Non-perennial river segments-those that recurrently cease to flow or frequently dry-occur in all river networks, and are globally more abundant than perennial (always flowing) segments. However, research and management have historically focused on perennial river segments. In this Review, we outline how non-perennial segments are integral parts of river networks. Repeated cycles of flowing, non-flowing and dry phases in non-perennial segments influence biodiversity and ecosystem dynamics at different spatial scales, from individual segments to entire river networks. Varying configurations of perennial and non-perennial segments govern each river network's physical, chemical and ecological responses to changes in flow regimes, especially in response to human activities. The extent of non-perennial segments in river networks has increased due to warming, changing hydrological patterns and human activities, and this increase is expected to continue.Moreover, the dry phases of flow regimes are expected to be longer, drier, and more frequent, albeit with high regional variability. These changes will likely impact biodiversity, potentially tipping some ecosystems to compromised stable states. Effective river network management must recognize ecosystem services (such as flood risk management and groundwater recharge) provided by nonperennial segments and ensure their legislative and regulatory protection, which is often lacking.