Waterlogging and secondary salinisation have become serious problems in canal irrigated areas of arid and semi-arid regions. This study examined hydrology and estimated the seasonal net groundwater recharge of an irrigated semi-arid region located in the Haryana State of India where about 500 000 ha area are waterlogged and unproductive, and the size of the waterlogged area is increasing, causing a threat to agricultural sustainability. Groundwater recharge analysis during the study period (1989–2010) revealed that percolation from irrigated fields was the main recharge component, with 48% contributing to total recharge. An annual groundwater table rise of 0.198 m was estimated for the study area. Since the groundwater table had been rising continuously, suitable water management strategies such as as conjunctive use of groundwater and canal water and changes in crop patterns by reducing rice crop areas against of other low-water crops such as sorghum are suggested to bring the groundwater table down to a safe limit and prevent further rise of the groundwater table.