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CADDIS Volume 2: Sources, Stressors & Responses

Physical Habitat

Ways to Measure Physical Habitat and Its Alteration

There are diverse measurements that may be used to quantify stream physical habitat, and a variety of publications are available that describe methods for measuring physical habitat in streams. Some of these publications are focused on fish habitat (Bain and Stevenson 1999) or have a state or regional focus (Simonson et al. 1994, Overton et al. 1997, Somerville and Pruit 2004, Doll et al. 2003).

Two general procedures, intended to be applicable nationwide, are available. The field methods for these procedures are designed to allow thorough collection of quantitative data representative of a stream reach. The documents outline methods used to measure and summarize physical habitat variables in the U.S. Environmental Protection Agency's Environmental Monitoring and Assessment Program (Kaufmann and Robison 1998, Kaufmann et al. 1999) and the U.S. Geological Survey's National Ambient Water Quality Assessment program (Fitzpatrick et al. 1998).

Physical habitat attributes Measurements
Stream size and channel dimensions Stream order
Stream catchment or watershed area (m2)
Thalweg depth (cm)
Wetted width (m)
Cross-sectional area (i.e., wetted width x thalweg depth) (m2)
Wetted width : thalweg depth ratio
Bank angle (degrees)
Bank undercut distance (m)
Bankfull width (m)
Bankfull height (m)
Channel gradient Water surface gradient (m/m or %)
Channel substrate size and type Mean substrate size class
Mean substrate diameter (mm)
Substrate embeddedness (%)
Percent substrate, specific size classes:
bedrock (>4000 mm)
boulder (250-4000 mm)
cobble (64-250 mm)
coarse gravel (16-64 mm)
fine gravel (2-16 mm)
sand (0.6-2 mm)
fines (silt/clay, <0.6 mm)
Percent substrate, coarse (>16 mm)
Percent substrate, sand + fines (<2 mm)
Percent substrate, wood
Percent substrate, organic detritus
Percent substrate, concrete
Percent substrate, hard pan
Relative bed stability
Habitat complexity and cover Percent, specific habitat types:
run or glide
impoundment pool
plunge pool
lateral scour pool
trench pool
backwater pool
dry channel
subsurface flow
Percent fast-water habitats (falls + cascades + rapids + riffles)
Percent slow-water habitats (glides + all pool types)
Percent pool (all pool types)
Channel sinuosity
Residual pool vertical profile area (m2)
Residual pool volume (m3)
Count of residual pools with residual depth >50 cm, >75 cm, >100 cm
Residual pool length (m)
Residual pool area (m2)
Residual pool depth (m)
Percent of pool volume filled with sediment fines
Areal cover, specific cover types (proportion)
filamentous algae
aquatic macrophytes
large woody debris
brush and small woody debris
overhanging vegetation
boulder and rock ledges
undercut banks
artificial structures
Areal cover, all types except algae and macrophytes (m2 or %)
Areal cover, large types (i.e., large wood, boulders, undercut banks, artificial structures) (m2 or %)
Areal cover, natural types (i.e., large wood, brush, overhanging vegetation, boulders and undercut banks) (m2 or %)
Large woody debris within active channel (i.e., submerged) [count or volume (m3)]
Large woody debris above active channel (i.e., not submerged) [count or volume (m3)]
Vegetation cover and structure in the riparian zone Percent, canopy density
Riparian canopy cover (proportion)
Riparian mid-layer cover (proportion)
Riparian ground-layer cover (proportion)
Riparian bare ground (proportion)
Anthropogenic alterations Riparian human disturbance, specific types
parks or lawns
row-crop agriculture
pasture or grass fields
culverts or bridge abutments
Channel-riparian interactions Incision height (m)

Alternatively, qualitative visual assessments that score various habitat characteristics on some scale (often from 0 to 20) and combine scores into an index have been widely used as well. Examples include U.S. EPA's Rapid Assessment Protocol Habitat Assessment (Barbour et al. 1999) and Ohio EPA's Qualitative Habitat Evaluation Index (QHEI) (Rankin 1989). In high gradient streams, the Rapid Habitat Assessment Protocol scores ten habitat characteristics: epifaunal substrate and available cover, embeddedness, velocity and depth regime, sediment deposition, channel flow status, channel alteration, frequency of riffles or bends, bank stability, bank vegetative protection, and riparian vegetative zone width (Barbour et al. 1999). The QHEI scores six habitat characteristics: substrate (type and quality), instream cover (type and quality), channel quality (sinuosity, development, channelization, and stability), riparian/erosion (width, floodplain quality, and bank erosion), pool/riffle (maximum depth, current available, pool morphology, riffle/run depth, riffle substrate stability, and substrate embeddedness), and gradient. While such assessment may be conducted more rapidly, direct measurements or estimates of physical habitat attributes more clearly define the habitat alterations at a site. Moreover, Bauer and Ralph (1999) found that measurements based on visual judgments, such as these qualitative visual assessments, were the least precise habitat variables, and they noted that percent pool has relatively low precision, because it is visually estimated and dependent on stream flow at the time of the observation. However, it should also be noted that some measurements listed in the preceding table also rely on visual estimates.

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