Fuji's upper surface has many relatively new fissures, while a mudflow layer made by Ko Fuji Kazan lies underneath. The mudflow layer does not let water pass through easily, so much of the more than 2 billion tons of rainwater and melted snow percolating into the fissures every year sinks down to the top of the mudflow layer, then comes out as springs near the mountain foot, forming lakes and rivers.

When molten rock flowed down around the mountain base, it formed lava fields. First the surface cooled and hardened, and then some parts of the liquid interior oozed out to leave behind a network of lava tunnels. These tunnels are now natural water pipes feeding the fairly large Five Fuji Lakes and other topographical features like the Eight Oshino Ponds, Shiraito Falls, the springs of the Kakita River, and Wakutama Pond.

The strata under the mountain, the lava tunnels and the huge lava fields create natural watercourses and barriers resembling the infrastructure around a hydroelectric dam.