He will be replaced by Deputy Administrator Andrew Wheeler as acting administrator, a former coal lobbyist who worked with Murray Energy CEO Bob Murray; was an aide for Jim Inhofe, the top climate science denier in the Senate; and who helped craft the Bush administration's ironically-named "Clear Skies" initiative, an effort to destroy the Clean Air Act.
Last month, while praising Pruitt's "fantastic job" at the EPA, the president admitted, "I'm not happy about certain things, I'll be honest".
Asked if the decision was his own or the EPA chief's, Trump responded, "it was very much up to him".
Mink mentioned several issues surrounding the EPA head, including his reported room-rent deal.
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"[Wheeler] will be similar to Pruitt in terms of the agenda - he understands the Trump administration and will carry out the agenda", Matthew Dempsey, a former colleague of Wheeler's who works with an energy lobbying firm told the Times.
For now, however, Trump was not giving any clues as to whose name he would send to the Senate as a permanent replacement for Pruitt.
He had also ordered his EPA staff to do personal chores for him, picking up dry cleaning and trying to obtain a used Trump hotel mattress for his apartment. According to CNN, the president spoke highly of Pruitt just a month ago, telling reporters that he was "doing a great job within the walls of the EPA", and that "we're setting records". Many of the EPA regulations Pruitt scraped or delayed had not yet taken effect, and the tens of thousands of lost coal mining jobs the president pledged to bring back never materialized.
Pruitt also was hampered by spending scandals related to security. Some 170 lawmakers signed a resolution calling for Pruitt to resign.
Mr Pruitt's resignation is the latest in a long list of White House departures since Mr Trump took office a year ago. Pruitt has increasingly come under fire for multiple allegations of abusing his power - from spending hundreds of thousands of dollars on first-class travel to a sweetheart real estate deal tied to a lobbyist with EPA business and attempting to secure a private business deal for his wife - among numerous allegations.
He was confirmed by the Senate on February 17, 2017, on a 52-46 vote, the most recorded "no" votes of any EPA administrator.
This comes as a series of ethics embarrassments have piled up for Pruitt throughout his tenure.