Due to increased population and urbanization, freshwater demand for domestic purposes has increased resulting in a smaller proportion for irrigation of crops. We carried out a 3-year field experiment in the Indus Plains of Pakistan on salt-affected soil (ECe 15·67–23·96 dS m−1, pHs 8·35–8·93, SAR 70–120, infiltration rate 0·72–0·78 cm h−1, ρb 1·70–1·80 Mg m−3) having tile drainage in place. The 3-year cropping sequence consisted of rice (Oryza sativa L.) and wheat (Triticum aestivum L.) crops in rotation. These crops were irrigated with groundwater having electrical conductivity (EC) 2·7 dS m−1, sodium adsorption ratio (SAR) 8·0 (mmol L−1)1/2 and residual sodium carbonate (RSC) 1·3 mmolc L−1. Treatments were: (1) irrigation with brackish water without amendment (control); (2) Sesbania (Sesbania aculeata) green manure each year before rice (SM); (3) applied gypsum at 100 per cent soil gypsum requirement (SGR) and (4) applied gypsum as in treatment 3 plus sesbania green manure each year (GSM). A decrease in soil salinity and sodicity and favourable infiltration rate and bulk density over pre-experiment levels are recorded. GSM resulted in the largest decrease in soil salinity and sodicity. There was a positive relationship between crop yield and economic benefits and improvement in soil physical and chemical properties. On the basis of six crops, the greatest net benefit was obtained from GSM. Based on this long-term study, combined use of gypsum at 100 per cent soil gypsum requirement along with sesbania each year is recommended for soil amelioration and crop production. Copyright © 2010 John Wiley & Sons, Ltd.