Habitat Assessment

Habitat assessments in rivers and streams evaluate the condition of the physical and water chemistry features in the
stream, and the physical features along the rvet banks (the riparian zone) such as channel type, amount of woody
debris, bank stability, and vegetation type.

Why do we assess habitat?

Healthy and intact habitat is critical for supporting
biological communities, protecting water quality, and
preserving the overall ecological integrity of aquatic
ecosystems. Fish, insects, and other organisms find food
and shelter near and in streams, lakes, and wetlands.
Vegetation growing in the riparian zone provides shade,
stabilizes sediment, and can filter pollutants before they
enter the waterbody.

Alterations to the physical structure of the habitat
surrounding waterbodies can negatively impact instream
physical characteristics, water chemistry, and aquatic
communities. Specifically, if vegetation in the riparian
zone is removed, runoff of sediment into the stream can
increase. As a result, stream embeddedness (the amount
of sediment covering "substrate," or bottom material)
changes as excess sediment fills pools and reduces the
available substrate for fish and other aquatic organisms to

Table 7. Examples of habitat parameters and why we assess them.

shelter. The water chemistry may also change as the
excess sediment alters turbidity and pH levels. These
changes affect the potential for the habitat to support
the aquatic community.

Habitat assessments help determine whether
alterations to the riparian zone or instream features
may negatively impact water quality and aquatic
communities. Table 1 lists examples of parameters
that habitat assessments evaluate and the reasons for
assessing each parameter. These parameters are from
the Rapid Bioassessment Protocols (RBPs), which is a
popular, efficient, and cost-effective method to assess
habitat. Evaluating changes in the condition of habitat
parameters helps anticipate potential effects on the
aquatic ecosystem, provides clues towards sources of
degradation, and can inform restoration project? and
waterbody management strategies.

Habitat Parameter

Why We Assess this Parameter

Channel flow status, or the percent
of existing channel that is filled with
water

The degree to which the stream channel is filled with water affects the amount of suitable
substrate for aquatic organisms. Low flows can expose riffles and logs, reducing areas of
good habitat.

Channel alteration, or any activity
that changes the natural channel

Streams that have been straightened, deepened, or diverted into concrete channels have
far fewer natural habitats for aquatic organisms than naturally meandering streams. For
example, streams that are dammed prevent fish passage upstream for spawning.

Vegetative protection, or plant cover
on the streambanks

Native vegetative protection allows the streambank to resist erosion, absorb nutrients,
resist instream scouring, and provide stream shading. Streambanks that have full, natural
plant growth are better for aquatic organisms than those without vegetative protection.

Riparian vegetative zone width, or
the width of the riverbank vegetation

The vegetative zone controls erosion, serves as a buffer to pollutants entering a stream
from runoff, and provides habitat and nutrient input into the stream.

Source: USEPA (1999)

For factsheets on other water quality parameters, visit:
epa.gov/awma/factsheets-water-quality-parameters.

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For more information about the CWA Section 106 Grants Program, visit:
epa.gov/water-pollution-control-section-106-grants.

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Habitat Assessment

What affects habitat condition?

Habitat condition is affected by both natural influences
and human activities, including:

Invasive species - Humans introduce and spread
normative species to an area that can cause harm.
Invasive aquatic vegetation, such as hydrilla, can
harm native aquatic and riparian vegetation by
altering water chemistry and outcompeting them for
space, light, and resources such as dissolved oxygen
and nutrients.

Flooding - Flooding can increase water depth, width,
and velocity, and it can alter the location of woody
debris (Figure 1), sediments, and substrate in and
around a waterbody. For example, flooding can bring
in or remove fish habitat (such as woody debris).

stream embeddedness can change as the sediment
settles on the stream bottom, where it can bury
important habitat features and bottom-dwelling
biota such as fish eggs and macroinvertebrates.

Figure 1. Example of woody debris in a stream. Credit:
Photo courtesy of Zach Prause

Excess sediment deposition - Excess sediment
deposition (Figure 2) refers to sediment that has
been washed into a waterbody from the nearby
landscape or from upstream sources. As a result,

Figure 2. Example of sediment deposition in a stream.
Credit: Photo courtesy of Laura Shumway

Channel and riparian modification - Human
disturbances - including channel straightening
(channelization), damming, or removal of riparian
vegetation - negatively affect habitat condition.
The removal of riparian vegetation is particularly
harmful and can change water chemistry, water
temperature, and turbidity.

