Federal regulators have finalized water-quality rules for Washington state tied partly to how much fish people eat, approving many aspects of the state’s plan but also setting some stricter limits than the state wanted.

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The Environmental Protection Agency on Tuesday finalized water-quality rules for Washington state tied partly to how much fish people eat, approving some aspects of the state’s plan but deciding in many cases to set stricter limits than the state had wanted.

The action comes years after contentious debate over the issue of how clean the state’s rivers and bays need to be so people can safely eat fish from those waters.

Businesses and local governments have argued that too strict rules could cost billions with little benefit to the environment, while Native American tribes and environmental groups said tougher rules are needed to reduce water pollution and protect those who eat fish.

The EPA said the combination of its own federal rules and parts of the state’s plan will protect residents who eat fish and shellfish from exposure to toxic pollutants.

Maia Bellon, director of the state Department of Ecology, said she’s disappointed the “state’s approach wasn’t accepted in its entirety.” The state worked hard to balance protecting human health and the environment while helping businesses and local governments comply, she said in a statement.

The EPA agreed with Washington state on several key factors used to regulate water quality, including dramatically raising the fish-consumption rate to 175 grams a day, which would protect people who eat about a serving of fish a day. But it did not approve the state’s plan for three major chemicals including PCBs, arsenic and mercury.

Factories, wastewater plants and other point-source polluters are not the source of these chemicals, and the EPA’s rule is “asking for big investments from the wrong people,” said Rob Duff, a senior policy adviser with the governor’s office.

In the case of PCBs, the EPA rule is 25 times more stringent than what the state had proposed, Ecology officials said.

Boeing, industry groups and cities and counties had argued that the EPA’s limits for PCBs and mercury would be costly and difficult to meet. Boeing declined Tuesday to comment on the decision.

Chris Wilke, executive director of Puget Soundkeeper Alliance, said the EPA got it right. “The state had kicked the can on mercury and PCBs, and EPA today said that we have to move forward with stronger regulations on those two. The main points that we were pushing on, we’re happy with the results.”

But Carl Schroeder with the Association of Washington Cities said he’s unsure how hundreds of wastewater plants will be able to comply with some of the new regulations, because no current technology exists, for example, to meet the standards for PCBs.

Both the EPA and the state had each been working on parallel versions of the rules after the federal government last year stepped in to ensure that Washington did a rule in time. The state submitted its plan to the EPA for approval in August.

The EPA was under a court order to finalize a plan by Tuesday, after environmental groups sued to force quicker action.

On Tuesday, the EPA approved nearly one-quarter of the pollution standards the state adopted and finalized its own updates for the remaining three-quarters.

The Northwest Pulp & Paper Association said it was “extremely disappointed” in EPA’s final rule. The rule fails to incorporate the input of private businesses and public agencies and “sets up a system for failure, litigation and permitting uncertainty,” the group said in a statement.

But Lorraine Loomis, who leads the Northwest Indian Fisheries Commission, praised the EPA for its leadership for finalizing “more protective water quality standards for everyone who lives here.”

“Strong water quality standards are important because they help protect us from toxins in our water that end up in the fish and shellfish we eat,” she said in a statement.