To understand how environmental change will modify community assembly and the distribution of organisms it is valuable to understand mechanisms that drive the occurrence of organisms across the landscape. Salinisation of agricultural land in southwest Western Australia, as a result of land clearing, is a widespread environmental change, which threatens numerous taxa, but provides an opportunity to elucidate such mechanisms. Although salinisation affects terrestrial fauna and flora, the greatest impacts are seen in wetlands and waterways. Many aquatic insect taxa colonise ephemeral water bodies directly as adults or by oviposition. Few empirical studies, however, evaluate the influence of abiotic factors, such as water body salinity, on the colonisation behaviour of aquatic fauna. We conducted a manipulative experiment using mesocosms to test whether colonising insect fauna select aquatic habitats based upon salinity. We found that halosensitive fauna selected less saline mesocosms for oviposition and colonisation, demonstrating that behaviour can influence the distribution of aquatic organisms. Additionally, we utilised field surveys of insects from ephemeral water bodies across a broad region of southwest Western Australia to determine if mesocosm results reflected field observation. The abundance of the same insect taxa and taxonomic groups in the field were highly variable and, with the exceptions of Culex australicus Dobrotworksy and Drummond and Anopheles annulipes Giles (Diptera: Culicidae), did not show similar patterns of distribution to those observed in the mesocosm experiment. Both mesocosm and field assemblages exhibited similar and significant trajectories associated with the salinity gradient, even though there were differences in assemblage structure between the two. Our findings give empirical support to the importance of behaviour in the spatial distribution and assembly of some aquatic insects.