Transit time of discharge is a hydrological characteristic used in water resource management. Previous studies have demonstrated large spatial variation in the mean transit time (MTT) of stream base flow in meso-scale catchments. Various relationships between topography and MTT have been reported. Although it is generally assumed that base flow MTT is controlled by the depth of the hydrologically active layer that recharges a stream, this hypothesis has not been tested in field studies. This study confirmed that the depth of hydrologically active soil and bedrock controls spatial variation in MTT. The study used isotopic and geochemical tracer data gathered in the 4.27 km2 Fudoji catchment, central Japan. The results, together with previously documented relationships between topography and MTT, indicate that the depth of the hydrologically active layer is sometimes, but not always, related to topography. A comprehensive understanding of the factors that control base flow production in mountainous catchments will require further study of the water flow path depths that recharge streams.