Runoff - Runoff from urban and agricultural areas
contains chemical contaminants and nutrient
pollution that harm habitat by affecting water
chemistry, causing algal blooms, eutrophication, and
altered pH levels. Riparian vegetation can absorb
and prevent runoff from entering a waterbody. When
vegetation is removed from the habitat, pollutant
runoff can increase.

Wh;

hat are EPA's recommended criteria for habitat condition?

EPA does not have recommended criteria for habitat
condition. However, water resource agencies have
developed methods for assessing and rating habitat
condition. Examples of these include:

The RBPs, which also report information associated
with optimal ratings for habitat parameters.
Information on the parameters in the RBPs field
data sheets are described in more detail below.

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Habitat Assessment

The National Aquatic Resource Survey (NARS)
habitat protocols for rivers, streams, lakes, and
wetlands which are more intensive sampling
methods (see EPA's website Manuals Used in the
National Aquatic Resource Surveys for NARS field
methods).

Source: USEPA (1999)

How do we assess habitat?

Using the RBPs, habitat is assessed in field data sheets,
which are a compilation often parameters used to
assess habitat condition. The field data sheets are
available for both high gradient streams and low gradient
streams (Figure 3). The RBPs data sheets are found in
Appendix A of EPA's Rapid Bioassessment Protocols for
Use in Wadeable Streams and Rivers Periphyton, Benthic
Macroinvertebrates, and Fish (1999). Other habitat
protocols typically collect information on similar types
of parameters but may be more or less quantitative and
time intensive. It is important to consider your objectives
to determine which protocol is most appropriate for your
program.

For the RBPs, during the habitat assessment, field staff
evaluate and rate parameters on a scale from 0 (poor)
to 20 (optimal) at each sampling reach. Descriptions of
the parameters and relative criteria are included in the
RBPs to ensure consistency in evaluations and ratings.

State agency protocols.

The optimal rating criteria for four RBP habitat
parameters in high gradient streams (steep sloped)
and low gradient streams (gently sloped) are in Table 2
below.

Figure 3. The Manistee River in Michigan, an example of a
low gradient stream. Credit: Photo courtesy of Zach Prause

Table 2. Examples of habitat parameters and their optimal rating criteria for high and low gradient streams.

Habitat Parameter

Optimal Rating Criteria

Channel flow status

Water reaches the base of both lower banks, and a minimal amount of channel
substrate is exposed.

Channel alteration

Channelization or dredging is absent or minimal; the stream has a normal
pattern.

Vegetative protection

More than 90% of the streambank surface and immediate riparian zone are
covered by native vegetation.

Riparian vegetative zone width

The width is larger than 18 meters; human activities have not impacted the zone.

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Habitat Assessment

The ratings are summed and compared to a reference
condition for a final habitat ranking. Field staff establish
reference conditions by monitoring sites that represent
the natural range of variation in minimally disturbed
habitat, water chemistry and biological conditions.

Weather can affect the conditions evaluated during the
habitat assessment. For example, storms can impact
the velocity, debris, sediment, and substrate present
in the waterbody. Thus, assessments should not be
conducted until after the impacts caused by inclement
weather subside.

What are the challenges of using habitat condition to assess water quality?

Habitat degradation may be the result of physical and/
or chemical alterations to waterbodies. Typically, habitat
assessments are conducted when collecting other
data. If field staff collect data at a site multiple times
each year, the habitat assessment may only need to
be conducted during one visit. If field staff collect data
just once a year or once every few years, the habitat
assessment should be conducted each visit. This allows
staff to evaluate how changes in habitat condition are
related to changes in other biological and chemical
indicators.

Using habitat condition to assess water quality can be
challenging because:

Methods for habitat assessments often rely on
the judgment of field staff and results may be
inconsistent from one field staff member to the next.
Adequate training is needed to ensure consistency in
applying methods.

Different types of waterbodies, such as low gradient
streams and high gradient streams, generally require
different methods for habitat assessment because
of varying habitat traits and optimal conditions.
For example, channel sinuosity (or meandering) is
evaluated in low gradient streams only. This can
complicate comparisons or summaries of results
among different waterbody types.

It is important to ensure that the right habitat
assessment methods are being applied comprehensively
and consistently to the given waterbody type.

EPA 841F210071 j December 2021

SERA

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