(CNN) Two of Environmental Protection Agency Administrator Scott Pruitt's closest aides at the agency resigned on Wednesday, an EPA official confirms to CNN.

Sarah Greenwalt, a senior counselor to Pruitt, and Millan Hupp, who worked as Pruitt's scheduling director, both resigned on Wednesday, the official told CNN. Their resignations are set to take effect late this week and early next week, the source said.

Hupp recently testified before the House oversight committee that she did many personal tasks for Pruitt, including house-hunting and inquiring about obtaining a used Trump hotel mattress.

Their resignations leave Pruitt increasingly isolated at the EPA, where he has lost the confidence of most of the agency's career staff and many conservative political appointees who feel that Pruitt's ethical lapses have done a disservice to the President's agenda.

Still, Pruitt earned President Donald Trump's praise earlier Wednesday.

"EPA is doing really, really well. And you know, somebody has to say that about you a little bit," Trump said. "EPA is doing so well...I think people are very happy with the job that's being done at the EPA."

Hupp and Greenwalt were also the two aides who were set to receive Pruitt-approved pay raises despite the White House's refusal to sign off on the raises.

The Atlantic first reported Hupp resigned. Greenwalt's resignation was first reported by The New York Times.

CNN has reached out to the EPA for comment and has not yet received a response.

In congressional testimony last month, Pruitt described Hupp as "a longtime friend of my wife and myself," but denied the raise was related to their friendship.

She spearheaded his apartment search when his lobbyist landlords soured on his continued presence in their Capitol Hill condo; booked his personal travel; and inquired with President Donald Trump's DC hotel -- located across the street from EPA -- about purchasing a used mattress Pruitt had heard was available.

Her personal work for Pruitt raised red flags among ethics experts. Federal employees are subject to specific rules designed to prevent officials from using their office for personal gain or taking advantage of subordinates.

The majority of Hupp's professional career has been at Pruitt's side. Since her 2014 graduation from the University of Oklahoma, she has worked for his various political operations, including a PAC and super PAC.

Greenwalt is an attorney who worked for Pruitt when he was attorney general. Her resume says she "provided legal counsel to the Attorney General."