Rivers are spatially organised into hierarchic dendritic networks. This unique physical structure and the associated directionality of physical flows set them apart from most other environments by regulating the dispersal of resident biota and therefore the distribution of biodiversity. The aim of this special issue is to highlight the importance of the river network on structuring biodiversity, particularly through metacommunity dynamics and associated dispersal processes. The issue covers a wide range of topics, including disease spread, nutrient uptake, trophic dynamics, effects of anthropogenic stressors and the joint roles of dispersal and environmental filtering. Contributions employ a broad range of approaches, including field and laboratory experiments, modelling, population genetics and conceptual synthesis. Although these studies represent just a sample of the research that is being performed on biodiversity and metacommunity dynamics in river networks, several important findings have emerged; a common theme being that the structure of the network and spatial dynamics clearly influence the dynamics of populations and communities, and their functions. By taking a broad taxonomic focus (from diatoms and protists to fish), and spanning a large geographic gradient (from the tropics to the subarctic), this special issue provides a broad look at the dynamics that occur in river networks relating to their unique makeup. We hope that this selection of studies spurs additional research on these interesting, globally important, yet severely threatened ecological systems.