In order to alleviate the impact of Haidong tunnel construction in the water diversion project in central Yunnan Province on groundwater environment, we investigated into the hydrogeological characteristics of karst water system and the groundwater environment in the tunnel route area by comprehensive means inclusive of hydrogeological survey and mapping, prospecting and observation, as well as analytical and numerical approaches. We also optimized the route scheme of Haidong tunnel in consideration of its impact on groundwater environment, and recommend the line B scheme which has less impact on groundwater environment. The present research offers a reference for the selection and comparison of tunnel scheme for water diversion project.