Habitat is a combination of physical and biological characteristics of an area (or areas) essential for meeting the food and other metabolic needs, shelter, breeding, and over-wintering requirements of a particular species. For some species habitat can be as small as individual rocks or pebbles in the streambed. For others it can include many miles of rivers, streams, floodplains, wetlands, and ocean.
At any scale – from individual rocks in a streambed to particular habitat types (riffles, pools, cascades) to an entire river system – the particular characteristics of an area will determine what species are likely to be present. The tendency of areas to form structurally and functionally distinct portions of the landscape (e.g. riffles, pools, runs, floodplains, headwater streams, tidal rivers) means that organisms that inhabit these areas often form distinct assemblages of species called communities. These communities of organisms plus the physical environment they inhabit are what constitute ecosystems.
Natural communities are more than just collections of organisms. Species that make up communities are interconnected by a variety of ecological relationships, such as nutrient cycling and energy flow, predator-prey relationships, competition, and interdependency. For example, a single stream reach may support a variety of salmonid fish species competing with each other for food and appropriate habitat. Diverse communities of invertebrates are essential for providing a food base throughout the year for fish. Disease organisms, parasites, or predators that differentially affect species will affect the balance of competition among these fish.
The presence or absence of fish can affect whether other species are able to utilize river or stream habitats. Many amphibians require aquatic habitats that are free of fish in order to successfully breed. These species may utilize floodplain pools or intermittent sections of streams as long as fish are not regularly present. On the other hand, numerous species of North American freshwater mussels require specific fish hosts in order to complete reproduction. Larval stages of these mussels, known as glochidia, attach themselves to the gills or fins of host fish (or in one case, host salamanders), a process essential for proper development and dispersal. The nature of these interdependencies is such that freshwater mussels are unable to occupy otherwise appropriate habitat if their particular fish hosts are not present.