Worldwide, the incidence of soil and water salinisation is increasing. This is particularly the case in irrigated agricultural regions and potentially in Australia’s intensively irrigated cotton-growing areas. This paper describes a broad scale approach to estimate this threat in the cotton growing areas of the lower Gwydir and Macintyre valleys using baseline soil and water information and a steady-state soil and water balance model. Results suggest with the current water quality and soil types, irrigated cotton production appears to be sustainable. Using the geostatistical method of indicator kriging and several ‘worst case’ scenarios in the model, areas that are at risk if saline water is used for irrigated agriculture are identified.