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Water Quality Issues


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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

Water quality is a key element which unites the natural resources of the Monterey Bay National Marine Sanctuary, the watersheds which drain to it, and our local communities. Although existing monitoring data are limited, water quality within the offshore marine waters of the Sanctuary appears to be in relatively good condition compared to other areas of the country. That is one of the reasons a Sanctuary was created here on the Central Coast. However, there are a number of ongoing water quality issues in the Sanctuary's watersheds and coastal areas which must be addressed to improve and sustain the region's rivers, wetlands, and harbors and to protect nearshore waters. Healthy watersheds and aquifers are also essential to the long-term viability of agriculture on the Central Coast, and to continuing its current role as a cornerstone of the region's economy.

Polluted runoff

The Sanctuary is adjacent to over 400 miles of California's coastline and includes Elkhorn Slough, one of the region's key wetland areas. This coastal area contains 11 major watersheds, ranging from forest and grazing lands to heavily agricultural and urbanized areas. The Sanctuary's watersheds receive rainfall, runoff from urban and rural lands, and return flows from irrigation which travel downhill to streams, rivers, wetlands, harbors and ultimately out to the Sanctuary. This runoff can pick up a variety of potential pollutants such as sediments, oils and grease, nutrients, pesticides, and pathogens, which can then be carried to the surrounding rivers and wetland areas that sustain many Sanctuary species. Polluted runoff is also known as "nonpoint source pollution" because the pollutants come from a variety of sources, rather than a single "point" source, such as industrial effluent discharged from a pipeline.

Many human activities have the potential to influence the water quality in the watersheds and the Sanctuary by contributing pollutants to runoff. All public and private land-uses, including urban and rural development, recreation and wildlife, industrial, and agricultural activities may affect water quality within these rivers and streams. Individually insignificant sources of polluted runoff build upon each other as the water travels downstream. Throughout the country there is increasing recognition that addressing these scattered "nonpoint" sources of pollution is critical to maintaining the health of natural resources and local communities. However, because of the complexity of the variables that affect nonpoint source pollution, including weather, climate, substrate, terrain, land use, etc., no single unified solution exists. Addressing polluted runoff requires a long-term collaborative effort among all the people who live and work in a

Addressing current water quality problems in the region's watersheds becomes particularly important as we look to a future with the expectation of increasing population and intensity of human land use activities along the Central Coast. This increased intensity stems from continuing urbanization in many coastal watersheds. Simultaneously, many parts of the region are experiencing an increase in agricultural land-use activities.

Agricultural impacts

The aspects of agriculture that potentially impact water quality include erosion and sedimentation, offsite transport of chemical fertilizers and pesticides, and microbial contamination. Stormwater, flooding, irrigation, and leaching can all mobilize substances that are beneficial while on-site, but become pollutants as they concentrate in neighboring streams, rivers, wetlands, and nearshore waters. Though each individual farm or ranch may contribute a relatively small amount of pollutants, the cumulative effects through the length of a watershed can be damaging. At the same time, the offsite movement of sediments, pesticides and nutrients can represent a long-term economic loss to the grower.

Many farmers, ranchers and forest landowners have already adopted a variety of management measures to reduce polluted runoff. Expanding and strengthening the conservation practices already begun by the industry can help protect our natural resources and sustain the long-term economic viability of agriculture. It can also improve the public perception of agricultural conservation issues, and increase recognition of the value that agriculture provides the Central Coast region.

Some management practices that address these issues may have long-term economic benefits for the grower or rancher, as well as improving habitat for fish and wildlife and reducing offsite damage to public trust resources. Costs for other practices may exceed any economic benefit to the agricultural landowner or operator, though the benefit to the public may be considerable. The WQPP encourages increased support for the development and implementation of economically feasible management improvements, and the development of incentives which allow implementation of marginally economic practices where substantial benefits to natural resources may justify public investment.

