The Great Barrier Reef is under threat from diffuse agricultural pollutants and potential climate change. Nitrogen loads are examined using the nitrogen surplus of simulated sugarcane production systems in the Tully–Murray catchment, comparing current management practice regimes with best management practice regimes under present day and future climate scenarios – nominally 2030 and 2070. These future scenarios are represented by increased carbon dioxide, increased temperature and increased rainfall variability. Simulation results suggest that the impact of potential climate change on diffuse agricultural nitrogen loads from sugarcane production in the Tully–Murray catchment to the Great Barrier Reef is likely to be small and negligible in comparison to the impacts of management practice change. Partial gross margin analysis suggests climate change will not noticeably alter the profitability of sugarcane production and, hence, is unlikely to be a driver of change for this land use in the Tully–Murray catchment. Improvements in water quality from sugarcane production are more likely to come from identification and adoption of best management practices.