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About This Document


Water Quality Issues

Management Practices for Agricultural Nonpoint Sources

Section 1: Agricultural Industry Networks

Section 2: Technical Information/Outreach

Section 3: Education and Public Relations

Section 4: Regulatory Coordination/Streamlining

Section 5: Funding Mechanisms/Incentives

Section 6: Public Lands and Rural Roads


Appendix A. Water Quality Protection Program Committee Members

Appendix B. TMDL Schedule for Impaired Waters in Sanctuary Watersheds.

Appendix C. Existing Laws and Programs Related to Agricultural Nonpoint Sources

Appendix D. Definitions of Acronyms

Monterey Bay National Marine Sanctuary and Central Coast Agriculture

The Monterey Bay National Marine Sanctuary (hereafter, "Sanctuary") is the largest marine protected area in the United States, and includes over 5000 square miles of water off California's Central Coast. It spans over 400 miles of coastline from Cambria in San Luis Obispo County to the Marin Headlands, extending as much as 53 miles offshore.

The area was given sanctuary protection by Congress and the National Oceanic and Atmospheric Administration (NOAA) in 1992, in recognition of its dramatic underwater topography, the diversity of its unique plants and animals, the presence of threatened/endangered species and abundant commercial fisheries, and its standing as an important research site. Within the Sanctuary and its shores are more than 50 species on government special status lists, perhaps the most prominent being the southern sea otter.

The Sanctuary boasts the greatest biodiversity in temperate regions of the world. It is home to 28 species of marine mammals, 94 species of seabirds, 345 species of fish, four species of turtles, more than 450 species of marine algae and 31 phyla of invertebrates. Within a dozen steps on the rocky shore, one may walk over 90 species of invertebrates associated with intertidal red algae and over 300 invertebrate species associated with a mussel bed. This diversity encompasses a wide range of environments, including estuaries, rocky coastlines, sandy beaches, subtidal reefs and soft bottoms, open ocean waters, and the deep waters of the Monterey Bay canyon.

The Sanctuary also includes the waters of Elkhorn Slough, one of the largest remaining wetlands in California and a key nursery ground for fishes. Dramatic migrations of shorebirds visit the Elkhorn Slough estuary, a key stop for feeding and weight gain before the birds continue on the "Pacific flyway." Congress designated the Sanctuary as a marine environment of special national significance, to be protected for the generations to come.


California's Central Coast is also home to another national treasure, the agricultural lands in its rich coastal valleys. The region's unique soils and year- round mild coastal climate sustain a 3 billion dollar agricultural industry which produces over 200 types of crops. These include the nurseries and brussel sprouts which thrive along the fog-shrouded San Mateo coast, the diverse row crops, berries and apple orchards of the warm Pajaro Valley, and the strawberry fields lining the steep lands surrounding the Elkhorn and Watsonville Sloughs. The rich soils of the broad flat lands along the Salinas River are the "Salad Bowl of the Nation", producing the majority of the country's lettuce and a diverse mix of vegetables, including broccoli, artichokes, celery, and cauliflower. Monterey County alone produces more than 80% of the nation's leaf lettuce, 70% of its artichokes, 55% of its broccoli and cauliflower, and more than one-third of its celery, strawberries and mushrooms.

Rolling grazing lands occupy the slopes of these valleys and much of the watersheds of San Luis Obispo, San Benito, Monterey and Santa Clara Counties, sustaining a cattle industry, providing habitat for wildlife, and improving recharge of local water supplies. In recent years, a portion of the grazing lands in Monterey County has been converted to vineyards. Steeper forested lands occupy much of the upper watersheds in Santa Cruz and San Mateo County, sustaining a timber industry, providing wildlife habitat and recreational opportunities for local residents.

Agricultural products from the region are shipped all over the nation and the world, and provide jobs for thousands of local residents. They are a cornerstone of the region's economy, along with the region's large tourist industry. The agricultural production on these lands also provides an aesthetically pleasing landscape which benefits both tourists and local residents alike. Agriculture is a multi-faceted asset to the region.

