Water extraction from rivers for development of irrigated agriculture is occurring from Cape York to the Kimberley. The challenge is to avoid the mistakes of the past and ensure that there is hydrological regime is still suitable for sustaining the downstream habitats, including estuaries and coasts. Our study examined the importance of catchment nutrient loads in fuelling estuarine and coastal productivity in estuaries in the southern Gulf of Carpentaria and the Northern Territory, to provide information on the likely impacts of water extraction. We measured primary productivity on intertidal flats and determined whether catchment nutrients stimulated productivity. These mudflats are an important feeding area for a range of fish and fisheries species, as well as migratory shorebirds. Our study found that all studied estuaries were nitrogen limited, such that a reduction in catchment nitrogen loads is likely to impact productivity in the longer term. This combined with the highly variable interannual flow regimes, and associated nutrient loads in many of these rivers means that there are significant risks from water extraction, particularly in low-flow years.