Restricted by terrain, a large number of tunnels have been built and are densely distributed in Chongqing. In karst areas, the construction of tunnels has given rise to a series of environmental and engineering negative effects. By integrating the geological background and groundwater chemical characteristics of the karst areas in Chongqing, the tunnel construction environment and engineering negative effects in this region are systematically sorted out, including inducing karst collapse, causing water body drainage and loss, affecting vegetation growth and distribution, reducing soil quality and causing soil pollution, altering the groundwater thermal pattern, inducing water and mad inrush in tunnels, and triggering surrounding rock collapse and structural damage. On this basis, the overall trends and directions for future research are identified: 1) Strengthen research and evaluation on the mechanism of tunnels’ impact on the stability of karst foundations. 2) Strengthen research on the identification of water conversion processes and drainage impact scopes as well as related protection measures. 3) Strengthen research on the response processes and mechanisms of soil and vegetation to tunnel construction. 4) Shift from “single-subject” to holistic research, and connect the “dual assessments” in karst tunnel sites.