The main objective of this work is to develop a hydrological model of the Upper Sebou watershed located in northwest of Morocco, by applying the agro-hydrological model SWAT (Soil and Water Assessment Tool). The modeling was carried out on a period of 14 years including 2 years as warm-up period, 5 years for calibration and 7 years for validation. The results indicated that R2 was 0.69 and NS was 0.70 in calibration period (2002–2006), while R2 was 0.61 and NS was 0.62 in validation period (2007–2013) which means this study showed a good agreement between simulated and observed monthly flow. The results obtained helped firstly to establish and understand the water balance at its different spatio-temporal scales, whose average annual precipitation during the study period is of the order of 431 mm, of which 69.3% is lost by evapotranspiration (298.7 mm). Surface runoff is approximately 37 mm, or 8.58% of the precipitation. As for the total flow in the river, it is of the order of 99.8 mm. And on other hand, this model helped to identify areas where soil loss is very high. This degradation is in fact closely related to the physical basin properties. However, the soil loss can reach a maximum value (more than 12.11 t/ha/year) upstream of the basin and a minimum value (less than 4 t/ha/year). The siltation rate of the retention dam was estimated at 2.12 Mm3/year.