Abandoned tailings and mine adits are located throughout the Boulder River watershed in Montana. In this watershed, all species of fish are absent from some tributary reaches near mine sources; however, populations of brook trout Salvelinus fontitalis, rainbow trout Oncorhynchus mykiss, and cut-throat trout O. clarki are found further downstream. Multiple methods must be used to investigate the effects of metals released by past mining activity because the effects on aquatic life may range in severity, depending on the proximity of mine sources. Therefore, we used three types of effects—those on fish population levels (as measured by survival), those on biomass and density, and those at the level of the individual (as measured by increases in metallothionein, products of lipid peroxidation, and increases in concentrations of tissue metals)—to assess the aquatic health of the Boulder River watershed. Elevated concentrations of Cd, Cu, and Zn in the water column were associated with increased mortality of trout at sites located near mine waste sources. The hypertrophy (swelling), degeneration (dying), and necrosis of epithelial cells observed in the gills support our conclusion that the cause of death was related to metals in the water column. At a site further downstream (lower Cataract Creek), we observed impaired health of resident trout, as well as effects on biomass and density (measured as decreases in the kilograms of trout per hectare and the number per 300 m) and effects at the individual level, including increases in metallothionein, products of lipid peroxidation, and tissue concentrations of metals.