Cotton is one of many agricultural industries in Australia heavily reliant on nitrogenous fertilizers and water storages to maintain high levels of production. Cotton-based farming systems are therefore labelled as potentially high-risk agricultural systems with respect to gases losses of nitrogen to the atmosphere. The on-farm study was undertaken at Dalby in the Darling Downs region of Queensland in north eastern Australia. The field was furrow irrigated and had been under continuous cotton (with winter bare fallow) for 10 years. An automated greenhouse gas measuring system (developed by Butterbach-Bahl et al.) was utilised that consisted of six chambers connected to sequential sampling unit, a gas chromatograph (equipped with both electron capture and flame ionization detectors for nitrous oxide and methane analysis respectively), and a Licor for carbon dioxide. The experiment also directly measured the specific losses of N2O and N2 from a single application of N fertiliser using 15N isotopically labelled urea. As there was little residual N in the profile after the previous crop, the grower applied 200 kg starter N in August 2006, and planted in late October, 2006. An application of 15N labelled urea (99% atom excess 15N) was made on 2 November in three (of the six) gas sampling chambers equivalent to 120 kg N/ha (treatment A), and 60 kg N/ha equivalent in the remaining three chambers (Treatment B). The grower applied 23 and 46 kg N as urea in the irrigation water, 98 and 135 days after the 15N urea was applied.