Benthic invertebrate assemblages were studied across four streams in the Sahtu Settlement Region of the Northwest Territories between July 2010 and October 2011 to provide information on biotic composition and associations with habitat and temporal factors. Overall diversity was similar for all streams, although taxonomic composition varied among the streams. Within streams, richness was highest in riffle and snag (woody debris) habitats and lowest in pools and leafpacks. A substantial portion of taxa (∼25%) would have been missed if only riffles had been sampled. Nearly 88% of individuals belonged to eight taxa, with >60% of individuals found in only two families (Chironomidae and Baetidae). While high within-family diversity was observed, samples were also characterized by large numbers of rare taxa, with large temporal differences in abundances. Future benthic assessments in northern streams would benefit from increased sampling effort to ensure representative samples for comparing streams or sites and approaches that target dominant families in the north (e.g., Chironomidae), which can provide a great deal of information on biodiversity when examined at the generic level. Likewise, further analysis of the seasonal compositional turnover for some assemblages may be necessary to distinguish anthropogenic responses from natural variability.