Cotton is one of many agricultural industries 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, nitrate leaching which contribute to environmental pollution. The inefficient use of fertiliser applied nitrogen also reduces profitability. Irrigated cotton grown on alkaline grey clay soils often use nitrogen fertilizer inefficiently, due largely to nitrogen loss (commonly 50 - 100 kg N ha-1) through denitrification. These and the heavier black clays (Vertosols) are the dominant soils in the cotton growing region of Australia and with their high water holding capacity are ideal environments for denitrification and associated losses of nitrous oxide (N2O) and N2. The nitrogen gases emitted also include ammonia, but it is N2O, a potent greenhouse gas with a Global Warming Potential (GWP) approximately 300 times that of carbon dioxide (CO2), which has fuelled debate. Field measurements using a portable automated gas analysis system were carried out on a typical furrow irrigated cotton farm near Dalby on Queenslands Darling Downs over the 2005/06 season. The impact of water run applications of fertiliser N on emissions were examined with half (three) the chambers placed within the irrigation furrow and the remaining three (with 50 cm extentions) placed over growing plants in the row .