Stormwater Permits


California regulates water pollution through the issuance of waste discharge requirements by the Regional Water Quality Control Board (Regional Board).

Permits can be individual, say a specific facility and its specific discharge, or general, such as facilities that discharge the same types of wastewater. The permits set limits on what may be dumped into our waters and where.  A power plant may be limited on how much it can raise the temperature of its discharge (heat is a pollutant); a shipyard may have to submit monitoring reports to gauge how much copper it discharges into the bay.

Coastkeeper reviews these permits to ensure that they contain adequate precautions to prevent harm of our waters.  The language can be numeric – so many milligrams of mercury per day, or narrative – no toxic substances in toxic amounts.  Sometimes we work directly with dischargers to achieve strong requirements; often we submit our comments to the Regional Board directly.  The board members review all the comments on a permit, take testimony from all sides and decide on the permit.  The Regional Board’s board members can approve the permit, approve it with modifications or deny it.

After approval of a permit, Coastkeeper reviews monitoring reports to ensure the facility meets its requirements.  If we see violations, we can bring litigation to correct the problems.  Every five years, the Regional Board must renew the permit, which gives another opportunity to evaluate the requirements and advocate for further protections or modifications. (back to top)

Learn more about permits in these categories:

Large Municipalities

Small Municipalities and Nontraditional Sources

Industrial Sources



Large Municipalities

commercial pollution san diego

Photo by Jackie Loza

Under the Clean Water Act, medium and large municipalities with populations of 100,000 or more are required to have a permit for their municipal separate storm sewer system (MS4). The systems are called “separate” storm sewer systems because they do not join with the sanitary sewer system, and the storm sewer system leads straight into our waters instead of into a treatment plant.

In San Diego, we’ve had several versions of the municipal stormwater permit. The region adopted our latest permit on May 8, 2013. It covers 18 cities in San Diego, along with San Diego County, the port and the airport, along with portions of South Orange County and Riverside County. The permit focuses on the health of our watersheds and requires all the municipalities within a watershed to create a Water Quality Improvement Plan. The Water Quality Improvement Plan, which will be crafted over two years with the help of public participation, will identify priority pollution conditions, strategies to address those problems, numeric goals and timelines to achieve those goals.

San Diego Coastkeeper worked for almost two years to get this new permit adopted, and we are committed to ensuring the Water Quality Improvement Plans help us get cleaner water faster. Public participation is important to ensuring these plans are robust, protect the environment and find creative ways to solve our water pollution problems in San Diego. To give your input on the plan, watch for notices on the Regional Clearinghouse and keep an eye on our blog for opportunities to participate. (back to top)

Small Municipalities and Nontraditional Sources

Small municipalities and nontraditional sources, like universities, schools, and military installations (sometimes called “Phase II” permittees) are usually covered by a general stormwater permit. In California, the State Water Resources Control Board adopted a general small MS4 permit, or Phase II MS4 permit, on February 5, 2013. (back to top)

Industrial Sources

The Clean Water Act assumes that some industrial facilities are more likely than others to create the type of pollution that can contribute to urban runoff problems. The Clean Water Act requires these facilities to do one of three things:

    1. prove that no stormwater runoff leaves the facility,
    2. apply for and be issued an individual stormwater permit or
    3. apply for coverage under a general industrial stormwater permit.

In California, the State Water Resources Control Board is revising the 1997 general industrial stormwater permit. We expect it will adopt a finalized permit in late 2013. The general industrial permit requires covered facilities to implement management measures that will achieve the performance standard of best available technology economically achievable and best conventional pollutant control technology. The general industrial permit also requires the development of a Storm Water Pollution Prevention Plan and a monitoring plan. The Storm Water Pollution Prevention Plan must identify sources of pollutants and the means to manage the sources to reduce storm water pollution. The general industrial permit requires covered facilities to submit an annual report each year on July 1. Facility operators may be able to participate in a group monitoring program. (back to top)


road pollution san diego

Photo by

Roads can significantly contribute to stormwater pollution and are covered under the Clean Water Act. In California, the California Department of Transportation (Caltrans) is responsible for the design, construction, management, and maintenance of the State highway system and is therefore subject to the Clean Water Act’s stormwater permitting requirements. On September 19, 2012, the State Water Resources Control Board issued the latest version of Caltrans’ stormwater permit, which became effective on July 1, 2013. Caltrans’ Storm Water Management Plan describes the procedures and practices used to reduce or eliminate the discharge of pollutants to storm drainage systems and receiving waters. Caltrans must submit a revised Storm Water Management Plan to the State Water Board for approval by July 1, 2014. (back to top)