Stream Structure & Function

A major component of water quality or stream health is the physical condition or habitat structure of the stream. Just like people need homes and grocery stores and transportation systems, the habitat structure of a stream needs to provide these things for aquatic life.  A diversity of flow, sizes of rock, woody debris, and other features provide for a diversity of places to live, places to find food and free movement to different parts of the stream. For example, deep pools in a stream can provide a place for fish to go during hot summer days when flows are low or in the deep winter when parts of the stream may be frozen. Some species of fish live most of their lives in the bigger sections of river, but go up into smaller streams to lay eggs where there is less competition for their young. Some insects prefer fast flowing water over rocks and have evolved ways to attach themselves to rocks so they can catch their food as it flows by. The more diversity of structure there is, the more life a stream system can support. Connectivity here is also key, structures like dams or culverts under bridges can stop the movement of fish, denying them access to parts of the river they may need to breed or expand populations. 

Components of Stream Habitat


Natural stream channels wind back and forth vs. channelized streams that are very straight.  Curves in a stream slow water down and provide areas that sediments can drop out and form point bars. Outer bends tend to have deeper pools that are scoured out during high flows. 


From beginning to end, how much elevation change is there? Even though we live in a fairly flat state, there is elevation change across the landscape with defined river valleys. The slope of a stream determines how quickly water flows, particularly at normal or low flows. Higher slope results in faster water flow and usually narrower channels. Sections of the river with little slope or elevation change, results in slower moving water that may spread out or form braided channels.

Riffle-Pool-Run Sequence

These are relatively defined sections of a natural stream. Riffles have rocks of various sizes across part or most of the channel width.  Riffles create a diversity of velocities or flow across the rocks and concentrate flow through a narrower section of the stream channel. Pools are deeper sections of the stream that have been scoured out by higher flow events or below larger riffles or bends in the river. Runs are the quiet, flat flowing sections of river between riffles. All of these features create unique habitat areas that support different species of aquatic life.


What makes up the bottom of the stream? Substrate types range from silt – fine clay, to sand, to gravel, to cobble (rocks from 3-9″) to boulders (rocks over 9”), as well as exposed bedrock in some places. While having some silt is very normal, it is not good when whole sections of stream are covered in silt or other fine materials so that there are no interstitial spaces (nooks & crannies) between the rocks.


The wetted edge of a stream ranges from very stable with vegetation to the edge of the water, minor erosion with some undercut banks or exposed tree roots to very incised (deeply cut) channels with lots of exposed soil, little to no vegetation, trees falling in or infrastructure compromised.  In urban/suburban areas where stormwater is quickly directed to the nearest stream via stormsewers and structures are built too close to streams, streambank erosion is usually a big problem. 

Riparian Area

This is the land that is along both sides of a stream. The riparian area usually includes the floodplain, which in healthy stream systems is connected to the stream and provides a place for high flows to safely spread out in big rain events. The quality of the vegetation along the riparian area is important in reducing erosion, and providing habitat for insects that lay their eggs in the water.

Backwaters & Oxbows

These are areas off the main channel of a stream where flow is very slow or connected to stream only in high flow events. These can be important nursery areas for small or juvenile fish, breeding areas for some species as well as important areas for amphibians and birds. 

In-stream Vegetation

In-stream vegetation is the aquatic vegetation that grows both completely in the water or grows up above the water. Aquatic vegetation plays a big role in providing in-stream habitat for small fish and macroinvertebrates, can help stabilize stream edges and can concentrate flows and enhance flow diversity in sections of stream.  Too much vegetation can also cause problems by slowing down and allowing sediment to build up, exacerbate the extremes of the diurnal dissolved oxygen cycle and suck oxygen out of the water when it dies back.  Like most things, it is all about balance.

Woody Debris and Tree Roots

Exposed tree roots along streambanks and downed trees or other woody debris in the water provides structure for fish – ask any fisherman! Here again, balance is key. Too much/fast erosion we lose too many trees and banks fall in and too much woody debris clogs waterways, backs up flow and can cause more erosion or flooding.  Using root wads, the root ball of a tree that has been cut down and turned on its side, is a common practice in stream restoration to create habitat.