Iowa DNR
River & Stream Biological Monitoring
Fish and Benthic Macroinvertebrate Surveys
Physical Habitat Assessments

Habitat - Instream Fish Cover

This portion of the physical habitat protocol is a visual estimation procedure that semi-quantitatively evaluates the type and amount of important types of cover for fish and macroinvertebrates. Alone and in combination with other metrics, this information is used to assess habitat complexity, fish cover, and channel disturbance.

A area 5 meters upstream and downstream of the transect (10m total) is visually examined for several fish cover types.

Fish Cover Type

Minimum Fish Size*


Filamentous Algae


Filamentous algae long enough (~>2”) to provide cover.



Rooted aquatic plants long/large enough to provide cover.

Woody Debris


Logs and woody debris that are >30cm (~1’) in diameter.

Small Brush/

Woody Debris


Logs, brush and other woody debris <30cm (~1’) in diameter.



Trees/roots that are inundated or could become inundated.

Overhanging Vegetation


Living or non-living vegetation within 1m of the water surface.

Undercut Banks


Undercut banks with a vertical depth of >1.5’ when measured from underside of the undercut to the bottom of the stream. When inundated it must provide enough cover for an adult fish.



Rocks >10’’ (250-4000mm) or the size of a basketball to a car.

Artificial Structures


Purposeful or incidental anthropogenic items (e.g. fish hide or tire).



Deeper water areas (> 2’) with slow to no current velocity.

*Juvenile fish include small-bodied species such as darters and minnows. Adult fish include large-bodied species such as suckers or trout.

Using the following 0 – 4 rating scheme an estimate of the aerial percentage represented by each cover type within the 10m area is made: 0 = absent, 1 = sparse (>0% to < 10%), 2 = moderate (>10% to 40%), 3 = heavy (>40% to 75%), and 4 = very heavy (>75%). It is permissible for the total aerial percentage for all cover types to equal more than 100% due to potential overlaying of cover types in three-dimensional space.

In early 2021, Watercress was added to the database as an additional Instream Fish Cover category. The category was added at the request of the Iowa DNR Fisheries Bureau to record the presence and amount of watercress on transects to aid in cold-water thermal classifications. Although watercress is listed under "instream cover", the watercress values are NOT included in the instream cover summary calculations. This may change in the future as more watercress data is collected and the summaries can be calibrated for its inclusion.

This page was created 3/30/2021 10:07:03 AM and was last updated 3/30/2021 10:27:34 AM