Draft Programmatic Environmental Impact Statement/Environmental Impact Report
San Francisco Estuary Invasive Spartina Project: Spartina Control Program
April 2003

5.0   Environmental Compliance

The following environmental laws and regulations are applicable to implementation of the proposed action.

5.1  Applicable Federal Laws, Regulations, Executive Orders, and Approvals

5.1.1 National Environmental Policy Act (42 U.S.C. 4321 et seq.)

This programmatic Environmental Impact Statement/Report (EIS/R) was prepared pursuant to regulations implementing the National Environmental Policy Act (NEPA). NEPA affects federally authorized projects. It was established to ensure that Federal projects or decisions incorporate considerations of environmental consequences into the decision-making process. NEPA establishes a process for input by affected parties through public noticing and scoping. This input is considered when analyzing a reasonable range of alternatives in an Environmental Assessment (EA) or EIS. The Notice of Intent (NOI) is included in Appendix A. When all key permits are obtained and the final EIS/R is released, a Record of Decision (ROD) will be filed.

5.1.2 Clean Water Act (33 U.S.C. 1252 et seq.)

The Clean Water Act (CWA) was enacted to restore and maintain the chemical, physical, and biological integrity of U.S. waters through the elimination of discharges of pollutants. Among other things, the CWA provided that continuing (point-source) pollutant discharges could not occur unless specifically authorized by permit, and it established permit programs for various forms of discharges, including the discharge of dredged materials. The main sections of the CWA that apply to dredging and dredged material disposal are Sections 401 and 404.

CWA Section 401

The Act requires Section 401 Certification that the permitted discharges of dredged or fill material comply with State water quality standards for actions within State waters or Federal water quality criteria for offshore waters. The State is required to establish water quality standards for all State waters including the territorial sea under Section 301 of the CWA. Compliance with Section 401 is provided by approval of a Water Quality Certification or waiver from the State Water Resources Control Board (SWRCB) or Regional Water Quality Control Board (RWQCB), and is a condition for issuance of a Section 404 permit, discussed below.

CWA Section 402

This section of the Act requires that the permitted project comply with National Pollutant Elimination Discharge System (NPDES) requirements. The State is required to establish waste discharge standards for all State waters, including the territorial sea under Section 301 of the CWA. Compliance with Section 402 is provided by approval of a NPDES permit from the SWRCB and RWQCB.

CWA Section 404

This section of the CWA addresses permits for dredged or fill material. It establishes guidelines for the discharge of dredged or fill materials and for the prevention of such discharges, individually or in combination with other activities, from having unacceptable adverse impacts to the ecosystem.

The U.S. Army Corps of Engineers (USACE) has the legal authority to regulate, through the issuance of a Section 404 permit, the discharge of dredged or fill material in inland waterways, wetlands, and territorial seas. The USACE must also provide notice and opportunity for public hearings. This section also requires the United States Environmental Protection Agency (EPA) to develop guidelines (the "404(b)(1) Guidelines," published separately at 40 Code of Federal Regulations (CFR) Part 230) that the USACE must follow in evaluating and issuing permits for the discharge of dredged or fill material. Although this section specifically applies to applications for Federal permits, and the USACE does not issue itself permits, the USACE policy is to apply the EPA guidelines to their projects as well.

5.1.3 Rivers and Harbors Act (33 U.S.C. 403, Section 10)

Section 10 of the Rivers and Harbors Act of 1899, authorizes the USACE to regulate virtually all structures or work within navigable waters of the United States (see 33 CFR Part 328.3 for definition of navigable waters). Virtually all projects in navigable waters must comply with Section 10, however the USACE does not issue Section 10 permits to itself for federally authorized projects. This programmatic EIS/R describes potential effects of the proposed action on wetlands and other waters.

