Bedrock topography is known to affect subsurface water flow and thus the spatial distribution of pore water pressure, which is a key factor for determining slope stability. Therefore, the aim of this study is to investigate the effect of bedrock topography on the timing and location of landslide initiation using 2D and 3D simulations with a hydromechanical model and the Local Factor of Safety (LFS) method. A set of synthetic modeling experiments was performed where water flow and slope stability were simulated for 2D and 3D slopes with layers of variable thickness and hydraulic parameters. In particular, the spatial and temporal development of water content, pore water pressure, and the resulting LFS were analyzed. The results showed that the consideration of variable bedrock topography can have a significant effect on slope stability and that this effect is highly dependent on the intensity of the event rainfall. In addition, it was found that the consideration of 3D water flow may either increase or decrease the predicted stability depending on how bedrock topography affected the redistribution of infiltrated water.