During the tunnel construction in the karst area, there is a great danger of water inrush, and the discharge of groundwater will lead to the geological disasters. The hydrogeology in Zhongliang mountain tunnel area was analyzed and the BP neural network optimized by the genetic algorithm is used for inverse analysis of the permeability coefficient of aquifer. The impact of tunnel elevation and the discharge of groundwater on groundwater environment change was studied, and the groundwater environment change with time was explored. The results show that water inrush during karst tunnels construction is most likely to occur on the interface between the aquifuge and the aquifer, and that tunnel elevation and the discharge of groundwater have both great impacts on the groundwater environment. The results indicate that the groundwater level drops rapidly and cannot return to the original level in the current drainage conditions. Consequently the discharge of groundwater should be controlled properly during construction. Measures should be also taken to protect the groundwater environment during construction and operation stage of tunnels.