The random medium theory is widely used in predicting the surface settlement caused by tunnel excavation, but the theory can not fully reflect the formation deformation mechanism in the stratum with groundwater, resulting in a certain deviation of surface settlement between the theoretical results and the actual results. In order to expand the application scope of random medium theory, based on the formation deformation mechanism, it is considered that the settlement caused by tunnel excavation in water rich formation mainly includes the formation loss caused by excavation disturbance and the increase of formation effective stress caused by underground seepage. Therefore, this paper combined the traditional random medium theory with groundwater seepage theory, and then deduced the theoretical solutions of surface settlement caused by tunnel excavation disturbance and underground seepage respectively, when superposing these two factors, the surface settlement value caused by the tunnel in water rich stratum is obtained. The reliability of the proposed method is proved by comparing the theoretical value with the numerical simulation result, and the surface settlement curves are in good agreement, in addition, the correctness of the proposed method is further verified by comparing with an engineering case. It is found that when only considering tunnel disturbance or underground seepage, the settlement caused by tunnel in water rich stratum is often underestimated, and when the two are combined, the settlement curve is close to the numerical results. After tunnel excavation, the surface settlement decreases rapidly in the early stage, and changes slowly in the later stage until the settlement tends to be stable, which is mainly due to the transformation of deformation mechanism from formation disturbance to seepage induction. The research results can provide reference for the settlement prediction and control of tunnel excavation in water rich stratum.