The vast Great Barrier Reef catchment area (GBRCA), spanning over 420,000 km², is notable for its diverse, nationally significant freshwater wetlands, many of which connect to the Great Barrier Reef World Heritage ecosystem. Monitoring these natural wetlands, under the government objective that their condition will improve, is undertaken by Queensland’s GBRCA Wetland Condition Monitoring Program, one of the most comprehensive, ongoing wetland monitoring programs in Australia. We outline how the Program design has engaged landholders and met challenges, such as the large spatial scale it covers to monitor ~240 randomly sampled and spatially balanced selection of wetlands on lands subject to a range of uses from mining, to cropping, grazing and conservation. The growing dataset has enabled us to report on condition since 2016 and the incorporation of new analytical methods will facilitate reporting on trend in coming years. Key outcomes of the Program include the release of biennial report cards, a flexible design enabling phased expansions from the GBRCA-wide scale program to incorporation of regional scale data and reporting and the ongoing participation of a wide range of landholders. By highlighting the challenges, solutions and results of the Program, we hope others engaged in or developing monitoring programs requiring complex designs will benefit from our experience.