Energy is a fundamental currency in food web ecology, needed for metabolic maintenance, growth, and reproduction. Prey energy content and nutritional value, rather than purely abundance, is important for determining food web functioning in coastal ecosystems vulnerable to drought or flood extremes. The Coorong estuary and hypersaline lagoon at the terminus of the Murray-Darling River system is exposed to altered flow regimes due to river regulation, water extraction, and climate change. We analysed spatial and temporal patterns in energy (kJ/g biomass) and energy density (kJ/m2) of benthic macroinvertebrates and fishes in the estuary and lagoon. Calorific values varied little between the estuary and lagoon regions. Energy density, however, decreased significantly between the estuary and lagoon for macroinvertebrates, following a salinity driven decrease in biomass. Apart from salt-tolerant small-mouth hardyheads dominant in the hypersaline lagoon, energy densities of fishes were also higher in the estuary. The region of highest energy densities contracted during low flow periods and expanded under higher flows. The spatial and temporal patterns of energy density in relation to flow enhanced our understanding of trophic dynamics in southern temperate estuaries exposed to climatic extremes, which can inform food web models to predict ecosystem responses under future change scenarios.