Although this document focuses on strategies to protect water quality from potential adverse impacts of agricultural land management, the program recognizes the importance of maintaining agricultural use of the lands for the long-term health of the watersheds. Relative to the extensive paved surfaces of urban areas, effectively managed agricultural lands can act to slow and capture stormwater runoff, provide sites for recharge, water storage and wildlife habitat, and reduce the impact of flood events. These lands also enrich the quality of life for watershed residents and visitors, providing green, aesthetically pleasing landscape, and jobs and tax revenues that sustain local communities.

Overview of Nonpoint Source Contaminants

An overview of nonpoint source issues in the Central Coast region is provided below. This section is based on a review of existing data and literature, as well as additional information provided by participants at agricultural workshops. Additional information on the literature cited is provided in the backnotes on page 56. Although the WQPP is addressing a much wider set of issues which impact water quality, including urban runoff and marinas and boating activities, only those issues which have an agricultural component are discussed here.


Soil management practices can have an effect on wetlands and waterways, fish populations, levels of toxic pollutants in water and sediment, and the economic viability of farm, range and forest lands. The most significant impacts in this region are caused by the accumulation of soils washed into surface waters by rain, particularly by winter storm events and periodic extensive floods. Although some natural level of sedimentation occurs in all watersheds, and flooding can overwhelm the most prudent land management, both offshore activities and land use practices can significantly increase the rate of erosion and sedimentation. Erosion occurs not only from agricultural areas, but from urban and rural development as well, including rural roads. These non-agricultural sources of erosion are included in the WQPP's Urban Runoff plan and in Section 6 of this document.

Transport of sediment is a natural function of a healthy hydrological system, but excessive sedimentation is a concern for the rivers, wetlands and harbors that border the Sanctuary. Although several studies have focused on specific sediment sources and problems, additional research is needed to fully understand all the functional variables in the various watersheds. Excessive sedimentation may smother riverine, estuarine and marine habitats, killing benthic (bottom-living) organisms, reducing colonization, interfering with feeding, covering spawning grounds important to fish such as steelhead and salmon, and reducing the number of plants emerging in wetlands. It can also fill wetland areas, reducing their natural ability to "treat" and slow runoff water as it makes its way to the sea, and cause perennial wetlands to evolve toward seasonal wetlands. Increased sediment in streams can result in sediment deposition in the stream channels, which can lead to severe streambank instability and increased flooding downstream. Sedimentation is also a main transport mechanism for persistent pesticides (see below) that adhere to soil particle surfaces.1

Anadromous fish (like steelhead and salmon) that spend part of their lives in the ocean and make use of local rivers to reproduce are particularly susceptible to human activities in the watersheds. Heavy sediment loads from rural developments and roads, agricultural activities, and urban areas can cause habitat degradation that contributes to fish population decline by burying the coarse gravel beds where they would normally deposit their eggs. Recently both the Coho salmon and steelhead populations on the Central Coast have been listed as threatened/ endangered species by the National Marine Fisheries Service and the State of California, increasing the level of interest in restoring and protecting the spawning habitat of these fisheries.2

Soil loss from farms, range and forest lands also has a variety of economic effects. Over the long term, reduced agricultural productivity through topsoil loss can be a significant economic loss to the agricultural landowner and manager, particularly in upland areas where soil layers are thin. Added to this are the costs of reduced water retention and percolation, and increased on-farm maintenance to control erosion or dispose of sediments. There are costs to all sectors of the community from sediments being in the wrong place (e.g., cleanup and disposal of sediments deposited on public roads, in channels and harbors). In addition, downstream transport of soils which contain relict loads of banned or discontinued persistent pesticides adsorbed to their surfaces has impeded dredging of sediment in areas such as Moss Landing Harbor, increasing annual dredging costs and making appropriate disposal of the dredged materials difficult. Control of excessive erosion and runoff is one of the most important issues for agricultural land management in the region's watersheds, since it can result not only in reduced sedimentation, but reduced transport of other contaminants as well.


