Hydraulic conductivity of the reservoir bottom stratum is one of the main factors affecting reservoir leakage. Studying the spatial variability of hydraulic conductivity can provide a scientific basis for the reliability analysis of the calculation results of reservoir leakage. Using the bottom stratum of the Beitang Reservoir as a case study, the parameter series were extended through Kriging interpolation. Then, the interpolated hydraulic conductivity was estimated by sequential Gaussian simulation which was carried out 500 times. Finally, the effect of the spatial variability of hydraulic conductivity on the uncertainty of calculated leakage was analyzed. The results show that the spatial structure of vertical hydraulic conductivity can be described by a spherical model, and it has a high spatial correlation within 1 210 m. As for the leakage calculated on July 16, 2005, the smallest value was 1 389. 49 m³/d, the largest value was 1 897. 30 m³/d, and the frequency of the calculated value falling into the range of 1 600 to 1 850 m³/d reached 77. 6%.