Water resources are precious in arid and semi-arid areas such as the Wadis of Iran. To sustainably manage these limited water resources, the residents of the Iranian Wadis have been traditionally using several water use systems (WUSs) which affect natural hydrological processes. In this study, WUSs and soil and water conservation measures (SWCMs) were integrated in a hydrological model of the Halilrood Basin in Iran. The Soil and Water Assessment Tool (SWAT) model was used to simulate the hydrological processes between 1993 and 2009 at daily time scale. To assess the importance of WUSs and SWCMs, we compared a model setup without WUSs and SWCMs (Default model) with a model setup with WUSs and SWCMs (WUS-SWCM model). When compared to the observed daily stream flow, the number of acceptable calibration runs as defined by the performance thresholds (Nash-Sutcliffe efficiency (NSE)≥0.68, -25%≤percent bias (PBIAS)≤25% and ratio of standard deviation (RSR)≤0.56) is 177 for the Default model and 1945 for the WUS-SWCM model. Also, the average Kling-Gupta ef?ciency (KGE) of acceptable calibration runs for the WUS-SWCM model is higher in both calibration and validation periods. When WUSs and SWCMs are implemented, surface runoff (between 30% and 99%) and water yield (between 0 and 18%) decreased in all sub-basins. Moreover, SWCMs lead to a higher contribution of groundwater flow to the channel and compensate for the extracted water by WUSs from the shallow aquifer. In summary, implementing WUSs and SWCMs in the SWAT model enhances model plausibility significantly.