Head deep into a gorge carved by a river
Shosenkyo, Kiyotsu, Nezame-no-Toko, Oboke and Oirase are gorges and valleys that rivers have cut through rock over a very long time. Walking paths, a tunnel through the cliff and a sightseeing boat let you go right down inside them. They are spread across Japan, so pick the one on your route, and check access in winter, when some close or are hard to reach in snow.
A gorge north of Kofu, in Yamanashi, where the river has carved granite into strange cliffs and pillars, protected as one of Japan's special places of scenic beauty. A path along the river winds between the rocks to Senga Falls, which pours through a crack in the granite. It is a bus ride of under an hour from Kofu Station, which is about 90 minutes from Shinjuku by limited express.
A tunnel about 750 meters long dug through the rock wall of a deep gorge in Niigata, with lookouts along the way where you peer out at the cliffs and the river below. At the far end, a shallow pool reflects the gorge like a mirror, an artwork made for a local art festival. On busy days you must book a time slot online, and in winter it may close for snow, so check the official site first.
A stretch of the Kiso River in Nagano where the water has worn granite into huge pale blocks, like giant boxes laid side by side. Its name means the bed of awakening, from the legend that Urashima Taro, the fisherman of a famous folk tale, woke from his long dream here. Paths lead down to the water so you can walk out among the rocks; it is about 30 minutes on foot from Agematsu Station on the JR Chuo Line.
A sightseeing boat that glides slowly through the gorge, giving you a close look at rock layers tilted almost on end and at potholes, round hollows ground into the rock by stones swirling in the current. The rock here is so unusual that the gorge is protected as a natural monument. Boats do not run after heavy rain.
A mountain stream that flows about 14 kilometers out of Lake Towada in Aomori, northern Japan, through a forest of beech and maple, past a long chain of waterfalls and rapids. A mostly flat path follows the water, so you can walk any stretch you like and take the bus back. In winter buses are limited and the path can be snowy, so check access before you go.