Estuarine fauna, flora and structure are subjected to extremely unstable environments caused by the physical and chemical changes that occur when freshwater flows enter estuaries. Within Australia, the development of water plans pertaining to river catchments have recently included the need to monitor the “health” of estuaries. In Queensland, one of the indicators suggested to monitor estuarine health within water plans was estuarine fisheries production. Fisheries production is often the only long term measure of the economic benefit of estuaries while also reflecting the environmental state of the estuary. Using a logical decision making framework to determine the appropriate temporal and spatial scales, we have shown that fisheries production and freshwater flows are highly correlated in time and space. Various measures of estuarine fisheries production were investigated, with decadal catch data, yearly recruitment indices, monthly growth rates and short term movement all being significantly and positively influenced by freshwater flow entering the estuary. We suggest that freshwater flows bring long and short term benefits to estuarine fisheries through enhanced biological productivity.