LAUSR

Approximately half of the global annual production of wastewater is released untreated into aquatic environments, which results in worldwide organic matter pollution in urban rivers, especially in highly populated developing countries. Nonetheless, information on microbial community assembly and assembly‐driving processes in organic matter–polluted urban rivers remains elusive. In this study, a field study based on water and sediment samples collected from 200 organic matter–polluted urban rivers of 82 cities in China and Indonesia is combined with laboratory water‐sediment column experiments. Our findings demonstrate a unique microbiome in these urban rivers. Among the community assembly‐regulating factors, both organic matter and geographic conditions play major roles in determining prokaryotic and eukaryotic community assemblies, especially regarding the critical role of organic matter in regulating taxonomic composition. Using a dissimilarity‐overlap approach, we found universality in the dynamics of water and sediment community assembly in organic matter–polluted urban rivers, which is distinctively different from patterns in eutrophic and oligotrophic waters. The prokaryotic and eukaryotic communities are dominated by deterministic and stochastic processes, respectively. Interestingly, water prokaryotic communities showed a three‐phase cyclic succession of the community assembly process before, during, and after organic matter pollution. Our study provides the first large‐scale and comprehensive insight into the prokaryotic and eukaryotic community assembly in organic matter–polluted urban rivers and supports their future sustainable management.