Nonpoint Source Program Banner - Panoramic photograph of Clear Lake

Nonpoint Source (NPS) Program

What is Nonpoint Source Pollution?

Nonpoint source (NPS) pollution, also known as polluted runoff, is the leading cause of water quality impairments in California. Nonpoint sources are major contributors of pollution to impacted streams, lakes, wetlands, estuaries, marine waters, harbors, bays, and ground water basins. Unlike pollution from distinct, identifiable sources, NPS pollution comes from many diffuse sources and is transported by rainfall, snowmelt, or irrigation water that moves over and through the ground. As the runoff moves, it picks up and carries away natural and human-made pollutants and deposits them into lakes, rivers, wetlands, ground water, and other inland and coastal waters. Common sources of NPS pollution include runoff from agricultural activities, including feedlots, grazing and dairies; runoff from urban areas; and erosion from timber harvesting, construction sites, and roads.

Nonpoint Source Programs

Nonpoint Source (NPS) pollution does not originate from regulated point sources and comes from many diffuse sources. The federal Clean Water Act (CWA) requires States to develop a program to protect the quality of water resources from the adverse effects of NPS water pollution. The NPS Program aims to minimize NPS pollution from land use activities in agriculture, urban development, forestry, recreational boating and marinas, hydromodification and wetlands. The NPS Program goal is to protect water quality and maintain beneficial uses.

The Central Valley NPS Program is guided by the 2020-2025 Nonpoint Source Program Implementation Plan. This implementation plan is updated every five years to reflect current priorities for NPS programs.

The Central Valley NPS Program encompasses several different programs to address NPS pollution. Some of the NPS programs in the Central Valley include the following. Each has its own work plan and fact sheet.

Delta Water Quality

Staff from the State Water Board and the Central Valley and San Francisco Bay Water Boards (collectively Water Boards) formed the Bay-Delta Team to improve coordination of the Water Boards' activities in the San Francisco Bay and Sacramento-San Joaquin River Delta (Bay-Delta). The Bay-Delta Team is charged with developing a short and long-term program for addressing impacts to beneficial uses of water in the Bay-Delta. In response to this charge, the Water Boards developed a 2008 Draft Strategic Workplan for Activities in the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (for a copy of the Strategic Workplan please contact Janis Cooke at

The Strategic Workplan, adopted in 2008, had a project timeline of five years. In 2013, the Strategic Workplan moved to a web-based format and in 2014 the Central Valley Water Board updated their Strategic Work Plan. Links to the Central Valley Water Board activities can be found on the Delta Water Quality Webpage.

Central Valley Salinity Alternatives for Long-Term Sustainability (CV-SALTS)

Elevated salinity and nitrates in surface water and groundwater are increasing problems affecting much of California, other western states, and arid regions throughout the world. In California, as surface and groundwater supplies become scarcer, and as wastewater streams become more concentrated, salinity and nitrate impairments are occurring with greater frequency and magnitude.

In 2006, the Central Valley Water Board, the State Water Board, and stakeholders began a joint effort to address salinity and nitrate problems in California's Central Valley and adopt long-term solutions that will lead to enhanced water quality and economic sustainability. Central Valley Salinity Alternatives for Long-Term Sustainability (CV-SALTS) is a collaborative basin planning effort aimed at developing and implementing a comprehensive salinity and nitrate management program. The goal of CV-SALTS is to maintain a healthy environment and a good quality of life for all Californians by protecting our most essential and vulnerable resource: WATER.

In July 2008, the Central Valley Salinity Coalition (CVSC) was formed. CVSC represents stakeholder groups working with the Board in the CV-SALTS effort. Its purpose is to organize, facilitate and fund efforts needed to fulfill the goals of CV-SALTS. CVSC coordinates the meetings of the CV-SALTS committees, maintains an independent web site, and manages the projects originating from this effort. Information and materials regarding the stakeholder committees and other activity, including the meeting schedule, are posted the CV Salts Webpage. Additional information may be found at the
Water Boards CV-SALTS Webpage.

Irrigated Lands Program

A range of pollutants can be found in runoff from irrigated lands, such as pesticides, fertilizers, salts, pathogens, and sediment. At high enough concentrations, these pollutants can harm aquatic life or make water unusable for drinking water or agricultural uses. The Irrigated Lands Regulatory Program was initiated in 2003 to prevent agricultural runoff from impairing surface waters. Waste discharge requirements (WDRs), which protect both surface water and groundwater, now address irrigated agricultural discharges throughout the Central Valley. The Central Valley Water Board adopted the first WDRs for irrigated agricultural discharges in December 2012 and has adopted WDRs for all regions in the Central Valley. The adopted WDRs are the product of four years of dialogue among a variety of interested parties, as well as public input received at numerous Central Valley Water Board meetings. Additional information may be found at the Water Boards Irrigated Lands Regulatory Program Webpage.

Forest Activities Program

The Forest Activities Program at the Central Valley Water Board addresses nonpoint source (NPS) activities in our forested headwaters. These activities primarily include; timber harvesting and fuels management, post-fire impacts assessment and mitigation, rural roads construction and maintenance, and off-highway vehicle use areas. All of these NPS activities in our forested lands have the potential to impact the beneficial uses of our surface waters. Additional information may be found at the Water Boards Forest Activities Webpage.

Confined Animal Facilities

Animal wastes may produce significant amounts of pathogens, nutrients, and salt contamination. Runoff from animal confinement facilities (e.g., stockyards, dairies, poultry ranches) can impair both surface and ground water beneficial uses. The Central Valley Water Board adopted General WDRs Order R5-2007-0035 (Dairy WDRs) in May 2007 to control the discharges from existing milk cow dairies in the Central Valley. In 2011, the monitoring and reporting program for the Dairy WDRs was revised to incorporate representative groundwater monitoring. Additional information may be found at the Water Boards Confined Animal Facilities Webpage.

Total Maximum Daily Load (TMDL) Implementation

Many of the streams in the Central Valley Region are listed as impaired under Section 303(d) of the federal Clean Water Act. Most of these impairments, such as pesticides, dissolved oxygen and salt are from nonpoint source pollution. Placement on the 303(d) list triggers an assessment that can lead to the development of a TMDL for the waterbody and associated pollutant/stressor on the list. Literally, the "total maximum daily load" is the amount of a certain pollutant that a specific water body or watershed can assimilate and still be safe for people, fish, and wildlife. The TMDL describes the causes of the impairment and outlines a plan for achieving water quality standards in the impaired water body using the regulatory authorities administered by the Water Boards.

There are several ways to implement the actions necessary to meet a TMDL, including the following:

  • Regulatory action(s) of a Water Board, such as a permit, waiver, or enforcement order.
  • Regulatory action(s) of another state, federal, or local agency.
  • Amendments of Water Quality Control Plans in the form of an Implementation Plan, describing the steps necessary to meet the TMDL.
  • Non-regulatory action(s), such as third party agreements and self-directed pollutant control.

Additional information and a complete list of adopted TMDLs for the Central Valley Water Board can be found on the Central Valley Water Boards TMDL and 303(d) List web page.

Contact Us

Program Contacts

Facts & Information

Fiscal Year 23/24 Annual Report Video
(Video will open in YouTube)

Additional Information regarding Nonpoint Source Pollution can be found on the following websites: