Biodiversity declined markedly over the past 150 years, with the biodiversity loss in fluvial ecosystems exceeding the global average. River restoration now aims at flood safety while enhancing biodiversity and has had success locally. However, at the scale of large river distributaries, the recovery remained elusive. We quantify changes in biodiversity of protected and endangered species over 15 years of river restoration in the embanked floodplains of an entire river delta. We distinguish seven taxonomic groups and four functional groups in more than 2 million field observations of species presence. Of all 179 fluvial floodplain sections examined, 137 showed an increase in biodiversity, particularly for fast-spreading species. Birds and mammals showed the largest increase, that is, +13 and +3 percentage point saturation of their potential based on habitat. This shows that flood risk interventions were successfully combined with enhancement of biodiversity, whereas flood stage decreased (-24 cm).