Because coral reefs are sensitive to land derived inputs of nutrient and sediment, there is concern worldwide for the effects of anthropogenic change in river catchments on reefs. Thirty-one river catchments drain directly into the waters of the Great Barrier Reef, NE Australia. This case study was undertaken on the floodplain of the Herbert River catchment in north Queensland, utilizing remote sensing and GIS to assess both spatial and temporal changes in freshwater wetlands and riparian forests. We demonstrate that there has been a very large reduction in the area of these ecosystems since European settlement in the mid nineteenth century, with an 80% decline in their extent since 1943. We provide a range of quantitative measures to show that the landscape diversity of these ecosystems has also declined. These changes are of importance in terms of regional, national and international trends. We argue that policy, planning and management reform is required if the remaining ecological, economic and social values of these systems and the adjacent Great Barrier Reef Marine Park are to be maintained.