This paper focuses on a typical shallow lake, Lake Changdanghu, which is subject to frequent hydrodynamic disturbances and suspended sediment deposition, resulting in reduced water clarity and the degradation of the grass-type ecosystem. Using a combination of long-term systematic observations and numerical simulations, the impact of terrain modification on the hydrodynamic characteristics of Lake Changdanghu and its resulting environmental improvements are systematically analyzed. The results indicate that there is a significant correlation between the wind wave intensity, suspended solids concentration of the water, and water clarity. The artificial shoal project effectively reduces the local wind wave intensity, increases the water area of the weak waves, and alters the flow structure and transport path of the lake. The wave reduction effect of the artificial shoal significantly improves the transparency of the local water, especially under high wind wave conditions, with a 60% increase in the sheltered area, significantly improving the physical habitat environment. Additionally, the flow resistance and guidance roles of the artificial shoal concentrate the impact of the poor water quality of the inflow in a local area, reducing its adverse effects on the main body of the lake. Our research demonstrates that for shallow lakes, the water transparency can be improved, the physical habitat conditions for aquatic vegetation can be enhanced, and grass-type ecosystems can be gradually restored through artificial intervention and vegetation recovery projects by reducing the wave energy, flow resistance, and guidance through the construction of artificial shoals. This approach achieves long-term maintenance of eutrophication control and water quality improvement in shallow lakes.