The Lamprey Eel Decline project conducted by the Confederated Tribes of Siletz Indians (CTSI) combined traditional ecological knowledge, scientific research and geographic information science. CTSI wanted to learn why the Pacific lamprey (Lampetra tridentata), a culturally and ecologically important species, was declining in the streams within their native land area. The project included interviewing native elders, characterizing stream habitat, monitoring water quality, creating a geographic information system (GIS) and educating tribal members on the cultural and ecological importance of the Pacific lamprey. Dynamic segmentation, a GIS data structure, was used to link standard stream survey data on the river unit scale to a base stream coverage (1:24,000). Dynamic segmentation efficiently associates georeferenced data to a linear feature, thus allowing the data to be readily assessable on desktop computer systems. To be more useful to the tribal and local resource managers, it is recommended that these GIS coverages of aquatic habitat should be used in conjunction with additional data coverages and basic regional models for watershed analysis and better management of aquatic ecosystems.