Globally, many coastal ecosystems are threatened by a decline in water quality from land-based runoff. However, dynamic and complex biophysical and socioeconomic interdependencies often hamper the reversal of this decline in water quality. This Special Issue illustrates an integrated approach to address deteriorating water quality from land-based runoff in the Tully basin to the Great Barrier Reef (GBR), Australia. Nitrate was identified as the key pollutant, and was mainly derived from sugarcane and banana farms. To achieve GBR water quality targets for chlorophyll a, the dissolved inorganic nitrogen (DIN) load needs to be reduced by at least 80%. Modelling shows that financially beneficial changes to management of sugarcane results in a 50% reduction in DIN load. However, larger reductions would come at a significant cost. An adaptive approach is proposed as a framework to assess (i) the efficacy of implementing the recommended management practices, and (ii) progress against set targets. Quantification of linkages between catchment management and coastal ecosystem health will help inform management strategies based on ecosystem performance measures. Verification of the efficacy of existing and exploration of innovative management strategies, as well as spatial and temporal prioritisation of their implementation, remain critical to achieve coastal ecosystem rehabilitation, including water quality improvement.