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Comparative studies of drainage and leaching in irrigated cotton (Gossypium hirsutum L.) based cropping systems in Australian Vertosols are sparse. Our objective was to quantify soil water storage, drainage, and leaching in four cotton-based cropping systems sown on permanent beds in an irrigated Vertosol with subsoil sodicity. Drainage was inferred using the chloride mass-balance method, and soil water storage and leaching were measured with a neutron moisture meter and ceramic-cup water samplers, respectively, from September 2005 to May 2011 in an ongoing experiment. The experimental treatments were: CC, cotton monoculture, summer cotton with winter fallow; CV, cotton–vetch (Vicia benghalensis L.) rotation with vetch stubble retained as in-situ mulch; CW, cotton–wheat (Triticum aestivum L.), with wheat stubble incorporated and a summer–winter fallow; and CWV, cotton–wheat–vetch, with wheat and vetch stubbles retained as in-situ mulch and summer and spring fallows. Soil water storage was generally highest under CW and CWV and least under CV. An untilled short fallow (~3 months) when combined with retention of crop residues as surface mulch, as in CWV, was as effective in harvesting rainfall as a tilled long fallow (~11 months) with stubble incorporation, as in CW. Drainage under cotton was generally in the order CW ≥ CWV > CC = CV, all of which were considerably greater than drainage during fallows. Except for very wet and dry winters, drainage under wheat rotation crops was greater than that under vetch. During wet winters, saturated soil in the 0–0.6 m depth of treatments under fallow resulted in more drainage than in the drier, cropped plots. No definitive conclusions could be made with respect to the effects of cropping systems on salt and nutrient leaching. Leachate contained less nitrate-nitrogen, magnesium, and potassium, but leachate electrical conductivity was ~6 times higher than infiltrated water. The greater salinity of the leachate may pose a risk to groundwater resources.