The time required for rainfall to travel through a hillslope and reach a stream (transit time) is a fundamental hydraulic parameter that reflects the diversity of flow paths, water storage capacities, and associated mixing at the catchment scale and is a useful indicator for water resource management [e.g., Kirchner et al., 2000; McDonnell et al., 2010; Stolp et al., 2010; Rinaldo et al., 2011]. The mean transit time (MTT) of stream base flow varies spatially among subcatchments within a meso-scale catchment, and a few studies have investigated the effect of landscape organization on the spatial pattern of MTT [e.g., McGlynn et al., 2003; McGuire et al., 2005; Hrachowitz et al., 2010a]. These studies followed standard hydrological concepts derived in part from the pioneering works of Tsukamoto  and Hewlett and Hibbert , which describe runoff generation as dependent on surface and subsurface topography. The ideas generated by this topography-dependent concept are variable source areas [Hewlett and Hibbert, 1967], partial contributing areas [Dunne and Black, 1970], TOPMODEL [Beven and Kirkby, 1979], representative elemental areas [Wood et al., 1988], and subsurface topography control [McDonnell et al., 1996]. However, in our survey of the literature, we found no common relationship between base flow MTT and topographic measures for a variety of catchments. Some studies have found a clear correlation between MTT and topographic measures, such as median catchment area and median hillslope length [e.g., McGlynn et al., 2003; McGuire et al., 2005], whereas others found less correlation with topography [e.g., Soulsby et al., 2006; Katsuyama et al., 2010].
 The basic theoretical concept of transit time suggested another possibility about its first-order (main) control. If the base flow draining a catchment is treated as a well-mixed, steady state system (e.g., a linear reservoir), then the MTT of base flow (MTT) is described as,
where Qb, the base flow, is the volumetric flow rate through the system and Vm is the volume of mobile water in the system during base flow [e.g., Zuber, 1986]. Generally, based on the water balance, Qb can be described as,
where R is the rainfall rate, ET is the evapotranspiration rate, qs is specific discharge during storm runoff, D is the deep water percolation rate, and A is the drainage area. The volume of mobile water can be described as,
where θm is the mean mobile water content per unit volume and dm is the mean depth of hydrologically active soil and bedrock. From equations (1)–(3), the MTT for base flow can be expressed as,
If the climate, vegetation, and underground materials that store water (e.g., soil and bedrock) are almost homogeneous throughout catchments, we can assume that the rainfall rate (R), evapotranspiration rate (ET ), and deep water percolation rate (D) are also similar. Furthermore, because the porosity of soil and bedrock commonly changes with depth [e.g., Harr, 1977; Katsura et al., 2008], we can assume that θm is a function of dm. That is, the spatial variability in MTT should be related to qs and dm. Hence, we can propose the hypothesis that spatial variation in the MTT of stream base flow in a meso-scale catchment is related to the mean depth of hydrologically active soil and bedrock (dm). We based this hypothesis on recent studies demonstrating that the depths of water sources contributing to hillslope runoff varied greatly with location within a catchment, even when the catchment had uniform bedrock geology, soil type, and land use [e.g., Uchida et al., 2008; Uchida and Asano, 2010]. Recent process studies and theoretical considerations have also tightly linked storage and flow path lengths to catchment response [Harman and Sivapalan, 2009; Sayama et al., 2011] and MTT [Soulsby et al., 2009; Hrachowitz et al., 2010b]. However, most studies investigating the spatial patterns of stream MTT in headwaters have not focused on the spatial pattern of dm because it is nearly impossible to measure directly [e.g., Soulsby et al., 2006]. The depth of hydrologically active soil and bedrock (dm) should be defined by the internal structure of the catchment, such as the distribution of porosity and mobile water in soil and bedrock; thus, it is not necessarily related to surface topography.
 Therefore, we tested the hypothesis stated above by examining the effect of spatial patterns of MTT on the headwaters of a 4.27-km2 catchment consisting of a nearly homogenous landscape of incised valleys and granitic bedrock covered with forest. To compare relative MTTs among locations, we used the degree of isotopic signal dampening [e.g., Maloszewski et al., 1983; McGuire et al., 2005; Tetzlaff et al., 2009b]. The concentration of dissolved silica (SiO2) was used as a tracer to identify the contributing depth of the flow path to stream discharge because previous studies of this catchment demonstrated that dissolved SiO2 increased with the depth of this flow path whereas contact time of groundwater with soil and bedrock had minimal impact [Asano et al., 2003; Uchida and Asano, 2010]. We also tested the effects of qs and topography on the spatial pattern of MTT.