5.1.4 Endangered Species Act (16 U.S.C. 1531 et seq.)

The Endangered Species Act of 1973, as amended (ESA) establishes a national program for the conservation of threatened and endangered species and the preservation of the ecosystems upon which they depend. Consultation with and an opinion statement from the United States Fish and Wildlife Service (USFWS) and National Marine Fisheries Service (NMFS) are required under Section 7 of this Act. Section 7(a) of the ESA further prohibits Federal agencies from jeopardizing the continued existence of listed and proposed species, and it requires Federal agencies to implement conservation programs for listed species. Section 9 of the Act prohibits the taking of listed species without authorization from the USFWS or NMFS. This EIS/R describes the potential programmatic effects of the proposed action on special status species. Consultation with the USFWS will evaluate measures to bring adverse effects to a level of "not likely to adversely affect." The USFWS will forward a concurrence determination on applicable special status species to NMFS.

5.1.5 Migratory Bird Treaty Act (16 U.S.C. 703 et seq.) and Executive Order 13186

The Migratory Bird Treaty Act (MBTA) governs the taking, killing, possession, transportation, and importation of migratory birds, their eggs, parts and nests. The take of all migratory birds is governed by the MBTA's regulation of taking migratory birds for educational, scientific, and recreational purposes and requiring harvest to be limited to levels that prevent overutilization. Further, the MBTA prohibits the take, possession, import, export, transport, selling, purchase, barter, or offering for sale, purchase or barter, any migratory bird, their eggs, parts, and nests, except as authorized under a valid permit (50 CFR 21.11). Certain exceptions apply to employees of the Department of the Interior to enforce the MBTA and to employees of Federal agencies, State game departments, municipal game farms or parks, public museums, public zoological parks, accredited institutional members of the American Association of Zoological Parks and Aquariums (now called the American Zoo and Aquarium Association) and public scientific or educational institutions.

Executive Order (EO) 13186 (effective January 10, 2001), outlines the responsibilities of Federal agencies to protect migratory birds, in furtherance of the MBTA, the Bald and Golden Eagle Protection Acts, the Fish and Wildlife Coordination Act, ESA, and NEPA. This EO specifies the following:

   The USFWS as the lead for coordinating and implementing EO 13186;

   Requires Federal agencies to incorporate migratory bird protection measures into their activities;

   Requires Federal agencies to obtain permits from the USFWS before any "take" occurs, even when the agency intent is not to kill or injure migratory birds;

   Requires a Memorandum of Understanding (MOU) between the Federal agencies within two years from the inception of EO 13186 (January 10, 2003);

   Outlines migratory bird protection specifications that are to be included in MOUs;

   Encourages Federal agencies to immediately begin implementation of the elements required by the USFWS to be included in MOUs;

   Requires the USFWS to develop a schedule for completion of the MOUs within 180 days from the signing of EO 13186; and

   Requires Federal agencies to notify the public of the availability of its MOU in the Federal Register.

5.1.6 Marine Mammal Protection Act (16 U.S.C. 1361 et seq.)

This Act prohibits taking or harassment of any marine mammals except incidental take during commercial fishing, capture under scientific research and public display permits, harvest by Native Americans for subsistence purposes, and any other take authorized on a case-by-case basis as set forth in the Act. The Department of the Interior, USFWS, is responsible for the polar bear, sea otter, marine otter, walrus, manatees, and dugong, while the Department of Commerce, NMFS, is responsible for all other marine mammals.

5.1.7 Federal Clean Air Act (42 U.S.C. Section 7401 et seq., as amended)

The Clean Air Act (CAA) is intended to protect air quality by regulating emissions of air pollutants. The CAA requires compliance with State and local requirements and prohibits Federal agencies from engaging in non-conforming activities.

5.1.8 Coastal Zone Management Act (16 U.S.C. 1456 et seq., as amended)

The Coastal Zone Management Act (CZMA) provides for the development and implementation of coastal management programs by the states. The Bay Conservation and Development Commission's (BCDC) coastal management program for the Bay, which was approved in 1977, is based on the provisions and policies of the McAteer-Petris Act, the Suisun Marsh Preservation Act of 1977, the San Francisco Bay Plan, the Suisun Marsh Protection Plan, and its administrative regulations. Under the CZMA, Federal agencies are required to carry out their activities and programs in a manner consistent with BCDC's coastal management program. To implement this provision, Federal agencies make consistency determinations regarding proposed Federal activities while applicants for Federal permits or licenses, or Federal financial assistance make consistency certifications. BCDC reviews these determinations and certifications, and concurs or objects based on a proposal's consistency with its laws and policies.

