Nonpoint Source Program


Nonpoint source pollution is the pollution of our nation's waters caused by rainfall or snowmelt moving over and through the ground, picking up and carrying pollutants (both natural and from human activity) and depositing them into lakes, rivers, wetlands, coastal waters, and ground waters. This pollution may be from agricultural runoff, including pesticides and herbicides and animal wastes; sedimentation from timber harvests or building construction; discharges from marinas and boating activities; mining wastes; septic system discharges; and runoff from urban areas [the latter are now covered under municipal NPDES permits and generally considered in the category of point source pollution for regulatory purposes]. In addition, modification of streams and river channels, construction of dams and impoundments and erosion of streambanks or shorelines (collectively known as hydromodification) are considered a form of nonpoint source pollution that often adversely affects the biological and physical integrity of surface waters.

Nonpoint source pollution is one of the top threats to the ecological health of San Francisco Bay and its tributaries and to coastal waters. San Francisco Bay is impaired due to exceedances of water quality standards for trace metals, such as mercury, and other pollutants, including polychlorinated biphenyls (PCBs) and diazinon, which are largely from nonpoint source pollution. Many other waterbodies in the Region are also impaired by pathogens, sediments, nutrients, metals, and pesticides.

Statewide Plan for NPS Pollution Control

In July 2000 the State Board and the California Coastal Commission developed the Plan for California's Nonpoint Source Pollution Control Program to reduce and prevent nonpoint source pollution in California, expanding the State's nonpoint source pollution control efforts by identifying 61 management measures that provide specific goals and practices for controlling NPS pollution from land use activities related to: (1) agriculture, (2) forestry, (3) urban areas, (4) marinas and recreational boating, (5) hydromodification, and (6) wetlands, riparian areas and vegetated treatment systems. The plan is available on the State Board's website

In August 2004 the State Office of Administrative Law approved the "Policy for the Implementation and Enforcement of the Nonpoint Source Pollution Control Program" (NPS Policy). The NPS Policy makes it clear that all NPS discharges must be under regulation - permitted Waste Discharge Requirements (WDRS), waivers of WDRs, or Basin Plan Prohibitions. The policy formally eliminates the previous "three-tiered approach" of voluntary compliance, regulatory-based encouragement (waivers), and regulation (permits and prohibitions).

NPS Activities in the San Francisco Bay Region

The primary causes of impairment in the San Francisco Bay Region are from activities associated with urbanization, agriculture, and hydromodification. We have identified the highest priority areas of focus for NPS management measures to be: 1) Runoff from confined animal facilities, 2) Runoff from urban areas, and 3) Hydromodification. The staff person(s) in our North and South Bay Watershed Management Divisions are responsible for watershed management activities, outreach activities, specific NPS issues, and contract management. We are currently managing over 15 Federal 319(h) NPS grants, as well as approximately 30 Proposition 13 grants, the majority of which are targeted to address NPS pollution. Past and present grants include equestrian facility improvements, dairy and rangeland water management practices, dam removal, creek restoration, and citizen monitoring projects.

A major focus of nonpoint source staff activities in Region 2 has been working with dairies in Marin and Sonoma Counties. We completed inspections and surveys of all dairies and awarded compliance merit awards to fourteen dairies that fully complied with State Standards and demonstrated a standard of excellence in running their facilities. In October 2003, the Board issued a general permit for dairies that were not fully in compliance and a waiver of WDRs for those meeting standards.

An important element of the Regional Board's approach to address NPS is to increase public awareness through education and outreach on the causes and control of NPS pollution to local agencies, developers, businesses, industry, home owners and renters, and school children, in order to promote the use of improved management practices to eliminate or reduce pollution. For example, in cooperation with the San Francisco Estuary Project, we have recently completed our sixth year of workshops for contractors and local municipalities on erosion control for construction projects. Region 2 has been a leader in developing construction-related guidance materials, including two videos (in English and Spanish) "Keep it Clean" and "Hold on to Your Dirt", an Erosion and Sediment Control Field Manual, and Guidelines for Construction Projects, which are available from the Association of Bay Area Governments (ABAG).

We have also developed a technical reference circular entitled A Primer on Stream and River Protection for the Regulator and Program Manager. This document provides a clear introduction to basic stream hydrology and geomorphology and gives technical assistance to applicants on permitting hydromodification projects. The primer has also been used for a statewide series of workshops to consultants, contractors, local agencies, and nonprofit groups. This primer is available on this website under "Available Documents" or through ABAG.

For More Information:

Region 2 NPS Program:

Jan O'Hara at Janet.O' (510) 622-5681 (for grazing waiver and confined animal facilities programs)

Leslie Ferguson at (510) 622-2344 (Grants Coordinator)

U.S. EPA information:

NPS Encyclopedia:
The NPS Encyclopedia is a guide that provides information on NPS in California, including descriptions of management practices and how they can be used to meet each management measure, their applicability to various situations in California, and their cost-effectiveness in different settings.

The State Board website's NPS page provides documents and further links to information sources at: