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 natural forest in Hokkaido, Japan. We mapped 65 extant- and palaeo- side channels (total 10.1 km long) along a 10.8 km length of the stream. More avulsions and side channels were present in stream reaches with a higher density of large wood and log jams. 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% dried. We have previously documented that spatially variable hydrological and biological processes shape diverse post-flood aquatic communities including fishes, amphibians, benthic macroinvertebrates, and planktons (Uno et al., 2022 Freshwater Biology). Direct estimates of the floodplain habitat contributions to the entire biodiversity show high contributions from the large wood and the diverse side channels to floodplain biodiversity. Many fish species utilize the hydrologically different side channels at different life stages, and the habitat complexity is crucial for the persistence of such species. Our results demonstrate 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 is potentially playing important roles sustaining such complexity, and further studies should investigate these mechanisms.