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 physical, chemical and ecological responses to changes in the flow regimes of each river network, especially in response to human activities. The extent of non-perennial segments in river networks has increased owing to warming, changing hydrological patterns and human activities, and this increase is predicted 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 non-perennial segments and ensure their legislative and regulatory protection, which is often lacking. Non-perennial segments of rivers undergo cycles of flowing, non-flowing and dry phases, influencing ecosystem dynamics and services across the river network. This Review describes the occurrence, ecology and future of these intermittent and ephemeral flows and highlights the importance of protecting these segments. Non-perennial segments comprise over half of the global river network. Ongoing climate change and human activities will further increase the occurrence of river drying.Recurrent cycles of flowing, non-flowing and dry phases influence exchanges of water, energy, nutrients and organisms between non-perennial segments and connected perennial waters.Physical, chemical and biological processes in non-perennial segments affect water quality and quantity, and ecological integrity in downstream receiving waters and entire river networks.Historically, river science and management have focused on perennial river segments, neglecting the ubiquity and importance of non-perennial segments. This imbalance has often led to environmental problems such as poor water quality, loss of biodiversity and alteration of natural flow regimes at the river-network scale.Sustaining the water quality and ecological integrity of entire river networks and associated downstream waters requires integrated management strategies that explicitly consider non-perennial segments and their connections with perennial ones.