This study examined the species composition of commercial fishery catches in the terminal system of Australia’s Murray River to evaluate their usefulness for understanding spatial and temporal variability of large-bodied fishes in response to restoration of flow and water levels following a period of drought. Over the period of the Millennium Drought (1998-2010) species structures differed in a large freshwater lake (Lake Alexandrina) with similarity between pre-, (1998-99 to 2001-02), and post-drought, (2010-11 to 2013-14), periods suggesting that recovery of these may have occurred in response to high freshwater discharge following the end of the drought. There was no evidence for such recovery in a smaller adjoining lake (Lake Albert) given variability in assemblage structures among years and differences between pre- and post-drought. During early- (2002-03 to 2005-06) and late- (2006-07 to 2010-11) drought, species structures were characterized by higher contributions from the exotic common carp and lower contributions from the native bony herring with the reverse occurring during pre- and post-drought. In estuarine habitat, trajectories of annual species compositions suggested that those from the post-drought period differed to those from prior to the drought in the Murray Estuary and South Lagoon but were broadly similar between these periods in the North Lagoon. These results updated a previous long-term study (1984/85 to 2008/09) which found that species with rapid growth and early maturation (opportunistic strategists), increasingly dominated catches while species with slow growth and late maturation (periodic strategists) declined. Updated data from the recent period of prolonged flooding indicated increasing contributions to catches from periodic strategists and declining contributions from opportunistic strategists.