Karst water resources represent a primary source of freshwater supply, accounting for nearly 25% of the global population water needs. Karst aquifers have complex recharge characteristics, storage patterns, and flow dynamics. They also face a looming stress of depletion and quality degradation due to natural and anthropogenic pressures. This prompted hydrogeologists to apply innovative numerical approaches to better understand the functioning of karst watersheds and support karst water resources management. The Soil and Water Assessment Tool (SWAT) is a semi-distributed hydrological model that has been used to simulate flow and water pollutant transport, among other applications, in basins including karst watersheds. Its source code has also been modified by adding distinctive karst features and subsurface hydrology models to more accurately represent the karst aquifer discharge components. This review summarizes and discusses the findings of 75 SWAT-based studies in watersheds that are at least partially characterized by karst geology, with a primary focus on the hydrological assessment in modified SWAT models. Different karst processes were successfully implemented in SWAT, including the recharge in the epikarst, flows of the conduit and matrix systems, interbasin groundwater flow, and allogenic recharge from sinkholes and sinking streams. Nonetheless, additional improvements to the existing SWAT codes are still needed to better reproduce the heterogeneity and non-linearity of karst flow and storage mechanisms in future research.