Whitman, a former New Jersey governor, said her resignation is effective June 27. She met with Bush at the White House on Tuesday afternoon to inform him of her decision, the agency said.
Whitman, in her letter, defended the administration's environmental policies which have been under attack by environmentalists as a series of rollbacks in protecting the nation's air, water and land.
"Our work has been guided by the strong belief that environmental protection and economic prosperity can and must go hand-in-hand," she wrote. "The EPA has built an enviable record of success that will result in significant improvements to the state of our nation's treasured environment."
She pointed to initiatives to reduce pollution from off-road diesel engines, a push to cut pollution from school buses and "our aggressive and effective efforts to enforce the nation's environmental laws."
She said she was proud of the EPA work under her leadership.
Whitman Resigns From EPA