It is increasingly recognized that riparian vegetation and wood play crucial roles in enhancing spatial heterogeneity in rivers. Historical removal of large wood and cutting of streamside forests around the world have simplified rivers and substantially reduced aquatic habitat complexity. To understand how (semi-)natural rivers sustain complex geomorphology and hydrology, and how they support aquatic diversity, we carried out an interdisciplinary field study in a stream flowing through a natural forest in Hokkaido, Japan. We mapped 65 side channels (a total of 10.1 km long) along a 9.2 km length of the main channel. More avulsions and side channels were present in stream sections with a higher density of large wood and logjams. At flood stage, 90% of the side channels were inundated with through-flowing river water, while the other 10% remain disconnected from the river and harbor stagnant water. At low flow, only 20% of the side channels had flow from the mainstream river, 46% contained stagnant water, and 34% were dry. In sum, the total surface area of side channels with permanent flow was 20%, side channels with transient flow were 9%, and disconnected side channels were 6% of the surface area of the main channel. We estimated the contribution of each habitat type with different hydrological regimes to the entire populations of aquatic animals in the studied segment. The analysis demonstrated that four out of eleven fish taxa, five out of 26 benthic macroinvertebrate taxa, three out of three plankton taxa, and two out of two amphibian taxa primarily utilized transient or disconnected channels. Furthermore, cohort analysis of dominant fish Salvelinus leucomaenis showed that they exhibit ontogenetic habitat shifts: they primarily utilize channels with transient flow as juveniles and then shift their primary habitats to channels with permanent flow, indicating the need for both types of habitats and their connectivity. Our results demonstrate form and process characteristic of the mostly lost and forgotten “baseline” of rivers in Japan; how geomorphologically and hydrologically complex a natural river can be; and how aquatic organisms rely on such complexity. Large wood potentially plays important roles in sustaining such complexity, and further studies should investigate these mechanisms.