Acid mine drainage (AMD) is a global problem that threatens nearby water sources, poses risks to aquatic ecosystems and humans, and has lasting environmental impacts. Conventional remediation of high fluoride and high acid mine drainage in one of the deepest and largest abandoned mine pits in eastern China was challenging due to its immense volume and vertical stratification, and was estimated to take nearly several years through pilot testing and monitoring. The Integrated Treatment Station (ITS), consisting of the pump and dosing tank, was designed to promote vertical mixing, with deep water being drawn to the surface by the pump and supplemented by an appropriate amount of neutralizer being added in the dosing tank, and then sprayed nearby. A three-dimensional (3D) k-ε hydrodynamic coupled water exchange model was established to predict the feasibility and optimality of the solution, and was also used to track the efficiency of the real treatment operation. There are three schemes, referred to as V1, V2, and V3. The first scheme, V1, involves a few high-capacity land-based ITS, while V2 employs many low-capacity floating ITS, and V3 uses a moderate number of low-capacity floating ITS, deployed in varying areas depending on the bathymetry. Based on the simulation results, after running V1, V2 and V3 schemes ran for 3 months, the water exchange efficiency of the total alkaline addition reached 71.37%, 76.18% and 81.56%, respectively, which can meet the efficiency requirements for AMD treatment. According to a comprehensive cost–benefit analysis, V3 was determined as the optimal solution for operation in AMD treatment. During the operation of the selected V3 scheme, the fluoride ion levels in the surface and bottom layers were monitored synchronously to assess the effectiveness of the treatment, and the total fluoride ion concentration showed a remarkable logarithmic decrease, with surface, bottom and total water body levels following a consistent downward trajectory as predicted by the model. The use of model simulation reduced the trial and error, increased the efficiency of AMD remediation, and greatly reduced the treatment time. Within approximately one year, the water had substantially achieved the treatment objectives. The study focuses on the entire AMD treatment process of a large-deep mine pit using a 3D numerical model to guide the design, optimization and implementation of the scheme, providing a successful demonstration of AMD water environmental remediation for a large mine pit.