Preferential flow through fractures in weathered bedrock is thought to influence the occurrence of deep－seated landslides. To better understand rainfall runoff processes involving such flow within bedrock layers, we conducted field observations in a granitic headwater catchment and developed a numerical model to simulate preferential flow. Observations of bedrock groundwater levels and spring discharge revealed distinct differences between high‐water and low‐water periods, particularly in the sharpness of fluctuations. To replicate this behavior, we employed a numerical model featuring a three‐tiered pipe system with varying drainage capacities, allowing for higher flow rates in the uppermost pipe. The simulation results suggest that numerical modeling can be used to estimate the structure of preferential flow within bedrock layers and indicate the presence of vertically distributed flow pathways with different drainage capacities in the studied catchment.