Elevated nutrient concentrations, particularly nitrates, are also of concern in several areas surrounding the Sanctuary. Nutrients can enter surface and groundwater from agricultural and urban sources, including agricultural and urban fertilizer application, human septage, waste from livestock and domestic pets, and from numerous natural sources including plant decomposition and wildlife. Elevated levels of nutrients from mixed sources have been reported in the Elkhorn Slough and Salinas River watersheds, Moro Cojo Slough, and in the Pajaro River and its tributaries including Llagas Creek and Watsonville Sloughs. Long-term monitoring studies indicate a marked seasonal increase in surface water nitrate concentrations in the Elkhorn Slough watershed since the 1970's, and very high year-round levels in the lower portions of the Salinas River in the 1990's.3

Concentration of nutrients in surface waters may result in the rapid growth of aquatic plants and plankton, decreasing biological diversity, clogging waterways and flood control channels, and leading to the depletion of oxygen in the water. Algal blooms have been observed in the Pajaro River and several tributaries, and in the Watsonville Slough System. Nutrient inputs can also cause algal blooms in coastal waters, leading some scientists to consider nutrients a contributing factor in the national and global rise in toxic "harmful algal blooms". Although surface waters are the primary focus of the WQPP, it is important to note that nutrients may also infiltrate groundwater supplies and may have public health consequences. There may be some supplementary benefits to groundwater quality from activities undertaken in connection with the Water Quality Protection Program.4

Elevated ammonia concentrations can result from urban, agricultural and natural nutrient sources, and may be toxic to fish. Data for the Watsonville Sloughs System, which receives runoff from agricultural lands, urban sources, and small acreage rural ranchettes, are routinely in excess of chronic ammonia toxicity limits for sensitive fish species. Additional recent data from the Pajaro watershed indicate high ammonia levels in several subwatersheds further upstream. Because there is no direct application of either anhydrous ammonia or aqua ammonia on agricultural lands in these subwatersheds, the presence of ammonia is the result of breakdown products from either agricultural or nonagricultural sources such as human or animal waste. Accurate source identification will therefore be necessary for development of effective controls.5


Old-generation Pesticides

The character of pesticides in use has changed over the last two decades, from persistent broad-spectrum compounds to products that decay rapidly and are generally applied to specific groups of target organisms. Many organochlorine pesticides that are now banned were used extensively in the past during an era in which their persistence and toxicity to non-target organisms was unknown. These now-banned pesticides were used throughout various watersheds, primarily for agricultural pest control but also for urban and rural uses such as mosquito abatement, structural fumigation, urban park and residential garden pest control. Many of these compounds have persisted in the soil longer than anticipated, adhering to fine soil particles on site, or moving downstream with eroding sediments to be deposited elsewhere.

Elevated levels of contamination from persistent pesticides such as DDT, aldrin, chlordane, dieldrin, toxaphene, endosulfan, etc. have been reported from sediment and/or shellfish tissue for the Old Salinas River Channel, Salinas River Lagoon, Moro Cojo Slough, Moss Landing Harbor, Elkhorn Slough, and Watsonville Sloughs, and in aquatic toxicity tests for subwatersheds draining to the Pajaro Lagoon. For several of these persistent compounds, the studies of the Watsonville Sloughs and Salinas River/Old Salinas River areas report some of the most severe pesticide contamination in the state. A recent study of sediments in the mid-portions of Monterey Bay also found DDT, probably related to discharges from the Pajaro and Salinas Rivers, but at relatively low levels.6

Although most of these persistent pesticides are currently banned (except for endosulfan and dacthal), they remain present in the soil and are transported in surface runoff, through the movement of sediment, to the water bodies and tributaries surrounding the Sanctuary. Their impact on water quality is generally not an issue related to current pesticide practices, but a sedimentation issue to be addressed through management practices that reduce controllable sediment sources. Many of the watershed and rivermouth concentrations exceed the levels of these compounds at which biological impacts have been observed in other areas.

