The EPA's failure to document has masked its process for overhauling major regulations like the Waters of the United States rule, the groups say.
"Under Scott Pruitt, the EPA has assumed a bunker mentality where paper trails are religiously avoided unless penned in invisible ink," Adam Carlesco, staff counsel for PEER, said in a statement. "By law, the American public has a right to know the basis for public health and anti-pollution decision-making that affects their lives."
The law in question is the Federal Records Act, which provides guidelines to government agencies on how they should create and maintain records of their activities.
A spokesperson for the EPA said the agency does not comment on ongoing litigation.
In their complaint, the groups cite news reports that Pruitt prefers to hold face-to-face meetings and avoids email to prevent his comments from being documented. They note that employees told The New York Times that Pruitt prohibits staff from bringing cellphones to meetings and discourages them from taking notes.
Pruitt said during a Senate oversight hearing last month that reports about the ban on note-taking at the EPA are inaccurate.
"I am very encouraging of the folks taking notes during meetings. Because I forget things often and we want to make sure we are keeping track of where we are heading on issues," he told the Senate Committee on Environment and Public Works.
The groups also point to the installation of a soundproof communications booth in Pruitt's office, which reportedly cost more than $25,000 and is the subject of an investigation by the EPA's inspector general.
Also named as defendants in the complaint are the National Archives and Records Administration and David Ferriero, the archivist of the United States. The groups claim the administration has failed to enforce the Federal Records Act by not taking action to investigate the EPA. Pruitt has defended the booth.
In an emailed statement to CNBC, a National Archives spokesperson said the Office of the Chief Records Officer of the United States has issued a formal inquiry and requested a response from EPA leaders to address the concerns raised by Citizens for Responsibility and Ethics in Washington.
"This matter is active and ongoing, and as is the case with all such allegations of improper recordkeeping, we consider each case seriously and expect that the agency complies with existing records management laws and regulations," said James Pritchett, the administration's director of public and media communications.
The latest lawsuit against Pruitt and the EPA comes as the administrator's travel habits are under increasing scrutiny. On Wednesday, South Carolina Republican Trey Gowdy, who chairs the House Oversight Committee, requested information about Pruitt's frequent first-class flights detailed in a series of recent news reports.