His deputy Andrew Wheeler will take over as acting head of the agency, Mr Trump said.
Scott Pruitt survived months of misconduct allegations by preserving his relationship with one person at all costs: President Donald Trump. Chmielewski also leveled new claims against the administrator, including "improper retaliation against EPA staff".
"There have been too many ethical lapses under Administrator Pruitt's watch and this decision is in the best interests of the agency and our country", she said in a statement.
In only 1.5 years at the agency, Pruitt has rolled back numerous Obama-era policies.
"Outstanding? Instead of protecting our air and water (Scott Pruitt) gave polluters unprecedented influence and access to the EPA", he said in response to Trump's praise of the outgoing EPA chief.
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Pruitt was a former Oklahoma attorney general who filed a number of lawsuits against the EPA, according to the agency's website. And later: "I count it a blessing to be serving you in any capacity".
"But Mr. Pruitt's brazen abuse of his position for his own personal gain has been absolutely astounding, rivaled only by the silence of far too many in Congress and in the White House who allowed Mr. Pruitt's unethical, and at times, possibly illegal behavior to go unchecked", the DE senator said in a lengthy statement.
Pruitt was recently harassed by a woman at a Washington restaurant, who urged him to "resign before your scandals push you out". As of last October, 67 environmental rules appeared to be under threat. Which means in the short term, the departure isn't likely to change the trajectory of the EPA.
Wheeler was registered to lobby for Murray Energy. the nation's biggest coal mining company until August 2017, Senate records show. "We can't afford more pollution and asthma attacks - our children's health and their future depends on it". Wheeler is a former coal industry lobbyist.
Before taking the job at the EPA, Wheeler worked as an energy lobbyist on Capitol Hill. This differs from Pruitt, who drew attention not only for his aggressive moves to cut back regulations but also for mounting scandals and questions about potential ethics violations. The main difference between the two, say conservation groups, is Wheeler will likely be more effective than Pruitt in dismantling EPA safeguards. In June, he told the Washington Examiner that he liked his current job and did not want to run the EPA.
Senator Kamala Harris, Democrat from California:"Just because Scott Pruitt resigned doesn't mean we've forgotten about the taxpayer funds he's misused or the damage he's done to our environment".