Irrigation of cotton while substantially increasing yields, presents several new problems to the industry. Perhaps the most immediate of these is deep drainage, which in turn poses water use efficiency and groundwater pollution problems. Excess root zone salinity and soil structural problems due to irrigation should also be issues of great concern. There are many factors that contribute to the development of these problems, the most crucial of which is the irrigation water quality and the soil properties. The expansion of cotton into areas such as the Darling Downs has seen the increasing use of higher conductivity, occasionally sodic groundwater for irrigation. With this trend set to continue, and with significant quality decline in surface waters predicted (MDBC Salinity Audit 1999), the need to investigate the extent of the problems this will cause is even more pressing.