Coal and water resources have played important roles in China’s social and economic development. Thus, accurate and reliable predictions of coal mine water inflow and aquifer water level variations are required to ensure mining safety and assess the impact of coal mining on groundwater aquifers. A three-dimensional numerical model was established for unsteady groundwater flows based on a conceptual hydrogeologic model. The numerical simulation predicted mine water inflow via repeated parameter adjustments and model identification and verification, and the simulated water inflow values were compared with the water inflow values predicted by the hydrogeological analytical method. Similarly, the numerical simulation also forecasted the changes in the water levels of the phreatic and karst fissure aquifers. The numerical simulation predicted greater water inflow than that determined by the big well method for the 5th coal seam of Panel 1, whereas the opposite results were obtained for the water inflow estimates for the coal seams in the other two panels. The calculated combined mine water inflows for the three mined panels were 14940 m3/day and 14774 m3/day using the big well method and the numerical simulation, respectively. A comparative analysis of the water levels in different periods showed that the water levels slightly decreased for both the mined and unmined cases, and the maximum variation differences between the unmined and mined cases were 1.39 and 2.72 m in the phreatic aquifer and karst fissure aquifer, respectively. The maximum water level decrease occurred in the northeast area of the coalfield. Based on this work, such results can be used by decision maker to improve mine safety and protect water resources.