This study aims at identifying historical patterns of meteorological, hydrological, and agricultural (inclusively biophysical) droughts in the Karkheh River Basin (KRB), one of the nine benchmark watersheds of the CGIAR Challenge Program on Water and Food. Standardized precipitation index (SPI), standardized runoff index (SRI), and soil mois- ture deficit index (SMDI) were used to represent the above three types of droughts, respectively. The three drought indices were compared across temporal and spatial di- mensions. Variables required for calculating the indices were obtained from the Soil and Water Assessment Tool (SWAT) constructed for the region. The model was calibrated based on monthly runoff and yearly wheat yield using the Sequential Uncertainty Fitting (SUFI-2) algorithm. Five meteorological drought events were identified in the studied period (1980–2004), of which four corresponded with the hydrological droughts with 1–3 month lag. The meteorological droughts corresponded well with the agricultural droughts during dry months (May–August), while the latter lasted for a longer period of time. Analysis of drought patterns showed that southern parts of the catchment were more prone to agricultural drought, while less influenced by hydrological drought. Our analyses highlighted the necessity for monitoring all three aspects of drought for a more effective watershed management. The analysis on different types of droughts in this study provides a framework for assessing their possible impacts under future climate change in semi-arid areas.