Native freshwater fish populations in many parts of southern and eastern Australia have undergone extensive declines since European settlement, and there is now considerable investment in trying to reverse this trend. A major focus for these efforts, both in terms of scientific research and management actions, has been directed towards addressing the impacts of habitat loss and flow alteration on opportunities for spawning, recruitment, and availability of, and access to, the necessary habitats for fishes to complete their life-cycle. Meanwhile, much less attention has been given to the impacts of altered flooding regimes on the production and carrying capacity of aquatic biota. Here we ask whether populations of high-trophic order native fish in regulated lowland rivers such as the Murray are presently limited by energy availability, either due to altered rates of production or altered energy flows, for example due to competition from introduced species. We assembled information on historical and contemporary native fish abundance and historic and present day estimates of basal energy production, and combined these data using simple food-web models. Our initial results suggest contemporary levels of riverine production are insufficient to support historical biomass estimates, and hence pose severe constraints on the outcomes that might be expected from traditional approaches to rehabilitating native fish populations. We discuss the implications of these results in terms of environmental flow management, and also discuss future research needs.