The construction of ecological islands in lake areas is an important practice for implementing the concept of “Lucid waters and lush mountains are invaluable assets” with significant ecological and economic implications. However, the construction of ecological islands inevitably alters the local hydrodynamic of the lake, which in turn affects sediment transport and engineering stability. This study focuses on the ecological island project in Hongze Lake, China’s fourth largest freshwater lake. Using MIKE3, a 3D hydrodynamic and wave numerical model is established, verified with field data and theoretical formulas, to analyze the effects of ecological island construction on both the overall and local hydrodynamics and wave of the lake. The results indicate that the current field changes in the Hongze Lake area are primarily influenced by strong winds, with wind direction and water level variations affecting water blockage and the lake current structure. The significant wave height increases in the upwind area and decreases in the downwind area with changing wind directions. Additionally, as wind speed and water levels increase, the significant wave height increases accordingly. After the ecological island is constructed, it forms a structure similar to a water-blocking barrier, causing an increase in flow velocity and significant wave height on the windward and current-facing sides. On the leeward side, however, due to the sheltering effect of the island, flow velocity and significant wave height decrease. Overall, the construction of the ecological island has differentiated impacts on the wind, wave, and current conditions at different locations in the lake area.