For the first time, Pillar Point Harbor has earned certification as a “Clean Marina,” meaning it exceeded standards for tidy facilities and pollution-free waterways.

Don’t go out for a swim behind the jetty quite yet — the harbor beaches are considered hazardous for humans. Just two days before the Clean Marina distinction, San Mateo County health officials tested the waters and found it contained dangerous levels of fecal bacteria. Signs warning about the risks are posted around the beaches.

How can a certified Clean Marina have dangerous water?

County and harbor officials say both messages are accurate. Pillar Point Harbor reportedly has been taking the right steps to keep the harbor sanitary, but factors out of its control have continued to make the waters among the most polluted in the county.

The source of the bacteria inside the harbor has been a contentious issue. Harbormaster Scott Grindy points to a longstanding theory that ranches upstream from the harbor have been the source of bacteria. That belief gained momentum recently from an ongoing study by the San Mateo County Resource Conservation District, he said. The study has not been released publicly yet, but Grindy said it indicated the high bacteria levels within the harbor were predominantly coming from animal waste.

“Obviously, we’re trying to make sure that people aren’t dumping sewage into the water,” Grindy said. “But no matter what you do, somebody’s still going to do it their way. … We’re not in control of the land above the harbor.”

Under the Clean Marina program, a team of marina experts toured Pillar Point Harbor last month to gauge local management practices. The visiting inspectors graded the harbor’s emergency readiness, ability to contain an oil spill and waste-handling procedures, among other items. In the end, Pillar Point Harbor received a high score, 92 out of 100.

The harbor water remains dirty, said county Environmental Health Director Dean Peterson, but he said that shouldn’t come as a surprise.

“We’re not talking about a horrible mess out there. After all, it’s a closed environment,” he said.

County health officials would be more alarmed if the harbor showed signs of human waste. That would imply sewage was leaking into the water, he said.

The harbor district in recent days has been working to repair an aging sewer line underneath various harbor buildings leased out to businesses. Work crews discovered the 4-inch sewer line under the building had a 2-inch gash running along its length. That and other pipe breaches led district officials to conclude the wastewater was draining into the ground.

Health officials examined the leak and determined it was not likely leaching sewage into the nearby water.

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