Failure to estimate capture efficiency, defined as the probability of capturing individual fish, can introduce a systematic error or bias into estimates of fish abundance. We evaluated the efficacy of multipass electrofishing removal methods for estimating fish abundance by comparing estimates of capture efficiency from multipass removal estimates to capture efficiencies measured by the recapture of known numbers of marked individuals for bull trout Salvelinus confluentus and westslope cutthroat trout Oncorhynchus clarki lewisi. Electrofishing capture efficiency measured by the recapture of marked fish was greatest for westslope cutthroat trout and for the largest size-classes of both species. Capture efficiency measured by the recapture of marked fish also was low for the first electrofishing pass (mean, 28%) and decreased considerably (mean, 1.71 times lower) with successive passes, which suggested that fish were responding to the electrofishing procedures. On average, the removal methods overestimated three-pass capture efficiency by 39% and under-estimated fish abundance by 88%, across both species and all size-classes. The overestimates of efficiency were positively related to the cross-sectional area of the stream and the amount of undercut banks and negatively related to the number of removal passes for bull trout, whereas for westslope cutthroat trout, the overestimates were positively related to the amount of cobble substrate. Three-pass capture efficiency measured by the recapture of marked fish was related to the same stream habitat characteristics that influenced (biased) the removal estimates and did not appear to be influenced by our sampling procedures, including fish marking. Simulation modeling confirmed our field observations and indicated that underestimates of fish abundance by the removal method were negatively related to first-pass sampling efficiency and the magnitude of the decrease in capture efficiency with successive passes. Our results, and those of other researchers, suggest that most electrofishing-removal-based estimates of fish abundance are likely to be biased and that these biases are related to stream characteristics, fish species, and size. We suggest that biologists regard electrofishing-removal- based estimates as biased indices and encourage them to measure and model the efficiency of their sampling methods to avoid introducing systematic errors into their data.