The total amount of water resources severely affects socioeconomic development of a region or watershed, which means that accurate quantification of the total amount of water resources is vital for the area, especially for the arid and semi-arid regions. Traditional evaluation of water resources only focused on the qualification of blue water, while the importance of green water was not fully considered. Therefore, the blue and green water resources in the Neishabour basin were evaluated by the SWAT and SWAT-MODFLOW models in this study. Furthermore, the Sequential Uncertainty Fitting program (SUFI2) which is one of the programs interfaced with SWAT, in the package SWAT-CUP (SWAT Calibration Uncertainty Programs), was used to calibrate and validate Neishabour hydrologic model based on river discharges. In this paper, results of calibration and validation are given for the river monthly discharge. Runoff data for four hydrometric stations in 2001-2011 were used to calibrate and validate this basin. The results show that p-factor, r-factor, R2 and NS, which were used to evaluate the ability of SWAT model, are about 0. 37, 0. 55, 0. 86 and 0. 85 and for validation are about 0. 29, 0. 83, 0. 7 and 0. 65 respectedly. The results show that the components of water resources, except for blue water, which SWAT-MODFLOW model estimates more, are similar in other cases. Therefore, two models were used to investigate the spatial variations of blue water in the watershed. The main difference was within the Neishabour plain, which could be due to the integrated ability of the model to simulate different processes, such as groundwater recharge and infiltration of the non-saturated zone. Moreover, the spatial distribution of the green water indicates that the amount of green water increases gradually towards Neishabur plain. The study of interannual variability of the blue and green water shows that the trends in precipitation, blue and green water have a relatively similar characteristic during the same period and in the winter, the lower temperature, the greater difference between the blue and green water. Also, the trend of the blue and green water changes is milder in the integrated model.