Hydrology and water quality drive multiple biological indicators in a dam-modified large river.

Freshwater biodiversity is increasingly threatened by dams and many other anthropogenic stressors, yet our understanding of the complex responses of different biotas and their multiple facets remains limited. Here, we present a multi-faceted and integrated-indices approach to assess the differential responses of freshwater biodiversity to multiple stressors in the Yangtze River, the third longest and most dam-densely river in the world. By combining individual biodiversity indices of phytoplankton, zooplankton, periphyton, macroinvertebrates, and fish with a novel integrated aquatic biodiversity index (IABI), we disentangled the effects of hydrology, water quality, land use, and natural factors on both α and β diversity facets in taxonomic, functional, and phylogenetic dimensions. Our results revealed that phytoplankton and fish species and functional richness increased longitudinally, while fish taxonomic and phylogenetic β diversity increased but phytoplankton and macroinvertebrate β diversity remained unchanged. Hydrology and water quality emerged as the key drivers of all individual biodiversity indices, followed by land use and natural factors, with fish and phytoplankton showed the strongest responses. Importantly, we found that natural, land use, and hydrological factors indirectly affected biodiversity by altering water quality, which in turn directly influenced taxonomic and phylogenetic IABIs. Our findings highlight the complex interplay of multiple stressors in shaping freshwater biodiversity and underscore the importance of considering both individual and integrated indices for effective conservation and management. We propose that our multi-faceted and integrated-indices approach can be applied to other large, dam-modified river basins globally.