Uranium mining activities have the potential to impact aquatic systems through mine drainage (runoff) and the release of treated effluent into nearby watersheds. Such anthropogenic exposure can lead to elevated concentrations of metals and major ions, which may impact aquatic biota. Previous studies have looked at the effects of water quality on aquatic biota within flooded pit lakes and natural lakes that have been exposed to various mechanisms of mining exposure. However, the literature often only examines the effects of a limited number of contaminants on a limited number of species. Researchers have rarely looked at the effects of multiple contaminants on species composition, biodiversity and ecosystem function in aquatic systems. This study uses a multivariate approach to look for relationships between water quality (24 variables), plankton species composition and abundance, biodiversity (richness and evenness) and ecosystem function among lakes exposed to mining activities (n = 18) and non-exposed reference lakes (n = 8). Lake water quality data was used to cluster lakes into groups. Lake groups were then overlain onto multivariate ordinations derived from species composition-abundance data to determine if species composition was related to water quality. Ecosystem function variables included planktonic phosphorus cycling and planktonic respiration. The classified lake groups clustered well on ordinations derived from species composition-abundance data suggesting that relationships exist between water quality and plankton species composition. However, ecosystem function was similar among the majority of lakes and flooded pits despite differences in species richness, species composition and species abundance. Only a small number of aquatic systems had ecosystem function properties that were different from the majority of lakes and pits.