In Tunisia, water used for irrigation is often saline, increasing the risk of salinization for soils and crops. In this study, an experiment was conducted on a tomato crop cultivated on a silty-clay soil irrigated with three different water qualities: 0, 3.5, and 7 dS·m−1. Experimental data were then used to calibrate and validate the Hydrus-1D model, which simulates water flow and salt transfer in soils. The successfully-calibrated and validated model was then used to study the combined effects of the soil osmotic and soil matrix potentials on root water uptake. The values of the root mean square error (RMSE), the coefficient of determination (CD), the modeling efficiency (EF), and the coefficient of residual mass (CRM) were close to their optimal values for both soil water content and soil electrical conductivity profiles, indicating the reliability of the model to reproduce water and salt dynamics. Relative yields (Yr), indirectly estimated using actual and potential root water uptake (transpiration), indicated that the multiplicative stress response model (using the S-shape model) satisfactorily simulates measured yields and reproduces the effects of irrigation with saline waters on crop yields. An alternative scenario using a reduction of water requirements by 50% was investigated to assess an irrigation method with considerable water savings. As the results show that relative yields, Yr, were only slightly reduced, the crop water requirements estimated by CROPWAT 8.0 must have been overestimated. The variation of the soil salinity in the root zone highlighted a high salinization risk in the short-term when water of 7 dS·m−1 is used for irrigation.