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On at least three occasions, the agency has blamed the process for harming drinking-water supplies. Each time it has been forced to backpedal after further study cast doubt on its findings.

Those incidents and others have eroded the EPA’s credibility among Republicans, some of whom surely will doubt any scientific findings released by the EPA over the next four years.

Sen. James M. Inhofe, Oklahoma Republican and one of the EPA’s loudest critics, recently asked, “Why should anyone trust their ‘science’ now?”

On Thursday, he blasted the EPA’s actions but commended Ms. Jackson for her honesty and congeniality — a sentiment shared by many other Republicans and leaders in the fossil-fuel industry, even those who disagree with Obama administration policy.

“She was one of the few at the EPA that was honest with me,” Mr. Inhofe said. “While so many other Obama administration appointees don’t tell the truth, she did, and I hope that is not the reason for her departure.”

But Mr. Inhofe and others say that although she may have been an upfront and honest public official, her efforts have been and will continue to be disastrous for American consumers and energy producers.

“From an energy and consumer perspective, it had to be said that the Jackson EPA presided over some of the most expensive and controversial rules in agency history. Agency rules have been used as blunt attempts to marginalize coal and other solid fossil fuels and to make motor fuels more costly at the expense of industrial jobs, energy security and economic recovery,” said Scott Segal, director of the Electric Reliability Coordinating Council, a coalition of energy companies. “The record of the agency over the same period in overestimating benefits to major rules has not assisted the public in determining whether these rules have been worth it.”

Although it is unclear whether Ms. Jackson’s resignation is tied to the growing furor around her use of secret email accounts, critics say she is simply getting out of town before the scandal grows.

“It is not only implausible that Lisa Jackson’s resignation was unrelated to her false identity, which we revealed, given how the obvious outcome and apparent objective of such subversion of transparency laws was intolerable,” said Christopher C. Horner, a senior fellow at the Competitive Enterprise Institute, which sued the EPA this year for records related to the secret emails.

“But it became an inevitability when, last week, the Department of Justice agreed [as a result of our lawsuit] to begin producing 12,000 of her ‘Richard Windsor’ alias accounts related to the war on coal Jackson was orchestrating on behalf of President Obama outside of the appropriate democratic process,” he said.