Seepage characterization from reservoirs is challenging for various environmental and water resource applications. Nonintrusive geophysical methods can achieve excellent detection results, but they cannot provide a quantitative description of the amount of seepage. Integrating geophysical methods with traditional hydrochemical and hydrologic methods enables simultaneous localization and quantitative analysis of heterogeneous reservoir seepage. Ground and waterborne electrical resistivity tomography are used to scan a reservoir under a typical cutoff wall antiseepage system, and the measurements reveal the northern preferential infiltration area. The hydrochemical results reveal that the seepage bypass of the cutoff wall has led to evident ion concentration variations in groundwater near the dam. Based on the geologic stratum information, the typical cutoff wall antiseepage system is divided into three scenarios for numerical simulation to calculate the seepage. The total seepage of the reservoir over 15 months is approximately 7.15 × 106 m3, which is consistent with traditional water budget methods. However, in the northern part of the reservoir, only 27% of the entire dam contributes 77% of the total seepage. All methods have confirmed that the heterogeneous seepage is caused by the absence of an antiseepage seal in the northern region, which should be a primary focus for future monitoring and operational efforts. With the geophysical results undergoing extensive cross-validation, the results from the preceding methods are comprehensively leveraged, effectively lowering uncertainties and overcoming the limitations of geophysical methods in quantitatively characterizing seepage.