The degree of overall impact of these compounds is uncertain in this region, but the high concentrations occurring at some sites raise significant concerns. Many of these compounds are fat-soluble and tend to accumulate and persist in fatty tissues of animals, especially shellfish and other aquatic species. Shellfish and other bottom-living organisms accumulate these pesticides as they feed, and other animals accumulate them by consuming contaminated fish or shellfish. DDT may accumulate in the tissue of predatory birds and has reportedly caused reproductive failure locally through weakening of eggshells. DDT found in tissues and eggshells is assumed to be the cause of near-complete reproductive failure of a breeding population of Caspian Terns in Elkhorn Slough in 1996. These terns reportedly hunt in the Watsonville Sloughs area as well as in Elkhorn Slough. Elevated levels of DDT have also been found in the tissues of sea otters in the Monterey Bay region, although it is not yet known what, if any, impact this may be having on the population.7

Although currently used compounds generally decay more rapidly than the historically-used organochlorine pesticides, some more persistent compounds still in use can accumulate in fairly high concentrations locally, particularly in rivers, lagoons, sloughs, and harbors where sediment deposition rates are high. Dacthal and endosulfan have been detected in sediments and tissues of local estuarine and freshwater animals at concentrations that cause concern. Dacthal is no longer manufactured, and its current use is limited to depletion of existing inventories. Due to its persistence in the environment, the use of endosulfan is restricted near all waterways. The Monterey County Agricultural Commissioner, for example, has prohibited its use on lands that may drain into the Salinas River or Elkhorn Slough.8

New-generation Pesticides

The newer generation pesticides decompose more readily. Potential impacts of currently used pesticides are extensively evaluated in the course of product registration by the U.S. Environmental Protection Agency and the California Department of Pesticide Regulation. Current pesticide use in the State of California is closely regulated, with 100% use reporting to the Agricultural Commissioner's office required for most pesticide use. However, monitoring for these compounds in the region's streams, rivers, wetlands and harbors is both difficult and expensive, and there is currently little data on their distribution and fate throughout the watersheds, due to funding constraints of the monitoring programs and difficulties in keeping up with new compounds as they are introduced.9

Most of the newer organophosphate and carbamate pesticides currently in use are not regularly monitored in the region's watersheds or coastal waters. A study in the Salinas Valley found no offsite migration of currently used pesticides from two parcels with appropriate management practices in place, although surface water runoff was minimal during the sampling period. Sediment monitoring for a few of the currently-used new generation pesticides did not find detectable levels in Monterey Bay.

However, limited data available from shellfish studies in the Salinas, Elkhorn and Pajaro watersheds indicate that chlorpyrifos, diazinon, and oxydiazinon may bioaccumulate, suggesting a certain degree of persistence in the environment. Diazinon has also been found in the subwatersheds draining to the Pajaro Lagoon. Additional monitoring should be conducted to determine the distribution and fate of a wider range of currently-used compounds to ensure that the newer pesticides are functioning as designed to be non-persistent and non-bioaccumulatable and do not run off into waterways. It also should be recognized that chlorpyrifos, diazinon and oxydiazinon are also used for non-agricultural uses such as urban/rural landscape maintenance, and their use in these urban areas is not subjected to the degree of supervision, regulation or reporting imposed on agricultural uses.10

