Bernhardt, whose past clients include oil companies and others with business before the Interior Department, became the agency's deputy secretary in 2017 and has led the department on an interim basis since former Secretary Ryan Zinkeresigned amid ethics scandals in January.
Trumptweeted Monday that Bernhardt "has done a fantastic job from the day he arrived".
If Bernhardt ascends to secretary, it would mirror the change of guard at the Environmental Protection Agency where last July Acting Administrator Andrew Wheeler, a former coal lobbyist, replaced Scott Pruitt, who stepped down after a series of probes into his conduct.
The interior department called its effort important to bolstering United States energy independence. Zinke had been facing multiple investigations into potential ethics violations at the time of his departure.
The Arizona Democrat Raul Grijalva, chairman of the House natural resources committee, said lawmakers would be watching to see whether Bernhardt's former industry ties were influencing his policy decisions.
"David Bernhardt spent much of his career lobbying for fossil fuel and agricultural interests, and the president putting him in charge of regulating his former clients is a ideal example of everything wrong with this administration".
Environmentalists were quick to criticize Trump's decision.
Critics have said Bernhardt is too close to his former clients who he sometimes represented in cases against the Interior Department.
Despite their letter calling him a "walking conflict of interest", the Senate confirmed Bernhardt on a 53-43 vote, and with strong support from Sen.
Republicans say Mr. Bernhardt's revolving-door experience makes him an informed regulator in matters before the agency.