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WASHINGTON — President Obama on Monday will nominate new leaders for the Energy Department and the Environmental Protection Agency, filling out his second-term team to tackle energy and climate issues.

Ernest J. Moniz, the director of the Massachusetts Institute of Technology's Energy Initiative, is set to take over for Steven Chu at the Energy Department. Gina McCarthy, the assistant administrator in charge of air and radiation at the E.P.A., is set to replace the departing administrator, Lisa P. Jackson. Both are subject to Senate confirmation.

The choice of Ms. McCarthy is likely to generate considerable opposition because she is identified with several of the Obama administration's most ambitious clean air regulations, including proposed greenhouse gas regulations for new power plants. Mr. Obama has pledged to address climate change in his second term, and he is expected to use the authority granted to the E.P.A. under the Clean Air Act to reduce climate-altering emissions from power plants and other major sources.

The nominations will be announced Monday morning at the White House, where Mr. Obama will also name Sylvia Matthews Burwell to be the director of the White House Office of Management and Budget.