Microcosm experiments with natural indigenous phytoplankton communities were conducted to assess the effects of waters from oil sands extraction processes, emphasizing the naphthenate and salt constituents. Process waters of varying ages (zero to eight years) remediation histories, and chemical composition were obtained from outdoor mesocosms and inoculated with phytoplankton assemblages from a reference lake in the study area. Community composition measures, including percentage model affinity (PMA) and canonical correspondence analysis (CCA), revealed significant community effects of water from systems less than five years old, with naphthenate concentrations greater than 20 mg/L, compared to water from the reference lake. Canonical correspondence analysis, PMA, and regression analyses further showed that naphthenate concentration was significantly correlated with community structure. Using CCA, groups of taxa characteristic of waters with > 20 mg/L naphthenates (including Botryococcus braunii, Gloeococcus schroeteri, Cosmarium depressum, Chrysococcus rufescens, Chromulina spp., Ochromonas spp., and Keratococcus spp.) were identified. Salinity, as reflected in conductivity, was positively correlated with naphthenate concentration and itself appeared to influence the community structure. The results confirmed an important role for naphthenates in ecological effects of process waters from oil sands mining, but the influence of covarying factors such as salinity requires further investigation.