The bill, which will be filed Wednesday, would let the Massachusetts Department of Environmental Protection administer a federal water quality protection program run by the federal Environmental Protection Agency.
Massachusetts is just one of four states — along with New Hampshire, Idaho and New Mexico — that still rely directly on the federal government to run the program.
Known as the National Pollutant Discharge Elimination System, the program regulates public and private discharges of wastewater and storm water.
Baker says his proposal will give the state direct oversight of water quality monitoring, assessment, and water quality standards programs.
The Republican governor has proposed spending $1.4 million to begin making the switch.