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Microbial abundance and diversity in river ecosystems are being increasingly investigated, yet a synthesized understanding is still lacking. Here, studies of microbial abundance and diversity along global rivers are systematically reviewed based on 814 investigations performed across 8376 sites. We found that riverine microbial investigations are extremely heterogeneous regarding the spatiotemporal distribution of the sampling sites, the environmental media concerned, the microbial groups and indices targeted, the methods used, and the physicochemical properties examined. More than 72.23% of the studies were performed in the last 8 years, with most studies conducted in Europe, China, and the United States, while other regions were poorly investigated. Most studies have examined microbes in water, but very few studies have systematically investigated microbes in water, sediments, and riparian soils. Bacteria are the most studied microbial taxonomic groups; microbes with resistance genes and nitrogen cycling genes are the most studied microbial functional groups. High-throughput sequencing has greatly expanded our understanding of microbial diversity along rivers. Nevertheless, the ecological implications of microbial diversity are still poorly understood. Regarding physicochemical properties, researchers tend to examine environmental parameters that are critical for shaping microbial communities, such as pH, nitrogen, and phosphorus. Future research should pay more attention to rivers that have not been well studied, especially large rivers. Additionally, microbial studies along rivers should be conducted in a more systematic way, taking the underinvestigated environmental media, microbial groups, microbial indices, and physicochemical properties into consideration. Advanced microbiology techniques, such as multiple omics technologies, should be increasingly applied.