Substantial emissions of nitrous oxide have been reported for sugarcane production systems in Australia. Estimates have ranged from the equivalent of 3 to 21% of nitrogen fertiliser applications, and the reason for this range is not clear. The highest emissions have been measured from acid sulphate soils, and chemical, rather than biological pathways have been suggested as important sources of nitrous oxide in these soils. However, other studies on acid sulphate soils have measured emissions closer to those from soils with more neutral pH. We used the APSIM farming systems model to investigate the degree to which the biological nitrous oxide-generating pathways represented in the model might account for, (1) the high emissions measured in some sugarcane crops grown on acid sulphate soils, and hence (2) provide a broader understanding of the basis for the wide range of nitrous oxide emissions associated with this important crop. The model, which is well-tested in sugarcane production systems, predicts denitrification and nitrification, and nitrous oxide emissions from these processes. As in many other models, the nitrogen cycling processes and nitrous oxide emissions are responsive to soil nitrate, ammonium, carbon, water contents and/or soil pH. We found a combination of high water contents (due to shallow water tables) and high soil carbon (~9%), similar to conditions at the site where the highest emissions were measured, were predicted to give similarly high emissions. Where average soil water and/or carbon contents were lower, predicted emissions were similar to those measured in other studies. Our results suggest that the biological nitrous oxide-generating pathways represented in the model are capable of producing the range of nitrous oxide emissions measured in sugarcane production systems, and that the contribution of chemical pathways need not be great. The results have important implications for understanding how nitrous oxide emissions from sugarcane may be mitigated.