Global climate shifts are likely to increase the frequency and severity of drought events in semi-arid and arid regions. These extreme hydrological events act to significantly shift the functional groups present in a given ecosystem. Abundances of many aquatic fauna have significantly declined, some near the point of extinction, as a result of extended drought. For fish, it is assumed that drought favours tolerant generalist species over more specialist species but questions remain as to the mechanisms of persistence and timescales over which these changes occur. Despite flooding that broke the Millennium Drought in 2010/11 in the Lower Lakes, South Australia, the once-abundant and diverse assemblage of native small-bodied fish had not recovered in recent years. We compared the post-drought littoral fish assemblages in the two lakes, which differ in hydrology and habitat availability. Catch per unit effort from fyke nets showed that common small-bodied fish were more abundant in Lake Albert than Lake Alexandrina. For all years sampled, Lake Albert showed a higher catch per breeding season than Lake Alexandrina. The total small-bodied fish catch per site for both lakes showed a negative trend through time although the ratio of alien to native fish also decreased through time. This trend in ratio was reversed in recent sampling, largely driven by an increase in the number of juvenile and small redfin perch (Perca fluviatilis). There were differences in the species present, their abundances and the functional groups between lakes. This study documents an ongoing decline in native small-bodied fish assemblages despite the end of drought conditions and indicates that management for alien fish species may be required before recovery of that assemblage is likely.