The cotton plant derived a large proportion of N nutrition from the soil organic pool (up to 70%) which is composed of N sourced from previous fertiliser application and the soil N pool that has built up over the millennia. The soil base is developing an equilibrium with the current land use. Over the last century for Australian agriculture has benefited from some soil chemical and physical properties inherited from the pre European condition. The size of the soil organic N pool is declining with the decline in soil organic carbon stocks, which means that in the future a greater rates on N fertiliser will need to be used to maintain agricultural yields. During the season 143 kg N ha-1 was lost, via atmospheric losses, run-off and deep drainage; and by far the largest losses were N2 from the soil surface. Nitrogen present in the run-off water equated ~8% of the applied fertiliser and this could be transformed into indirect N2O-N. The IPCC estimates of flux overestimate indirect emissions by a factor of at least 3.7. Applications of IPCC methodology to estimate indirect N2O emissions are unlikely to be accurate. A better understanding of the processes controlling N2O production, and attempts to reconcile top-down and bottom-up estimates are necessary if we are to develop better estimate and mitigate indirect N2O emissions.