San Diego Region - Bay Cleanup Program

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Welcome to the Bay Cleanup page of the California Regional Water Quality Control Board San Diego Region. Several sampling and cleanup efforts are underway in San Diego Bay, small craft harbors, and coastal lagoons in southern Orange County and northern San Diego County.

Copper in Marina Waters

Schiff, Kenneth. 2006. Extent and magnitude of copper contamination in marinas of the San Diego Region, California. Southern California Coastal Water Research Project Technical Report No. 483. See the narrative report.
Dissolved copper, bivalve toxicity, and TIE. Data for this project will be posted on the Division of Water Quality Website under the Surface Water Ambient Monitoring Program (SWAMP).

San Diego Bay Report, City of San Diego

This report summarizes the San Diego Bay data from the Southern California Coastal Water Research Project (SCCWRP) Bight'98 regional monitoring program for the Southern California Bight. The San Diego Bay report documents intensive sampling during the summer of 1998 in the Bay. Download this report from Public Downloads below.

Bill in Congress to allow sewage disposal into harbors

A House of Representatives bill, H.R. 1027, would allow recreational boats to dispose of treated sewage into more than 50 state no-discharge zones, including Dana Point Harbor, Oceanside Harbor, Mission Bay, and San Diego Bay. Read the August 12, 2003 response from the State Water Resources Control Board to the California Congressional delegation.

Vessel Bottom Paint

Activities to address the effects of copper-based anti-fouling paint include a survey of underwater hull cleaners by John Conway, Marine Fouling and Underwater Hull Cleaning in San Diego Bay, available below; research on underwater hull cleaning best management practices (Southern California Coastal Water Research Project); research to evaluate non-toxic hull paint (University California Sea Grant); and participation on the proposed San Diego Advisory Committee for Environmentally Superior Antifouling Paints. See Copper Emissions From Antifouling Paint Final Report, by Kenneth Schiff of SCCWRP.

Boater and Marina Information and Invasive Species on Boat Hulls

UC Cooperative Extension, Coastal Resources Program focuses on a few topics and provides links to resources on many other issues that affect the coast, its people and resources. It provides research-based information on: Aquatic Invasive Species (coastal), Quagga/Zebra Mussel Invasion (lakes), Nontoxic Antifouling Strategies, and Boating & Marina Pollution Prevention.

Total Maximum Daily Load (TMDL)

A Total Maximum Daily load project for dissolved copper at the Shelter Island Yacht Basin in San Diego Bay may be viewed at this San Diego Regional Board Website. Other San Diego Bay and Mission Bay TMDL programs for diazinon, metals and bacteria may also be viewed at this site.

Sediment Sampling

Sediment sampling programs include compliance monitoring by permit holders, triad sampling under the Bay Protection and Toxic Cleanup Program, and a Bight'98 regional monitoring program for marine waters from pt. Conception to south of Ensenada, Baja California Norte. View the Bight '98 reports. Compliance point source and storm water monitoring reports are not yet available on the web but reports may be viewed at the Regional Board office with appointment.

Toxic Hot Spots

In 1999 the State Water Resources Control Board adopted the Bay Protection Program Consolidated Toxic Hot Spot Cleanup Plan, which incorporated seven regional cleanup plans for bays and estuaries throughout California. View the Bay Protection Program reports. The agenda folder material for the San Diego Regional Plan may be downloaded from files listed at the bottom of this page.

Shipyard Cleanup

See information on shipyard sediment cleanup.


Visit the State Water Resources Control Board Website for reports of bioaccumulation in caged mussels placed throughout California's coastal waters.


John Largier's San Diego Bay Circulation report is now available for download. See the list of files below.


The county of San Diego has online information about bacteria at public swimming beaches

San Diego Interagency Water Quality Panel

The San Diego Interagency Water Quality Panel (Bay Panel) produced a framework for a San Diego Bay coordinated monitoring program, part of which was carried out in 1998 under the Bight '98 Regional Monitoring Program. View the Panel's draft Comprehensive Management Plan at the San Diego Bay Project of the San Diego Super Computer Center.

SCCWRP Regional Monitoring

View the Southern California Coastal Water Research project Bight '98 sampling reports.

Storm Water

Get information on the City of San Diego's Think Blue campaign.

Please contact Vicente Rodriguez at (619) 521-3966 or at should you have questions about bay cleanup.

Public Downloads

(All files are viewable using Adobe Reader 8.0 or higher unless noted)

Date Description
Ecological Assessment of San Diego Bay: A component of the Bight'98 Regional Survey:
Copper Emissions From Antifouling Paint Final Report, by Kenneth Schiff of SCCWRP
John Largier: San Diego Bay Circulation Final Report
Marine Fouling and Underwater Hull Cleaning in San Diego Bay
Moderate-Priority Site Cleanup Plans
Hot Spot Decision Tables
Regional Toxic Hot Spot Cleanup Plan
Responses to hot spot comments
Hot Spot Cleanup Plan Information