Agriculture and the Sanctuary's plants and animals are linked by their mutual dependence on the marine waters which generate the region's unique coastal climate. They are also linked by the drainage patterns of the local watersheds as water flows from the mountains to the flood plains and rivers, and out to sea. Additional links and partnerships between the Sanctuary and agriculture will be needed to protect and sustain our unique natural resources, the area's vital agricultural and tourist economies, and quality of life for local residents.

Water Quality Protection Program

The Water Quality Protection Program (WQPP) is a partnership effort to enhance and protect the physical, chemical and biological conditions in the Sanctuary and its adjacent watersheds. The map on page 1 shows the WQPP's broad geographic range, including 5000 square miles of marine waters and 11 major watershed areas with over 7000 square miles of land. Land use in this diverse region includes urban and suburban development, extensive areas of irrigated croplands, managed timber lands, grazing lands and other agricultural activities. Extensive public lands with diverse multiple uses are also present, including lands under the management of the federal, state and local governments. As water passes over any of the land uses in the watershed, it can pick up a variety of potential pollutants such as sediments, oils and grease, nutrients, pesticides, and pathogens which can be transported to the region's rivers, wetlands, harbors and nearshore waters.

In addition to diverse land uses, the region also encompasses a large number of county and municipal jurisdictions, various special districts, portions of two Regional Water Quality Control Boards (RWQCBs), and the overlapping jurisdictions of at least ten state and federal agencies which deal with water quality issues. This mix of land uses and agency responsibilities requires an approach that cuts across jurisdictional and political boundaries and focuses on watersheds.

The WQPP implements a key element of a Memorandum of Agreement (MOA) signed by eight federal, state, and local agencies during Sanctuary designation in 1992. Signatories to the Agreement are: the National Oceanic and Atmospheric Administration; the U.S. Environmental Protection Agency, Region IX; the California Environmental Protection Agency; the California State Water Resources Control Board; the San Francisco Regional Water Quality Control Board; the Central Coast Regional Water Quality Control Board; the California Coastal Commission; and the Association of Monterey Bay Area Governments.

Twenty-seven federal, state and local agencies, public and private groups are now working together with cities, harbors, businesses, and the agricultural community to address a range of water quality and watershed issues (Appendix A). These issues include regional monitoring and data sharing, urban and agricultural runoff, marinas and boating activities, wetland/riparian issues and point sources of pollution. A main focus of the program is to more efficiently integrate the large number of existing programs and projects related to these issues, eliminate gaps and redundancies, and pool resources to address problems. The WQPP provides a cooperative process through which governmental agencies, public and private interests can develop and carry out feasible strategies to reduce transport of pollutants to Sanctuary waters, while sustaining economic productivity.

The program uses a stewardship approach to water quality issues, rather than a "top down" regulatory approach. This means working with a wide variety of stakeholders in the community to identify issues and develop practical solutions that meet environmental needs and sustain the region's economic viability. Priority strategies have already been identified and refined for three general issues, working with a variety of local groups to evaluate the feasibility of recommendations, their environmental benefits, and economic impacts. These strategies are part of three detailed action plans published during 1996 addressing urban runoff, regional monitoring and data sharing, and marinas and boating activities. Implementation of these completed plans has begun, using staff from a variety of agencies, cities and harbors, nonprofit groups, volunteers, and supplementary grant funding. During the past several years the program has been working with the agricultural community on the development of a plan to address agricultural water quality issues.

Development of Agricultural Strategies

Participation in the initial development of this document was obtained during a series of three workshops held in Salinas, Watsonville and Half Moon Bay in 1996/1997. Participants were invited by phone, mail, and Farm Bureau newsletter inserts from a broad range of interest groups, including growers and ranchers, agricultural interest groups, resource management agencies, and environmental groups. Outreach presentations were also made to a variety of agricultural groups to invite their participation in the program and solicit comments.

The water quality issues and strategies presented in this document build on the wide range of suggestions made by various individual participants at these first workshops. Recognizing that much research has been conducted by various organizations and implemented by industry on effective agricultural management practices, the strategies are intended to build on many of the positive actions which are already underway to address water quality issues, and develop effective partnerships for watershed protection.

The long list of comments and suggestions from the initial three workshops were combined into a single outline and organized by issue. Drafts of these comments and suggestions were mailed to all parties invited to the workshop for their review, and additional comments on the drafts were incorporated.

The outline of workshop results was then used to develop draft descriptions of potential strategies, using a basic "What, Why, How, Who" format. The descriptions indicate what the strategy is intended to do, why it is needed, how it would be carried out, and who should be involved. In addition, a short section describing "performance measures" has been added to each strategy to determine success in implementation. The strategy drafts building on workshop comments were written by the WQPP staff and various members of the WQPP committee, with overall review by committee members as well as by some of the original workshop participants. Note that references to institutions and their roles in implementing this plan are proposals put forth by the planning team. Ultimate authority to proceed on and implement any of these proposed strategies remains with the institutions themselves.

The draft strategies were reviewed and revised during 1998 and early 1999 in a series of meetings which included representatives from the Farm Bureaus of six counties (San Mateo, Santa Cruz, Monterey, San Luis Obispo, Santa Clara and San Benito), the California Farm Bureau Federation, the Sanctuary, Regional Water Quality Control Boards 2 and 3, Natural Resources Conservation Service (NRCS), and the University of California Cooperative Extension (UCCE). A key outcome of these meetings was the addition of several strategies in Section 1 focused on implementation of nonpoint management practices via industry organizational networks composed of Farm Bureau members and other agricultural groups. The WQPP committee also reviewed and commented on the document. Revisions included modification of strategies and omission of recommendations which were deemed inappropriate.

The resulting draft was then distributed to interested parties, and three public workshops were held (in Watsonville, Salinas, and Half Moon Bay) during the summer of 1999 for final public comments. The Sanctuary greatly appreciates the time and expertise, ideas, and criticisms toward improving this plan, contributed by over 200 individuals at the various workshops and meetings.

This document is not intended to alter existing legal authority, or to serve as the basis for greater regulation, but rather for greater cooperation among public agencies which share management responsibilities affecting water quality, farmers, ranchers and other interested parties in accomplishing their shared goal of protecting and enhancing the resources of the region.

Process for Implementation and Tracking Success

These new strategies are designed to strengthen and complement existing programs in the region which promote voluntary adoption of conservation measures. Implementation will require major commitments of effort and funding from the variety of agencies, public and private organizations identified in the individual strategies. The WQPP committee will work to facilitate overall implementation of the plan, including identifying and beginning projects which can be undertaken with existing resources or modification of existing practices, and working together to identify and recruit resources for strategies which will require supplementary staff or funding. They will also work closely with the Central Coast Farm Bureau Coalition to facilitate industry's involvement in carrying out the plan.

Implementation will be funded through a mix of in-kind services from participating agencies and organizations such as the Farm Bureaus, existing resources, and external grant funds. The general priority for implementation has been set in terms of "high" and "medium" priority strategies based on several factors, including: greatest benefit to water quality; general ease or difficulty in actual implementation; efforts currently underway onto which some strategies can naturally "piggyback"; and in many cases, the necessary linkages between key strategies which should be implemented together for maximum effectiveness.

Early implementation of some of the strategies has already begun, such as the agricultural industry network and pilot projects in Section 1, and the development of regulatory coordination/permit streamlining in Strategy 4-2. In addition, several grants have either been submitted, already obtained or are under development with various partners which can begin to carry out other parts of the plan in limited geographic areas, especially for those strategies related to technical assistance. Other strategies (or parts thereof) can be readily implemented, with minimal additional resources, by including new materials into existing programs or by redirecting staff time/focus to include watershed or nonpoint source information. Additional grants or other external funding sources will need to be secured in order to carry out many of the other strategies. A long-term stable funding source will be needed to ensure comprehensive implementation of the plan throughout the Sanctuary region.

Each of the recommended strategies includes specific short-term "performance measures" by which to evaluate successful implementation of that strategy. Long-term success of the program as a whole&emdash;that is, demonstrable improvements in regional water quality&emdash;will be measured over time by data collected through the coordinated regional monitoring program currently under development (see below), including both government and high-quality citizen monitoring data. In addition, records from implementation tracking of management practices and voluntary self-monitoring conducted by growers and ranchers (see strategy 1-3) will be collected by the county Farm Bureau Coordinating Committees, summarized on a subwatershed level, and forwarded to the RWQCBs. The RWQCBs will then share that information with the WQPP committee and the committee members' constituencies.

The Sanctuary and the WQPP committee will play an active role in facilitating and coordinating implementation of the plan as a whole with the many partners in this effort, although the Sanctuary is not the lead agency for implementing most of the individual strategies. This will include working with various groups to identify and initiate projects which can be accomplished with existing resources, attracting additional resources where needed, tracking progress of the plan as a whole over time, and facilitating the development of modifications as needed based on the success or problems encountered with the plan. It will also provide a liaison with the Central Coast Farm Bureau Coalition to facilitate implementation of the plan, and between these agricultural efforts and the other WQPP efforts underway addressing urban runoff, marinas and boating, and regional monitoring.

Nonpint Source Regulatory Authorities

The WQPP prefers a voluntary stewardship approach to addressing agricultural sources, and that approach is reflected in the new strategies recommended later in this document. However, it is important to recognize that there are a number of existing and upcoming state and federal regulatory mandates focused on nonpoint sources.

Each of the State's nine Regional Water Quality Control Boards (RWQCBs) are responsible for administering regulations established by the Federal Clean Water Act and the California Water Code (Porter-Cologne Water Quality Control Act). Their administration of the Code is overseen by the State Water Resources Control Board (SWRCB).

Basin Plans

The Porter-Cologne Act directs each of the RWQCBs to develop a regional water quality control plan, or "Basin Plan." Basin Plans describe the beneficial uses of each of the region's water bodies, including warm and cold water habitat, fish spawning, recreation, drinking water supply and several others. The Basin Plans describe the water quality which must be maintained in order to allow those uses, and the actions which are necessary to achieve those water quality objectives.

The RWQCBs implement the Basin Plans by issuing and enforcing state Waste Discharge Requirements and federal NPDES permits (National Pollutant Discharge Elimination System, pursuant to the Clean Water Act) for waste discharged to land or surface waters which can potentially affect water quality.


Many of the waterbodies in the Central Coast do not meet water quality objectives or support beneficial uses. Section 303(d) of the Clean Water Act requires states to develop a list of water bodies that do not meet water quality standards without application of additional pollutant controls. States are then required to develop a strategy for bringing those water bodies back into compliance through a process called a Total Maximum Daily Load (TMDL).

A TMDL is a process of assessing pollution problems, identifying responsible parties, proposing implementation measures and timelines (including the installation of management measures), and developing a monitoring strategy.

TMDLs for various categories of nonpoint pollution such as sediments, nitrates and/or pesticides are scheduled for development in several Central Coast watersheds over the coming years, including Salinas, Pajaro, San Lorenzo and Pescadero (Appendix B). If voluntary efforts over the next few years can demonstrate increasing implementation of management measures and ultimately improvements in water quality, then there may be no need to move to higher levels of regulatory involvement. It is also possible that waterbodies may eventually be removed from the 303(d) list if voluntary efforts demonstrate that water quality standards are being attained. However, detailed watershed assessments on the sources of pollution and their improvement over time would be necessary for the RWQCBs to recommend removals from the 303d list.

California's Nonpoint Source Plan

California's Nonpoint Source Plan requires that the State ensure implementation of appropriate management measures for nonpoint source pollution. The RWQCBs implement California's Nonpoint Source Management Plan using a three-tiered approach:

  1. Voluntary implementation of management measures to achieve water quality standards. This tier offers landowners the greatest degree of flexibility and "self-determination" in deciding which management practices are most appropriate for their situation.

