The moving particle semi-implicit method (MPS) has been employed to numerically simulate fluid flows. Further, some studies have used the MPS method to solve the Darcy-Brinkman equation, which also expresses fluid flow in porous media. However, these studies simulated flows only in porous media with high permeability, not in relatively low permeability. Thus, this study developed a numerical simulation method that employs Navier-Stokes equations to describe flow in surface water and the Richards equations, derived from the Darcy law and the law of conservation of mass, to describe water flow in porous media, and it uses the MPS method to discretize those equations. This numerical simulation method was then evaluated by comparing the numerical simulation results with previously obtained experimental results for fluid draining from the bottom of a column, which was first packed with silica sand saturated with water and then filled with water to 25 cm above the top surface of the sand, which had an intrinsic permeability of 1.737 x 10-11 m2, a porosity of 0.402, van Genuchten parameters of 0.231 kPa-1 and 9.154, a residual gas saturation of 0.0, and a residual water saturation of 0.178. The numerical simulation was able to simulate the decrease in the level of the surface water above the silica sand in the column, similar to the column experimental results. However, the decrease in the saturated water in the silica sand obtained by the numerical simulation was almost consistent with the experimental results.