If approved by the Senate, Scott Pruitt, the attorney general in Oklahoma, will lead the agency, which Trump has pledged to "dismantle".
The EPA was tasked with instigating President Obama's Clean Power Plan (CPP) — a programme designed to lower carbon emissions in the US beyond 2022.
The rules should enable the US to slash emissions by 32% below 2005 levels by 2030, said the White House in 2015 when the plan was announced.
As Attorney General, Pruitt has taken a leading role in a group of states suing the EPA over the CPP — court action which has stalled the CPP in a federal court.
It is not the first time Pruitt has had a run-in with the EPA.
According to the New York Times, in 2011, Pruitt sent a letter to the EPA stating regulators were overestimating the amount of air pollution from the drilling of new gas wells in Oklahoma.
The paper claims, following an open-records request, the letter was instead drafted by oil and gas company Devon Energy, and copied with minor changes on to Pruitt's office stationery before being sent to the EPA.
The New York Times found Pruitt had sent more letters, similarly drafted by the oil and gas lobby, to the US's interior department and President Obama.
Pruitt's links with the fossil fuel industry go deeper. Harold Hamm, chief executive of major oil and gas firm Continental Resources, who acted as energy advisor to Donald Trump's election campaign, was also chairman of Pruitt's re-election campaign for attorney general in 2014.
Hamm had been tipped to become the new energy secretary in the Trump administration but ruled himself out for the role in early December.
In May, Pruitt wrote an article for conservative news magazine National Review.
In it he states: "Global warming has inspired one of the major policy debates of our time. That debate is far from settled. Scientists continue to disagree about the degree and extent of global warming and its connection to the actions of mankind."
The environmental lobby has unsurprisingly criticised the nomination.
Friends of the Earth climate and energy program director Benjamin Schreiber said: "By appointing Oklahoma Attorney General Scott Pruitt to head the Environmental Protection Agency, Donald Trump has made it clear that he intends to wage war on clean air and clean water. Trump has also put our climate in peril and shown he is out of step with the American people.
"As the Attorney General, Scott Pruitt did the bidding of the oil and gas industry and fought many of the laws he will now be tasked to enforce. He helped 'Big Oil' turn Oklahoma into an Earthquake zone.
"With this EPA pick, Donald Trump is putting all Americans at risk. Friends of the Earth is committed to stop Trump and Pruitt from undermining environmental protections."
UK-based Energy and Climate Intelligence Unit (ECIU) director Richard Black, added: "It's unclear to what extent Mr Pruitt will be able to deliver, or what impact four years of trying will have in the real world.
"Many US states, headed by California, are heading inexorably in a clean energy direction, and both they and environment groups are promising legal action if the new administration tries to turn back the clock. It's notable too that some Senators have pledged to fight Mr Pruitt's nomination."
Democratic Party presidential-primary nominee Bernie Sanders tweeted: "Trump's nominee to lead EPA, Scott Pruitt, is a climate denier who's worked closely with the fossil fuel industry. That's sad and dangerous."