidance or minimization of medium level of effects is recommended.

Mitigation for medium level effects may be required if effects can not be avoided or minimized.

3. High A high level of effect arises from an action that occurs for a long time across a large area, or destroys a sensitive habitat type (i.e., eelgrass). The effect is usually considered a permanent loss. Avoidance or minimization of high level of effects is recommended. Mitigation for high level effects will be required if effects can not be avoided or minimized.

B. Types of Effects

Types of effects that are expected to result from the proposed maintenance dredging and associated activities are described below. While there is overlap among some of the effects (for instance many of things affect the availability of prey) these are the generally accepted categories of the environmental effects of dredging on EFH (Hanson et al. 2003).

1. Direct removal/burial of organisms

a. Prey: Many EFH species forage on infaunal and bottom-dwelling organisms, such as polychaete worms, crustacean, and other EFH prey types. Dredging may adversely effect these prey species at the site by directly removing or burying these organisms (Newell et al.

1998, Van der Veer et al. 1985) and providing substrate for invasive species (see section V.B.8). Recolonization studies suggest that recovery (generally meaning the later phase of benthic community development after disturbance when species that inhabited the area prior to disturbance begin to re-establish) may not be quite as straightforward, and can be regulated by physical factors including particle size distribution, currents, and compaction/stabilization processes following disturbance. Rates of recovery listed in the literature range from several months to several years for estuarine muds (McCauley et al.

1976, Oliver et al. 1977, Currie & Parry 1996, Tuck et al.1998, Watling et al. 2001) to up to

2 to 3 years for sands and gravels (Reish 1961, Thrush et al. 1995, Watling et al. 2001, Gilkinson et al. 2005). Recolonization can also take up to 1 to 3 years in areas of strong current but up to 5 to 10 years in areas of low current (Oliver et al. 1977). Thus, forage resources for fish that feed on the benthos may be substantially reduced before recovery is achieved. Based on available literature, NMFS will assume recovery of prey resources will not occur within one year.

b. Refugia: Dredging activities and the activities of associated equipment may directly damage or destroy spawning nursery and other sensitive habitats such as emergent marshes and subaquatic vegetation, including eelgrass. Direct removal of eelgrass can occur when eelgrass is growing within the project footprint to be dredged (Sabol et al. 2005). Eelgrass may be directly damaged by the dredging vessels and barges themselves. Impacts may result from the dredging vessel grounding, direct damage from propellers, and anchor scour.

Eelgrass is also susceptible to damage by burial resulting from the sediments re-suspended during dredging, dredge material disposal, and from the prop wash associated with dredging vessels.

2. Turbidity/siltation Dredging and dredge disposal activities may result in greatly elevated levels of fine-grained mineral particles, or suspended sediment concentration (SSC), and organic particles in the water column. The finer grain sediments, silts and clays, are more readily suspended and settle out slower than course sediments, such as sand and gravel. Dredging in areas with fine sediments are likely to have greater turbidity impacts than dredging in areas with coarse sediments (Sabol et al. 2005).

Turbidity plumes of suspended particulates reduce light penetration through the water column.

Limited light availability has been identified as the primary factor controlling depth distribution, density, and productivity of eelgrass (Dennison & Alberte 1982, Dennison & Alberte 1985, Dennison & Alberte 1986, Zimmerman et al. 1991). Reductions in light available at the eelgrass canopy due to dredging-related turbidity may result in eelgrass loss, especially where eelgrass is growing at or near its lower depth limit. Even slight reductions in light availability result in lower rates of photosynthesis for subaquatic vegetation (Dennison 1987). Furthermore, phytoplankton productivity in the water column may be reduced as a result of elevated turbidity and increased light attenuation (Cloern 1987).

While fish in San Francisco Bay are exposed to naturally elevated concentrations of suspended sediments resulting from storm flow runoff events, wind and wave action, and benthic foraging activities of other aquatic organisms (Schoellhammer 1996), dredging induced concentrations of suspended sediments may be significantly elevated to have direct effects on fish behavior. If suspended sediment loads remain high for an extended period of time, fish may suffer increased larval mortality (Wilber & Clarke 2001), reduced feeding ability (Benfield & Minello 1996) and be prone to fish gill injury (Nightingale & Simenstad 2001a). Additionally, the contents of the suspended material may react with the dissolved oxygen in the water and result in short-term oxygen depletion to aquatic resources (Nightingale & Simenstad 2001).

