In this study, using borehole logs and microtremor data, we demonstrate that the relationship between the shallow-subsurface (to maximum depths of a few decameters) properties in a valley-bottom lowland and the surrounding upland varies in the along-stream direction. Borehole logs were collected to assess geological structures, and microtremor array observations were used to model S-wave velocity structures and obtain ground-motion characteristics along survey lines across each valley of the Kanda (Zenpukuji) and Furukawa (Shibuya) rivers in the Musashino Upland, Tokyo, central Japan. Microtremor data reveal that the average S-wave velocity in the valley-bottom lowlands of the downstream area is generally low. This low value is ascribed to the occurrence of thick, soft, muddy sediments with S-wave velocities of <150 m/s beneath the lowlands. Particularly, in areas where soft sediments are ~15 m thick, marked peaks occur at low frequencies of 1.5-1.6 Hz in the microtremor H/V spectra. These areas correspond to areas that sustained severe building/house damage during the 1923 Kanto Earthquake. In contrast, the average S-wave velocity in the valley-bottom lowlands of the middle to upper reaches of the rivers is generally high. The gravel beds of Pleistocene terrace deposits have suffered minimal erosion from small rivers, meaning that these rivers flow on gravel beds, and soft sediments are lacking or very thin beneath these reaches. Therefore, the valley-bottom lowlands in the middle and upper reaches are characterized by hard ground. In contrast, the surrounding uplands are composed of volcanic-ash soil of the Kanto Loam and the muddy Tokyo Formation, which form softer ground compared with the valley-bottom lowlands. Therefore, it is important to accurately document the change in thickness of soft deposits in the along-stream direction beneath the valley-bottom lowlands and the lithologic and physical properties of the strata in the surrounding upland area for robust seismic-hazard assessment.