Types of Runoff Pollution

The toxic secret below the surface of San Diego Bay — and many of our inland and coastal waters — tells a different story than the glamorous shimmer it gives during the day. A five-year cleanup at the industustrial waterfront will improve some of the harmful pollution lurking in the bottom of the bay, but these contaminants continue to persist:



Boats typically used copper-based antifouling paints to prevent buildup of marine organisms on a vessel’s hull. The copper in antifouling paints leaches into the water to prevent marine life accumulation on the bottom of the boat. However, even at relatively low levels, copper poisons a variety of aquatic organisms and persists in the environment. The large number of boats in San Diego’s marinas and the relatively small tidal action has resulted in elevated levels of dissolved copper that exceed water quality objectives and threaten wildlife and marine habitat.

High levels of copper threaten several areas in San Diego Bay, including Shelter Island. The San Diego Regional Water Quality Board developed a plan to reduce copper to safe levels in Shelter Island through the Shelter Island Yacht Basin Total Maximum Daily Load.

Coastkeeper works with the Port of San Diego, recreational and commercial boaters, marina owners and other interested groups to reduce copper in San Diego Bay. (back to top)


pier-fish-warning-sMercury bioaccumulates, or builds up, in fish tissue. When fish contain unsafe levels of mercury, they are unsafe to eat, especially for children and pregnant women. To warn children and pregnant women of the dangers of eating fish from the bay, the Port of San Diego posted all piers along San Diego Bay with fish consumption advisories. Unfortunately, anglers – many who come from underserved populations– still catch and eat fish from the bay, resulting in serious human health risks.

Much of the legacy pollution in San Diego Bay comes from the shipyards and Navy facilities that line the eastern shore of the bay. In 2003, Coastkeeper and Natural Resources Defense Council successfully sued Southwest Marine (now BAE), the Navy’s largest ship repair and maintenance facility on the West Coast, on charges that it failed to implement required measures to prevent toxins from flowing into San Diego Bay.This case reached its conclusion when the United States Supreme Court refused to hear the shipyard’s final appeal. Southwest Marine had challenged the September 1999 U.S. District Court ruling, later upheld by the U.S. Court of Appeals Ninth Circuit, which required the shipyard to improve their stormwater pollution prevention practices and found the company liable for $799,000 due to recurring permit violations. (back to top)


We don’t want insects in our homes, in our food or on our flowers, so we rely on very toxic chemicals to kill them. Unfortunately, these chemicals kill bugs indiscriminately, even those beneficial to our food web. Research definitively shows two popular and widely used pesticides, diazinon and chlorpyrifos, are lethal or cause harm to organisms living in creeks and rivers.

Monitoring in the late 1990s found that Chollas Creek, a local stream that drains into San Diego Bay, had consistent and high levels of toxicity. Further research demonstrated that concentrations of diazinon caused the toxicity as it flowed into the creek with urban runoff, particularly during rain events. The federal government placed Chollas Creek on its list of unhealthy waters, known as the 303(d) List, for toxicity from diazinon. In 2002, the San Diego Regional Water Quality Control Board adopted a plan to reduce diazinon in Chollas Creek.

Fortunately, the U.S. Environmental Protection Agency (U.S. EPA) has also taken federal action to address pesticide toxicity issues. Due to the mounting evidence that diazinon caused widespread toxicity in our water, the U.S. EPA created a phase-out and elimination program in 2001. Diazinon is no longer available for sale for any indoor or outdoor residential use. Similarly, in 2000, EPA began phasing out almost all over-the-counter sales of chlorpyrifos.

With specific pesticides like chlorpyrifos and diazinon now banned, residential users largely turned to a new class of pesticides called pyrethroids. Tests now detect pyrethroids in creeks and rivers throughout California. Recent research has also determined that pyrethroids cause toxicity detected in creeks and rivers in California. The widespread problems caused by pyrethroids led the California Department of Pesticide Regulation’s to evaluate some 600 pyrethroid products on the market in August 2006. In mid-2012, the state decided not to ban the pesticide altogether, but instead limit the application of pyrethroids.

Watch this video to learn more about pesticides in San Diego Bay. (back to top)

Water SamplePathogens

Pathogens are disease-causing microorganisms and include viruses, bacteria and protozoa – and they make us sick. These microbes infect us through our skin and mucous membranes and when we drink contaminated water. The resulting illnesses range from mild to severe symptoms (skin rashes, sore throats, ear, eye and respiratory infections, stomach aches, minor or serious cases of nausea and dysentery and fever). The ultimate origin of these pathogens is the feces of any warm-blooded animal, including humans, pets, livestock and wild animals.

It is difficult, costly and time intensive to measure every type of pathogen in San Diego’s waters. That is why when water quality volunteers monitor our local waters, they measure indicator bacteria – E. coli and Enterococcus, microbes that are associated with pathogens and are easily and cheaply measured. These fecal indicator bacteria correlate with an increased risk of illness and help us understand the risk posed to recreational users.

At Coastkeeper, we recognize the health, environmental and economic impact of pathogen pollution in San Diego’s waters. There are too many water bodies in the San Diego region that are polluted with pathogens. That is why we worked with the Regional Water Quality Control Board and local municipalities to develop a Total Maximum Daily Load (TMDL) plan to reduce the amount of pathogenic pollution reaching our waters. This plan will address pathogen pollution at 20 beaches and creeks in five watersheds in Orange County and eight watersheds in San Diego County. The combined watersheds affected by this TMDL cover roughly 1,740 square miles. The TMDL tries to separate and identify the pathogens that stem from human-related activity from natural ones and sets aggressive interim targets for reduction over ten to twenty years. This plan was finalized in February 2010.

In addition to working with regulatory agencies and local government, Coastkeeper also actively monitors our creeks, rivers and lagoons for pathogens. We do this on a monthly basis to better understand how much pathogen pollution exists in our local waters. We are also developing a wet weather monitoring program in Chollas Creek to capture more information during rainstorms – a critical period of high inputs into water bodies. (back to top)


plastic-bottle-of-water-sImagine taking a nice stroll along one of San Diego’s many rivers or streams. Certainly, your mental image does not include trash strewn everywhere.

In addition to its unsightliness, trash in our waters clogs our streams, harbors harmful bacteria and poses an ingestion hazard to wildlife. Sadly, 80 percent of all the marine debris found in our oceans comes from inland sources.

According to our beach cleanup data, the most common trash we find in our streams is cigarette butts and household trash, including plastic cups, plastic bags and wrapping materials, fast-food wrappers, plastic bottles and other plastic containers. Cigarette butts are toxic to aquatic organisms and plastic breaks down into easily swallowed bits, choking the wildlife that lives in and near our waters.

Read more about the impacts of marine debris. (back to top)