Study region: This study focuses on the Nari River Basin in Baluchistan, southwestern Pakistan-a semi-arid region characterized by complex karst topography, sparse hydrological data, and increasing water resource stress due to climate variability and human activities. Study focus: The primary aim of this research is to assess the hydrological modeling of karst watersheds using the Modified Soil and Water Assessment Tool (SWAT) model, specifically in regions with limited hydrological data. The study incorporates modifications to the SWAT model to improve its performance in simulating the groundwater recharge processes in karst aquifers, where original SWAT model often fall short due to complex flow characteristics. New hydrological insight: (1) We developed a modified SWAT model that integrates a novel three-zonal conceptualization of the karst system-epikarst, vadose, and phreatic zones-into its hydrological structure. (2) The enhanced model demonstrated a similar to 10 % improvement in NSE during calibration and validation compared to the original SWAT. It better captured flood peaks and low-flow events under arid conditions. Parameter sensitivity improved significantly, with the CN2 t-value increasing by 50 % and the p-value decreasing by 80 %. (3)This three-zonal approach provides a more physically representative modeling framework for karst basins in data-scarce arid regions and offers a transferable methodology for improving groundwater recharge and discharge simulation under climate change.