Mine water damage has put the safe back mining of coal resources under serious threat, leading to a series of irrational mining behaviours of coal resources, which affects the safety of coal mines and at the same time has a serious impact on the environment. Fault structures are an important cause of water inrush from the coal mine floor. Studying the activation mechanism of the hidden faults of floor water inrushes is significant for the prevention and control of these accidents. Hidden faults’ activation law was explored under the highly confined water pressure and mining using a method that combines numerical simulations and geophysical exploration technology, and targeted measures were developed for prevention and control. The results demonstrate that under confined water and mining, shallow and deep fractures of hidden faults develop in floor. Fracture development has high probability toward the cutting hole direction. A smaller influence of the confined water pressure results in a water-inrush risk, a lower plastic failure of the floor, and an activation degree of the hidden faults. The bottom plate has a water-inrush threat. Waterproof floor layer’s grouting reinforcement can effectively prevent and control floor water inrushes.