Abstract: The estimation of seepage at dam site is important to the design of hydropower station. A synthetic 3-D groundwater flow model is built by using Visual MODFLOW 4. 0 under ideal conditions and the WALL boundary package is used to describe the dam, which can well depict the seepage characteristics at the dam site. Taking the analytical solution of the related specifications as a contrast, for the water budget analysis by ZoneBudget, we discussed the influence of budget unit arrangement on the seepage calculation of dam foundation and around dam. The comparison shows that there is a relatively large difference between the seepage numerical solution and the analytical solution, and the latter has a larger uncertainty. Moreover, the numerical simulated value increases with the budget range of ZoneBudget; therefore, the influence of budget unit arrangement on calculation results should be fully demonstrated.