The agro hydrological model SWAP3.03 was used for two wheat crops, cultivars “Ghods” and “Rowshan” under different irrigation regimes. The field study was conducted during 2005-2006 growing season in the Research Field of Birjand University. Different qualities of irrigation water (namely 1.4, 4.5 and 9.6 dS/m) obtained from three local wells were used in a factorial plot design with four levels of water depths (namely, 50, 75, 100 and 125% of ETc). The model was initially calibrated with respect to the winter wheat crop coefficients, based on a study in the province of S. Khorasan. The simulated values fitted well the trend of actual crop production for various amounts and qualities of irrigation water. Maximum yield was obtained for a deficit irrigation of 75% ETc with the best water quality, that of 1.4 (dS/m). Results also showed that different levels of water and salinity stress would affect crop production. The correlation coefficients between the simulated and actual crop production were 0.72 for “Ghods” and 0.83 for “Rowshan”, both statistically significant at 1% level. As compared to the actual yield, the Average simulated yield was 15% higher for “Ghods” and 10% lower for “Rowshan”. A t-test showed that such deviation between simulated and observed values were not lower than required for significant differences. The results of this study, therefore, show that SWAP3.03 model is a useful tool to estimate wheat production under different levels of water and salinity stress.