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WASHINGTON — When the Environmental Protection Agency administrator, Andrew Wheeler, accused California of allowing “piles of human feces” on city streets to contaminate sewer systems, leaders of the agency’s West Coast region hastily convened an all-hands meeting of the San Francisco staff.
At that meeting, E.P.A. officials informed staff members that Mr. Wheeler’s torrent of allegations about the state’s water pollution were exaggerated, according to five current and former E.P.A. officials briefed on internal discussions. Moreover, the accusations, contained in a Sept. 26 oversight letter, had been developed without the knowledge of the California-based staff, which would normally issue such notices.
Instead, it was put together by a small group of political appointees in Washington assigned specifically to target California, according to three current E.P.A. officials.
Senior leaders of the agency defended the process, pointing to legitimate issues with California’s air quality and water systems.
“Unlike previous administrations that were complacent with noncompliance, this administration will not let these serious environmental failures languish,” said Michael Stoker, the administrator of E.P.A. Region 9, which includes California. He added that he was aware of Mr. Wheeler’s letter before it went out and agreed that it was warranted.
But the unusual manner in which Mr. Wheeler’s accusations were compiled and delivered bolsters suspicions voiced by Gov. Gavin Newsom of California and others that the Trump administration is retaliating against California, a liberal state that has consistently defied the president’s deregulation agenda. In recent weeks the Trump administration has fought bitterly with California over immigration, the president’s tax returns and homelessness.
But nowhere are the complaints more jarring and the threats more specific than in the environmental arena, where, nationwide, the Trump administration has been easing off enforcement. Critics of the Trump administration have accused E.P.A. officials in Washington of clamping down on environmental standards in California while averting their gaze from similar or worse situations elsewhere.
“There’s no question here that the administration is targeting California, because, ironically, California has played an outsize role as an aggressive regulator of environmental pollution,” said Richard Lazarus, a professor of environmental law at Harvard University.
Tensions between the state and the federal government have increased sharply in recent months, aggravated by a feud over California’s authority under the Clean Air Act to set automobile emissions standards that are stricter than those of the federal government.
California officials struck a deal in July with four automakers willing to abide by the state’s tougher gas mileage standards in defiance of Mr. Trump, a move that reportedly enraged the president. The E.P.A. then formally revoked California’s authority, which triggered a lawsuit from the state and 13 others that follow California’s stricter standards and want to preserve their authority to enact tougher environmental rules.
In the weeks that followed, the Trump administration made a series of increasingly severe accusations against the state, including the Sept. 26 letter that accused California of failing to meet clean water standards and hundreds of “deficiencies that have led to public health concerns.”
It charged that California was out of compliance on a long list of regulations, including arsenic and lead levels in water, and it detailed a litany of bacteria issues affecting the state’s drinking water.
Under normal protocol, the agency’s regional office in California would be in charge of any communications detailing particularly challenging problems, according to the five current and former E.P.A. officials who asked not to be identified because they were not authorized to publicly discuss internal agency discussions.
Cynthia Giles, who served as assistant administrator for the E.P.A.’s enforcement office during the Obama administration, said ordinarily the agency would compile a lengthy history of trying and failing to solve a state’s problems before the E.P.A. administrator would send a letter like Mr. Wheeler’s, which included a veiled threat that funding through the Clean Water Act could be at risk. That history does not exist in the case of California.
“If this were an actually serious policy concern about a state’s performance,” she said, “it’s inconceivable that this wouldn’t be a subject of discussion for months, if not years, between the region and state.”
In fact, according to the latest review of California’s performance under the Clean Water Act, the state’s rate of “significant noncompliance” was below the national average. It also had more stringent pollution limits and tougher monitoring than many other states.
California, the country’s most populous state, does face numerous environmental compliance problems, but E.P.A. officials said many other states have violations at least as serious. California is generally acknowledged to be one of the states that works hardest to resolve its environmental problems.
“California is the place that has innovated more than anywhere else on air pollution and other regulations,” said William K. Reilly, who served as administrator of the E.P.A. under the first President George Bush. “Everybody knows that.”
Mr. Stoker, who is based in Los Angeles, did not attend the all-hands meeting on the day Mr. Wheeler delivered his letter. Instead, it was led by the office’s regional counsel, Sylvia Quast. Other top agency officials, including the directors of the offices of compliance and water, also attended. The regional office has since held at least one other meeting to discuss Mr. Wheeler’s accusations.
The message from the E.P.A.’s leadership in California has been consistent: Mr. Wheeler’s office bypassed the people who know the most about the state and work most closely with state and local officials. The office has been rerouting requests for the data that supports Mr. Wheeler’s accusations to Washington because the San Francisco office does not have it. They have also advised staff members concerned that the letters have undermined the E.P.A.’s working relationship with the state to tell their counterparts at California agencies that the letter is purely political and that the regional office had nothing to do with it.
On Tuesday, two senior E.P.A. officials acknowledged that the concerns expressed in the letter did not originate from the regional office. They also asserted that questions over process and turf should not overshadow genuine problems with California’s air and water quality.
The officials said Mr. Wheeler’s interest arose from two main sources: Concerns that Representative Nanette D. Barragán, Democrat of California, expressed to Mr. Wheeler at a House Energy and Commerce Committee hearing in March about discolored tap water in Compton, Calif., and a National Public Radio segment in August detailing how a spiraling homeless crisis in San Francisco had led to streets strewn with needles and human feces.
Ms. Barragán accused the E.P.A. leadership of hypocrisy, since it has proposed to cut $300 million from a fund used to help states pay for water projects. She said in a statement Mr. Wheeler “is using my legitimate inquiry to disingenuously and opportunistically rebuke California’s environmental efforts in his politically skewed letter.”
California’s senators, Dianne Feinstein and Kamala Harris, both Democrats, have requested that the E.P.A.’s inspector general investigate whether the agency’s accusations against California were politically motivated. Last week more than 600 former E.P.A. officials signed a letter calling for a federal investigation into what they called an “inappropriate threat of use of E.P.A. authority” against California.
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