NPDES Stormwater

The goal of the Storm Water Program is to prevent or minimize the discharge of pollutants contained in storm water runoff to waters of the state. During rainfall events, water runs across surfaces which may be contaminated by pollutants (such as motor oil, litter, etc). The storm water runoff is often directed into storm drains which then discharge to nearby creeks and rivers. Common pollutants contained in storm water runoff include:

  • Sediment - construction or other activities expose and loosen soils, while vehicles break-up pavement. Excessive sediment in water can effect the respiration, growth, and reproduction of aquatic organisms, cause aesthetic impacts to receiving streams and affect spawning habitat for salmonids.
  • Nutrients - sources include fertilizer, lawn clippings, and car exhaust, which contain nutrients like phosphorous and nitrogen. An overabundance of nutrients can accelerate the growth of algae, which is a key factor in the decline of water clarity in Lake Tahoe and other water bodies.
  • Heavy metals and toxic chemicals - sources include cars (brake pads, engine wear, etc), pesticides and herbicides. Maintaining and cleaning transportation vehicles can release solvents, paint, rust, and lead. These chemicals may poison organisms or cause serious birth defects.
  • Bacteria- sources include failing septic tanks, sewer overflows, decaying organic material, and the improper disposal of household pet fecal material. Some bacteria found in storm water runoff can result in disease. Beach closures result from high bacteria levels.

Recent studies have shown that storm water runoff is a significant source of water pollution, causing declines in fisheries, restrictions on swimming, and limiting our ability to enjoy many of the other benefits that water provides (USEPA). The federal Storm Water Permit Program attempts to curtail storm water pollution by requiring some specific industries and municipalities to obtain a permit for storm water discharges. The permit regulates the permittees activities to ensure the proper management of pollution sources. There are three types of permits required under the federal program: Construction, Industrial, and Municipal permits.

Industrial Permits

Storm water discharges to surface waters from companies involved in manufacturing operations, transportation facilities where vehicles are maintained (maintenance includes fueling and washing), landfills, hazardous waste sites, and other similar operations must be covered by a storm water discharge permit. For coverage under the state's industrial storm water general permit, each facility must submit an application to the State, prepare and implement a Storm Water Pollution Prevention Plan, and monitor the flow of pollutants leaving the site. Although the plan does not have to be submitted to the Regional Board, the permittee must keep the plan available to onsite inspectors and submit an annual report to the Board. With State approval, the general permit allows group monitoring, where only selected facilities within a group are monitored in order to characterize the whole group. Also, a company may be exempt from all or part of the general permit if industrial materials (including wastes, products, machinery, roof exhausts, etc.) are not exposed to rain.

Construction Permits

The major pollutant expected from construction sites is erosion-related, where large amounts of sediment laden water flows into storm drains. Construction activities that involve more than one acre of land disturbance must obtain a permit for discharges of storm water. Construction on sites of less than five acres that are part of a larger project that covers more than five acres also must be permitted. However, construction activities that essentially maintain existing facilities, and do not involve a change in the slope of the land, are not required to be covered under a permit. The State's general permit for discharges of storm water from construction activities requires the site owner to apply with the State, to prepare and implement a Storm Water Pollution Prevention Plan, and to monitor the effectiveness of the plan. The plan does not have to be submitted to the Regional Board, but must be on site and available to inspectors. The plan must also address post-construction control of pollutants in storm water. The size criteria for permit coverage will drop to 1 acre in March, 2003.

Municipal Permits

The Municipal Storm Water Permitting Program regulates storm water discharges from municipal separate storm sewer systems (MS4s). Storm water is runoff from rain or snow melt that runs off impervious surfaces such as rooftops, paved streets, highways or parking lots and can carry with it pollutants such as: oil, pesticides, herbicides, sediment, trash, nutrients, bacteria and metals. The runoff can then drain directly into a local stream, lake or bay. Often, the runoff drains into storm drains which eventually drain untreated into a local river, creek, or lake.
Urban areas commonly include large impervious cover which contributes to an increase in runoff flow, velocity and volume. As a result streams are hydrologically impacted through streambed and channel scouring, instream sedimentation and loss of aquatic and riparian habitat. In addition to hydrological impacts, large impervious cover contribute to greater pollutant loading, resulting in turbid water, nutrient enrichment, bacterial contamination, and increased temperature and trash.
Municipalities are designated into the permitting program based on population. Municipalities with populations over 250,000 are designated as large MS4s, 100,000-250,000 as medium MS4s and less than 100,000 as small MS4s. Large and medium municipalities are designated as Phase I MS4 Permittees and small municipalities are designated as Phase II MS4 Permittees. Additionally, Federal and State operated facilities can be designated as non-traditional small MS4s. Types of facilities can include universities, prisons, hospitals, and military bases.

Phase I Program

There is one Phase I MS4 permit in the North Coast Region, Order No. R1-2015-0030. This permit regulates the discharge of pollutants from the City of Santa Rosa, portions of unincorporated County of Sonoma, Sonoma County Water Agency, the City of Cotati, the City of Cloverdale, the City of Healdsburg, the City of Rohnert Park, the City of Sebastopol, the City of Ukiah, and the Town of Windsor.


Each Co-Permittee (except Cloverdale) has developed a draft Non-Storm Water BMP Plan (BMP Plan) to eliminate or minimize the discharge of pollutants to the MS4 related to select types of discharges. The discharges are allowable non-storm water discharges provided they meet all required conditions in the MS4 Order, are not a significant source of pollutants, and are conducted as specified in the Co-Permittee's approved BMP Plan. The Executive Officer is considering approval of these BMP Plans, pending public comment. Comments on the BMP Plans must be submitted by 5:00 p.m. on November 30, 2015.

Phase II Program

There is one state wide general permit which regulates the discharge of pollutants from small MS4s, State Water Board Order No. 2013-0001 DWQ. In the North Coast Region the following municipalities have been designated as small MS4 and are currently responsible for implementing the requirements of Order No. 2013-0001.

Mendocino County
City of Fort Bragg
Portions of Unincorporated Mendocino County

Humboldt County
City of Eureka
City of Arcata
City of Trinidad
City of Fortuna
Portions of Unincorporated Humboldt County
Humboldt State University

Siskiyou County
City of Yreka

Sonoma County
Sonoma State University
Petaluma Coast Guard Training Center

State of California Department of Parks and Recreation

Phased Program

The Storm Water Program is a National Pollutant Discharge Elimination System (NPDES) Program, and is currently being implemented in two phases. The November 16, 1990 Federal Register describes the requirements of the Phase I Regulations and the December 8, 1999 Federal Register describes the Phase II regulations. The State of California carries out the Storm Water Regulations according to the California Water Code Section 13399.