Data from the state's pesticide use reporting system indicates that total pounds of pesticide applied in the Central Coast region (and other areas of the state) increased over the time period from 1991 to 1995. It is important to recognize that total pounds of pesticide applied does not provide a measure of pesticide load in the environment, and it is currently not known what, if any, environmental impacts there may be in the region's waterways. Potential factors contributing to the 1991-1995 increase included changes in weather patterns, increases in agricultural acreage and total crop production, greater pest problems, increased compliance with reporting requirements, lack of alternative pesticides due to suspended or canceled pesticides or to increases in pest resistance, increased intensity of use, and changes in reporting requirements of organic products. In addition, some of the increase may have been due to shifts from the few remaining old-generation, persistent, broad-spectrum pesticides still in use to new-generation products that break down more readily and must be applied more often, and are highly pest-specific, requiring more chemicals to do the job previously done by one. Note that the 1996 Summary of Pesticide Use Report Data indicates that total pounds applied in 1996 statewide were somewhat less than the previous year (though still higher than the total pounds applied during the years 1991 to 1994).11

The limited water quality monitoring data that are available do not suggest a crisis situation with currently-used pesticides. More adequate monitoring for these compounds in the watersheds should be developed to detect any potential problems.

Microbiological Contamination

Microbiological contamination also occurs in some watersheds from mixed sources including urban runoff, confined animal facilities, rural ranchettes, poorly functioning septic systems, and wildlife. Elevated concentrations of coliform bacteria have been reported for Watsonville Sloughs, stemming from mixed sources. Coliform bacteria are relatively harmless microorganisms that live in the intestines of animals and aid in the digestion of food. Fecal coliform bacteria are a subgroup of this collection of bacteria which are associated only with the fecal material of warm-blooded animals. The presence of fecal coliform in water sources indicates fecal contamination, which in turn indicates possible contamination by pathogens or disease-producing bacteria or viruses. Elevated concentrations of coliform bacteria from mixed sources in Elkhorn Slough have resulted in the loss of a significant shellfish culturing industry. There have also been localized problems in some watersheds along the San Mateo Coast apparently due to bacterial contamination in creeks from nearby rural ranchettes. Existing limited microbiological data from these reports do not allow quantification of the relative contribution of urban, agricultural and wildlife sources.12

Regional Monitoring Needs

Although the studies cited above present significant information on water quality issues, the lack of adequate long-term monitoring data for watershed and coastal areas was identified as a concern by workshop participants. There are a number of federal, state and local monitoring programs operating within the region (including State Mussel Watch and the Toxic Substances Monitoring Program), as summarized in Tetra Tech's 1995 report. Most of these programs have a limited focus and generally work independently of other monitoring efforts.

The need for coordinated monitoring and databases which can provide readily accessible and understandable information to characterize the health of the Sanctuary and its watersheds was identified and addressed in WQPP's Action Plan II. Work has been initiated by the Central Coast RWQCB in conjunction with the California Department of Fish and Game (CDFG), municipal dischargers, the Sanctuary, and others to develop a coordinated regional monitoring program. The program includes development of a centralized database which can incorporate data from the various government monitoring programs in the region. In addition to collecting data from existing monitoring programs, the RWQCB has recently received funding to collect water quality data in various central California watersheds on a 5-year, rotational basis. This will not only provide baseline data for establishing water quality trends, but will allow for the detection of pollution problems and for the evaluation of various conservation measures implemented by both point and nonpoint source dischargers, including agricultural management practices.

In parallel with the RWQCB's effort to coordinate regional governmental monitoring programs is an effort led by the Coastal Watershed Council and the Center for Marine Conservation, in association with the Sanctuary's WQPP. The Sanctuary Citizen Watershed Monitoring Network is coordinating and providing training for the existing volunteer monitoring programs in the Sanctuary's watersheds. Data collected from approximately 20 citizen monitoring programs will be displayed in a standardized database, and linked to the RWQCB's database of monitoring programs. These volunteer groups are being provided with standardized training and sampling protocols to ensure collection of high quality data. Trainers also emphasize the need to sample from public access locations and to work on private lands only with the permission of the landowner.

In addition, grower self-monitoring is addressed in Sections 1 and 2 of this document. Water quality data generated from agricultural self-monitoring, compiled by the Farm Bureaus at a subwatershed level to protect the privacy of the individual landowners, will eventually be linked into the coordinated regional monitoring program. These three related monitoring efforts will help resource managers further evaluate the overall health of the waters that drain into the Sanctuary. The self-monitoring data will also provide valuable information to growers and ranchers regarding the effectiveness of management practices.

The need for more adequate monitoring data, especially for sediments, was of particular concern to the participants in the WQPP's agricultural workshops in Half Moon Bay, due to a relative lack of information for the San Mateo Coast. The recommendation for additional monitoring in this area led to the development of a proposal for a joint project by the San Mateo County Resource Conservation District, the Sanctuary and the San Mateo County Farm Bureau which includes sediment characterization, monitoring and outreach on source control for the Pescadero watershed. This project was recently funded by the San Francisco Regional Water Quality Control Board and work will begin in 1999.

Notes for "Water Quality Issues" Section

  1. References regarding sedimentation in rivers, wetlands and harbors that border the Sanctuary: ABA Consultants, 1989; AMBAG, 1984; Habitat Restoration Group, 1996; Questa Engineering, 1995; NOAA, 1995; San Mateo County RCD, 1997; SWRCB, 1993a; USGS, 1992; Balance Hydrologic, 1998.

    References regarding effects of excessive sedimentation: Mathias & Moyle, 1992; Jurik, et al., 1994; Questa Engineering, 1995.

    References regarding sediment as transport mechanism for persistent pesticides: Kleinfelder, 1992, 1993; Werner, et al., 1993.

  2. Reference regarding effects of sedimentation on spawning habitat: Nelson, et al., 1987.
  3. References regarding elevated nutrient levels reported in local rivers and sloughs: Caffrey, et al., 1997; Habitat Restoration Group, 1991; Habitat Restoration Group, 1996; Greenlee and Ricker, 1981; Questa, 1995; San Jose State University, 1994; RWQCB, 1998.

    Reference regarding increase in surface water nitrate concentrations in the Elkhorn Slough watershed and in the lower portions of the Salinas River: Caffrey, et al., 1997.
  4. References regarding algal blooms reported locally: Greenlee & Ricker, 1981; RWQCB, 1998; Questa, 1995.

    Reference regarding "harmful algal blooms": Anderson, 1999.

    Reference regarding nitrates in groundwater supplies: Monterey County Water Resources Agency, 1990.
  5. References regarding ammonia data: Questa, 1995; RWQCB, 1998.
  6. References regarding reports of elevated levels of contamination from persistent pesticides: Habitat Restoration Group, 1996; Kleinfelder, 1993; Ladd et al., 1984; Oakden and Oliver, 1988; Questa Engineering, 1995; SWRCB, 1990, 1991, 1995a, b; Santa Cruz County, 1997; Stephenson et al., 1995; Hunt et al., 1999; USGS, 1997.
  7. References regarding DDT impacts: Crump, 1991; Parkin, 1997; Nakata et al., 1998.
  8. Reference regarding local detection of dacthal and endosulfan: SWRCB, 1995a.
  9. Reference regarding monitoring of new-generation pesticides: TetraTech, 1995.
  10. References regarding new-generation pesticides: CDFG, 1997; SWRCB, 1995a; Hunt et al., 1999.

    Reference regarding no offsite migration of pesticides in two parcels in the Salinas Valley: Kleinfelder, 1993.
  11. References regarding increase in total pounds of pesticide applied from 1991 to 1995: University of California, 1999; CDPR, 1998. Reference regarding total pounds of pesticide applied during 1996: CDPR, 1999.
  12. References regarding coliform bacteria data reported for Watsonville Sloughs and Elkhorn Slough: Questa, 1995; Elkhorn Slough Technical Advisory Committee, 1995.
  13. Reference for the California Rangeland Management Plan: SWRCB, 1995c.


Reviewed: April 11, 2024
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