How environmental conditions influence current distributions of organisms at the local scale in sensitive High Arctic freshwaters is essential to understand in order to better comprehend the cascading consequences of the ongoing climate change. This knowledge is also important background data for paleolimnological assessments of long-Term limnoecological changes and in describing the range of environmental variability. We sampled five limnologically different freshwater sites from the Fuglebergsletta marine terrace in Hornsund, southern Svalbard, for aquatic invertebrates. Invertebrate communities were tested against non-climatic environmental drivers as limnological and catchment variables. A clear separation in the communities between the sites was observed. The largest and deepest lake was characterized by a diverse Chironomidae community but Cladocera were absent. In a pond with marine influence, crustaceans, such as Ostracoda, Amphipoda, and calanoid Copepoda were the most abundant invertebrates. Two nutrient-rich ponds were dominated by a chironomid, Orthocladius consobrinus, whereas themost eutrophic pond was dominated by the cladoceran Daphnia pulex, suggesting decreasing diversity along with the trophic status. Overall, nutrient related variables appeared to have an important influence on the invertebrate community composition and diversity, the trophic state of the sites being linked with their exposure to geese guano. Other segregating variables included water color, presence/absence of fish, abundance of aquatic vegetation and lake depth. These results suggest that since most of these variables are climate-driven at a larger scale, the impacts of the ongoing climate change will have cumulative effects on aquatic ecosystems.