The present study extends the numerical manifold method to include the hydro-mechanical model to investigate the effect of water flow in fractures on the stability of rock structures, particularly slopes. The proposed flow model is verified by a simple 2-D flow problem in a homogeneous aquifer. Combining the water flow model with the earlier developed fracture evolution technique, the entire failure process of the rock slope due to a heavy rain is simulated. The results illustrate that the developed numerical manifold method can not only determine the trigger factor of the crack initiation but also model the failure processes related to crack initiation, propagation, block formation, detachment and sliding due to the water effect successfully. Copyright © 2014 John Wiley & Sons, Ltd.