Rivers and streams include lotic (running water) ecosystems, flowing from elevated uplands or underground springs to deltas, estuaries, and lakes. They are defined primarily by their linear structure, unidirectional flow regimes, and close interaction with the surrounding landscape. Individual rivers drain catchments separated by watersheds.

Channels that make up a river system can be classified into stream orders, with 1^st order streams having no tributaries, 2^nd order streams having 1^st order tributaries, 3^rd order having 2^nd order tributaries and so on. The world’s largest rivers are 10^th-12^th order. Flow regimes depend on stream order and rainfall patterns in the catchment (except in regulated rivers and spring-fed streams), which vary from year-round to seasonal to episodic. Stream gradients determine flow velocity and turbulence, bank and substrate structure, and habitat variability, but flow variability depends on regional climate and local weather. River systems in arid zones may remain dry for several years.

These factors act as selection filters, differentiating lotic ecosystems and their species’ traits amongst flow regimes, and between uplands and lowlands. Productivity tends to increase from uplands to lowlands, and is driven both by allochthonous energy sources that contribute coarse organic matter from terrestrial ecosystems in adjacent riparian zones and upper catchments, and by autochthonous energy synthesis by biofilms or phytoplankton. Phytoplankton is important downstream in larger, slower rivers that carry smaller organic particles and more dissolved organic matter. Erosion and depositional processes depend on the gradient and position of a stream reach within a catchment, and are fundamental to the downstream passage of nutrients and organic matter, and their exchange between river ecosystems and surrounding land. Anthropogenic nutrient inputs increase downstream and vary with land use. Rivers with extensive peatlands in their catchments are rich in tannins, which reduce light penetration through the water column, increase acidity, promote microbial activity that thrives on dissolved organic carbon, and thereby reduce oxygen levels, productivity and biotic diversity, although endemism may be high. Streams in cold climates freeze over in winter, imposing seasonal constraints on productivity and the movement of organisms. Much of the biotic diversity resides in or on the stream benthos.

Trophic webs are more complex in large rivers due to greater resource availability and niche diversity, and species-catchment area relationships. Invertebrate detritivores consume fragments of organic matter, providing resources for predatory macroinvertebrates and fish, which in turn support larger predatory fish, waterbirds, reptiles, and some mammals. Specialised species-level traits are associated with different flow regimes and life history strategies often align with patterns of resource availability. For example, suspension feeding is common in high flow velocities, cold tolerance and seasonal dormancy occur in freeze-thaw streams, life cycles are geared to autumnal leaf fall in temperate forested catchments, and desiccation tolerance and dormant life stages dominate in episodic rivers.