In the Indus Basin of Pakistan, multi-strainer shallow tubewells often called 'skimming wells' are used to extract groundwater from thin fresh lenses underlain by saline groundwater. Most of these wells face problems such as deteriorating water quality and reduction in discharge due to inadequate design and poor operational and management strategies. This paper evaluates the current practices of farmers in the Chaj doab area of Pakistani Punjab and suggests improvements in design and operation of skimming wells to ensure long-term sustainability of irrigated agriculture in the area. The effect of existing design and operation of skimming wells on pumped groundwater quality was evaluated using MODFLOW. To study the long-term effects of skimmed groundwater use on crop production and soil salinity development, the soil water flow and solute transport model SWAP was applied. The results revealed that farmers could reduce the number of strainers from 16 to 6 without reducing the anticipated discharges. For the conditions considered, the maximum discharge of skimming wells should be 4'8 L/s and they should not be operated for more than 2'4 h per day. Increasing discharge rate or daily operational hours can disturb the interface between fresh and saline groundwater resulting in reduced quality pumped groundwater. Weekly operational schedules together with recommended discharge rate and operational hours will be the best strategy to use skimmed groundwater for achieving optimal crop yields while maintaining root-zone salinity within acceptable limits. To avoid aquifer degradation, skimming wells should be used for supplemental irrigation rather than full irrigation of crops. Due to low discharge rates, skimming wells cannot be used to irrigate crops through surface irrigation methods.Therefore, pressurised irrigation methods should be used. The results also suggest that continuation of present irrigation practices could lead to serious problems of land and aquifer degradation. Therefore, farmers need to adjust their irrigation and leaching requirements annually considering crop evapotranspiration, precipitation, and salinity status of soils.