Interflow is an important water source contributing to river flow. It directly influences the near-surface water cycles for water resource management. This study focuses on assessing the interflow potential and quantifying the interflow in the downstream area along the Kaoping River in southern Taiwan. The interflow potential is first determined based on the modified index-overlay model, which employs the analytical hierarchy process (AHP) to calculate the ratings and weightings of the selected factors. The groundwater and surface water flow (GSFLOW) numerical model is then used to link the index-overlay model to quantify the interflow potential for practical applications. This study uses the Monte Carlo simulations to assess the influence of rainfall-induced variations on the interflow uncertainty in the study area. Results show that the high potential interflow zones are located in the high to middle elevation regions along the Kaoping River. Numerical simulations of the GSFLOW model show an interflow variation pattern that is similar to the interflow potential results obtained from the index-overlay model. The average interflow rates are approximately 3.5 × 104 (m3/d) in the high elevation zones and 2.0 × 104 (m3/d) near the coastal zones. The rainfall uncertainty strongly influences interflow rates in the wet seasons, especially the peaks of the storms or heavy rainfall events. Interflow rates are relatively stable in the dry seasons, indicating that interflow is a reliable water resource in the study area.