Managing receiving-water quality, ecosystem health and ecosystem service delivery is challenging in regions where extreme rainfall and runoff events occur episodically, confounding and often intensifying land-degradation impacts. We synthesize the approaches used in river, reservoir and coastal water management in the event-driven subtropics of Australia, and the scientific research underpinning them. Land-use change has placed the receiving waters of Moreton Bay, an internationally-significant coastal wetland, at risk of ecological degradation through increased nutrient and sediment loads. The event-driven climate exacerbates this issue, as the waterways and ultimately Moreton Bay receive large inputs of nutrients and sediment during events, well above those received throughout stable climatic periods. Research on the water quality and ecology of the region’s rivers and coastal waters has underpinned the development of a world-renowned monitoring program and, in combination with catchment-source tracing methods and modeling, has revealed the key mechanisms and management strategies by which receiving-water quality, ecosystem health and ecosystem services can be maintained and improved. These approaches provide a useful framework for management of water bodies in other regions driven by episodic events, or where novel stressors are involved (e.g., climate change, urbanization), to support sustained ecosystem service delivery and restoration of aquatic ecosystems.