5.1.9 Fish and Wildlife Coordination Act (16 U.S.C. 661 et seq.)

The Fish and Wildlife Coordination Act (FWCA) provides a procedural framework for the consideration of fish and wildlife conservation measure in Federal and federally permitted or licensed water development projects. When a water body is proposed to be controlled or modified by a Federal agency or by any public or private entity under Federal permit or license, the Federal lead agency must consult with and consider the recommendations of the USFWS, the California Department of Fish and Game (CDFG) (in California) and, for projects affecting marine fisheries, NMFS. The FWCA is applicable to ACOE and EPA evaluation of CWA Section 404 and the Marine Protection, Research, and Sanctuaries Act (MPRSA) Section 103 permits. However, because the USFWS is the Federal lead agency for this EIS/R, they will coordinate pursuant to this Act.

5.1.10 Magnuson-Stevenson Fishery Conservation and Management Act

Prior to completion of the project, the USFWS has a statutory requirement under Section 305(b)(4)(B) of the Magnuson-Stevenson Fishery Conservation and Management Act (MSFCMA) to consult with NMFS with respect to any action authorized, funded, or undertaken, or proposed to be authorized, funded, or undertaken that may adversely affect essential fish habitat (EFH).

5.1.11 National Historic Preservation Act (16 U.S.C. 470 et seq.)

The National Historic Preservation Act (NHPA) protects historic and prehistoric resources from impacts by Federal projects and requires consultation (under Section 106) with the State Historic Preservation Officer (SHPO). Compliance with the NHPA would be necessary for any undertaking. The USFWS, the Advisory Council on Historic Preservation, and SHPO, pursuant to Section 800.13 of the regulations (36 CFR 800.13) implementing Section 106 of the NHPA, entered into a Programmatic Agreement (PA) to streamline the cultural resource compliance process for low-impact projects. Applicability of this PA to project activities would be determined depending on project specifics, and the PA would apply only to activities for which the USFWS is the federal lead agency. For the proposed action, a request for cultural resource compliance will be submitted to the Regional Archaeologist, Region 1, in Portland, Oregon.

5.1.12 Executive Order 11990 - Protection of Wetlands

EO 11990 requires Federal agencies to follow avoidance, mitigation, and preservation procedures with public input before proposing new construction in wetlands. This EO directs Federal agencies to avoid to the extent possible long and short-term effects associated with the destruction or modification of wetlands and to avoid direct or indirect support of new construction in wetlands wherever there is a practicable alternative. Specifically, Federal agencies are directed to:

   Provide leadership and take action to minimize the destruction, loss, or degradation of wetlands, and to preserve and enhance the natural and beneficial values of wetlands in carrying out the agency's responsibilities when acquiring, managing, and disposing of Federal lands and facilities; and providing federally sponsored, financed, or assisted construction and improvements, or conducting Federal activities and programs affecting land use.

This EO does not apply to the issuance of permits (by Federal agencies), licenses, or allocations to private parties for activities involving wetlands on non- Federal property.

5.1.13 Executive Order 11988 - Floodplain Management

This EO directs Federal agencies to avoid to the extent possible the long and short-term adverse impacts associated with the occupancy and modification of floodplains and to avoid direct or indirect support of floodplain development wherever there is a practicable alternative. Specifically, Federal agencies are directed to:

   Provide leadership and take action to reduce the risk of flood loss, to minimize the impact of floods on human safety, health and welfare, and to restore and preserve the natural and beneficial values served by floodplains in carrying out its responsibilities for acquiring, managing, and disposing of Federal lands and facilities, providing federally sponsored, financed, or assisted construction and improvements and conducting Federal activities and programs affecting land use.

This EIS/R describes the potential effects of the proposed actions on floodplains.

