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The East River (Dong Jiang), a major tributary of the Pearl River (Zhu Jiang, the second largest river in China by discharge), is situated in southern China, which has the highest rates of urbanization and development on Earth. The East River also provides 80% of Hong Kong’s water supply. However, there have been no ecological studies to examine the combined impacts of changes in land use and water quality degradation on this river ecosystem. We tested the hypothesis that land-use disturbance and water quality degradation would significantly reduce benthic biodiversity in the East River by investigating macroinvertebrate community composition and relating it to data on water quality and catchment condition. The percentage of total impervious area within each catchment (%TIA—an indicator of land-use disturbance) was negatively related to a composite water quality index—the ERWQI—we developed for the East River. Modeling by partial least squares projection to latent structures (PLS) showed that family richness and relative abundance index (RAI) of macroinvertebrates were strongly influenced by both %TIA and ERWQI. Multi-response permutation procedure (MRPP) tests showed highly significant differences in family richness composition and RAI of macroinvertebrates among sites in the upper, middle, and lower course of the East River. MRPP also revealed differences in the family richness composition of nighttime drift samples between upper and middle site groups. Abundance (individuals m−3) and total family richness of drifting macroinvertebrates at each site were positively related to %TIA (range: 1.0–8.5%), while drift biomass was negatively related to dissolved oxygen and positively related to total suspended solids. Thus, human disturbances associated with land-use changes (increasing %TIA) and nutrient inputs severely degraded ecosystem integrity and the water quality of the East River and thereby reduced aquatic biodiversity. [ABSTRACT FROM AUTHOR]