To examine how food resource availability links with natural variation in primary productivity in the Moonie River, south-west Queensland, the diets of two native Australian fish species (Nematalosa erebi and Macquaria ambigua) were examined from fifteen waterholes in February, May and September 2006. N. erebi diets reflected strong ‘boom and bust’ patterns of food consumption, with high concentrations of benthic (non-filamentous) algae during boom (flow) times, moving to higher concentrations of filamentous algae and detritus during bust (no flow) periods. M. ambigua diets were primarily dominated by aquatic insects in all sampling periods. Although there was no clear ‘boom to bust’ pattern in relation to flow, M. ambigua secondary prey consumption revealed a compensatory switch between high energy prey (crustaceans) during more productive periods with terrestrial insects during less productive periods. The ability of both species of fish to switch from high to low concentrations of food quality under a variable environmental background allows them to persist through both high productive and low productive periods. This interaction between native biota and variable ‘boom’ and ‘bust’ conditions, and how changes to the natural hydrology will affect it is an important consideration of any future water resource development plans.