5.1.14 Executive Order 13112 - Invasive Species

The National Invasive Species Management Plan was developed in response to EO 13112 in 1997. This EO established the National Invasive Species Council (Council) as the leaders in development of the plan. It directs the Council to provide leadership and oversight on invasive species issues to ensure that Federal activities are coordinated and effective. In addition, the Council has specific responsibilities including: promoting action at local, State, tribal, and ecosystem levels; identifying recommendations for international cooperation; facilitating a coordinated network to document, evaluate, and monitor invasive species' effects; developing a web-based information network on invasive species; and developing guidance on invasive species for Federal agencies to use in implementing NEPA. The Council is comprised of the Secretaries of Agriculture, Commerce, Interior, Treasure, Defense, Transportation, State, and the Administrator of the EPA, and they have developed nine plan priorities, that provide direction for Federal agencies. The plan priorities are as follows:

   Leadership, coordination, and development of State and Federal partnerships

   Prevention (a risk-based approach)

   Early detection and rapid response

   Control and Management


   International Cooperation


   Information Management

   Education and Public Awareness

The proposed project would implement the San Francisco Estuary Invasive Spartina Project (ISP), which is a regionally coordinated approach to controlling, or eradicating, populations of non-native Spartina in San Francisco Bay. Although there is no formal international cooperation taking place on this issue, the Federal and State lead agencies have shown that the proposed project is consistent with the plan by:

   Providing effective leadership in development of the ISP,

   Determining prevention measures to curtail further spread,

   Coordinating with researchers at the San Francisco Estuary Institute, UC Davis, and Bodega Marine Lab, to develop early detection methods and rapid response techniques,

   Conducting experiments to determine effective control and management techniques,

   Developing a preliminary approach to restoration following control,

   Establishing working relationships with researchers to further understand the biology and ecology of the target species,

   Creating an archive of data and reports, and serving as a clearinghouse for information regarding Spartina biology and ecology and the efficacy of control efforts in California and elsewhere, and

   Developing and implementing a public education and public awareness program.

Additional details regarding this plan can be found at the following Internet address: http://www.invasivespecies.gov/council/.

5.1.15 Executive Order 12898 - Environmental Justice in Minority and Low Income Populations

The objectives of EO 12898 include identification of disproportionately high and adverse health and environmental effects on minority and low-income populations that could be caused by a proposed Federal action. Accompanying EO 12898 was a Presidential Transmittal Memorandum that referenced existing Federal statutes and regulations, including NEPA, to be used in conjunction with the EO. The EIS/R analyzes the environmental, social, and economic impacts on minority and low-income populations and complies with this EO.

5.1.16 Indian Trust Assets, Indian Sacred Sites on Federal Land - Executive Order 13007, and American Indian Religious Freedom Act of 1978

These laws protect Indian Trust Assets; accommodate access and ceremonial use of Indian sacred sites by Indian religious practitioners, and avoid adversely affecting the physical integrity of such sacred sites; and protect and preserve the observance of traditional Native American religions, respectively. Compliance with these laws, regulations, and Executive Orders is the responsibility of the federal land manager. The USFWS' Regional Cultural Resources Office would be available to provide assistance in the review the proposed action for potential effects on cultural resources of Native Americans.

5.2  Applicable State Laws, Regulations, and policies

5.2.1 California Environmental Quality Act (P.R.C. 21000-21177)

The California Environmental Quality Act (CEQA) contains requirements similar to NEPA and requires the preparation of an EIR prior to implementation of applicable projects. CEQA requires significant impacts to be mitigated to a level of insignificance or to the maximum extent feasible, and that less damaging alternatives be considered. The State or local lead agency is responsible for CEQA compliance.

