Multidimensional biodiversity framework reveals divergent responses of benthic organisms to multiple stressors in a highly urbanized river basin

Freshwater biodiversity faces an unprecedented decline from multiple stressors, yet conventional assessment approaches often inadequately capture complex ecological responses, especially in heavily urbanized river systems. Here we implemented a multidimensional biodiversity framework in China’s most urbanized basin─the Pearl River Basin─to investigate how macroinvertebrate and diatom communities respond to spatial factors and multiple stressors across climatic, hydrological, water quality, and land-use gradients. Based on two-year surveys at 50 sites (2020–2021), we found that (1) Basin-scale α-diversity increased longitudinally, whereas β-diversity decreased, with macroinvertebrates showing pronounced diversity attenuation in urbanized middle and downstream; (2) Spatial factors explained 61.0–83.1% of explained variance in macroinvertebrate α-diversity, indicating dispersal limitation as the primary assembly mechanism. In contrast, environmental drivers accounted for 66.2–77.5% of explained variance in diatom communities, reflecting stronger environmental filtering. Additionally, stochastic processes played an important role in shaping the assembly of both groups. (3) Multidiversity indices demonstrated significantly enhanced sensitivity to influence factors (84.9% for α-diversity and 12.9% for β-diversity), outperforming single-taxon metrics in detecting community-level responses to multiple pressures. Our findings highlight the importance of integrating taxonomic, functional, and phylogenetic diversity across levels when assessing ecosystem responses to complex environmental stressors, with direct implications for more effective biodiversity monitoring and conservation in human-disturbed river basins.