Geochemical and hydrological data from abandoned mine watersheds demonstrated that (1) point sources of pollution fail to account for total receiving watercourse metal load at higher flows and (2) an inverse relationship exists between river flow and pH due to peatland runoff. Quantifying the varying importance of point and diffuse pollution sources enabled prediction of treatment benefits for a major point source of pollution in one watershed. Instream zinc load increases with river flow (∼3 to 14 kg Zn/d) due to diffuse groundwater and surface runoff pollution sources at higher flows. Lab tests demonstrated that metal release from the streambed, driven by pH decreases at higher flows, also contribute to increased downstream metal loads. Predicting point source treatment benefits demonstrates major instream improvements at low flow (zinc decreases from >800 to 120 μg Zn/L). At higher flows treatment benefits diminish (Zn decreases from 240 to only 200 μg Zn/L) due to the greater influence of diffuse sources. A quantitative understanding of the variable importance of point and diffuse sources of pollution, and instream processes of metal attenuation and release, is crucial to evaluating the benefits of treatment to downstream water quality.