The occurrence of drought is one of the natural phenomena and an inseparable part of climate change and natural hazards that can occur anywhere. Hydrological drought is used to indicate the reduction of surface flows and the drop in the levels of underground water reservoirs, lakes, and rivers. The present research was conducted to determine the values of the base flow index and to assess its effectiveness in identifying the type of flow regime and conducting a regional analysis of hydrological drought in the HalilRood watershed. For this purpose, three homogeneous hydrological drought zones were established based on the threshold level and cluster analysis. The base flow index was then calculated on a daily scale using daily discharge data from ten hydrometric stations within these homogeneous zones. The results showed that the regional average of the annual base flow index is 0. 38, with a standard deviation of 0. 193 over the long-term statistical period, and that the range of the base flow index is 0. 12–0. 29. Based on the 70th, 80th, and 90th percentiles, the river flow regime was divided into four classes, revealing that 100% of the watershed sub-basins in the study area exhibited an unstable regime. Additionally, the results of drought zoning indicated that hydrological drought occurred at a threshold level of 70 in the southeast of the region near the Dehroud hydrometric station, and at levels of 80 and 90 in the northwest near the Baft and Cheshme-Arus stations. The findings of this research can be utilized for assessing underground water supply, managing water supply systems, irrigation management, monitoring hydrological drought, and developing regional models for estimating water resource reserves in areas lacking statistical data.