To understand the impacts of debris flows on the distribution of an amphipod with limited dispersal ability in the context of stream networks, we surveyed the presence of Gammarus nipponensis in 87 headwater streams with different legacies of debris flow occurrence within an 8.5-km2 mountain catchment. The amphipod was present in only 7% of the streams impacted by debris flows after 1977; in contrast, it was present in 69% of the streams that had older or no debris flow occurrence. The absence of the amphipod in certain headwater streams did not appear to be related to water chemistry because pH and calcium concentrations differed little among streams within the catchment. In addition, survival rates of individuals incubated in streams with the amphipod present and absent did not differ significantly. Debris flows appeared to displace amphipod populations, and the absence of amphipods in streams for more than 30 years after debris flow occurrence suggests that considerable time is required for the recovery of populations. Because of geographic isolation from the source of colonists, headwater streams in the uppermost sections of the catchment and those indirectly connecting to the main stream via tributaries appear to be at greater disadvantage for receiving colonists from other areas and thus population recovery. Copyright © 2012 John Wiley & Sons, Ltd.