  2. Regulatory-based encouragement of management measures. RWQCBs can waive Waste Discharge Requirements on the condition that management measures are implemented, or alternatively, RWQCBs or the SWRCB can enforce management practices indirectly by entering into agreements with other agencies that have authority to enforce the implementation of such management practices.

  3. Issuance of Waste Discharge Requirements. The implementation of management measures may be necessary in order to meet waste discharge limitations. RWQCBs and the SWRCB have a variety of enforcement tools, including cease and desist orders and administrative civil liability, that can be used in response to noncompliance.

The Regional Board's preferred approach is voluntary action by private landowners and individuals to identify specific nonpoint sources on their lands and to implement appropriate management measures for their control. However, the Regional Boards have both the authority and the responsibility to require the implementation of management measures, if the voluntary actions of landowners are insufficient to meet water quality standards and to protect beneficial uses.

CZARA Section 6217

Polluted runoff is also addressed under Section 6217(a) of the Coastal Zone Act Reauthorization Amendments of 1990 (CZARA). The State Water Resources Control Board and the California Coastal Commission are in the process of updating the Nonpoint Source Plan to address the requirements of CZARA. This includes both a detailed 5-year implementation plan describing when, where and how program implementation will occur, and a more general 15-year implementation strategy for achieving full implementation of the 6217(g) management measures.

The updated plan includes the WQPP as an implementation of CZARA on the Central Coast. Although the plan will not require implementation of specific practices, it will include identification of general management measures and a menu of practices addressing erosion and sediment control, the application of nutrients and pesticides, confined animal facilities, grazing management and irrigation water management.

CZARA requires that the State provide enforceable policies and mechanisms to implement appropriate management measures. Voluntary actions by individual landowners are the strongly preferred approach under CZARA; however if voluntary actions are not sufficient to protect water quality, then CZARA requires that other actions be pursued by the state, using the authorities identified in the CZARA implementation plan, such as the RWQCB.

Regional Boards and the WQPP

The WQPP is a collaborative effort of many agencies and organizations within the watersheds of the Sanctuary. The Regional Boards are active participating members of the WQPP and signatories to the MOA which created the program.

The MOA outlines the existing authorities and roles of the eight signatory agencies, and describes the WQPP's role in recommending priority actions to address point and nonpoint pollution. An appeal process to the State Water Resources Control Board (SWRCB) is included should potential disagreements arise between the RWQCBs and the Sanctuary on water quality permit issues and the adequacy of protection of Sanctuary resources. However, as outlined in the MOA, primary regulatory authority on water quality issues still resides with the Regional Boards and the State Board, not the WQPP. As indicated above, both the Regional Boards and the WQPP prefer to encourage a voluntary approach to addressing agricultural nonpoint issues.


WQPP efforts will be closely coordinated with the development of TMDLs and CZARA to conserve limited water quality planning and implementation funding, and to ensure that participants will not be subjected to conflicting approaches. Participation in the WQPP can provide a "window of opportunity" to enhance and protect water quality, and may offer landowners a chance to influence the TMDL process by helping to determine effective management practices, which in turn could help shape potential regulatory requirements.

Other Programs

A variety of other federal, state and local agencies, public and private organizations have regulatory and non-regulatory programs addressing agricultural practices and water quality issues. Many of these programs can assist in facilitating voluntary implementation of management measures. A brief description of these agencies and programs is provided in Appendix C.

Ongoing communication among these various programs and pooling of resources to address issues is an important function of the WQPP. This document is not intended to alter existing legal authority, or to serve as the basis for greater regulation, but rather for greater cooperation among public agencies which share management responsibilities affecting water quality, farmers, ranchers and other interested parties in accomplishing their shared goal of protecting and enhancing the resources of the region. The WQPP respects the concern of the region's farm and ranch families for the privacy and productive use of their farms and ranches.

Reviewed: September 08, 2023
Web Site Owner: National Ocean Service

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