Water-quality, streambed-sediment, and biological data were collected in the Clark Fork-Pend Oreille and Spokane River basins as part of the U.S. Geological Survey’s National Water-Quality Assessment Program and are presented in this report. These river basins compose the Northern Rockies Intermontane Basins study unit which was selected to include a river system that has a mixture of forested, agricultural, urban, and developing areas. Waterquality samples were collected from 28 surface-water sites and 86 ground-water sites from June 1998 to September 2001. Data collected included measurements of physical properties and chemical analyses of concentrations of major ions, trace elements, nutrients, organic carbon, pesticides, volatile organic compounds, and radiochemical constituents. Streambed-sediment and biological tissue samples were collected from 41 sites and analyzed for trace elements and organochlorine compounds. Benthic algae were collected to determine chlorophyll concentration and areal density.