Freshwater wetlands of the Moreton Bay Region and Bay islands are prominent landscape features of high biodiversity performing essential ecological functions and providing ecosystem services. This paper reviews the types, extent, biodiversity and ecology of freshwater wetlands in the region, and documents the main threats to wetland ecosystems. These wetlands are protected and managed under Queensland and federal legislation, international obligations and a range of laws, policies and programs administered by government agencies. Important initiatives include the Queensland Wetlands Program, the Healthy Waterways and Catchments and Resilient Rivers alliance, and Queensland’s water management plans. The ongoing challenge for those managing the Moreton Bay Region and Bay islands is to appreciate the importance of freshwater wetlands as essential landscape components and sources of valuable ecosystem services, and to recognise how human activities threaten their biodiversity, integrity and future in spite of rigorous monitoring, dedicated management programs and conservation initiatives. Recommendations to ensure the future of freshwater wetlands in the Moreton Bay region and Bay islands include: (i) sustaining and enhancing wetland biodiversity, functions and ecosystem services in the context of expanding human populations, growing demands for water and infrastructure, and likely threats associated with climate change; (ii) increasing support for research, monitoring, communication and management of freshwater wetlands on the mainland and Bay islands; and (iii) maintaining a well-coordinated holistic approach to integrated land, water and wetland management based on sound multidisciplinary science, societal values and expectations, and partnership arrangements (such as the Healthy Waterways and Catchments and Resilient Rivers Alliance).