The intensification of irrigated agriculture is required for attaining food security. It could result, however, in water resources problems of waterlogging and secondary salinization. To assess different management strategies in solving the problems, the current study used a simulation model SaltMod in a command area of north-west India which faced the problems of salinization and waterlogging. Following the thriving testing in the course of calibration and validation, it was used for studying various water management alternatives for the command area. The analysis of different scenarios shows that watertables in the command would persist to go up under the normal conditions. Thus, right management alternatives, for example, increased groundwater use, rice area reduction, and reduced canal water use are recommended. The ideal scenario revealed that small changes of 3–6% in input values would contain the problems of the study region.