Sedimentary rocks are normally characterized by a stratification structure with high connectivity. According to the combinations of rock formations, they can be divided into permeable strata and impermeable strata. Due to the influence of post-stage tectonic events and the Karst phenomenon, the hydrogeological conditions are complicated. The groundwater level varies significantly in sedimentary rocks under the control of topographic variations. For underground engineering construction where the foundation is buried below groundwater level, changes may occur in the replenishment relationship between surface water bodies and groundwater runoff resulting from a large-scale excavation, which consequently makes an adverse effect on the water environment of the surrounding cities. This paper aims to highlight the impact of underground engineering projects on the water environment in Karst areas. Based on the study on characteristics of different types of sedimentary rocks in southern China, such as Karst development characteristics, water-rich characteristics of rock masses, groundwater environmental conditions in cities with a mountainous topography, and types of underground engineering, this paper analyzes the impact modes and treatment principles of projects distributed in spots, large expanse, and line under different geological conditions. The research results have been widely used in the construction of urban subways in a highly developed Karst stratum in southern China, which fully satisfies the requirements of projects.