The direct extraction of clear water from a sandy river is a difficult task and can only be achieved through specific engineering measures. This paper proposes an artificial percolation riverbed structure for extracting clean water from sandy rivers, using a numerical simulation to study the flow field distribution characteristics of the structure under clean water conditions. The main conclusions are as follows: When the percolation vortex tube opening rate is 1.4%, the vortex tube with or without opening the percolation hole has little influence on the distribution characteristics of the flow field in the artificial riverbed, and the purpose of water extraction can be achieved while constructing a helical flow field. The axial flow velocity and circumferential flow velocity of the vortex tube cross-section under different Reynolds numbers show the distribution of a low-flow velocity close to the center of the vortex tube, and a high-flow velocity close to the vortex tube side-wall area. The average axial flow velocity and average circumferential flow velocity of the vortex tube show a trend of increasing and then decreasing distribution along the axial axis of the vortex tube in the direction of the sediment transport flume. The mean axial flow velocity of the vortex tube along the axis of the vortex tube toward the sediment transport flume and the mean circumferential flow velocity both show a distribution trend of increasing and then decreasing. At the junction of the vortex tube and the sediment transport flume, there are obvious pressure changes, and the pressure changes drastically under the same horizontal line. Along the direction of the bottom line of the vortex tube, the pressure at the vortex tube is obviously greater than that at the sediment transport flume. The vortex of the artificial percolation riverbed is mainly concentrated in the vicinity of the vortex tube, and the maximum value of the vortex intensity generally occurs at the junction of the vortex tube and the sediment transport flume. With the increase in the Reynolds number, the vortex intensity has an overall increasing trend, and the distribution of the vortex is more complex. This study helps to elucidate the distribution characteristics of the flow field in the artificial percolation riverbed, and it provides a reference basis for the future study of the flow field of artificial percolation riverbeds of sandy rivers.