5.2.2 Porter-Cologne Water Quality Control Act (C.W.C. Section 13000 et seq.; C.C.R. Title 23, Chapter 3, Chapter 15)

This Act is the primary State regulation addressing water quality and waste discharges (including dredged material) on land. The Act's requirements are implemented by the SWRCB at the State level, by the San Francisco Bay Regional Water Quality Control Board (SFBRWQCB) in the Bay Area, and by the Central Valley Regional Water Quality Control Board (CVRWQCB) in the Delta. The dividing line between the SFBRWQCB and the CVRWQCB is in the vicinity of Chipps Island in Suisun Bay. Additionally, the SWRCB requires a Permit to Appropriate Water for actions including diversion of surface waters to non-riparian land or for seasonal storage of unappropriated surface waters.

5.2.3 California Endangered Species Act (Fish and Game Code Section 2050
et seq.)

This Act provides for recognition and protection of rare, threatened, and endangered plants and animal species. The Act requires State agencies to coordinate with the CDFG to ensure that State authorized/funded projects do not jeopardize a listed species. The Act prohibits the taking of a listed species without authorization from the CDFG.

5.2.4 McAteer-Petris Act

The McAteer-Petris Act, first enacted in 1965, created BCDC to prepare a plan to protect the Bay and shoreline and provide for appropriate development and public access. The McAteer-Petris Act directs BCDC to issue or deny permit applications for placing fill and extracting materials, or changing the use of any land, water, or structure within its jurisdiction, which includes the Bay, shoreline band, saltponds, managed wetlands, and certain waterways. Such permits are issued or denied in accordance with the provisions of the McAteer-Petris Act and Suisun Marsh Preservation Act, and the policies of the San Francisco Bay Plan (Bay Plan) and the Suisun Marsh Protection Plan. The shoreline development aspect of the McAteer-Petris Act ensures that prime shoreline sites are reserved for priority uses, such as ports, water-related industry, airports, wildlife refuges, and water-related recreation. The Act also ensures that public access to the Bay is provided to the maximum extent feasible for each development project, and that shoreline development projects are designed in an attractive and safe manner. Under the CZMA, Federal agencies are required to carry out their activities and programs in a manner consistent with BCDC's coastal management program.

The Bay Plan was adopted in 1968, signed by the California Legislature in 1969, and has been implemented with several amendments by BCDC. The Bay Plan established the framework for a permit program that provides for protection of the Bay and its natural resources, as well as development of the Bay and shoreline while minimizing the amount of fill. Several relevant Bay Plan policies are summarized below.

Fish and Wildlife Policies of the Bay Plan

The benefits of fish and wildlife in the Bay should be insured for present and future generations of Californians. To this end, remaining marshes and mudflats around the Bay, including water volume, surface area, and freshwater inputs of the Bay should be maintained.

Specific habitats that would prevent the extinction of species, or maintain or increase species populations that would provide substantial public benefits should be protected, whether in the Bay or on the shoreline behind dikes.

Water Quality Policies of the Bay Plan

Bay marshes, mudflats, water surface area. and volume should be maintained and increased wherever possible. Freshwater inputs should also be maintained at a level sufficient to protect Bay resources and beneficial uses. Water pollution should be avoided.

Water quality in the Bay should be maintained at a level that will support and promote beneficial uses of the Bay, as identified in SFBRWQCB's Basin Plan.

Tidal Marshes and Tidal Flats Policies of the Bay Plan

Marshes and mudflats should be maintained to the fullest extent possible, to conserve fish and wildlife, and abate air and water pollution. Activities that eliminate marshes and mudflats should be allowed only for purposes providing substantial public benefits and only if there is no reasonable alternative. These areas should be protected in the same manner as open water areas.

Proposed activities (fills, dikes, piers) should be thoroughly evaluated to determine their effects on marshes and mudflats so as to minimize harmful effects.

Former marshes should be restored, existing marshes should be augmented, new marshes created where appropriate (by selective placement of dredged material), and the quality of existing marshes should be improved whenever possible.

The proposed project would take place in salt marsh and mudflat habitats that are subject to policies of the Bay Plan. Although the proposed project does not involve the import or discharge of fill, some control methods, such as mechanical ripping/shredding would result in a redeposition of sediment due to the ground disturbances associated with equipment. The primary goal of the proposed project is to restore infested marshes to a more natural [native] condition for the benefit of marsh and mudflat-dependent species that prefer or require native marsh habitat. To the extent that the project would restore these habitats over the long-term, the project is consistent with Bay Plan policies.

