The coast is clear: Water good at most Bay Area beaches

There might be one upside to the drought, and it's just in time for the holiday weekend.

Bay Area beaches are cleaner and healthier than ever, because so little rain has washed dangerous bacteria and other pathogens into San Francisco Bay and the Pacific coastline, according to a report released Thursday by Heal the Bay.

"Dry weather has meant less urban runoff. This is all great heading into Memorial Day weekend, but we shouldn't have a false sense of security," said Amanda Griesbach, a water-quality scientist for the Santa Monica environmental group. "Next year, especially if we have an El Niño cycle, things could be very different."

Heal the Bay's 24th annual survey of 650 West Coast beaches showed some of the highest-ever grades for cleanliness, with 95 percent of California's beaches receiving "excellent" or "good" marks.

The group looked at the amounts of harmful bacteria from sewage leaks, pollution runoff and industry - pathogens that are flushed into creeks and storm drains and ultimately onto the beaches.

When people or wildlife come into contact with the bacteria, they're likely to suffer from gastrointestinal problems like diarrhea, skin rashes, or eye, ear or lung infections.

In San Francisco, the beaches with the highest grades - an A or A+ - include Aquatic Park Beach at the Hyde Street Pier, Ocean Beach at Balboa Avenue, and Baker Beach.

Most Marin and East Bay beaches also received high scores.

Troublesome lagoon

The Peninsula saw some challenges. Marina Lagoon in San Mateo is a perpetual low scorer, and 2013-14 was no exception. In fact, it ranked as the second-worst beach in the state, largely because it's enclosed and shallow and the water tends to stagnate.

Pillar Point near Half Moon Bay also received poor grades, and was singled out as a "beach bummer."

In San Francisco, Windsurfer Circle near Candlestick Point also received an "F."

But the award for worst beach in the state went to one that's also among the most popular. Cowell Beach in Santa Cruz, near the Beach Boardwalk amusement park, has some of the highest concentrations of pathogens in California, according to the report.

The reason is an aging sewer system, Griesbach said. Untreated sewage leaches into the groundwater and into the San Lorenzo River and then flows into the ocean. Sometimes, especially at high tide, the pollution meets great kelp forests, creating a bacteria-rich stew of raw sewage and rotting kelp along a shoreline crowded with surfers, kayakers and splashing kids.

"The good news is that state funding is on the way to fix the problem," Griesbach said. "It's frustrating to see the same beaches on the list every year, but sometimes it takes a long time to prod these agencies into acting. This is one of those situations."

Improving drains

In San Francisco, the Public Utilities Commission is working on increasing the capacity of its sewer and storm drain system and diverting excess runoff, to decrease the chance of sewage overflowing.

Avalon on picturesque Catalina Island, off the coast in Los Angeles County, was one of the biggest success stories this year, as the city spent more than $6 million to rebuild its corroded sewer system. The beach went from being one of the state's worst to one of the best.

The Bay Area has its own host of aging sewer systems Most older cities in the Bay Area have cracked and leaking sewer pipes, said Deb Self, director of San Francisco Baykeeper.

Raw sewage, pharmaceuticals, drain cleaners and other toxic substances can leach into the groundwater and creeks, causing myriad problems for wildlife, people and the environment, she said.

Not only does harmful material leak out, but sometimes unwanted things make their way into the sewers, Self said. Twice, she said, she has opened the toilet in her East Bay home to find baby possums - which had apparently taken up residence in the sewer line.

"Cities need to be held accountable for their aging infrastructures," she said. "There's just a lot of deferred maintenance."

Carolyn Jones is a San Francisco Chronicle staff writer. E-mail: carolynjones@sfchronicle.com