Background <p>Microbial communities, which drive most ecological processes and functions, contain not only a few highly abundant species but also a large number of rare species. However, little is known about the relative importance of abundant and rare microorganisms to network complexity and biogeochemical cycling, especially at large spatial scales. Here, we investigated nitrifying and denitrifying communities using high-throughput sequencing of archaeal <i>amoA</i> and bacterial <i>amoA</i>, <i>nirK</i>, and <i>nirS</i> genes, and we determined nitrification and denitrification rates in channel sediments, riparian rhizosphere soils, and riparian bulk soils of 30 rivers across China.</p> Results <p>Rare nitrifiers and denitrifiers exhibited broader environmental thresholds than abundant taxa. Co-occurrence network analysis revealed that all topological features (e.g., node degree and eigenvector centrality) had higher values for rare taxa than for abundant taxa. In addition, major modules (i.e., clusters of closely interconnected microbes) in the network were mainly composed of rare taxa, indicating that rare taxa play a vital role in maintaining the network complexity of nitrifying and denitrifying communities. Random forest analysis showed that nitrification rates were significantly associated only with the β-diversity of rare bacterial nitrifiers. Denitrification rates were largely influenced by the β-diversity of both rare and abundant <i>nirK-</i>type denitrifiers. These results suggested that rare microbial taxa play an important but previously underestimated role in biogeochemical processes.</p> Conclusions <p>Overall, this study highlights that, compared with abundant taxa, rare taxa contribute more to microbial network complexity and nitrogen cycling processes in river ecosystems at the continental scale.</p>