Findings and Policies 5, 6, and 7 concerning tidal marshes and tidal flats around the Bay were amended in April 2002:

   5. Any tidal restoration project should include clear and specific long-term and short-term biological and physical goals, and success criteria and a monitoring program to assess the sustainability of the project. Design and evaluation of the project should include an analysis of: (a) the effects of relative sea level rise; (b) the impact of the project on the Bay's sediment budget; (c) localized sediment erosion and accretion; (d) the role of tidal flows; (e) potential invasive species introduction, spread, and their control; (f) rates of colonization by vegetation; (g) the expected use of the site by fish, other aquatic organisms and wildlife; and (h) site characterization. If success criteria are not met, appropriate corrective measures should be taken.

   6. Non-native species should not be used in habitat restoration projects. Any habitat restoration project approved by BCDC should include a program for the periodic monitoring of the site for non-native species and a program for control and, if appropriate and feasible, eradication should an introduction occur. The use of non-native plant species in public access landscape improvements should be avoided where a potential exists for non-native plants to spread into the Bay, other waterways, or transition zones between tidal and upland habitats.

   7. BCDC should continue to support and encourage the expansion of scientific information on the arrival and spread of invasive plants and animals, and when feasible, support the establishment of a regional effort for Bay-wide eradication of specific invasive species, such as non-native cordgrasses.

5.2.5 Executive Order W-59-93 - California Wetlands Conservation Policy

In August 1993, the Governor announced the California Wetlands Conservation Policy. The goals of the policy are to establish a framework and strategy that:

   Ensures no overall net loss and achieve a long-term net gain in the quantity, quality, and permanence of wetlands acreage and values in California in a manner that fosters creativity, stewardship, and respect for private property.

   Reduces procedural complexity in the administration of State and Federal wetlands conservation programs.

   Encourages partnerships to make landowner incentive programs and cooperative planning efforts the primary focus of wetlands conservation and restoration.

The EO also directed the California Resources Agency to establish an Interagency Task Force to direct and coordinate administration and implementation of the policy.

The Resources Agency and the departments within that agency generally do not authorize or approve projects that fill or harm wetlands. Exceptions may be granted for projects meeting all the following conditions: the project is water-dependent; there is no other feasible alternative; the public trust is not adversely affected; and the project adequately compensates the loss.

5.2.6 State Lands Commission Policies

California became a State on September 9, 1850, and thereby acquired nearly 4 million acres of land underlying the State's navigable and tidal waterways. Known as "sovereign lands," these lands included the beds of rivers, streams, and sloughs; non-tidal lakes; tidal navigable bays and lagoons; and tidal and submerged lands adjacent to the entire coast and offshore islands of the State from mean high tide line to 3 nautical miles offshore. These lands are managed by the California State Lands Commission (SLC). The State's interest in these lands consists of sovereign fee ownership, or a Public Trust easement implicitly retained by the State over sovereign lands sold into private ownership. They can only be used for public purposes consistent with the provisions of the Public Trust, such as fishing, water-dependent commerce and navigation, ecological preservation, and scientific study. Use of these lands for dredging and dredged material disposal activities, may require written authorization from the SLC. Some of the alternative project components under consideration in this EIS/R may be subject to the jurisdiction of the SLC. Therefore, coordination with the SLC will be fulfilled when required for a specific project. Public and private entities may apply to the SLC for leases or permits on State lands for many purposes. Therefore, coordination with the SLC would be necessary.

5.2.7 California Clean Air Act

The California Air Resources Board (CARB) and local air districts are responsible for developing clean air plans to demonstrate how and when California will attain air quality standards established under both the Federal and California Clean Air Acts. For the areas within California that have not attained air quality standards, CARB works with local air districts to develop and implement State and local attainment plans. The local air quality districts in the Bay Area will review the EIS/R and coordinate with the California Coastal Conservancy or the USFWS as the proposed project and specific treatment methods are implemented.

