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Flow regulation in gravel-bed rivers impacts the hydrology, sediments and morphology, riparian vegetation, and vertical connectivity with the hyporheic zone. In this context, previous works have suggested that flood events may have riverine morphological and ecological benefits. In a Mediterranean-climate river system, we analyzed the impact of a 18-year return period flood on river morphology, riparian vegetation, fish aquatic habitat quality, and hyporheic exchange in a dam-regulated gravel-bed river, Serpis River (Spain). We collected pre- and post-flood riparian vegetation distributions and bathymetries, which were used to develop two-dimensional surface and three-dimensional subsurface numerical models to map surface and hyporheic hydraulics. Results show that the large flood removed the invasive giant reed from large areas, reshaped the in-channel morphology by forming new bars and pools, and enhanced the complexity of the flow field and the hydro-morphological diversity. The habitat availability for the endemic Eastern Iberian chub (Squalius valentinus) and invasive bleak (Alburnus alburnus) increased. Hyporheic exchange showed limited change under losing conditions, but noticeable under neutral ambient groundwater condition. This study corroborates the beneficial effects that flood events or high flow releases may have on regulated streams and the potential use of high flow pulse as a restoration tool., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)