The cultural and ecological importance of fork-tailed catfish, Neoarius graeffei, in northern Australia is linked to its energy stores, or how fat fish are. Water resource development that alters river flow has the potential to impact the energy stores of fork-tailed catfish. We investigated the influence of flow and habitat on the energy reserves of fork-tailed catfish during the dry season in an intermittent wet–dry tropical river using data collected in three years with different flow volumes from a variety of habitats, i.e. different mesohabitats (tributary, main-channel) and pool sizes. Julian day was included to describe seasonal trends. We used mesohabitat and pool size to reveal where fork-tailed catfish had the most energy reserves and flow-year and Julian day to reveal when reserves were greatest. Body condition and the quantity of intramuscular and coelomic fat were used to describe energy reserves. Predictive models created for each metric revealed that fork-tailed catfish body condition and intramuscular fat were greater in years following moderate to high wet-season flow, smallest in a year following very low flows and decreased as the dry season progressed. Coelomic and intramuscular fat of fork-tailed catfish was also lower in smaller pools. There was no association between mesohabitat and energy store. These when and where hydro-ecological patterns highlight the importance of wet season flows and groundwater-fed refuge pools for fork-tailed catfish energetics in this wet–dry tropical river. Intermittent rivers flowing through wet–dry tropical savanna habitats are under increasing threat globally and the results of the present study illustrate how flow variation may impact on biota and influence their continued survival and functional roles.