Estuaries are particularly susceptible to climate change and drought resulting in atypical changes to freshwater flows. How such changes in flow impact on the ecology of estuarine fishes may depend on how a species moves in response to changing flow conditions. Acoustic telemetry was used to interpret fine-scale movements of two co-inhabiting estuarine fish species, black bream, Acanthopagrus butcheri and estuary perch, Macquaria colonorum in relation to freshwater flows, season and moon phase. We found black bream to be highly mobile, regularly travelling the length of the estuary and into the neighbouring estuaries. In contrast, estuary perch had particular home ranges and made occasional, upstream or downstream movements. Possibly influenced by freshwater flows, estuary perch moved at greater rates in the Tambo compared to fish in the Mitchell. Black bream resided in the upper estuary during winter and spring and the lower estuary during summer and autumn, whereas estuary perch remained in the upper estuary throughout the year, with occasional downstream movements in winter and spring. This study revealed 1) significantly large increases in freshwater flows result in mass downstream movements in both species, 2) fish moved upstream during full moons and 3) there are contrasting spatio-temporal patterns in movement between species. The results from this study highlight that estuarine fishes are likely to show differential sensitivity to the impacts of drought and climate change and illustrate how acoustic telemetry methods can be used to determine the environmental needs of fishes and help efforts to conserve and manage estuaries worldwide.