<p>Bacteria and eukaryotes are integral to the ecological functioning of river systems, while little is known about the spatial patterns and driving mechanisms of different abundance taxa in karst mountainous rivers. The 16S and 18S rRNA amplicon sequencing was used to examine microbial community composition and assembly processes in the surface water of the Tongzi River. The results showed that the community compositions of total and abundant bacteria and eukaryotes formed distinct clusters according to their geographic areas. Similar pattern of community composition was observed in total and abundant taxa. Co-occurrence networks incorporated most abundant taxa and the node-level topological properties of abundant taxa in both bacterial and eukaryotic networks were significantly higher than those of rare taxa. The keystone taxa identified by Zi/Pi analysis were both belonged to abundant taxa. Overall, these findings indicated that the bacterial and eukaryotic community structure and distribution were primarily governed by abundant taxa. Abundant taxa were more strongly influenced by spatial variation than rare taxa. Stochastic processes dominated the assembly of both bacterial and eukaryotic communities. Among the environmental factors analyzed, Oxidation–Reduction Potential (ORP) was the most important factor influencing the bacterial and eukaryotic communities. Furthermore, eukaryotic communities were more sensitive to environmental variations than bacterial communities. The results expand our understanding of the importance of abundant taxa in microbial community assembly in the karst mountainous river.</p>