A strong driver of water quality change in the Great Barrier Reef (GBR) is the pulsed or intermittent nature of terrestrial inputs into the GBR lagoon, including delivery of increased loads of sediments, nutrients, and toxicants via flood river plumes (hereafter river plumes) during the wet season. Cumulative pressures from extreme weather with a high frequency of large scale flooding in recent years has been linked to the large scale reported decline in the health of inshore seagrass systems and coral reefs in the central areas of the GBR, with concerns for the recovery potential of these impacted ecosystems. Management authorities currently rely on remotely-sensed (RS) and in situ data for water quality monitoring to guide their assessment of water quality conditions in the GBR. The use of remotely-sensed satellite products provides a quantitative and accessible tool for scientists and managers. These products, coupled with in situ data, and more recently modelled data, are valuable for quantifying the influence of river plumes on seagrass and coral reef habitat in the GBR. This article reviews recent remote sensing techniques developed to monitor river plumes and water quality in the GBR. We also discuss emerging research that integrates hydrodynamic models with remote sensing and in situ OPEN ACCESS Remote Sens. 2015, 7 12910 data, enabling us to explore impacts of different catchment management strategies on GBR water quality.