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The water and sediments of urban rivers are spatially heterogeneous because of the influence of environmental and anthropogenic factors. However, the spatial and functional diversity of bacterial communities in urban river sediments are unclear. We investigated the spatial distribution of microbial compositions in sediments in Qingdao section of the Dagu River, and the effects of sediment physiochemical properties on the variation were explored. Among the seven heavy metals analyzed, only the average concentration of Cd significantly exceeded the safety limit for sediments. The detailed composition and spatial distribution of bacterial communities fluctuated substantially between sites along the river. Bacterial datasets were separated into three clusters according to the environmental characteristics of sampling areas (the urbanized, scenic, and intertidal zones). For the urbanized zone, Acidobacteria, Firmicutes, Gemmatimonadetes, Bacteroidetes, and Gammaproteobacteria were significantly enriched, implying the effects of human activity. In the intertidal zone, Alphaproteobacteria and Deltaproteobacteria were significantly enriched, which are associated with S redox processes, as in the marine environment. Variation partitioning analysis showed that the amount of variation independently explained by variables of Na, Al, total S and Zn was largest, followed by sediment nutrients, while heavy metals and pH explained independently 13% and 9% of the variance, respectively. Overall, microbial structures in the Dagu River exhibited spatial variation and functional diversity as a result of natural and anthropogenic factors. The results will enable the prediction of the changes in urban river ecosystems that maintain their ecological balance and health. Image 1 • Microbial communities exhibit spatial variation and functional diversity in the Dagu River. • The microbial variation explained by variables of Na, Al, total S and Zn was largest. • Sediment nutrients explained the second largest portion of the microbial variation. Both natural and anthropogenic factors contribute to the spatial variation of microbial communities in the Dagu River. [ABSTRACT FROM AUTHOR]