Northern Saskatchewan, Canada is home to a uranium milling operation that discharges a complex milling effluent containing nutrients, cations and anions, and many metals including selenium (Se). Se has the potential to accumulate in a system even when water concentrations are low. This study evaluated the effects of treated uranium milling effluent and contaminated sediment in combination and in isolation to determine the contribution and importance of each source to fathead minnow (Pimephales promelas) reproduction and survival. Trios of fathead minnows were allocated to one of four treatments for 21-days where the following were evaluated; survival (adult and 5 day larval), larval deformities, reproductive effects (egg production, spawning events) and metal tissue burdens (muscle, gonad, eggs and larvae). In addition Se speciation analysis was conducted on fish tissues. Effects were solely effluent-mediated with little contribution observed due to the presence of contaminated sediments. The contaminated sediments tested were taken from the actual receiving environment and represented the sediment composition found in greatest abundance. Results showed egg production significantly increased in the effluent treatments compared to the reference water treatments. Although egg production increased following effluent exposure, there was reduced hatching and larval survival and a significant increase in skeletal deformities in 5 day old larvae. Despite these effects on the offspring, when examined in an integrated manner relative to increased egg production, the mean number of normal larvae did not differ among treatments. Total selenium significantly increased in the effluent exposed, algae, female muscle, gonad, eggs and larvae in addition to other metals. A shift in the proportion of species of selenium was evident with changing exposure conditions. Biofilm/algae was key in the transfer of available Se into the food chain from the water and a source of direct dietary exposure in fish and possibly invertebrates.