The living arrangement, first reported by ABC News, was for $50 a night at a Capitol Hill condo co-owned by the wife of a top lobbyist.
EPA Inspector General Arthur Elkins said in the letter that he will add to existing investigations in response to requests from members of Congress, hotline complaints, and issues raises by the federal government's top ethics official.
Elkins wrote that his office will now review Pruitt's living arrangements, travel spending, use of staff and expenditures for security and travel, approvals of hiring and salary decisions, use of subordinates time, and reassignment or demotion of staff who objected to spending decisions.
The letter was sent to multiple Democrats that requested investigations into Pruitt, including Rep. Don Beyer, D-Va., and Rep. Ted Lieu, D-Ca., and Sen. Tom Carper, D-Del.
Some of those questions are already ongoing, including reviews of the cost of Pruitt's expanded security detail and the use of frequent first-class flights that Pruitt says were recommended for security reasons. Those reports are expected to be published this summer.
Pruitt previously denied any knowledge of the raises but admitted in congressional testimony on Thursday that he delegated authority to Jackson and did know at least one of the aides was seeking a raise, though he did not know the amount.
Pruitt said during congressional hearings on Thursday that he "has nothing to hide" and that he wasn't aware of some of the specific amounts being spent such as the $43,000 spent on a secure booth for his office or the amounts of raises for certain staffers.
On the cost of his first-class travel, Pruitt has said his security detail recommended he fly first-class for safety reasons. He said he now flies coach.
EPA ethics officials have said that Pruitt's living arrangement for much of his first year in Washington did not violate gift rules because it was a comparable rate to other rentals in the area. But the officials have also said that they didn't have all the information at the time they made the initial finding and that their statements only apply to whether it was an improper gift, not if it was a conflict of interest.