Background and Aims <p>The increasing construction of dams on rivers around the world has created a unique and highly fragile ecosystem type, namely the reservoir riparian zone. The artificial dam operations impose inundation stress on riparian zones. However, how inundation stress influences the relationships between biodiversity and ecosystem function (BEF) in reservoir riparian zones remains unknown.</p> Methods <p>We investigated 64 transects (a total of 192 plots) along three world-renowned giant reservoirs in China (i.e., the Three Gorges, Danjiangkou, and Xiaolangdi reservoirs), and tested how inundation stress affects plant richness, soil bacterial and fungal richness, ecosystem functions (i.e., plant productivity, pools of soil carbon, nitrogen and phosphorus, and soil enzyme activities related to organic matter decomposition), and BEF in reservoir riparian zones.</p> Results <p>We found that riparian plant richness tended to decrease with increasing inundation intensity, but soil microbial richness showed no significant difference across the inundation intensity gradient, indicating that soil microbial diversity was more resilient under inundation stress compared to plant diversity. Riparian plant productivity of the Danjiangkou and Xiaolangdi reservoirs decreased as inundation intensified, and the carbon hydrolases activity and pools of soil carbon, nitrogen and phosphorus were not affected by inundation intensity. Notably, soil microbial diversity-ecosystem function relationship was weakened by intensified inundation stress, whereas plant diversity-ecosystem function relationship was strengthened.</p> Conclusion <p>These findings provide large-scale evidence that inundation stress enhances the functional importance of plant diversity but weakens that of soil biodiversity, and emphasize the divergent responses of above- and below-ground biodiversity-ecosystem function relationships to inundation.</p>