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Abiotic conditions are important considerations in the species sorting process, which ultimately determines the distribution and abundance of species. Freshwater ecosystems will be impacted by ongoing temperature rise and other anthropogenically induced changes, such as nutrient enrichment and eutrophication. Changing characteristics of freshwater habitats will likely impact organisms in numerous ways, including through effects on colonization dynamics. Species are expected to colonize habitat patches where fitness will be the highest for themselves and their offspring, and how habitat selection interacts with changing environments remains an important question. We conducted a warming experiment to test the habitat selection preferences of aquatic beetles and hemipterans between habitat patches (mesocosms) of varying temperatures (via heaters), nutrient addition, and their interaction. Overall, insect abundance and richness were higher in unheated patches, with taxon-specific variation in response to heating. Although nutrients had limited effects on environmental conditions in mesocosms, their addition had no significant effects on insects. Insect assemblages had unique structures across heating treatments, with lower beta diversity and higher effective numbers of species in the warmest mesocosms. Our data support the importance of spatial variation in abiotic factors during the habitat selection process, and in determining species distributions and abundances as shallow lentic ecosystems are impacted by rising global temperatures.