The health of South East Queensland’s waterways has been monitored for over 22 years through the Ecosystem Health Monitoring Program (EHMP) and communicated annually via a Report Card. A major component is estuarine-marine water quality monitoring across 18 estuaries and Moreton Bay. In 2015 new indicators representing seagrass and benthic habitat quality were added to the program. A recent analysis of long-term patterns in water quality found that it had improved in many parts over two decades. Similarly, seagrass extent was found to improve, expanding across parts of Western Bay regions, typically subjected to poor water quality. In contrast, trends in benthic habitat quality, as indicated by the mud-content of bottom sediments show a system undergoing rapid change, with the broader ecological consequences of these changes remaining largely unclear. This highlights the importance of integrating multiple indicators, that reflect whole of ecosystem components and component processes, to support a richer understanding of ecosystem trends. This is enabled by continued research and implementation of novel monitoring approaches. Ensuring the diversity of environmental and cultural values of the region's waterways are reflected in monitoring programs also remains critical.