A three-year effort to end fecal coliform pollution on the Samish River that threatens tidal shellfish beds has been declared “a failure” by Gov. Chris Gregoire.

Her stern criticism of the Clean Samish Initiative came during an April 6 meeting of state agency heads involved in a monthly assessment of the effectiveness of government programs.

The Samish initiative seeks to reduce the amount of fecal coliform in the river through education, more frequent water quality monitoring and on-site farm and septic inspections.

Fecal coliform can get into the river from failing septic systems and animals defecating in or near the water. Typically, the highest levels of fecal coliform in the river are detected after heavy rainfalls.

To date the initiative has spent nearly $1 million in federal, state and local money. But Gregoire said there was little tangible success to report.

“We need to accept the fact that we’ve failed and take immediate steps to correct the fact that we’re losing 4,000 acres (of shellfish beds in the Samish Bay),” she said.

Since the presentation earlier this month, some state and local officials have bristled at Gregoire’s remarks, saying the initiative has not been a failure and that conditions in the river are improving for both shellfish and salmon.

Closures in the bay are nothing new. But now the state is poised to downgrade the shellfish beds to what is called “conditional approval” status.

That means the bay would automatically close when the river rises by a certain number of feet per second. That rate changes depending on the month. The bay would be closed for five days or until water samples show it’s cleared up again.

The three commercial shellfish companies that harvest crops out of Samish Bay have each had to adjust their schedules to the frequent bay closures. They’ve learned to haul their harvested shellfish out of the bay when they see the rain coming, before it can wash contaminants into the water that make their products unsafe to eat.

Ron Shultz, policy director for the Washington State Conservation Commission, said the effort in the Samish River has been a success on many levels, but with fewer tangible results than the governor would like.

The initiative monitors water quality, provides education to landowners and identifies hotspots for fecal coliform, he said.

“What they aren’t doing is linking those actions to the hot spots,” he said. “The governor was pushing very hard to get action. From where she sits, it’s a very legitimate question. ‘I see a lot of people working toward something, but I don’t see progress. Why not?’”

Gregoire’s question is of particular importance because the Samish initiative is similar to a process outlined in a bill now on her desk.

The measure, which has bipartisan support, would put into law the “Ruckelshaus Center process,” which was the result of three years of work by the center done at the behest of the Legislature.

Gregoire has until May 10 to sign the bill. The program seeks to protect what are called “critical areas” — fish and wildlife habitat, wetlands and aquifer recharge areas — through the new process instead of the state’s Growth Management Act.

But to five Washington American Indian tribes, the process lacks teeth.

“We think that we need regulations to protect the environment,” said Larry Wasserman, environmental services director for the Swinomish Tribe. “You see what’s happening on the Samish Bay. That’s a program where we have the current county critical areas ordinance in place, and the shellfish beds remain polluted. … A voluntary program is not going to meet the tribe’s goal of recovering fisheries.”

Wasserman thinks the legislation will not help situations in critical watersheds.

“It will hurt in this regard: If there’s an illusion of a solution, then there will be less incentive to actually deal with the problem in an effective way,” he said.

The Ruckelshaus Center process is similar to the Clean Samish Initiative, said Shultz of the conservation commission. The difference is that with the proposed process, the county would be required to show the state conservation commission that it had met benchmarks within five years of crafting a plan to clean the waters. The plan would be reviewed by a technical panel of scientific experts, he said.

There is also a potential of increased enforcement actions from the state Department of Ecology, Shultz said.

“If the county believes they would benefit from enhanced enforcement from Ecology, the bill says the county can request that,” he said. “If the Legislature passes it and the governor signs it, it’s a priority. We will retask existing resources to make it happen.”

But, like most everything else, it hinges on whether there is money available, Shultz said.

Samish Bay shellfish farmers are used to the status quo, and even though shellfish beds will be downgraded, nothing much would change.

The state Health Department has closed the bay to commercial harvesting about 30 times in the past 2 1/2 years, with most closures lasting at least five days.

Scott Blau, a fourth-generation shellfish grower at Blau Oyster Co., said the move to conditionally approved status basically puts on paper the way they’ve been operating in recent years.

Bill Dewey, spokesman for Taylor Shellfish Farms, which operates out of several bays in the state, said the added attention from the governor could bode well for producers in the bay.

“I appreciate the governor’s interest in the problems here. She recognizes that Samish Bay is sort of a classic nonpoint pollution watershed, and if we can’t deal with these problems here then we’re not going to have any success cleaning up the Sound by 2020,” Dewey said, referencing the goals of the governor’s Puget Sound Partnership.

Dewey said a statewide emphasis on cleaning up Samish Bay — as somewhat of a poster child for the overall project — could speed up the local effort.

Gregoire said she wants to see a plan in six months that addresses the condition of Samish Bay and would produce results by year’s end.

“Standing down and doing nothing is destroying 4,000 acres,” she said. “That is unacceptable.”

Skagit County water quality analyst Rick Haley told county commissioners Tuesday that the county will redouble its efforts on the river “in response to the governor’s charge.”

“We are taking it very seriously,” Haley said. “We should not lack for resources, and if we ask for something from the state, we should get it.”