Advanced habitat assessment


The habitat assessment process involves rating many different habitat conditions as optimal, suboptimal, marginal or poor based upon criteria (descriptions and a rating scale) included on the survey data sheets. The optimal category is a description of conditions that meet natural expectations; suboptimal includes descriptions of criteria that are less than desirable, but satisfies expectations under most circumstances; marginal is a description of moderate levels of degradation with severity at frequent intervals throughout the reach; and poor are descriptions of criteria for streams that have been substantially altered with severe degradation characteristics.  Descriptions of the habitat conditions are provided below followed by a brief description of each condition.  For additional information go to Chapter 5 of the US EPA’s Rapid Bioassessment Protocols.  The conditions here should be applied when describing the habitats of rocky-bottom streams and rivers.



Embeddedness refers to the extent to which rocks (gravel, cobble, and boulders) are surrounded by, covered, or sunken into the silt, sand, or mud of the stream bottom. Generally, as rocks become embedded, fewer living spaces are available to macroinvertebrates and fish for shelter, spawning and egg incubation. To estimate the percent of embeddedness, observe the amount of silt and sand sediments overlying and surrounding the larger gavel and cobble size particles.  You should base your embeddedness assessment on the composition of the materials that you observe.  Embeddedness is always evaluated in the riffles used for your macroinvertebrate collections.  In most cases the best person(s) to comment about this condition is the person(s) collecting macroinvertebrates.  If cobble and gravel are easy to remove from the riffle and there is little sand or silt either in the net or suspended during collections, embeddedness is minimal.  In some cases chemicals (i.e. those associated with polluted coalmine drainage) cement the substrate together and cause severe embeddedness. 




Sediment deposition is an estimate of the amount of sediment that has accumulated and the changes that have occurred to the stream channel as a result of deposition. Deposition occurs from large-scale movement of sediment. Sediment deposition may cause the formation of islands, point bars (areas of increased deposition usually at the beginning of a meander that increase in size as the channel is diverted toward the outer bank) or shoals, or result in the filling of runs and pools. Usually deposition is evident in areas that are obstructed by natural or manmade debris and areas where the stream flow decreases, such as bends. High levels of sediment deposition are symptoms of an unstable and continually changing environment that becomes unsuitable for many organisms. Sediment deposition should be rated throughout your reach and should not be confused with embeddedness.  Sediment deposition is probably the most difficult condition to assess.  It is a natural process and bars often form in streams that are very stable and have little sediment from the surrounding land or few problems with erosion.  When assessing this condition look for indicators that are unusual or beyond what is expected to be normal for the stream.  The most effective way to learn is to view many different stream types representing both degraded and natural conditions.  In most cases island formation, especially in small streams (1st through 3rd order), is an indication of excessive deposition.  The most common cause for unusual or un-natural deposition in most streams is human encroachment (i.e. structures such as bridges, roads, culverts etc. to close to the stream or built so that the stream is narrowed) and bank erosion. Steep sloping banks with exposed surfaces are more likely to erode.  Undercut banks can often erode but are sometimes very stable if covered with vegetation, tree roots and rocks.  Look for deposition around eroding banks, especially if they show bare soils consisting mostly of fine materials (fine gravel, sand and silt).  Hard surfaces no matter how steep or undercut are less likely to erode.





Riffle frequency estimates the sequence of riffles and thus the heterogeneity occurring in a stream. Riffles are a source of high-quality habitat and diverse fauna; therefore, an increased frequency of occurrence greatly enhances the diversity of the stream community. For high gradient streams where distinct riffles are uncommon, a run/bend ratio can be used as a measure of meandering or sinuosity. A high degree of sinuosity provides for diverse habitat and fauna, and the stream is better able to handle surges when the stream fluctuates as a result of storms. The absorption of this energy by bends protects the stream from excessive erosion and flooding and provides refuge for benthic invertebrates and fish during storm events. To gain an appreciation of this parameter in some streams, a longer segment or reach than that designated for sampling should be incorporated into the evaluation. In some situations, this parameter may be rated from viewing accurate topographical maps. The "sequencing" pattern of the stream morphology is important in rating this parameter. In headwaters, riffles are usually continuous and the presence of cascades or boulders provides a form of sinuosity and enhances the structure of the stream. A stable channel is one that does not exhibit progressive changes in slope, shape, or dimensions, although short-term variations may occur during floods.




Attachment sites includes the relative quantity and variety of natural structures in the stream, such as cobble (riffles), large rocks, fallen trees, logs and branches, and undercut banks, available as refuge, feeding, or sites for spawning and nursery functions of aquatic life. A wide variety and abundance of submerged structures in the stream provide macroinvertebrates and fish with a large number of niches, thus increasing habitat diversity. As variety and abundance of cover decreases, habitat structure becomes monotonous, diversity decreases, and the potential for recovery following disturbance decreases. Riffles and runs are critical for maintaining a variety and abundance of insects in most high-gradient streams and serving as spawning and feeding refuge for certain fish. The extent and quality of the riffle is an important factor in the support of a healthy biological condition in high-gradient streams. Riffles and runs offer a diversity of habitat through variety of particle size, and, in many small high-gradient streams, will provide the most stable habitat. Snags and submerged logs are among the most productive habitat structure for macroinvertebrate colonization and fish refuge in low-gradient streams. However, "new fall" will not yet be suitable for colonization.




Patterns of velocity and depth are included for high-gradient streams under this parameter as an important feature of habitat diversity. The best streams in most high-gradient regions will have all four patterns present: slow-deep (pools); slow-shallow (glides); fast-deep (runs); and fast-shallow (riffles).




Channel alteration is a measure of large-scale changes in the shape of the stream channel. Many streams in urban and agricultural areas have been straightened, deepened, or diverted into concrete channels, often for flood control or irrigation purposes. Such streams have far fewer natural habitats for fish, macroinvertebrates, and plants than do naturally meandering streams. Channel alteration is present when artificial embankments, riprap, and other forms of artificial bank stabilization or structures are present; when the stream is very straight for significant distances; when dams and bridges are present; and when other such changes have occurred. Scouring is often associated with channel alteration.




The degree to which the channel is filled with water is the channel flow status. The flow status will change as the channel enlarges (e.g., aggrading stream beds with actively widening channels) or as flow decreases as a result of dams and other obstructions, diversions for irrigation, or drought. When water does not cover much of the streambed, the amount of suitable substrate for aquatic organisms is limited. In high-gradient streams, riffles and cobble substrate are exposed; in low-gradient streams, the decrease in water level exposes logs and snags, thereby reducing the areas of good habitat. Channel flow is especially useful for interpreting biological condition under abnormal or lowered flow conditions. This parameter becomes important when more than one biological index period is used for surveys or the timing of sampling is inconsistent among sites or annual periodicity.

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