BP Products North America has agreed to pay more than $275,000 (£194,668) in penalties to resolve alleged air and water violations in Indiana.
The company will also take steps to reduce around 23,500 pounds of emissions annually from the Whiting petroleum refinery.
Located on the southwestern shore of Lake Michigan, BP operates the nation’s sixth largest petroleum refinery, producing up to 430,000 barrels of oil a day.
In March 2014, the US Coast Guard and Environmental Protection Agency (EPA) responded when BP discharged up to 39 barrels of oil into Lake Michigan.
The EPA launched an investigation following the incident and found the energy giant “failed to implement its spill prevention, control and counter measure plan and failed to provide appropriate containment to prevent a discharge of oil”.
It also found BP exceeded the limits of its wastewater discharge permit in April and November 2011.
The company has now agreed to install new monitoring equipment, implement an inspection and cleaning schedule for a wastewater treatment device and enhance storm water controls to prevent unauthorised discharges.
Earlier this month BP agreed to pay out $175 million (£121.5m) to its shareholders over claims the oil giant misled them about the severity of the Gulf of Mexico oil spill in 2010.