Management agencies documented a decline in the mountain whitefish ( Prosopium williamsoni) population on the Big Lost River, and unscreened diversions were recognized as a potential factor for this decline. Research suggests the Big Lost River mountain whitefish population is genetically unique, and it has been petitioned for protection under the Endangered Species Act. In 2007, a basin-wide synopsis of diversions was conducted to describe relative entrainment and identify diversions that entrained the most mountain whitefish. This larger scaled synopsis facilitated a more precise assessment of entrainment by a subset of diversions in 2008. In 2008, the volume that was diverted and the available stream-flows were assessed to identify correlations between discharge and increased entrainment. Lastly, a stage-structured population matrix model was used to describe the potential effect that entrainment is having on the mountain whitefish population. Entrainment was evaluated in canals using multiple-pass electrofishing depletions in conjunction with block-nets. Entrainment was estimated using simple or stratified random population estimates. Entrainment varied widely among diversions and between water years. Variations in entrainment were attributed to seasonal patterns, population densities, and the physical characteristics of the diversion. A positive correlation was identified (R² = 0.81) between the number of mountain whitefish entrained and the volume of water diverted annually. I observed substantial numbers of fish entrained by two diversions on the upper Big Lost River. I illustrate how reducing entrainment at these diversions will increase recruitment to adulthood and increase the viability of the population overall.