| Summary: | Abstract Forest degradation caused by deer overabundance has become a worldwide problem in recent decades. Overgrazing by deer not only affects terrestrial ecosystems but also spreads to aquatic ecosystems. Mass consumption of forest floor vegetation by deer creates denuded slopes and increases sediment inputs into adjacent rivers. In addition, rivers have upstream–downstream continuum structures, whereby the effects of degradation events in forests at upstream sites may spread to larger ecosystems downstream. However, few studies have examined the indirect effects of deer overabundance on downstream ecosystems. I examined the relationships between population dynamics of 13 fish species and habitat characteristics at a downstream site over the course of 11 years after forest floor degradation by deer overconsumption in a 36.5‐km2 catchment area of the Yura River in the Ashiu Research Forest, Japan, which is well‐protected from anthropogenic influences. During my 11 years of observation, characteristics of stream habitats changed from a predominantly coarse substrate to a fine substrate. I observed a remarkable decrease in one species (Tribolodon hakonensis) and increase in another species (Pseudogobio esocinus), and these changes were reasonably consistent with the increase or decrease in their preferred habitat types in the sampling site. This study showed long‐term habitat changes in a stream after forest floor degradation due to deer overconsumption in its catchment area and demonstrated that fish populations reacted to these changes. This study suggests that catchment‐level management, including forest ecosystem conservation, is necessary to solve fundamental problems in stream ecosystems.
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