Listed as a threatened species in 1992, the Bliss Rapids snail (BRS; Taylorconcha serpenticola) was originally thought to be associated primarily with spring habitat; however, recent sampling has found BRS to be sparsely distributed throughout 31 km of the Snake River (Idaho). BRS found in near shore areas are affected by rising and falling water levels associated with dam operation. We used a two-stage survey sampling design to estimate population size, density and occupancy rates for BRS in two reaches influenced by different dams. Whether dam operation (load following vs. run of river) had a significant effect on BRS depended on the response variable and the type of statistical test. Comparisons of overall population estimates were less sensitive than pair-wise comparisons of individual locations; comparisons of snail population size and density tended to be significant more often than percent occupancy. Results also differed by year and reach. Our task is to translate these disparate results into estimates of the number of BRS killed or injured and the amount of critical habitat that would be lost under different scenarios of dam operation.