We sampled the fish fauna of 9 small natural estuaries and 2 constructed estuarine lakes in Australia's dry tropics over 15 mo to detail the dynamics of fish assembly structures over time. The estuaries chosen were small enough that the cast net sampling method which we used could cover the full extent of the estuary, obviating the problem that within-estuary migration might lead to the false appearance of assemblage change over time. Temporal patterns in assemblage structure were consistent across the natural estuaries, overprinting complex spatial differences. Nursery ground utilisation and assemblage composition were intimately interlinked. In natural estuaries, assemblage change was a function of changes in both probability of encounter of individual species and in species compositions, and the recruitment, growth and subsequent emigration from the estuaries of juveniles was the main contributor to overall assemblage change. In contrast, in artificial lakes where connectivity with offshore sources of recruits was restricted, species compositions were attenuated and temporal change was not driven by the recruitment of offshore species.