Defects in geomembranes significantly contribute to leakage in impermeable reservoirs, the assessment of reservoir leakage related to geomembrane defects remains experimental, with no reported research on methods for estimating defective leakage in impermeable reservoirs. A numerical simulation inversion model for determining the permeability coefficient of defective geomembrane layers in impermeable reservoirs was developed based on the localization of macroscopic defects and monitoring data. Subsequently, a numerical simulation method was proposed to estimate defective leakage in geomembrane impermeable reservoirs. Based on on-site monitoring data, the numerical simulation inversion results show that the permeability coefficient of the defective geomembrane impermeable layer was 5.0 × 10-5 m/s, corresponding to the area of 4 m2. The total seepage flow and the flow of per unit width section due to geomembrane defects were both influenced by the reservoir water level. At a maximum reservoir water depth of 14.4 meters, the reservoir leakage reached about 857 m3/d. Furthermore, there was a discernible influence range, with the leakage of per unit width section decreasing as the distance from the center of the defect center increased. The research provides an approach for leakage evaluation and safe operation of geomembrane reservoirs in practical applications.