Dramatic environmental change is expected in the Arctic, yet little is known about the occurrence and community composition of microcrustaceans in Arctic lakes and how this will be influenced by future environmental change. We sampled and calculated relative abundances of microcrustacean species in 54 lakes on Ellesmere Island, Canada. New species records on Ellesmere Island included Daphnia umbra, Tachidius discipes, and Artemeopsis stefanssoni. Daphnia middendorffiana/tenebrosa was the most common taxon and often dominated microcrustacean assemblages, likely a result of its pigmentation, which offers resistance to ultraviolet radiation. Species richness was positively associated with nutrients, dissolved organic carbon (DOC), temperature, calcium, and conductivity and negatively affected by elevation. In contrast to most findings in temperate systems, we detected a negative relationship between species richness and surface area. Community composition was influenced by DOC, nutrients, and elevation but was also related to spatial variables, suggesting that spatial gradients in environmental conditions and dispersal are important drivers of differences among sites. Arctic ecosystems are expected to change rapidly in the coming years because of climate change and ozone thinning, and we expect that associated changes in DOC, temperature, and nutrients will affect microcrustacean species richness and distribution throughout the landscape.