The common bully (Gobiomorphus cotidianus), a small-bodied New Zealand native fish species, was used to monitor population impacts of multiple effluents in the Tarawera River, New Zealand. In an initial survey, the absence of reproductive development at the expected spawning time for common bully was observed in a population downstream of effluent discharges. Subsequently, we examined the hypotheses that the observed changes were due to effluent exposure, migratory patterns, or genetic differences between populations. Liver detoxification enzyme activity and stable isotopes provided evidence against upstream migration of sexually mature bully. The observed presence of developed gonads in the downstream population during winter season resulted in the rejection of the hypothesis that reproductive failure was due to effluent exposure, and it was concluded that there were substantial differences in reproductive timing. Genetic analyses of two upstream, one downstream, and one population from a nearby coastal river indicated the upstream (reference) and downstream (effluent exposed) bully in the river formed genetically distinct populations. The identification of a nearby river population with similar reproductive timing and high genetic similarity to the effluent-exposed population suggests that the observed differences in the genetics of the downstream population were not caused by effluent exposure. The genetic analysis did highlight the lack of downstream dispersion and gene flow in the river which could possibly be related to anthropogenic stress.