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The Indiana Department of Environmental Management (IDEM) administers the Clean Water Act Section 401 Water Quality Certification (WQC) Program. IDEM regulates the placement of fill materials, excavation (in certain cases), and mechanical clearing of wetlands and other waterbodies. IDEM draws its authority from the federal Clean Water Act and from Indiana's water quality standards. IDEM regulates activities in conjunction with the U.S. Army Corps of Engineers. Any person who wishes to place fill materials, excavate or dredge, or mechanically clear (use heavy equipment) within a wetland, lake, river, or stream must first apply to the Corps of Engineers for a Clean Water Act Section 404 permit. If the Corps of Engineers decides a permit is needed, then the person must also obtain a Clean Water Act Section 401 water quality certification from IDEM.

Under Clean Water Act Section 401, IDEM reviews the proposed activity to determine if it will comply with Indiana's water quality standards. The applicant may be required to avoid impacts, minimize impacts, or mitigate for impacts to wetlands and other waters. IDEM will deny water quality certification if the activity will cause adverse impacts to water quality. A person may not proceed with a project until they have received a certification from IDEM. A key goal of the program is to insure that all activities regulated by IDEM meet the no-net-loss of wetlands policy.