The state agency in charge of protecting Florida’s environment has allowed the dumping of millions of gallons of waste from a shuttered Manatee County phosphate plant into an aquatic preserve at the mouth of Tampa Bay.

Since Oct. 22, the state Department of Environmental Protection has allowed the Piney Point Phosphates plant to pump 10-million gallons of water with elevated levels of acid and nitrogen into Bishop Harbor, just north of the Sunshine Skyway bridge.

“That’s an aquatic preserve, very pristine grass beds — everything we want the bay to have,” said Suzanne Cooper of the Agency on Bay Management, an arm of the Tampa Bay Regional Planning Council. “This is very bad news.”

DEP officials say they had little choice but to allow the plant to discharge the treated water after Tropical Storm Gabrielle dumped more than 18 inches of rain on the area in mid September. The storm caused so much flooding at the phosphate plant that it raised fears of an accidental spill of highly acidic, untreated water that could have killed thousands of fish and wreaked untold environmental damage on the bay. “Obviously nobody wanted to do the treat-and-discharge, but the choice was between that or an uncontrolled discharge,” said Janet Llewellyn, DEP’s deputy director of water resource management.

DEP officials abruptly halted pumping Monday after local officials raised concerns about the effects on water quality in the Terra Ceia Aquatic Preserve and the bay — and about the fact that DEP had not notified most of them about what was going on.

Not even the aquatic preserve’s own personnel, who work for DEP, were aware of the pumping, Llewellyn said.

“Now we’re trying to get everybody better coordinated,” she said.

After a month of pumping up to 500,000 gallons a day from the plant, the waters of Bishop Harbor have become “a little murky,” said Rob Brown, Manatee County’s water quality administrator.

During the fall and winter “the tides are not as strong and the harbor doesn’t flush as well,” he explained. If the nitrogen persists into the summer, it could lead to an algae bloom and fish kills, he said.

Brown questioned why DEP was not better prepared for Gabrielle, noting that other phosphate plants in Manatee County did not experience similar problems. He said Manatee officials had urged DEP to prepare for the rainy season, but Llewellyn said she was not aware of any such warnings.

DEP’s emergency order allowing the pumping, signed Oct. 16 by Secretary David Struhs, called for sending up to 68-million gallons of water from the plant into Bishop Harbor over six months, although Brown said, “I don’t know if we could’ve handled 120 days of this.”

But the court-appointed receiver overseeing the plant’s operation, Tampa attorney Louis Timchak, predicted the pumping will resume at some point.

“We’ve stopped it temporarily, and we’re looking at the options that are available,” Timchak said. But he added that daily monitoring shows that so far “there has been no algae bloom and no fish kill.”

Piney Point has a long history of environmental disasters, dating back to the fish kills and cattle poisonings that occurred after it opened in the 1960s. During the next 20 years its owners were repeatedly fined after discharges killed trees and forced the hospitalization of workers.

In 1989, a sulfuric acid spill forced the evacuation of hundreds of people. Two years later three workers died in industrial accidents at the plant, and the accidental release of a toxic cloud of sulfur gases sickened more than a dozen nearby residents.

The plant’s last owner closed it in 1999 and went bankrupt. But it still contains a mountain range of phosphogypsum stacks, which hold the highly acidic water. Pumps keep it circulating within the mounds to prevent it from leaking into the groundwater. Because of the bankruptcy, this year Florida Power & Light threatened to turn off electricity to the pumps, which could have resulted in a spill. So the U.S. Environmental Protection Agency took over the plant, then handed oversight to DEP.

DEP wants to seal off the stacks completely but must await a decision by a bankruptcy judge before that can happen, Timchak said.

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