San Diego Coastkeeper Urges Water Board for Stormwater Permits

June 1, 2026 (San Diego, Calif.) — Today, San Diego Coastkeeper with California Coastkeeper Alliance filed a petition with the San Diego Regional Water Quality Control Board aimed at reducing stormwaterdriven pollution from privately-owned commercial, industrial, and institutional sites that generate runoff into the Lower San Diego River.

Under the federal Clean Water Act, advocacy organizations like Coastkeeper can petition regulators to address regulatory gaps that lead to water pollution. Thousands of privately-owned properties in San Diego and throughout California are not being held accountable for their disproportionate contributions to toxic metals, nutrients, and other pollution in local watersheds.

The petition demands that the San Diego Regional Water Quality Control Board (Regional Board) exercise its authority under the federal Clean Water Act to require stormwater permits for privately-owned commercial, industrial, and institutional, often referred to as “CII,” sites throughout the Lower San Diego River watershed. Because stormwater pollution accounts for more than half of the total pollution entering our waterways each year, these contaminated discharges must be controlled for the ecosystem to regain its health.

Under current law, municipalities – not private commercial owners – bear the legal and financial burden of addressing stormwater pollution. The San Diego Municipal Stormwater Permit regulates the public storm drain system, but private CII facilities that generate a disproportionate share of pollutants remain completely unregulated.

“Commercial and industrial sites occupy just 11% of the Lower San Diego River watershed, yet they generate an estimated 31% of the phosphorus that is degrading the San Diego River,” says Phillip Musegaas, executive director of San Diego Coastkeeper. “These facilities have benefited from a regulatory blind spot for decades. That ends now.”

Coastkeeper has identified an estimated 1,200–1,800 significant private facilities — including big-box retailers, shopping centers, auto-related businesses, industrial parks, and institutional campuses — whose stormwater runoff drains into the San Diego River, Forester Creek, Los Coches Creek, Alvarado Creek, and Murphy Canyon Creek. Each of these valuable waterways are currently on California’s list of impaired water bodies, failing to meet water quality standards for multiple pollutants including nitrogen, phosphorus, bacteria, low dissolved oxygen, toxicity, and benthic community degradation. Excess nutrients, such as nitrogen and phosphorus, can cause harmful algal blooms that create toxins, which can move up the food chain and present public health risks. They also depress oxygen levels resulting in fish kills and ecological dead zones.

The Clean Water Act’s Residual Designation Authority is designed precisely for situations like this. Once a regulator determines that a category of stormwater discharges “contributes to a violation of a water quality standard,” it is legally obligated to require permits for those discharges. As detailed in this petition, evidence of CII contribution to pollution in the community is overwhelming, and therefore mandatory designation is required.

This petition follows a directly analogous precedent: in November 2024, the EPA determined permits are required for CII stormwater discharges in the Dominguez Channel and Alamitos Bay/Los Cerritos Channel watersheds in the Los Angeles area – watersheds facing comparable conditions of CII-driven toxic metal impairments. The Lower San Diego River presents conditions that are in some respects more acute than those found in the Los Angeles-area watersheds.

“Regulators have both the authority and obligation to require permits for commercial, industrial, and institutional stormwater discharges that are polluting local waterways,” says Sean Bothwell, executive director for the California Coastkeeper Alliance. “Our petition demonstrates that similar action is not only justified here, but urgently needed across California to ensure private corporate polluters – not the public – are on the hook to address these water quality violations.”

Under federal regulations, the Regional Board must act on the petition within 90 days, determining whether to require new stormwater controls for major CII dischargers. If the Board designates these sources for regulation, an estimated 1,200–1,800 facilities in the Lower San Diego River watershed would need to obtain Clean Water Act permits and implement measures such as on-site green infrastructure, stormwater capture and reuse, treatment systems, or funding for regional projects – actions that would not only reduce pollution but also advance San Diego’s water supply reliability and drought resilience goals.

California Coastkeeper Alliance filed similar petitions at several other Regional Water Boards across California today, including one each in Ontario, Salinas, Santa Rosa, and the Bay Area and two in the Sacramento region. The organization is working with State legislators and has also approached the State Water Resources Control Board to encourage the development of a statewide policy and permit that would hold commercial, industrial, and institutional facilities accountable for the water pollution generated on their properties. The goal of such an effort is to increase mitigation efforts and require commercial landowners to make the needed investments to protect public waterways from pollution generated on private property.

To receive a copy of the petition or to learn more about the statewide effort, contact Sean Bothwell at 949-291-3401 or [email protected]. To speak with someone about this effort in the San Diego area, contact Patrick McDonough at 760-525-6838 or [email protected].

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ABOUT SAN DIEGO COASTKEEPER – San Diego Coastkeeper is a 501(c)(3) non-profit corporation founded in 1995 to protect and restore San Diego County’s bays, beaches, watersheds, and ocean for the people and wildlife that depend on them. Coastkeeper balances community outreach, education, science, advocacy, and legal enforcement to promote clean water stewardship and a healthy coastal ecosystem. For more information, visit www.sdcoastkeeper.org

ABOUT CALIFORNIA COASTKEEPER ALLIANCE – California Coastkeeper Alliance represents Waterkeepers programs statewide as they fight for drinkable, swimmable, fishable waters for all Californians. CCKA defends and expands California’s protective legislation and strengthens the function of our State Water Board. For more information, visit www.cacoastkeeper.org or @CA_Waterkeepers on social media.