Mission Bay draws an estimated 15 million visitors a year. Jim Sundquist is one of them. He considers himself a “frequent flyer” to Mission Bay, and has been for more than 70 years.
Sundquist, who lives in El Cajon, is a longtime sailor who first brought his daughter and now brings his grandchildren to Mission Bay to swim in the water and play in the sand.
When Sundquist’s foot was cut while walking along the East Mission Bay shore last week, he became a little anxious when he looked over a recently released report on water quality in the bay.
The “2025 Mission Bay Water Quality Monitoring Report,” published by San Diego Coastkeeper, gathers data on the levels of E. coli and Enterococcus bacteria, as well as dissolved oxygen; nutrients like nitrogen, phosphorus and suspended solids; and heavy metals like copper, zinc and barium.
The levels San Diego Coastkeeper documented included bacteria spikes after rain events, persistently high nutrients at creek inflows and metals exceeding safety standards during storms.
“I’ve got [Chronic Lymphocytic Leukemia], an autoimmune issue, so where I never thought about cutting myself before, now I do,” he said this week. “I used some antibiotic ointment on my cut and haven’t had any adverse reaction so far… What’s going on with our beaches and bays? I saw warning signs about swimming in Coronado, and now there’s fear about Mission Bay. It makes me want to know just what’s going on.”
San Diego Coastkeeper’s findings show that Mission Bay’s water quality problems are real — but the full picture is more complicated.
The 2025 monitoring report documents pockets of pollution in some of San Diego’s most popular recreation areas. Experts say the data matters, even if the risk appears low.
The report shows that 10 testing sites in the bay frequently fail to meet state water quality standards for bacteria, nutrients and heavy metals.
The report found that bacteria levels spiked at all sites following rain events, with phosphorus concentrations exceeding water quality objectives at Rose Creek 75 percent of the time and at Tecolote Creek 83 percent of the time. Zinc levels in Rose Creek exceeded standards in three out of four samples.
“The creek inflows represent persistent hotspots that warrant attention and further investigation,” said Marie Diaz, marine programs manager at San Diego Coastkeeper.
The most immediate public health concern centers on Rose and Tecolote creeks, which funnel the city’s storm drain system directly into the bay. Fecal indicator bacteria — the standard measure for pathogen risk in enclosed bays — exceeded state standards 58 percent of the time at Rose Creek and 50 percent of the time at Tecolote Creek.
Chronic contamination concerns
The report found that Rose and Tecolote Creek had elevated levels even during dry weather, indicating chronic contamination sources that extend beyond storm runoff.
“The persistence of bacterial contamination during dry weather strongly suggests that further investigation into aging infrastructure and other chronic pollution sources is warranted,” San Diego Coastkeeper programs manager Diaz said.
Suspects include cracked sewer lines, failing private laterals and illicit discharges into the storm drain system, she said.
Courtney Brown, a staff attorney with San Diego Coastkeeper, adds that “unlike wastewater, stormwater is not treated before it enters local waterways.”
“Instead, it flows through streets and storm drains, carrying harmful pollutants such as bacteria, oil, pesticides, heavy metals and litter directly into our beaches, ocean and coastal ecosystems.”
While the water from sinks and toilets travels to a treatment plant before being discharged, the water that hits the street carries pet waste, fertilizer, motor oil, and more, and goes straight into the storm drain system — then out into Mission Bay with no treatment.
Meanwhile, the city of San Diego faces a $5 billion stormwater infrastructure deficit — a gap that San Diego Coastkeeper describes in its report as “near collapse.”
Much of the underground system was built decades ago and designed simply to move rainwater away from streets, not to handle the complex mix of pollutants that flow through a modern urban watershed.
“The conditions documented in Mission Bay reflect the cumulative impacts of decades of underinvestment in infrastructure systems that were not designed for today’s population, land use, or regulatory standards,” Diaz said.
A different take
Researchers who have studied Mission Bay for decades urge caution before drawing sweeping conclusions — not everyone reads the data as a straightforward crisis narrative.
Dr. Richard Gersberg, professor emeritus of environmental health at San Diego State University and a longtime researcher of Mission Bay water quality, says the picture is more nuanced.
He pointed to a study conducted in the mid-2000s (“Recreational Water Contact and Illness in Mission Bay, California” for the Southern California Coastal Water Research Project) that found health effects among bay swimmers — primarily skin rash and diarrhea, and mostly in children ages 5 to 12 — were less severe than the bacterial exceedance rates alone would predict.
A separate study from around the same period — “Mission Bay Clean Beaches Initiative Bacterial Source Identification Study” for the State Water Resources Control Board — used DNA ribotyping to identify the sources of fecal bacteria in the bay, Gersberg said, and found that roughly 70 percent came from birds rather than humans.
That finding has significant implications, Gersberg said.
“While birds excrete the same indicator bacteria as humans, many of the pathogens most dangerous to people are human-specific,” Gersberg said.
If avian sources are driving the majority of dry-weather violations — which is when people most commonly swim — the actual disease risk may be lower than the exceedance percentages imply, he said.
Gersberg also noted that when he analyzed data from nine monitoring sites spanning 1999 to 2020, concentrations at most sites either held steady or declined over time, though only three of the nine showed statistically significant decreases.
“I wouldn’t make any rash conclusions,” he said, “but I don’t think things are getting worse.”
He doesn’t dismiss concerns, saying that wet-weather contamination is real, and driven by the kind of urban runoff that sends pet waste, metals and nutrients rushing through storm drains into the creeks and bay after every significant rain.
He said he would support the city building treatment wetlands at creek inlets and said that properly designed wetlands that hold water for five to 10 days can effectively remove bacteria and metals.
Coastkeeper monitoring continues, grows
San Diego Coastkeeper is expanding its monitoring program beyond the standard parameters — not a surprise after its testing revealed up to 31 different “forever chemicals” known as polyfluoroalkyls, PFAS, in a single sampling event in Mission Bay.
In Mission Bay, potential PFAS sources include industrial and commercial facilities located upstream along Rose Creek and Tecolote Creek, as well as wastewater and urban runoff moving through highly developed areas of the watershed.
“The widespread detection of PFAS is concerning because these chemicals are highly persistent, accumulate in the environment, and have been linked to a range of health impacts, including certain cancers, immune system effects and developmental concerns,” Diaz said. “However, the findings do not necessarily indicate an immediate public health emergency for people swimming or paddling in Mission Bay. Instead, they point to a broader and long-term contamination problem that is becoming increasingly apparent throughout watersheds across San Diego County and the nation.”
The group is also championing long-term stormwater funding and holding upstream polluters accountable under the Clean Water Act.
Earlier this year, San Diego Coastkeeper and the Coastal Environmental Rights Foundation were victorious in a lawsuit that pressed SeaWorld to permanently end its summer fireworks displays, which have been going on since 1968.
Attorney Brown said the recent legal settlement and the California Coastal Commission’s approval earlier this month of SeaWorld’s new drone light show program will permanently phase out traditional fireworks displays.
“The water quality and ecological impacts of fireworks are well documented and have been a longstanding source of pollution in Mission Bay,” she said. “Transitioning away from fireworks to drone shows will result in a much cleaner and safer environment for all who enjoy the bay.”
Sundquist says he’ll keep coming back regardless of the bacteria concerns — Mission Bay is too much a part of his life to stay away.
For dedicated beachgoers like Sundquist and others, Diaz acknowledged that “Mission Bay’s challenges were created over decades, and addressing them will require sustained public pressure, scientific monitoring, infrastructure investment and political will.”
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