Water, bed sediment, and biota were sampled in streams from Butte to near Missoula as part of a long-term monitoring program in the upper Clark Fork basin; additional water samples were collected in the Clark Fork basin from sites near Missoula downstream to near the confluence of the Clark Fork and Flathead River as part of a supplemental sampling program. The sampling programs were conducted in cooperation with the U.S. Environmental Protection Agency to characterize aquatic resources in the Clark Fork basin of western Montana, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water samples were collected periodically at 23 sites from October 2007 through September 2008. Bed-sediment and biota samples were collected once at 13 sites during August 2008.