In 1991, the Tribes formed the Division of Environmental Protection within the Natural Resources Department. The purpose of the Division is to protect human health and the environment for all Reservation residents. When created, the Division consisted of three programs: Air Quality, Water Quality, and Shoreline and Aquatic Lands Protection. Two of the three, Air and Shoreline programs, had been functioning for several years prior to 1991, but within a different organizational structure. A new program, Solid and Hazardous Waste, was added to the Division in 1993. The Division Manager presently handles solid waste issues with assistance from the Solid/Hazardous Waste Specialist and handles Pesticides issues with the assistance of the Pesticides Specialist . In 2003 the Tribal Brownfields Response Program was created.
In 2006, the Pesticides program was added to the Division and in 2007, the Underground Storage Tank/Leaking Underground Storage Tank Program was added.
Mission Statement: "To advocate for the protection, restoration, effective management and health of the air, land, water and biological resources of the reservation environment through education, planning, conservation, cooperation and regulation. While perpetuating cultural values and the quality of life of the people of the Flathead Indian Reservation."