The seepage effect of rock and soil in the process of encountering water follows a nonlinear coupling law between water and rock. According to the permeability of rock and soil during softening with water, changes in particles in rock and soil are related to permeability mechanisms. Based on the assumption of connection between particles in rock and soil, changes in particles before and after water infiltration, the mechanism of water–rock interaction, and the damage to rock and soil are analyzed herein. Combined with fractal theory and percolation theory, the random failure characteristics and nonlinear behavior of water in rock and soil are studied. At the same time, with the help of Fluent 17.0 software, the seepage process of rock samples in water is numerically simulated and analyzed. Taking the permeability coefficient of rock samples, the mass flow rate of water, and the internal pore water pressure of rock samples as tracking objects, it is found that there are obvious nonlinear characteristics in the process of water–rock interaction. The seepage–stress coupling between water and rock forms negative resistance to water seepage. The water infiltration is a slow and then accelerated process and tends to be stable. Research has shown that the coupling effect of seepage between water and rock increases the damage inside the rock and soil, and its permeability fluctuates randomly at different time steps. This feature is a common manifestation of fractal properties and percolation within rock and soil particles. At the same time, there is a non-equilibrium variation law of pore water pressure inside the rock and soil. This leads to a continuous strengthening of the seepage effect, reaching a stable state. The results of this study are crucial. It not only reveals the mechanism of interaction between water and rock but also correlates the degree of internal damage in rock and soil based on the seepage characteristics between water and rock. The conclusions can provide some reference value for relevant construction methods in the analysis of the formation of water flow characteristics, the prevention of rock slope seepage disasters, and the control of water inrush in tunnel excavation.