In Australia, the average temperature and frequency of drought events are predicted to increase due to human-induced climate change. This is likely to have impacts on freshwater ecosystems by altering hydrologic regimes, water chemistry and reducing available habitat. This will affect water availability and so potentially change assemblage structures of aquatic macroinvertebrates. Under these scenarios, aquatic macroinvertebrates are likely to rely on permanent waterbodies as a source of refuge during extended periods of drought. Ecological research associated with the importance of refugia from drought have tended to focus on natural lakes and wetlands rather than anthropogenic waterbodies. Therefore, we compared macroinvertebrate assemblages from potable and waste water storages with those from nearby natural waterbodies using both kick samples and rock scrubs. We also examined relationships between macroinvertebrate assemblages with macrophyte diversity, water quality parameters and habitat characteristics recorded at each location. These results illustrate the degree to which macroinvertebrate assemblages from anthropogenic water storages are representative of those in adjacent natural ecosystems, and hence, whether the water storages have the potential to provide possible refuge for macroinvertebrates during drought periods. The findings of this study will be shared with local water managers and will therefore improve the management of similar anthropogenic water bodies to enhance the conservation of aquatic biodiversity in the region.