Reducing pollutants, such as nitrogen and sediment from sugarcane lands, in the Great Barrier Reef catchment is important for protecting the resilience of the World Heritage listed ecosystem. Modelling is used to predict the change in water quality in response to typical changes in sugarcane management. To accomplish this, workshops were conducted with groups of 15 to 20 industry experts in each of the major sugarcane growing regions and a range of typical agronomic management, appropriate for each region, was elicited. APSIM was used to simulate a farm in each of the three regions Burdekin Delta, Mackay, and Tully, to estimate the expected pollutant loads from each farm. Each in silico farm is represented by a combination of soil, climate and the range of management derived from the workshops. Simulated pollutants include erosion and dissolved inorganic nitrogen (DIN), from both leaching below the root zone and in runoff. To quantify and rank the effect of changes in management on pollutants exiting farms least squared regressions were estimated using model output. Results are presented for the key management of nutrient and irrigation rates, tillage, and fallow crop scenarios. We found the rate of applied mill mud had the greatest effect on DIN exiting sugarcane paddocks both via leaching and in runoff (Figure 1) and the amount of tillage had the greatest effect on erosion (Figure 2).