It has been suggested that pipe flow and bedrock groundwater play important roles in storm runoff generation. We examined the effects of pipe flow on storm runoff generation and the roles of bedrock groundwater in rainfall-runoff phenomena in a steep headwater catchment in central Japan. Measurements of pore water pressures, pipe flow, and streamflow showed that when the total rainfall amount was 70 mm, the dominant runoff process shifted to pipe flow. Temperature measurements indicated four key points: (1) During base flow conditions (streamflow 0.2 mm h-1) the source of pipe flow was the same as the streamflow; (3) the transient groundwater at the upper hillslope was commonly dominated by the preevent soil water; and (4) only after the large storms with wet antecedent conditions, was water emerging from the bedrock and mixing with preevent soil water in the transient saturated area at the upper hillslope. Both the hydrometric and temperature measurements indicated that once pipe flow occurs, the contributing area of streamflow extended to upper hillslope, and the transient groundwater at the upper hillslope was delivered to the stream via preferential flow paths, shortcutting the normal mixing process through the soil matrix.