The diversity and distribution of aquatic benthic invertebrate communities of 17 lakes and 3 shallow ponds near Iqaluit and Rankin Inlet, Nunavut, Canada, were examined to assess patterns with respect to environmental gradients. Macroinvertebrates were collected using 500 µm mesh D-nets, and collected specimens were identified and enumerated; a total of 40 taxa were identified. Multivariate analyses (Redundancy Analysis) of relative abundance (%) data identified habitat (dominant substrate type), water chemistry, nutrients, and food/productivity (total phosphorus, total nitrogen, sulfate, dissolved oxygen, chlorophyll a), physical characteristics (maximum depth), catchment-related properties (lake elevation), and climate-related properties as significant environmental gradients influencing community composition. Ecosystem-scale lake characteristics had the greatest influence on benthic communities, followed by substrate type; however, there were substantive amounts of community variation influenced by the interaction between lake characteristics, substrate type, and regional differences. A number of environmental variables may have been significant due to differences in their values when comparing Rankin Inlet region sites versus Iqaluit region sites. The results agree with other studies indicating that benthic invertebrate communities are influenced by environmental gradients acting at different scales ranging from local, within-lake scales to large, regional scales.