5.3  Regional Plans and Policies

5.3.1 Baylands Ecosystem Habitat Goals

The San Francisco Bay Area Wetlands Ecosystem Goals Project began in 1995. It was a cooperative effort among nine State and Federal agencies, the EPA, USFWS, NMFS, California Resources Agency, California Coastal Conservancy, CDFG, SFBRWQCB, SWRCB, and BCDC, and nearly 100 scientists. The Project's vision was presented to the public in the Goals Project's final report, the Baylands Ecosystem Habitat Goals Project (Goals Project 1999). The Baylands Ecosystem Habitat Goals were adopted into the Bay Plan. SFBRWQCB uses the goals to evaluate projects that are proposed for permitting and some cities adopted the goals into their local plans. The goals are implemented through cooperative efforts of the agencies and stakeholders.

The principal objective of the Goals Project was to develop a concept for the types, quantities/acres, distribution of wetlands and related habitats needed to restore and sustain a healthy baylands ecosystem. The timeframe for achieving these goals is several decades, and it provides a habitat approach, rather than a species-based approach, although the authors recognize the importance of monitoring individual species that are indicators of ecosystem health. Regional and subregional goals are described in the Goals Project. The regional (Bay-wide) goals are summarized below because the proposed project is expected to occur Bay-wide. Regionally, the goals for restoration are as follows:

   Develop a diverse mosaic of habitats. The mosaic should include large patches of tidal marsh connected by corridors to enable movement of wildlife and birds; complexes of salt ponds managed for resident and migratory shorebirds and waterfowl; extensive areas of managed seasonal ponds, large expanses of managed marsh; continuous corridors of riparian vegetation along tributary streams and rivers; restored beaches, natural salt ponds and other unique habitats; and undisturbed patches of transitional habitats including grasslands, seasonal wetlands, and forested areas (Goals Project 1999).

More specifically, the goals include:

   Restoration of large areas (1,000+ acres) of tidal marsh or connected patches centered around existing populations of special status species such as California clapper rail or salt marsh harvest mouse. These areas would encompass salinity gradients that permit movement to alternate areas in response to freshwater flows. Priority sites for this type of restoration would include the Bay margin and specifically, areas adjacent to tributaries where freshwater enters the Bay that provides a diversity of microhabitats such as pans and large channels.

   Re-establish natural transitions from mudflat to marsh, and marsh to uplands, and establish buffers from developed areas to transitional zones.

   Manage former salt ponds (as well as diked agricultural lands no longer in production) for waterfowl and shorebirds. Managed ponds adjacent to important shorebird foraging areas would provide the most benefit to a large number and diversity of species.

The primary goal of the proposed project is to restore infested marshes to a more natural (native) condition for the benefit of marsh- and mudflat-dependent species that prefer or require native marsh habitat. While it is recognized that the proposed project would impact habitats and species within the Bay, large areas of mudflat and intertidal marsh habitat are substantially degraded by the presence of non-native cordgrass, and the decline of these habitats may contribute to the regional decline of several special status and mudflat/marsh-dependent species over time. To the extent that the project would restore these habitats over the long-term, the project is consistent with the Habitat Goals as described in the Goals Project.

5.3.2 Comprehensive Conservation and Management Plan

The Comprehensive Conservation and Management Plan (CCMP) plan was prepared in 1993 as part of the San Francisco Estuary Project. The plan establishes wetland ecosystem goals, a regional wetlands management plan, and geographically focused cooperative efforts to protect wetlands. The CCMP presented strategies to protect and restore the health of the San Francisco Estuary. The plan found that the region's wetlands were subject to uneven protection efforts and called for a coordinated intergovernmental system to ensure maximum protection, restoration, and management of wetlands. BCDC is the lead agency to assist in developing and implementing local wetland protection programs to minimize impacts of urbanization on wetland and agricultural resources. The CCMP presents a blueprint of 145 specific actions to restore and maintain the chemical, physical, and biological integrity of the Bay and Delta.

