River ecosystems drain the landscape through hierarchical series of fluvial channels, beginning with small headwater streams, and enlarging, ultimately, to estuaries meeting the sea. Several conceptual models provide unifying concepts about the connections of rivers with the landscape in terms of ecosystem properties such as processing of energy and matter, habitat, biodiversity, and resilience in the face of disturbance. Major groups of riverine biota are described. Human activities pose threats to river ecosystems, including placing land from forests, grasslands, and wetlands into urban or agricultural uses, dams, pollutant loadings, alteration of natural drainage characteristics, introduced species, overharvesting, and climate change. River ecosystems are clearly important and at risk. Their direct economic importance to societies includes their use in transportation, water supply, energy, and provision of harvestable products. Their indirect importance, sometimes termed essential ecosystem services, includes their fundamental role as biogeochemical transformers of energy and matter, physical transformers of the landscape (shaping the land through fluvial processes), and the provision of a wide variety of ecological habitats along the river continuum. Historically, the assessment of river ecosystems was hindered by two factors. First, on a practical basis, it is difficult to adopt a single methodology by which to assess the state of a large river system from headwaters to mouth. Many of the methods that were developed for small-stream study are not easily adapted to the higher order parts of the system, and at the other end of the continuum, oceanographic methodologies may be designed for scales of study that are larger than rivers. Second, until the development of scale-spanning river paradigms such as the river continuum concept, ecological studies of rivers tended to consider a river in isolation from its watershed; as is now widely recognized, upstream processes in the watershed (including human-accelerated land use change) have major downstream effects on rivers.