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Comparative research on the effects of soil and crop management practices in cotton farming systems on the quality of drainage water in irrigated Vertisols has not been reported in the literature. The objective of this study was to quantify drainage water quality in the subsoil (0.6, 0.9, 1.2m) of sodic and non-sodic Vertisols under selected crop rotations, viz. continuous cotton (Gossypium hirsutum L.), cottondolichos (Lablab purpureus L.) and cottonwheat (Triticum aestivum L.). The experimental sites were located at the Australian Cotton Research Institute (ACRI) near Narrabri and on two commercial cotton farms near Wee Waa and Merah North in northern New South Wales, Australia. A cottonwheat rotation was sown at Wee Waa and ACRI; wheat stubble was incorporated in the former and retained as in situ mulch in the latter. At Merah North, there were three cropping sequences; viz. continuous cotton, cottonwheat, and cottondolichos sown between 1993 and 2000 in adjacent plots with identical land management histories. The three treatments were sown with cotton during the 20002001 and 20022003 growing seasons, wheat during the 2001 winter and sorghum during the 20012002 growing season with stubble being incorporated. Drainage water was sampled with 50-mm diameter ceramic-cup samplers from depths of 0.6, 0.9 and 1.2m in six sites in each plot and irrigation water from the head ditch after irrigation between mid October and late February during the cotton-growing seasons of 2000-2001 and 20022003. Soil water extracted from the ceramic-cup samplers was analysed for pHw, ECw, Cl-, NO3--N, K+, Ca2+, Mg2+ and Na+. Salt and nutrient concentrations in drainage water varied among sites, and reflected variations in soil properties, fallow length since the preceding crop, fallow rainfall and irrigation water quality. Salinity and SAR of drainage water were many times higher than those of irrigation water. Salinisation and sodification of shallow groundwater reserves under irrigated cotton in Vertisols are, therefore, a distinct possibility. Salinisation and sodification of the root zone may occur in cotton-based rotations that result in poor subsoil structure and, thus, limited drainage even when irrigated with water of a quality that is generally accepted as being reasonable’. Copyright (c) 2013 John Wiley & Sons, Ltd.