Pruitt had become a constant source of embarrassment to a president who had entered Washington promising to "Drain the Swamp."
VIDEO: Notable firings, resignations under the Trump administration
Notable firings and resignations under the Trump administration
Pruitt has faced an array of ethical questions about his travel spending, security costs, dealings with industry lobbyists and misuse of government resources.
He had denied wrongdoing in the face of multiple congressional and oversight inquiries.
Despite the scandals, Trump has been approving of Pruitt's efforts to reduce regulations that the administration says curb business growth. Trump writes on Twitter, "Within the Agency Scott has done an outstanding job."
VIDEO: What to know about the controversies surrounding EPA administrator Scott Pruitt
Scott Pruitt: Controversies surrounding the EPA administrator
Activists have argued those cuts have endangered the environment.
Trump tweets that Deputy Administrator Andrew Wheeler will assume the acting administrator position Monday.
Trump praised Pruitt's performance in the tweets, saying he had done an "outstanding job" as EPA administrator.
Andrew Wheeler, Pruitt's deputy, will take over as acting administrator Monday, Trump said in the tweets.
"We have made tremendous progress and the future of the EPA is very bright!" Trump tweeted.