Subfossil chironomid head capsules have been used extensively as proxies to characterise past environmental conditions of waterbodies. To date, their potential to distinguish between temporary and permanent waterbodies has not been determined. This study set out to assess if subfossil chironomid head capsules could be used to distinguish between temporary and permanent floodplain wetlands from the Ovens River, south-eastern Australia. Twenty-six taxa were collected in both wetland types: one taxon (Paracladopelma spp.) was found exclusively in permanent wetlands; and five taxa (Cladopelma spp., Cryptochironomus spp., Microchironomus spp., Microtendipes spp. and Cricotopus spp.) were found exclusively in temporary wetlands. The overall concentrations of chironomid head capsules were greater in permanent than temporary wetlands. Furthermore, eight taxa were found in significantly higher concentrations in permanent than temporary wetlands but, apart from the unique taxa, the concentrations of no other taxa were significantly greater in the temporary than permanent wetlands. The temporary and permanent wetlands had distinct chironomid assemblages, as evidenced by the abundance and presence/absence data. This study highlights the importance of heterogeneity in the environment to maintain chironomid diversity and suggests that chironomid subfossils have the potential to be useful in palaeoecological studies aiming to reconstruct past changes in hydrology.