Summary Simulation models can be important tools for analyzing and managing irrigation, soil salinization or crop production problems. In this study a mathematical model that describes the water movement and mass transport of individual ions (Ca 2+ , Mg 2+ and Na + ) and overall soil salinity by means of the soil solution electrical conductivity, is used. The mass transport equations of Ca 2+ , Mg 2+ and Na + have been incorporated as part of the integrated model WANISIM and the soil salinity was computed as the sum of individual ions. The model was calibrated and validated against field data, collected during a three year experiment in plots of maize, irrigated with three different irrigation water qualities, at Thessaloniki area in Northern Greece. The model was also used to evaluate salinization and sodification hazards by the use of irrigation water with increasing electrical conductivity of 0.8, 3.2 and 6.4 dS m −1 , while maintaining a ratio of Ca 2+ :Mg 2+ :Na + equal to 3:3:2. The qualitative and quantitative procedures for results evaluation showed that there was good agreement between the simulated and measured values of the water content, overall salinity and the concentration of individual soluble cations, at two soil layers (0–35 and 35–75 cm). Nutrient uptake was also taken into account. Locally available irrigation water ( EC iw = 0.8 dS m −1 ) did not cause soil salinization or sodification. On the other hand, irrigation water with EC iw equal to 3.2 and 6.4 dS m −1 caused severe soil salinization, but not sodification. The rainfall water during the winter seasons was not sufficient to leach salts below the soil profile of 110 cm. The modified version of model WANISIM is able to predict the effects of irrigation with saline waters on soil and plant growth and it is suitable for irrigation management in areas with scarce and low quality water resources.