Understanding hydrological connectivity is one of the main objectives in hydrological research. Hydrological models have been proved to be an efficient tool for a better understanding of hydrological connectivity. Conceptual models have shown certain advantages compared to physically-based distributed models in terms of data requirement and computational time. However, the hydrological connectivity in conceptual models is usually not well represented. In this study, the Soil and Water Assessment Tool (SWAT) was selected for further improvements to have a better representation and simulation of hydrological connectivity. SWAT is a semi-distributed hydrological model used to simulate the effect of land use management practices on water, sediment, and nutrient yields at a basin scale. SWAT has been tested and applied worldwide. However, the non-spatial characteristic of the hydrologic response unit (HRU) concept used in SWAT has been identified as one of the main disadvantages for modeling hydrological connectivity. In this study, the hydrologic routing subroutine of SWAT was examined and the groundwater subroutine was modified to account for hydrological connectivity in porous and karst-dominated aquifers. Results show that the current hydrologic routing subroutines of SWAT are not able to simulate hydrological connectivity between river segments in the river network. The Muskingum routing method in SWAT could (1) cause unphysical oscillations in the simulated streamflow and (2) overestimate the evapotranspiration loss in the river and results in a hydrologic disconnectivity during low flow periods. For improving the representation of hydrological connectivity in the subsurface porous aquifer, the multicell aquifer model was proposed and incorporated into SWAT. The modified model, the so-called SWAT-MCA model, was validated in two basins located in Niedersachsen, Germany. The results show that the SWAT-MCA model could well simulate the regional groundwater flow and return flow from aquifer to stream. For improving the representation of hydrological connectivity in the karst-dominated aquifer due to interbasin groundwater flow (IGF) was added to SWAT, the SWAT_IGF was developed. The developed model was applied in a karst area located in the Southwest Harz Mountains, Germany. The model was validated with the observed streamflow and spring flow. Results show that the SWAT_IGF could well represent the hydrological connection due to interbasin groundwater flow in karst areas. The modified models, SWAT-MCA and SWAT_IGF could be applied for other regions to regional groundwater flow in porous aquifer and IGF in karst-dominated aquifers.