This thesis provides significant insight into the effect of seasonal patterns of flooding on estuarine function in the wet-dry tropics by exploring the impact of seasonal freshwater flow on benthic biota in the wet-dry tropical Norman River estuary of northern Australia. This thesis also describes the construction of a model designed to predict the potential impact of freshwater flow regulation on key estuarine biota. Flow regimes in the wet-dry tropics are characterised by seasonal patterns of summer wet season floods and low or no freshwater flow for the rest of the year. Few studies exist on wet-dry tropical estuaries, and none have sampled the estuary before, during and after wet season floods of different magnitude. Research within this thesis has increased the understanding of estuarine function in the wet-dry tropics, and the short and long term impacts of the magnitude of wet season flooding on benthic biota (meiofauna and microphytobenthos) was identified. These findings were combined with information on commercially important banana prawns (Penaeus merguiensis) in the Norman River estuary to construct a Bayesian Network (BN) model. The model explored the drivers of change in the Norman River estuary under currently natural patterns of flow, and the likely impact of future water resource development on banana prawns and their key food source, meiofauna and MPB (microphytobenthos).