SAN JOSE — In a move that could cost San Jose thousands of dollars in fines and lead to punitive cleanup orders, state wildlife officials have filed an environmental complaint against the city, claiming it’s violating pollution laws for failing to adequately clean up homeless encampments along Coyote Creek, one of Silicon Valley’s most troubled waterways.

The action by the State Department of Fish and Wildlife not only escalates the homeless issue politically, it also means state water regulators will investigate whether trash, human waste and other refuse from homeless encampments — already a recognized public nuisance — causes ecological damage similar to a factory dumping chemicals into local water channels.

“Basically what it comes down to,” said Fish and Wildlife Lt. Byron Jones, who filed the complaint Wednesday with the San Francisco Bay Regional Water Quality Control Board, “is they accept the encampments, they feel no sense of urgency to remove them, nor have they ever. It’s always been about the next cleanup. It’s never been about ending the practice of illegally camping and being in proximity to water.”

Although the department previously has taken on government agencies like Caltrans, Jones said, this is the first time guardians of the state’s wildlife have pursued a California city for essentially allowing the homeless to create a waterborne pollution threat to fish in the streams and, by implication, to humans who come into contact with the water.

Jones — a retired 22-year veteran of the San Jose Police Department — spent the past two years directing the efforts of local Fish and Wildlife wardens to remove homeless encampments from Coyote and Los Gatos creeks and the Guadalupe River. His complaint charges that city administrators and police “have refused to remove the encampments and protect the water.”

San Jose City Attorney Rick Doyle said the problem is not new. He recalled encampment cleanups during the 1990s, when the city had more financial wherewithal to deal with the squalor, that didn’t prevent the county’s most dispossessed citizens from returning to the water’s edge.

“I know people would like us to move faster, but given the finite resources, I think we’re doing what we can at this point,” Doyle said. “I wouldn’t agree that we are allowing this. We do have a coordinated effort with the water district, so it’s not as if we’re not doing anything. But unfortunately, it’s a larger problem than we have resources to meet immediately.”

Environmentalists called the move significant.

“It’s a long term intractable social justice issue that has not been brought to an environmental enforcement action in this way before,” said Jason Flanders, program director at San Francisco Baykeeper, an environmental group that monitors the health of local waterways. “So it’s an important gesture.”

State water pollution regulators said they will examine the case carefully.

“It is a big deal,” said Bruce Wolfe, executive director of the Regional Water Quality Control Board. “The Clean Water Act requires any type of discharge into the creek or bay needs a permit. We’re the agency that issues the permits. When it’s identified that there’s an unpermitted discharge, that’s considered a violation of the Clean Water Act.”

In previous cases of industrial pollution, fines have reached as high as $10,000 a day, though Wolfe indicated that drawing a direct line between a city’s lax oversight of homeless encampments and permitting illegal toxic discharges might be difficult.

“I welcome the opportunity to see if we can use this as a way to clarify that this is significant,” he said, “and that you can’t just say out of sight, out of mind. This may be a way to trigger looking at homeless encampments as a source of pollution that we need to better address.”

In an interview, Jones also implicated the Santa Clara Valley Water District as responsible for failing to fulfill its obligation as custodian of the creeks and streams it owns.

In January, the water district released a report showing that it and the city spent $275,542 last year and removed 2,011 cubic yards of debris from homeless encampments along creeks and rivers in Santa Clara County.

The two agencies, who have a joint agreement to keep working on cleanups at least through 2018, have heard an increasing chorus of public complaints in recent years as San Jose — which has the fifth-largest number of homeless people of any U.S. city — has struggled with homelessness amid the recession and sky-high housing prices.

“It’s a very complex issue. Our actions have been to collaborate with all the agencies involved in a way that’s more than just a Band Aid,” said Marty Grimes, a water district spokesman.

But Jones, the Fish and Wildlife warden, said not nearly enough has been done.

“You build a granny unit on the back of your house that doesn’t meet city code, they’ll red tag and make you tear it down,” he said. “But they’ll allow 50 or 100 people in encampments to sit right next to a river without any facilities and never lift a finger to do anything about it.”

Some environmentalists who have worked years to restore the health of Silicon Valley creeks agreed the city, the water district and the regional water board need to do more.

“I feel very bad for the homeless people that they are stuck there,” said Mondy Lariz, director of the Santa Clara County Creeks Coalition. “But they are damaging the creek and the ecosystem. Something needs to be done.”

Contact Bruce Newman at 408-920-5004. Follow him at twitter.com/BruceNewmanTwit