Soil salinity in the coastal areas of Mazandaran province in the north of Iran is a big problem that threats the cultivation of rice which is the major crop in this region. In this study, the latest version of DRAINMOD-S and AquaCrop models were used to simulate the salt concentration in the soil profile of paddy field with shallow and saline groundwater. This research was carried out in a physical model, located at the meteorological research center of agricultural and natural resources campus of University of Tehran in 2018. The physical model was divided into two boxes (each with dimension of 1*1*1.9 m) by an isolated sheet; one box was conditioned with shallow and saline groundwater (as SSG treatment) and another box with shallow and nonsaline groundwater as a control treatment (NSG). The concentration of saline groundwater was considered to be 20 dS m−1, equal to the salinity of groundwater in agricultural lands of the coastal zone of the Caspian Sea. Both boxes were irrigated with tap water with a salinity of 0.94 dS m−1. After evaluating the models for simulation of salinity in the soil profile of NSG treatment, the best values of MBE, RMSE, NRMSE, d, and R2 were 0.02 dS m−1, 0.07 dS m−1, 2.85%, 0.91 and 0.89 for DRAINMOD-S model and zero, 0.05 dS m−1, 2.11%, 0.93 and 0.84 for AquaCrop models. The results indicate a fairly good correlation between the observed and simulated data. Also, the parameters of MBE, RMSE, NRMSE, d, and R2 were calculated to evaluate the performance of the model in estimating salt concentration changes in three depths of soil. The best values for these parameters in the SSG treatment were −0.04 dS m−1, 0.10 dS m−1, 1.95%, 0.95 and 0.96, for DRAINMOD-S and −0.01 dS m−1, 0.09 dS m−1, 1.82%, 0.96 and 0.93 for AquaCrop, respectively. In general, comparing the measured and simulated soil salinity illustrated that DRAINMOD-S and AquaCrop could be used as a useful tools to predict and simulate the soil salinity changes trend. Also, the accuracy and performance of DRAINMOD-S in higher salinity levels was more than the ones of AquaCrop, because DRAINMOD-S model is a more specific model for salinity issues.