Surface runoff significantly impacts the region's ecosystem and is closely linked to sustainable development and human well-being. The mathematical model SWAT running in an ArcGIS environment was used to estimate surface runoff in the Kubaisa watershed. The period simulated in this model is 31 years, sufficient to give good results regarding surface runoff volume and water yield contribution from each sub-watershed. The Kubaisa watershed has an area of 2485.50 km2 and comprises six sub-watersheds. The watershed consists of 172 HRUs distributed among sub-watersheds depending on the variation in soil layers, land use, vegetation, and slope. The volume of water calculated from the annual surface runoff rate for the simulation period was about 2699 million cubic meters, and its value was higher than the volume of water calculated from surface runoff due to lateral flow, groundwater discharge, and the contribution of each sub-watershed to the water yield. The highest value in water yield was in 2012, and the largest contribution was made by the sixth sub-watershed; thus, the difference is temporal and spatial in terms of water yield. Finally, through the analysis of multiple scenarios, the difference in hydrological response units is controlled by the difference in surface runoff, discharge, and water yield to the watershed. For this purpose, the SWAT model divides the watershed into many different units and starts the simulation on their basis.