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ABSTRACT Much of life on Earth is at the mercy of currents and flow. Residence time (τ) estimates how long organisms and resources remain in a system based on the ratio of volume (V) to flow rate (Q). Shortτshould promote immigration but limit species establishment, while longτshould favour species that survive on limited resources. Theory suggests these opposing forces shape the abundance, diversity and function of flowing systems. We experimentally tested how residence time affects a lake microbial community by exposing chemostats to aτgradient spanning seven orders of magnitude. Microbial abundance, richness and evenness increased non‐linearly withτ, while functions like productivity and resource consumption declined. Taxa formed distinct clusters of short‐ and long‐τspecialists consistent with niche partitioning. Our findings demonstrate that residence time drives biodiversity and community function in flowing habitats that are commonly found in environmental, engineered and host‐associated ecosystems.