Effluent from anthropogenic inputs can affect fish assemblages in aquatic ecosystems by altering species richness, diversity and trophic structure. To investigate the effects of a bleached kraft pulp mill effluent (PME) and municipal sewage treatment plant (STP) discharge on fish assemblages in a temperate reservoir, we combined standard ecological methodologies with stable isotope analysis of δ13C and δ15N. Total catch, species richness, diversity and coefficient of community loss indicated lower species richness and diversity at sites exposed to PME, whereas sewage-exposed assemblages had intermediate richness and diversity relative to reference sites. Stable isotope analysis of δ13C and δ15N revealed that many species fed at higher relative trophic positions in the presence of both effluents and showed shifts towards increased reliance on littoral-derived and benthic-derived carbon at sites downstream of the PME discharge. Fishes at PME-influenced sites had also generally higher condition factor whereas fishes at STP-influenced sites were more variable in condition factor. These differences may, in part, be due to decreased species diversity at these sites and to nutrient enrichment manifest from the effluent discharge. While standard fisheries and ecological methodologies and stable isotope analysis have been separately used in other studies of anthropogenic effects on fishes, their integration in this study provides greater resolution than either could alone. Copyright © 2011 John Wiley & Sons, Ltd.