How hyporheic invertebrates at relatively shallow depths cope with floods and sediment movements that involve vertical and horizontal distribution shifts is not well known. This study examined the responses of macroinvertebrate communities in both benthic and hyporheic zone (30–50 cm deep from the riverbed) to a flow release at a fine temporal resolution (a few hours prior to and four days after an artificially caused flood) of a gravel-covered point bar so that immediate responses to the event can be described. Hyporheic communities exhibited little change during the flood, whereas benthic communities exhibited substantial decreases in total abundance. Most strikingly, at the taxon level, numerically dominant hyporheic species at relatively shallow depths, Alloperla ishikariana, increased substantially in the hyporheic zone, and its increase was positively correlated with deposited sediment depth (up to 45 cm). This study suggests that flood-induced sediment deposition drives rapid invertebrate colonization of the hyporheic zone. This can be perceived as refuge use of the benthic zone by hyporheic species in association with sediment deposits, which is a new conceptual framework for explaining how hyporheic invertebrates can persist through flood events by adapting to dynamic sediment movements. Experiments using artificial floods provide promising opportunities for challenging hyporheic studies.