This study investigates the permeability evolution in floor fault damage zones under stress–seepage–damage coupling, with a focus on water inrush risks caused by confined water upward conduction during deep mining. A stochastic fracture geometry model of the fault damage zone was developed using the discrete fracture network (DFN) model and the Monte Carlo method. Based on geological data from a mining area in Shandong, a multiphysics-coupled numerical model under mining-induced conditions was established with COMSOL Multiphysics. The simulations visually reveal the dynamic evolution of damage propagation patterns in the floor strata during working face advancement. Results indicate that the damage zone stabilizes after the working face advances to 80 m, with its morphology exhibiting strong spatial correlation to regions of high seepage velocity. Moreover, increasing confined water pressure plays a critical role in driving flow field evolution.