In Punjab, Pakistan, scarcity of canal water has lead to a rapid growth of the number of tube wells, pumping poor quality groundwater. In recent years, concerns have been expressed about the threat of salinization through the increasing use of tube well water for irrigation purposes. This paper reviews research results of a model study on the impact of irrigation practices, i.e., irrigation quantity, quality and frequency, on soil salinity and crop transpiration of cotton and wheat in a conjunctive use environment. Four fields with a different soil texture and irrigation water quality were selected and monitored during three cropping seasons. The agro-hydrological model SWAP93 was used to analyse the water flow and salt transport for the prevailing conditions. In the calibration process, the simulated water and salt balance appear to be sensitive to rooting depth, crop factors, actual soil evaporation and the soil retention function. Two concepts were used to account for fieId-scale heterogeneity of water infiltration and preferential flow. Taking into account this heterogeneity, the percolation losses increase, while the leaching of salts decreases. The calibrated model was used to evaluate the effects of various irrigation practices on salinization and crop transpiration. The irrigation water quantity, in terms of under-irrigation, has a greater impact than the quality of the irrigation water. Irrigation frequency may have a significant impact on the water and salt balance, especially on sandy soils. Finally, long term effects of current irrigation practices are discussed, in relation to the different soils in the study area. Soil texture appears to affect crop transpiration and salinization considerably.