Microbes inhabit virtually all river ecosystems, influencing energy flow and playing a key role in global sustainability and climate change. Yet, there is uncertainty about how various taxonomic groups respond to large‐scale factors in river networks. We analysed microbial community richness and composition across six European Atlantic catchments using environmental DNA sequencing. Our findings reveal different drivers for diversity and composition: land use is pivotal for eukaryotes, while climate and geology are crucial for prokaryotes. A strong regional influence shapes these communities, with warmer, drier regions (Portugal and France) differing from cooler, wetter ones (Northern Spain, Ireland and the United Kingdom). These patterns suggest potential indicators for global change, such as taxa resistant to temperature increases and water scarcity, or those sensitive to land use changes. [ABSTRACT FROM AUTHOR]

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