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Previous studies conducted in the Elk River watershed showed that selenium concentrations are higher in aquatic biota in lentic compared to lotic habitats of the system having similar water selenium concentrations. Studies have also shown that water selenium concentrations have increased over time (~10% per year) and recent annual average concentrations have ranged up to 0.044 mg/L in areas downstream from mine discharges. For the present study, trophic transfer of selenium was characterized in lotic versus lentic habitats using concentrations measured in field-collected samples and assuming a three-step food chain of water to the base of the food web (biofilm), to benthic invertebrates, and then to westslope cutthroat trout (WCT) ovaries. Food chain models were developed for each habitat type (lotic and lentic) by combining linear regression equations for the three transfer relationships, allowing for prediction of fish ovary concentrations from water concentrations. Greater accumulation of selenium in lentic areas was mostly attributable to greater uptake at the base of the food chain compared to lotic areas. Enrichment/trophic transfer factors for selenium at all levels of the lotic and lentic food chains decreased and then became near constant as exposure concentrations increased. The lotic model predicted little increase in WCT ovary selenium concentrations over an eightfold increase in water concentrations (~0.005-0.040 mg/L), accounting for the lack of observed increase in within-area fish tissue concentrations over time despite increasing trends in water concentrations.