Natural channel design or two-stage design also recognizes that rivers and streams support both aquatic and terrestrial ecosystems. Natural channel design provides habitat for aquatic organisms such as fish, amphibians, insects, mollusks, and plants and contributes to stream networks, which provide food sources and migration routes for mammals and simultaneously supports a great diversity of birds. A lot of this habitat is created through riffle and pool sequencing.
Riffles are the lifeblood of the stream. The riffle area is a natural grade control that accelerates the water column producing a variety of flow velocities that oxygenate the stream and volatilize pollutants. The riffle pool sequence provides the fast currents and clean substrates that are essential for the colonization of bacteria, periphyton, macro-invertebrates, and spawning beds for fish. That acceleration of flows also creates the pools or deep water areas that are essential for sustaining fisheries during low flows. Constructing riffles and runs in degraded channels restores the variety of flow velocities and micro pools necessary to support aquatic ecosystems. Before the restoration of the Town Branch, it had one good pool and only a handful of decent riffle habitats. After the restoration, approximately 80 new riffles and pools were created.