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 ). Short τ should promote immigration but limit species establishment, while long τ should 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 a τ gradient spanning seven orders of magnitude. Microbial abundance, richness and evenness increased non‐linearly with τ , while functions like productivity and resource consumption declined. Taxa formed distinct clusters of short‐ and long‐ τ specialists 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.