The heterogeneous temporal and spatial distribution of fresh water and rapid population growth in recent decades have led to problems in supplying required water resources for various uses. Therefore, new mathematical models have been developed to study the complex hydrological processes. In this study, SWAT model in Samalqan catchment with area of 1148 km2 was used to simulate the flow. In the modeling process, the basin was divided into 21 sub-basins and 402 hydrological units. Modeling of watersheds has uncertainties due to limited access to enough hydrological data. For this purpose, model calibration and validation were performed using SUFI2 algorithm for 1995 to 2012 and 2012 to 2014, respectively. Based on the sensitivity analysis results, the parameters RCHRG_DP (value of penetration into the deep aquifer), GWQMN (amount of water in the shallow aquifer to produce the base stream), ALPHA_BF (groundwater reaction coefficient), SOL_AWC (soil available water capacity) and CN (SCS curve number) had the most effect. The results showed that the values of Nash-Sutcliffe index and R2 coefficient were 0. 65 to 0. 80 for calibration period and 0. 40 to 0. 65 for validation period. Out of the total inflow into the basin, 87% is spent on evapotranspiration, 3. 2% for surface runoff, 3% for infiltration and the rest is related to changes and moisture storage in soil. Since no estimation of water balance components in this basin has been done so far, this research can provide useful information about the water balance of the basin and help to plan water resources more accurately.