CCMP Priorities

In August 2001, the priorities of the CCMP were reorganized and refined. The #2 priority is: "Reduce the impact of invasive species on the San Francisco Estuary through prevention, control, eradication and education."

5.3.3 Bay Area Air Quality Management District

Air quality permits are required by State law in the San Francisco Bay Area: Alameda, Contra Costa, Marin, Napa, San Francisco, San Mateo, Santa Clara and the southern portion of Solano and Sonoma counties. Air quality permits are issued by the Bay Area Air Quality Management District (BAAQMD), a regional government agency responsible for controlling air pollution. Situations for which a permit application must be submitted include:

   Construction or installation of new equipment that may cause air pollution;

   Existing equipment operations without a valid Permit to Operate;

   Modification of existing permitted equipment;

   When equipment is transferred from one location to another;

   Installation of abatement equipment used to control emissions.

By granting a permit, BAAQMD indicates that a project or the proposed equipment would meet air quality standards. Both large and small businesses and their activities are covered by BAAQMD rules and regulations. Typical large businesses requiring permits include bulk petroleum operations, refineries, and power plants. Typical small businesses include dry cleaners, gasoline service stations, auto body shops, coating operations and printers. Permits for new or modified facilities must be obtained before construction or use of equipment is initiated.

5.4  Local Laws, Regulations, and Permits

The lead agencies recognize that counties and cities around the Bay have local policies, ordinances, zoning designations and restrictions, permit requirements, and special districts (i.e., East Bay Regional Park District, mosquito abatement districts, flood control districts, etc.) within their jurisdictional boundaries. While the analyses contained herein are intended to provide sufficient information for most Federal and State permits and approvals, additional information or details regarding the application of treatment methods may be needed by cities, counties, or special districts before Spartina control efforts may be implemented at a particular site.

5.5  Agency Jurisdiction and Project Approvals

Table 5.5-1 summarizes the agencies with jurisdiction over the proposed project, applicable laws and authorizations or permit approvals needed to implement the proposed project.

Table 5.5-1  Agency Jurisdiction and Project Approvals


Applicable Law or Regulation

Authority or Permit Action


U.S. Environmental Protection Agency


Clean Water Act (CWA)

Clean Air Act (CAA)

NEPA compliance

CWA Section 404(b)(1) guidelines compliance

CAA Section 309 compliance

U.S. Army Corps of Engineers


Clean Water Act (CWA)

Rivers and Harbors Act (RHA)

CWA Section 404 permit and Section 404(b)(1) guidelines compliance

RHA Section 10 permit

U.S. Fish and Wildlife Service


Endangered Species Act (ESA)

Fish and Wildlife Coordination Act


ESA Section 7 Biological Opinion and Incidental Take Statement

National Oceanic and Atmospheric Aadministration Fisheries (formerly National Marine Fisheries Service)


Marine Mammal Protection Act (MMPA)

Magnuson-Stevenson Fishery Conservation and Management Act

ESA and MMPA Section 7 Biological Opinion and Incidental Take Statement


California Coastal Conservancy

California Environmental Quality Act (CEQA)

CEQA compliance and funding approvals

Department of Fish and Game


California Endangered Species Act (CESA)

California Public Resources Code (CPRC)

CESA Section 2081 permit

CPRC Section 1601 Streambed Alteration Agreement

State Lands Commission

California Public Resources Code (CPRC)

Permits for work on State lands

Air Resources Board

California Clean Air Act

Review EIS/R for compliance with local attainment plans


San Francisco Regional Water Quality Control Board


San Francisco Bay Area Basin Plan


CWA Section 401 certification or waiver

CWA Section 402 National Pollutant Discharge Elimination System (NPDES) Permit

San Francisco Bay Conservation and Development Commission


(Federal) Coastal Zone Management Act

McAteer-Petris Act

Coastal Development Permit(s)


Air Pollution Control or Mosquito Abatement Districts

Local policies

Permits to use chemical methods or conduct controlled burns

Agricultural Commissioners

Local policies

Authorization or permits for conducting prescribed burns


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