Nested Delft 3D and Hydrus 1D models were applied to simulate variations in the hydrological process of tidal creeks, soil water, and salt transport in the soil profile of the reconstruction area in the Yellow River Delta under six gate dam scenarios. The results showed that the gate dam set up near the sea area was more conducive to reducing the variation range of water depth in the reconstruction area. The water depth changes in scenarios with 6 m gate valves were higher than those with 3 m sluice valves in the same gate dam location. The variations in surface water salinity, cumulative flooding time, flooding frequency, and cumulative infiltration in each scenario were similar to those for water depth. Rapid changes in soil water and salt content occurred in each scenario in periods without flooding. The fluctuation of soil salt content in different soil layers was contrary to the changes in soil water content. The overall difference in the soil salt contents and soil water content of the soil profile in scenarios with a gate dam near the sea was relatively larger than that of those with a gate dam near the shore. Obvious differences in both the soil water content and soil salt content between scenarios with 3 m and 6 m gate valves were not observed. Our results contribute to the understanding of the function of gate dams in controlling soil water and salt content in coastal wetlands.