Agrohydrological models that simulate soil moisture and salinity profile are useful tools for improving irrigation management and increasing irrigation efficiency and crop yield. In this study soil moisture and salinity profile were simulated by AquaCrop software, and compared with field measured soil moisture and salinity data. This study was carried out as split plot design (factorial form). Treatments consisted of three levels of irrigation water salinity (S1, S2, S3 corresponding to 1.4, 4.5, 9.6 dS/m) as main plot, two wheat varieties (Ghods and Roshan) and four levels of irrigation water amount (I1, I2, I3, I4 corresponding to 125, 100, 75, 50% of crop water requirement) as sub plot. Based on the results, soil moisture and salinity profiles were moderately sensitive to volumetric water content at the field capacity (θFC), and soil water content at the saturation (θSat) levels, respectively. Overally, the model accuracy in estimation of the moisture was higher than that in estimation of soil salinity at the soil profile. For Roshan cultivar, the average values of NRMSE, NME, d, CRM and R2 for the simulated soil water contents were 11.72%, 26.81%, 0.79, 0.045, and 0.62, while for the simulated soil salinity they were 24.2%, 52.81%, 0.72, 0.187, and 0.58, respectively. For Ghods cultivar, the average values of these parameters for simulated soil water contents were 11.8%, 26.87%, 0.79, 0.055, and 0.61, while for the simulated soil salinity they were 24.6%, 52.97%, 0.72, 0.193, and 0.57, respectively. The model estimated soil moisture at the deeper soil layers and salinity at the surface soil layers more accurate than those in the surface and deeper soil layers, respectively. According to the statistical indices, the AquaCrop model’s accuracy in estimation of the soil moisture at different depths and times was higher than that in estimation of salinity.