Variation in the intensity of predation across the well-known environmental gradient of freshwater habitats from small, ephemeral ponds to large, permanent lakes is a key factor in the development and maintenance of aquatic community structure. Here, we present data on the distribution and abundance of four species of Chaoborus (Diptera: Chaoboridae) across this environmental gradient. Chaoborus show a distinct pattern of species sorting when aquatic systems are divided into fish and fishless environments, and this pattern is consistent with species traits known to influence their vulnerability to fish predation (i.e., pigmentation, diel vertical migration [DVM] behavior, and body size). To test whether fish are the drivers of this pattern, we created a gradient in fish density by stocking bluegill sunfish (Lepomis macrochirus) into 15 experimental ponds in southwestern Michigan, USA, and then allowed Chaoborus species to colonize. There was clear evidence of species sorting along the predation gradient; Chaoborus americanus was most abundant in the fishless ponds, C. flavicans was neutral in response to fish, and C. punctipennis and C. albatus were most abundant at high fish biomass, a response consistent with their field pattern. Furthermore, prey preference experiments confirm that size selective predation and differences in Chaoborus species traits contribute to the pattern of Chaoborus abundance and distribution.