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The urbanized areas around San Diego Bay and throughout the San Diego Bay Watershed require continual efforts to reduce or eliminate sources of pollution that can be carried by rainfall runoff to the bay.


a storm water runoff channel

Stormwater Management Program

The San Diego Bay is a treasured resource for local businesses, residents, and visitors. People come to the bay to fish, swim, and boat in its waters, view its wildlife and enjoy the diverse shoreline. The Bay is also used by maritime operations to import and export goods into the region and as a location for ship building and repair. The Bay is also the receiving water for discharges originating from within the 444-square miles of the San Diego Bay Watershed. Controlling urban runoff or discharge that is not entirely composed of rain water is critical to preserving the Bay’s resources.

As environmental steward and manager of State lands surrounding San Diego Bay, the Port of San Diego (Port) works to improve and protect bay water quality.

The Stormwater Management Program is a major element of the Port of San Diego's commitment to by preventing, reducing, and eliminating the discharge of polluted stormwater into San Diego Bay. The program is multifaceted with education, required administrative and operational business practices, structural pollution controls, monitoring and enforcement measures in place to prevent pollution.  The extent of the program includes municipal operations, commercial and industrial businesses and collaboration with other cities and jurisdictions that also convey stormwater to the Bay.

The Environmental Protection Department works with the Port’s Marketing and Communications Department on pollution prevention campaigns like #ThatsMyBay to help educate the public on how they can help prevent pollution.  

Click For Tenant Facility Stormwater Resources

Let’s All Do Our Part! Stop Irrigation Runoff

Irrigation water is prohibited from entering the storm drain system. Irrigation runoff can pick up pollutants that accumulate on the ground like dirt, bacteria, trash, and motor oil, and may send it into the nearest storm drain. Eventually, bacteria and other pollutants in the storm drain system would enter our creeks and beaches untreated. By preventing over-irrigation and unnecessary outdoor water use, you can help to prevent polluted water runoff from entering our storm drain system and waterways.

What Can You Do?

  • Get advice from a professional (landscapers or local public agencies) on how to keep runoff out of the stormwater system.  
  • Redirect sprinkler heads away from your yard drain
  • Repair leaking or broken sprinklers
  • Temporarily cover your yard drain with a bowl or mat when watering
  • Water in short cycles to allow water to absorb into the soil
  • Water in the early morning or late evening when it is cooler outside
  • Replace thirsty landscapes with drought-tolerant or native plants

The City of San Diego’s Water Survey Program offers the commercial landscape and commercial/industrial water use survey programs free of charge to commercial, industrial and institutional customers in the City of San Diego. 

Report Pollution

If you observe any of the following occurring, please immediately notify the Port:

  • Power washing or mobile detailing operations whose runoff is flowing into the sidewalk, curb and gutter, street, or a storm drain;
  • Over-irrigation where water is running off into the streets or storm drain system; 
  • Landscape crews using hoses to wash down driveways or gutters into the street; or
  • Restaurants washing their mats or equipment outdoors and allowing the runoff to flow into the streets or alleyways.

Know How to Use Pesticides, Herbicides and Fertilizers

Chemical pesticides, herbicides, and fertilizers can adversely impact human health or environmental quality. The proper use and management of chemicals materials and soils used in landscaping eliminates or minimizes erosion and the discharge of pollutants to the storm drain system. Chemical pesticides, herbicides, and fertilizers should be used only as a last resort and sparingly. Don't fertilize before a rainstorm. And remember, to not overwater your landscape, irrigation runoff is an illegal discharge! For more information on how to landscape sustainably visit San Diego Sustainable Landscapes Program.

The Port has an Integrated Pest Management (IPM) Policy, BPC No. 737. The purpose of this policy is to reduce the use of pesticides to all Port facilities and is applicable to all operations, contracts, and relevant agreements. IPM combines biological, cultural, physical, and chemical tools to minimize health, environmental, and financial risks. 

The Port is partnering with the University of California Agriculture and Natural Resources Cooperative Extension in San Diego County on an IPM for Landscape Professionals Webinar Series. To learn more and register visit 

Properly manage and dispose of used oil and toxic materials 

Used oil and other toxic materials can cause pollution if they aren’t stored or disposed of properly. Used oil and other toxic materials should be stored under cover, labeled, and with secondary containment. For information on how to properly dispose of used oil and other toxic materials visit Waste Free SD.

