Sugarcane is the dominant crop in the coastal regions of north eastern Australia. This is also an environmentally sensitive region as catchments drain into world heritage-listed aquatic and marine ecosystems of the Great Barrier Reef. Farmers in these regions are having to adopt farming systems that reduce losses of chemicals from farms, to reduce the environmental impact on these ecosystems. In the face of these pressures, the question arises whether climate change may influence the effectiveness of both production and water quality improvements. To address this question we used the APSIM farming-systems model to investigate the complex interactions between soil type, sub-regional climatology, climate change projections and management. We represented management practices such as tillage (including controlled traffic), fallow management and nitrogen (N) inputs in the study as these are part of the farming systems being promoted in the region to improve water quality. Three GCM/IPCC story lines were chosen to represent a range of potential future climates for 2030. In all of these, rainfall decreased and temperature increased relative to the historical climate. The study predicted that sugarcane yields increase with ‘mild’ climate change, but reduce under more severe change relative to current production. Also, the improvement in farm management needed to meet water quality improvement goals will not be greatly affected by climate change. However, without any interventions, the frequency of years with very high N losses, and hence extreme ecological risk, was predicted to increase by up to 10-15%. Compared with traditional practices, improved management practices were predicted to reduce N losses by up to 66% during these years. The results are substantially influenced by assumptions about the effects of elevated atmospheric CO2 concentration on plant assimilation rates and the characterisation of extreme climate events, with both issues deserving further study.