Pillar Point Harbor can sometimes resemble a toilet bowl of bacteria, but researchers report that there is no single culprit for the contaminants.

The taxpayer-funded San Mateo County Resource Conservation District delivered results Saturday from a study started in 2007 to investigate why Capistrano Beach is sometimes brimming with fecal bacteria. After three years of sampling and 50 DNA tests, the study found no single source for the pollution. Cow, dog and human waste were each detected in the waters, but none were found to be the primary polluter.

“There is no smoking gun,” said Karissa Anderson, RCD conservation associate. “We were able to eliminate some of the possible causes but not to find the primary source.”

The research did find some significant factors that contributed to the waste. During rainy weather, bacteria associated with dog waste would show up in high levels along drainage channels flowing from El Granada out to Capistrano Beach and Deer Creek, on the eastern side of the harbor. Alternatively, during dry weather, microbes associated with cow manure would appear in high concentrations, but only in the Deer Creek drainage.

Anderson said it was a little surprising that man’s best friend was, in effect, doing his business in the harbor waters. But upon reflection it made sense, she said, because the storm drains were flushing everything out to sea from all the front yards, parks and fire hydrants in the upstream neighborhoods.

“Anything that builds up on the landscape is going to end up in the mouth of the drains,” she said. “If you weren’t picking up (after your dog), that’s going into the storm system.”

Evidence that some humans might not be using the toilet properly was also detected. Bacteria that thrive in human waste were found in “minor” amounts during wet weather, but the research team dismissed it as an insignificant factor. Live-aboard boats, the study found, were also not a significant source of the harbor pollution.

To researchers’ surprise, they found the hordes of seagulls flocking around the harbor docks were not a major bacteria source.

For years, health inspectors have considered Pillar Point Harbor area beaches to be among the filthiest on the Peninsula, but they’ve been perplexed as to why the harbor showed high bacteria levels. RCD staff began studying the harbor waters in 2007, but the project stalled soon after its first year as a result of a state budget freeze. Funding was restored in 2011, allowing researchers to finish the project.

Researchers concluded that most bacteria inside the harbor stemmed from the upstream watershed, and it wasn’t being dumped directly into the harbor. There was evidence that sediment and vegetation inside of storm drains were retaining bacteria and then releasing it during periods of heavy rainfall.

To clean up the harbor in the future, RCD staff is recommending cleaning out the sediment and vegetation in the storm drains. Installing a row of native grasses or other plant life along the inflow of storm drains could also help filter out bacteria, Anderson said.

RCDs plan to compile a final report on their findings by the end of the month.

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