Fish living in the Moonie River, must cope with a range of environmental stresses associated with the unpredictable and highly variable hydrological regime of this dryland river. To investigate spatial and temporal variability in fish condition in the Moonie River we examined tissue lipid and water content of two ecological generalists: bony bream (Nematalosa erebi) and yellow belly (Macquaria ambigua) on three occasions (February, May, September 2006) in disconnected waterholes following summer flooding in January 2006. We predicted that fish condition would be highest in February due to the feeding benefits provided by flooding and condition would diminish thereafter as waterholes dried and food resources became limiting. We also predicted fish condition would vary among waterholes due to site-specific differences in waterhole physical character. Preliminary analysis revealed that fish body condition results were dependent on fish size. Larger bodied yellowbelly and bony bream individuals (>80 mm S.L.) had the best (fattest) body condition in February and their condition worsened thereafter. The condition of small (<80 mm S.L) yellowbelly showed little variation over time, while small bony bream were fattest in May 2006. In general, fish condition was not related to waterhole physical character, however bony bream were fatter in waterholes with a weir structure compared to waterholes with no weir structure, while the opposite trend was apparent for yellowbelly.