This study was conducted on the Kootenai River, Idaho to provide insight on sampling requirements to optimize future monitoring effort associated with the response of fish assemblages to habitat rehabilitation. Our objective was to define the electrofishing effort (m) needed to have a 95% probability of sampling 50, 75, and 100% of the observed species richness and to evaluate the relative influence of depth, velocity, and instream woody cover on sample size requirements. Sidechannel habitats required more sampling effort to achieve 75 and 100% of the total species richness than main-channel habitats. The sampling effort required to have a 95% probability of sampling 100% of the species richness was 1100 m for main-channel sites and 1400 m for side-channel sites. We hypothesized that the difference in sampling requirements between main- and side-channel habitats was largely due to differences in habitat characteristics and species richness between main- and side-channel habitats. In general, main-channel habitats had lower species richness than side-channel habitats. Habitat characteristics (i.e., depth, current velocity, and woody instream cover) were not related to sample size requirements. Our guidelines will improve sampling efficiency during monitoring effort in the Kootenai River and provide insight on sampling designs for other large western river systems where electrofishing is used to assess fish assemblages.