Over the past 30 years, reclamation projects and related changes have impacted the hydrodynamics and sediment transport in the Bohai Sea. Three-dimensional tidal current models of the Bohai Sea and the Yellow Sea were constructed using the MIKE 3 model. We used a refined grid to simulate and analyze the effects of changes in coastline, depth, topography, reclamation, the Yellow River estuary, and coastal erosion on tidal systems, tide levels, tidal currents, residual currents, and tidal fluxes. The simulation results show that the relative change in the amplitude of the half-day tide is greater than that of the full-day tide. The changes in the tidal amplitudes of M2, S2, K1, and O1 caused by coastline changes accounted for 27.76–99.07% of the overall change in amplitude from 1987 to 2016, and water depth changes accounted for 0.93–72.24% of the overall change. The dominant factor driving coastline changes is reclamation, accounting for 99.55–99.91% of the amplitude changes in tidal waves, followed by coastal erosion, accounting for 0.05–0.40% of the tidal wave amplitude changes. The contribution of changes in the Yellow River estuary to tidal wave amplitude changes is small, accounting for 0.01–0.12% of the amplitude change factor. The change in the highest tide level (HTL) is mainly related to the amplitude change, and the correlation with the phase change is small. The dominant factor responsible for the change in the HTL is the tide amplitude change in M2, followed by S2, whereas the influence of the K1 and O1 tides on the change in the HTL is small. Reclamation resulted in a decrease in the vertical average maximum flow velocity (VVAM) in the Bohai Sea. Shallower water depths have led to an increase in the VVAM; deeper water depths have led to a decrease in the maximum flow velocity. The absolute value of the maximum flow velocity gradually decreases from the surface to the bottom, but the relative change value is basically constant. The changes in the tidal dynamics of the Bohai Sea are proportional to the degree of change in the coastline. The maximum and minimum changes in the tidal flux appear in Laizhou Bay (P-LZB) and Liaodong Bay (P-LDB), respectively. The changes in the tidal flux are related to the change in the area of the bay. Due to the reduced tidal flux, the water exchange capacity of the Bohai Sea has decreased, impacting the ecological environment of the Bohai Sea. Strictly controlling the scale of reclamation are important measures for reducing the decline in the water exchange capacity of the Bohai Sea and the deterioration of its ecological environment.