Quantification of seepage in disconnected river-aquifer systems is significant for local water management and groundwater pollution control, especially in areas with water shortage or contamination. The vadose zone under riverbeds usually exhibits a multi-layered structure, particularly when paved with low permeability liners. To evaluate the impact of engineering solutions to seepage under such conditions, we proposed an approach by combining GIS and the minimum flux in saturation layer (MFSL) method. MFSL can calculate the stable seepage rate by assessing the dominant low permeability layers (including but not limited to the liners) in multi-layered disconnected river-aquifer systems. We used MFSL to calculate local seepage rate, and used GIS to extend the results to a regional scale. The reliability of MFSL is discussed by comparing the results with the double ring infiltration test, the numerical simulation by HYDRUS, and the methods of stream package in MODFLOW, including its improved form. A case study was conducted in the Yongding River with river-aquifer seepage calculated under various conditions, including different river water levels (i.e., under the designated water level, drought stage level, flood stage level and flood inundation level) and with/without low permeability liners (i.e., ecological membranes or geomembrane). Results showed that low permeability liners could greatly reduce the seepage rate. However, if an unlined inundation area exists, the seepage rate may increase greatly. The results indicated that the proposed method was reliable and convenient for calculating long-term, large area seepage in disconnected river-aquifer systems especially those paved with liners.