A major cyanobacterial bloom in the Curdies River estuary in early 2022 raised considerable concern in the local community about the health of the river’s catchment. The Curdies River runs through one of Australia’s most productive dairy regions and little of the original native forest remains. Concerns that elevated levels of nutrients in the river might lead to such blooms have been expressed for many years and have been the subject of previous investigations and action plans. Using long-term water quality data, we investigated how patterns of phosphorous and nitrogen enrichment have been altered over the last 30 years. Whilst we found some evidence that management strategies and changed water treatment practices has reduced total phosphorous concentrations under low-flow conditions, concentrations were unaltered under high-flow conditions, and total nitrogen concentrations in high-flow conditions were increasing. Worryingly, levels of both substantially exceed Victorian Government environmental objectives regularly. In contrast to an environmental risk assessment conducted in 2005, we found that high concentrations of both phosphorous and nitrogen were associated with high levels of turbidity, suggesting that erosion of sediments with high levels of nutrients as a result of historic and current land-use practices are the likely major source of nutrients in this system. This pattern appears to have previously been masked by point-sources. Our results underscore the challenges faced in improving the health of Australian freshwater and brackish systems, especially in the light of ongoing climatic changes which are likely to exacerbate the risks of adverse events, such as cyanobacterial blooms, in these systems.