Jurisdictional Runoff Management Program (JRMP)

The Port’s Jurisdictional Runoff Management Program (JRMP) was developed in accordance with the requirements of the San Diego Regional Water Quality Control Board (Regional Board) Order No. R9-2013-0001, as amended by Order No. R9-2015-0001 (NPDES Permit #CAS0109266, Municipal Permit).

The JRMP addresses the discharge of pollutants and urban runoff flow to the municipal separate storm sewer system (MS4) to the maximum extent practicable (MEP). The JRMP focuses on three major phases of urban development including development planning, the construction, and the existing development or existing use phases as well as illicit discharges and connections.

The Port JRMP document serves as an informational document that provides an overall account of the program to be conducted by the Port during the five-year life of the Municipal Permit. The Port JRMP document has been developed to meet the conditions of the Municipal Permit and to assist the Port in addressing the highest and focused priority water quality conditions identified in the San Diego Bay Watershed Water Quality Improvement Plan (WQIP), as appropriate. The Port has identified bacteria, metals, and trash as priority pollutants for San Diego Bay and is focusing resources on addressing these pollutants. The San Diego Bay WQIP and other watershed-related information are located on the Project Clean Water website.

The JRMP program’s focus is on controlling discharges from upstream sources and areas within the Port jurisdictional boundary to the MS4 that the Port owns and operates. The program’s overall goals are to achieve receiving water quality improvements and contribute to watershed efforts to meet the San Diego Bay WQIP goals for highest and focused priority water quality conditions, as appropriate. The JRMP utilizes Port-specific activities as well as watershed-based strategies. The main emphasis of the program is education. The programs described herein are effective as of June 27, 2015. The JRMP is updated as needed to ensure continued compliance the Municipal Permit. 

Stormwater Documents


For additional information on stormwater issues across the State of California and the nation, see:

SDCWA and Sweetwater Authority also provide a variety of resources relating to water conservation activities and incentives that help to reduce the potential of irrigational runoff.

Overview - San Diego Bay Watershed

What is a watershed?

A watershed is the area of land where all of the water that drains from the surface goes into the same place or common body of water. Watersheds come in all shapes and sizes. They cross county, state, and national boundaries.

San Diego Bay Watershed

The San Diego Bay Watershed encompasses a 415 square mile area that extends more than 50 miles to the east - all the way to the Laguna Mountains. A large portion of the watershed land area lies north of the border with Mexico and south of Interstate 8. The watershed is comprised of three smaller watersheds: Pueblo San Diego, Sweetwater, and Otay. The major water courses feeding San Diego Bay include the Sweetwater River, the Otay River, Chollas Creek, Paleta Creek, Paradise Creek, and Switzer Creek.

San Diego's Watershed (PDF Map)

The San Diego Bay watershed transects all or portions of seven cities (San Diego, National City, Chula Vista, Imperial Beach, Coronado, Lemon Grove, and La Mesa), along with unincorporated areas of the County of San Diego, the San Diego County Regional Airport Authority, and the Port of San Diego. Nearly half of the population of San Diego County lives and works in the San Diego Bay Watershed. Most of these people live and work in close proximity to San Diego Bay itself —certainly one of the finest natural resources in the region, the State, and the nation.

Watershed management planning involves the identification of issues and concerns that are related to the watershed in which they occur, rather than the jurisdiction in which they are found. Watershed management planning is based on the recognition that problems that may originate upstream and are generally carried down-stream by the flow of water.

For more information on the San Diego Bay watershed and local watershed planning efforts, visit Project Clean Water.

Total Maximum Daily Loads

What is a TMDL?

A Total Maximum Daily Load (TMDL) is a "pollution budget" for a water body (such as a stream, creek, bay or lagoon). It sets limits on the amount of pollution that a stream or other water body can tolerate and still maintain water quality standards.TMDLs require an assessment of priority issues and actions needed to restore water quality. TMDLs are issued on a watershed basis, involving multiple government agencies and other groups.

San Diego Bay Watershed TMDLs

The Regional Water Quality Control Board has adopted several TMDLs for the San Diego region. The TMDLs in the San Diego Bay watershed include:

Chollas Creek

Shelter Island

  • Dissolved Copper: Shelter Island Yacht Basin Dissolved Copper TMDL (Adopted 2005)
  • Indicator Bacteria TMDL: Project II - Baby Beach in Dana Point Harbor and Shelter Island Shoreline Park in San Diego Bay (adopted 2008)
  • Learn more about the the Port's efforts to reduce copper pollution through the Copper Reduction Program