3. Contaminant release

Dredging can disturb aquatic habitats by resuspending bottom sediments and, thereby, recirculating toxic metals, hydrocarbons, hydrophobic organics, pesticides, pathogens, and nutrients into the water column (USEPA 2000, SFEI 2008). Any toxic metals and organics, pathogens, and viruses, absorbed or adsorbed to fine-grained particulates in the sediment, may become biologically available to organisms either in the water column or through food chain processes. Dredging can also expose sediments that are more highly contaminated than previous surface sediments causing degradation of benthic and water column habitat. For further discussion of contaminant effects see Appendix 1.

4. Release of oxygen consuming substances The disposal of dredged material can change the chemistry and the physical characteristics of the receiving water at the disposal site by introducing chemical constituents in suspended or dissolved form. The introduction of nutrients or organic material to the water column as a result of the discharge can lead to a high biochemical oxygen demand (BOD), which in turn can lead to reduced dissolved oxygen, thereby potentially affecting the survival of many aquatic organisms.

Increases in nutrients can favor one group of organisms such as polychaetes or algae to the detriment of other types.

5. Entrainment Dredging may result in the direct uptake of aquatic species by the suction field generated at the draghead or cutterhead of a hydraulic dredge (Reine & Clarke 1998). Definitive information in the literature shows that elicit avoidance responses to the suction dredge entrainment occurs for both benthic and water column oriented species (Larson & Moehl 1990, McGraw & Armstrong 1990). However, demersal fish are more likely to become entrained because they reside on or in the bottom substrates (Reine & Clarke 1998). Entrainment of prey species is an adverse effect to EFH through the reduction in the quality of the habitat for managed species. Entrainment of demersal fish by mechanical dredges, though rare, has also been documented1. Disposal of dredged material may result in the direct uptake of aquatic species, both EFH species and their prey, when an offloader is used to transport material. Entrainment can occur when a pump intakes water to generate the slurry (typically an 80:20 mixture of water and dredged material) that an offloader requires for material transport.

6. Noise Dredging equipment and dredging related activities can generate underwater sound pressure waves that may adversely affect the ecological functioning of EFH. Sources of these underwater sounds originate from vessel propellers, pumps, generators, and from dredge buckets and dragheads coming in contact with the substrate (Clarke et al. 2002, Dickerson et al. 2001).

These pressure waves have been shown to injure and kill fish (e.g.,, CalTrans 2001, Longmuir & Lively 2001, Stotz & Colby 2001, Stadler, pers. obs. 2002). Injuries associated directly with dredging are poorly studied, but include rupture of the swimbladder and internal hemorrhaging (CalTrans 2001, Abbott & Bing-Sawyer 2002, Stadler, pers. obs. 2002). Sound pressure levels (SPL) 100 decibels (dB) above the threshold for hearing is thought to be sufficient to damage the auditory system in many fishes (Hastings 2002).

1 Personal communication from J. Crocker, National Marine Fisheries Service, Protected Resources Division, 55 Great Republic Drive, Gloucester, MA, 01930, February 2010.

7. Adjacent habitat Though dredging or disposal activities may be confined to a localized area, tides and currents can have a significant influence on the dispersal of suspended sediments into the adjacent areas.

Indirect impacts to adjacent undredged areas may occur as a result of increased turbidity and possibly siltation associated with dredging activities (Sabol et al. 2005).

8. Invasive species The introduction of exotic species into estuarine and marine habitats has been well documented (Rosecchi et al. 1993, Kohler & Courtenay 1986, Spence et al. 1996). Exotic fish, shellfish, pathogens, and plants can enter the environment from industrial shipping (e.g., as ballast), recreational boating, aquaculture, biotechnology, and aquariums. Dredging activities contribute to the establishment of invasive species in several ways. Barges and hydraulic dredges that travel into San Francisco Bay carrying ballast waters from other areas can directly transport and introduce invasive species. The maintainence of shipping channels via dredging may indirectly lead to transport of invasive species by allowing large vessels (able to travel from far distances) access to the Bay. Additionally, the act of removing soft-bottom sediments and their associated biotic assemblages during dredging creates an area of disturbance which is extremely susceptible to recolinization by invasive species, often resulting in the displacement of native species. As a result, dredging can increase both the number of new invasive species entering the bay and the distribution and abundance of existing invasive species in the bay. Finally, disposal of non-native species with dredged materials at dipsersive in-Bay sites also allows increased distribution and abundances of existing invasive species.

The transportation of nonindigenous organisms to new environments can have many severe impacts on habitat (Omori et al. 1994). Long-term impacts of the introduction of nonindigenous and reared species can change the natural community structure and dynamics, lower the overall fitness and genetic diversity of natural stocks, and pass and/or introduce exotic lethal disease.

Overall, exotic species introductions create five types of negative impacts: 1) habitat alteration,

2) trophic alteration, 3) gene pool alteration, 4) spatial alteration, and 5) introduction of diseases.

Habitat alteration includes the excessive colonization of exotic species which preclude the growth of endemic organisms. The introduction of exotic species may alter community structure by predation on native species or by population explosions of the introduced species. Spatial alteration occurs when territorial introduced species compete with and displace native species.

Although hybridization is rare, it may occur between native and introduced species and can result in gene pool deterioration. Non-native plants and algae can degrade coastal and marine habitats by changing natural habitat qualities. Introduced organisms increase competition with indigenous species or forage on indigenous species, which can reduce fish and shellfish populations. Long-term impacts from the introduction of nonindigenous and reared species can change the natural community structure and dynamics, lower the overall fitness and genetic diversity of natural stocks, and pass and/or introduce exotic lethal diseases. The introduction of exotic organisms also threatens native biodiversity and could lead to changes in relative abundances of species and individuals that are of ecological and economic importance. The introduction of bacteria, viruses, and parasites is another severe threat to EFH as it may reduce habitat quality. New pathogens or higher concentrations of disease can be spread throughout the environment resulting in deleterious habitat conditions.

9. Alteration to hydrodynamic regimes and physical habitat Dredging may modify current patterns and water circulation of the habitat by changing the direction or velocity of water flow, water circulation, or dimensions of the water body traditionally used by fish for food, shelter or reproductive purposes.

C. Effect by action

1. Dredging Certain effects of dredging are ubiquitous and do not vary significantly in the level of intensity among the various equipment types. Acre-for-acre of bottom substrate disturbed, the effects of a hydraulic dredge are assumed equivalent to mechanical dredges in terms of the direct removal/burial of organisms, influencing invasive species abundance and distribution, and alteration of hydrodynamic regimes and physical habitat. However, for other effects, such as turbidity, noise, and entrainment, the nature of these direct and indirect effects, and the level of those effects vary by the types of equipment used, site specific conditions, and sediment type at the site.

a. Mechanical dredging: Mechanical dredges are moderately precise but typically generate more suspended sediments throughout the water column than hydraulic dredges. Sediments may become suspended due to the bucket’s impact to the bottom, material washing from the top and side of the bucket as it passes through the water column, sediment spillage as it breaks the water surface, spillage of material during barge loading, and intentional overflow in an attempt to increase the barge’s effective load (Nightingale & Simenstead 2001). A study characterizing the spatial extent of turbidity plumes during dredging operations in Oakland Harbor found the closed bucket dredge generated elevated concentration of suspended sediments. Ambient Total Suspended Sediment (TSS) concentrations were typicall less than 50 mg/l. While exact plume trajectories were dynamic, turbidity levels above ambient were detected up to 400 meters both up- and down-current from the source.

But in general, significantly elevated TSS concentrations greater than 225 mg/l were detected up to 250 meters from the source (MEC Analytical Instruments, Inc. 2004).

In general, mechanical dredges produce a complex combination of several different types of repetitive sounds which may be intense enough to cause injury to fish, though the intensity, periodicity, and spectra of emitted sounds differ among the dredge types (Clarke et al. 2002, Dickerson et al. 2001). The most intense sound impacts are produced during the bucket’s impact with the substrate, with peak sound pressure levels (SPL) of 124 dB measured 150 meters from the bucket strike location (Clarke et al. 2002). Entrainment is not an impact typically associated with mechanical dredges.

i. Clamshell: A clamshell dredge if properly maintained and operated may be effective in dredging sediments without resulting in excessive turbidity plumes. However, when not properly maintained or operated, clamshell dredges may generate significant concentrations of suspended sediment throughout the water column. Clamshell dredges have a repetitive sequence of sounds generated by the winches, bucket impact with the substrate, closing and opening the bucket, and sounds associated with dumping the dredged material into the barge. Although clamshell dredges generate less turbidity than excavator dredges, high turbidity is common during routine operations.

ii. Environmental bucket: Modifications to the traditional clamshell bucket design results in less sediment re-suspension than the traditional clamshell. The enclosed nature of this type of bucket is intended to reduce the amount of sediment that spills out of the bucket during digging, lifting through the water, or exiting the water surface. Hayes et

al. (1984) found that environmental buckets provided up to 35 to 45 percent reduction of suspended sediment in the middle and upper water column compared to the conventional clamshell. Other than the reduction in suspended sediment, the effects of the environmental bucket are comparable to those of the traditional clamshell dredge.

iii. Excavator: Excavator dredges result in the highest suspended sediment concentrations throughout the water column, as much as 2.5 times higher than that of all other dredge equipment (LaSalle 1990).