Predicting the impacts of climate change on aquatic ecosystems in the Subarctic is challenging due to the presence of permafrost and the wide range of geomorphologic conditions found across this heterogeneous landscape. To accurately predict how fish and wildlife will be impacted by climate change, it is critical to identify the habitat requirements of important prey such as macroinvertebrates. To better understand spatial heterogeneity in macroinvertebrate populations and identify key habitat requirements, we compared taxonomic richness, relative abundance, and density of macroinvertebrate populations in seven different lake basin types, spanning a large latitudinal and elevational gradient of subarctic Alaska. We used nonparametric statistics and NMDS to relate macroinvertebrate community metrics to landscape characteristics such as sedimentary deposit type, permafrost extent, geomorphology, and lake basin type, as well as chemical conditions within the lakes. Macroinvertebrate richness was highest in areas with continuous permafrost, largely driven by richness in dipterans. Lake water chemistry influenced taxa richness, relative abundance, and densities of both macroinvertebrates and microcrustaceans. Invertebrate densities were greatest in regions (parks) with higher nutrient concentrations and specific conductance, with higher relative abundance of dipterans in older landscape terrains (Yedoma) while a higher relative abundance of microcrustaceans was found in landscapes with little peat accumulation (sand dunes). As climate-driven permafrost thaw continues across the subarctic, shifts in pH, specific conductance, and calcium are likely to occur due to changes in active layer thickness and surface and groundwater flow paths that drive nutrient and solute delivery. Changes in invertebrate relative abundance and density are most likely to occur in ETOC and Diptera, two of the most ecologically important invertebrate groups found in subarctic lakes.