The regulation of freshwater flow into estuaries has been identified as a potential threat to estuarine ecosystem structure and function, and the productivity of fisheries in particular. Correlative studies are one means by which associations between freshwater inputs and commercial landings have been identified. The study compared monthly landings of five species of finfish and two species of crustacean with monthly and 6-month running means of river discharge, climatic variables (temperature and rainfall) and the area of vegetated habitat (saltmarsh, mangrove and seagrass) for 11 temperate estuaries on the NSW coast. The monthly climatic and discharge record covered a 10-year period (1997-2007). High river discharge and rainfall were associated with higher catches of flathead (Platycephalus spp.) and Mullet (Mugil spp.), a result consistent with subtropical estuaries to the north. We found no relationships between landings and river discharge for any of the other species, which included school prawns (Metapenaeus macleayi). Temporal variability at a monthly time-step was more consistently associated with variation in temperature, reflecting seasonal variation in activity, and possibly fishing effort. Landings of several species showed strong habitat relationships, with greater seagrass area consistently associated with higher catches of blue swimmer crab (Portunis pelagicus), and intertidal wetlands (mangrove and saltmarsh) with mud crab (Scylla serrata), school prawns, flathead, and mullet (Mugil spp.), a result consistent with habitat-scale surveys. The results draw into question the efficacy of dam releases as stimulants of fisheries productivity in the region, although the effects of flow on juvenile populations and catadromous species were not studied.