Taylor Shellfish Farms crew members unload oysters on Samish Bay in Washington state. The company has seen its operations disrupted because of high bacteria levels. (ANDY BRONSON/THE BELLINGHAM HERALD)

Nearly every time heavy rain falls in north Puget Sound in Washington state, high levels of fecal bacteria flow into Samish Bay, disrupting work at Taylor Shellfish Farms, the largest shellfish producer in the United States.

The bay has been choked by many sources, including animal and human waste, broken septic tanks and farmland runoff. It’s been so bad the past two years that health officials have closed the bay to shellfish harvesting for more than 100 days.

Now state officials have responded with an ambitious cleanup campaign for Puget Sound, the nation’s second-largest estuary, just behind Chesapeake Bay — which also is struggling with an unhealthy diet of urban wastewater and agricultural runoff.

In Washington state, they’ve stepped up inspections, in some cases going door-to-door to track down who is contributing to the pollution. Antipollution workers are using DNA testing to pinpoint whether waste is coming from humans or animals.

Much of the pressure for action has come from the top. This year, the state downgraded the health status of 4,000 acres of commercial shellfish beds in Samish Bay, angering Gov. Christine Gregoire (D). She declared that cleanup efforts had failed and ordered a turnaround by September 2012.

“We’re not going to flush — literally flush — 4,000 acres down the drain of prime shellfish-growing area,” Gregoire said.

More than 20 organizations have come together in an attempt to clean up Samish Bay by the governor’s deadline. In May, the Puget Sound Partnership, a state agency created four years ago to lead cleanup efforts, released a 10-point plan for the bay.

Among other things, it calls for stepped-up inspections, portable restrooms for recreationists, more fencing and more education of dairy farmers and other landowners.

Rick Haley, a water quality analyst with a local public works department, said Skagit County had sent dozens of waste samples to laboratories for DNA testing — at a cost of $160 per sample — to determine where the pollution was coming from. Haley said the testing was preliminary and the county wasn’t ready to discuss its results.

Bill Dewey, a spokesman for the Taylor Shellfish Farms in Samish Bay, said the work could go a long way in determining whether similar efforts would pay off elsewhere in the sound.

“What’s at stake is whether we’re going to be able to clean up the rest of Puget Sound,” he said. “Samish Bay is pretty much a classic rural watershed. There isn’t any urban center. . . . We’re talking about runoff from pastures and failing septic systems and things that are more problematic in these rural areas. If we can’t do it in the Samish, then we’ve got a lot of other areas in the Puget Sound where we’re in trouble.”

While cleanup is already in high gear at Samish Bay, there’s a long-range plan for all of Puget Sound. Among the goals to achieve by 2020: Poisons would be reduced enough to allow for the safe consumption of fish, populations of Chinook salmon and Pacific herring would be on the rise and all beaches would meet fecal bacteria standards so people could swim, kayak and scuba dive without fear of illness.

Fecal bacteria levels have been a persistent problem on the sound, not only on Samish Bay. Last month, for example, health officials closed Twanoh State Park on Hood Canal to swimming after tests detected high bacteria levels in the water.

Gerry O’Keefe, the executive director of the Puget Sound Partnership, is trying to tamp down any expectations of a quick cleanup.

Addressing reporters at Samish Bay in July, he said: “We know that we’re not going to be able to do this overnight. It’s taken us 150 years to get to where we are today. It’s going to take us a while to get out of it.”

Instead of “pointing fingers at each other” to assign blame for the pollution, O’Keefe said everyone could contribute to the cleanup.

To that end, the partnership has been running a campaign urging the public to pick up after the 1.2 million dogs that live on the sound.

According to the partnership, the waste from the dogs is equal in volume to what would be produced by a city of 300,000 people.

— McClatchy Newspapers