In an effort to protect water quality at the source, some communities are currently developing and implementing plans to manage activities within their watersheds in a manner that protects their water systems from nonpoint source pollution. The U.S. Environmental Protection Agency (EPA) has allowed local governments to establish natural vegetative buffers (greenways) along stream corridors in lieu of incurring other EPA enforcement actions associated with violations of the Clean Water Act. This paper identifies the role of GIS and greenways in protecting water quality and aquatic and stream corridor habitats, describing an ongoing greenways project in Jefferson County, Alabama, and the supporting role of GIS in that project.