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Estuaries are under threat from changes in freshwater flows resulting from anthropogenic impacts and climate change, with unknown consequences for estuarine biota. In the past decade, significant rain deficits in south-eastern Australia have coincided with a decrease in commercial catches of black bream Acanthopagrus butcheri, an important commercial and recreational fish species that spawn in estuaries. We investigated the temporal and spatial distribution of black bream eggs and larvae, and copepods—preferred larval prey—in relation to the hydrology of the Mitchell River, a drought-stricken tributary of Australia’s largest estuarine lagoon system. We collected eggs, larvae, zooplankton and water quality data at multiple depths from 8 sampling sites over 7 fieldtrips from August to December 2008. The hydrology of the Mitchell River during this study was highly complex and influenced by freshwater flow …