Also on Tuesday, new details emerged about the lobbying of the E.P.A. by J. Steven Hart, the lobbyist whose wife had last year rented a $50-a-night condo to Mr. Pruitt. Congressional investigators on Tuesday provided The New York Times with an email in which Mr. Hart asked Mr. Pruitt for help in getting three people appointed to the E.P.A.’s prestigious Science Advisory Board. They had been recommended by Smithfield Foods, a company that was a client of Mr. Hart’s lobbying firm​, and its Smithfield Foundation, a charitable subsidiary.

The email was sent in August 2017, a few weeks after Mr. Pruitt had moved out of the apartment, but at a time when he still owed money to Mr. Hart’s wife.

Representative Frank Pallone Jr. of New Jersey, ​the leading Democrat on the House committee that helps oversee E.P.A. operations, ​called the email “further proof that Administrator Pruitt has consistently misled Congress and the public about the extent to which the special interests providing him with gifts have sought specific favors from E.P.A. in return.”

The E.P.A. press office did not respond to a request for comment. A spokesman for Williams & Jensen, the lobbying firm that Mr. Hart left last month, did not respond to a request for comment.

The departures of Mr. Perrotta and Mr. Kelly from the E.P.A. come as some of Mr. Pruitt’s top staffers privately have begun expressing frustration with his stewardship of the agency. When asked at a congressional hearing last week about the spending and the ethical questions hovering over his tenure, Mr. Pruitt denied knowledge of the decisions, blaming them instead on his senior staff.

As the investigations into Mr. Pruitt have grown, so has scrutiny of Mr. Perrotta and Mr. Kelly. Neither responded to emails or phone messages seeking comment on Tuesday afternoon.

Mr. Pruitt on Tuesday praised his two former aides, while Democrats seized on their resignations to renew calls for Mr. Pruitt to step aside.