Wetland ecosystems around the world are being degraded by many anthropogenic pressures, leading to significant changes in water quality, such as increased salinity, which in turn have severe implications upon biotic communities. Lakes Alexandrina and Albert are shallow fresh waterbodies situated at the terminus of the Murray-Darling Basin and, along with the Coorong, form a Ramsar Wetland of International Importance but water regulation and extraction have seen freshwater flows into the Lakes significantly reduced. Under recent severe drought conditions, water quality further altered within the lakes, so investigating the ecological response to such changes is vital for appropriate management of this wetland. Habitat models are a useful tool for this purpose. Using five years of macroinvertebrate and environmental monitoring data from eight lakeshore sites, we investigated which environmental variables are important in influencing macroinvertebrate assemblages in the Lakes by developing habitat models using nonparametric multiplicative regression within the software Hyperniche. Macroinvertebrate data included 79 families dominated by microcrustaceans, dipteran larvae, and amphipods. Models were developed for all families but only nine taxa produced robust models. The nine taxa included crustaceans, gastropods, dipterans, ephemeropterans and oligochaetes. Physico-chemical variables, including water quality and sediment grain-sizes, were more frequently predictors of the modelled macroinvertebrate distributions than macrophyte genera. The results of the study provide important information to managers regarding how macroinvertebrate assemblages respond to environmental conditions, which can then be used to inform the allocation of environmental water.