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CADDIS Volume 2: Sources, Stressors & Responses

Physical Habitat

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Authors: M.B. Griffith, B. Rashleigh,
K. Schofield

This section deals with the candidate causes associated with the geomorphologic and vegetative features of a stream channel. Degraded physical habitat is a leading cause of impairment in streams on 303d lists. According to Kaufmann et al. (1999), six attributes are the principal determinates of the physical habitat structure provided by a stream:

  1. Stream size and channel dimensions
  2. Channel gradient
  3. Channel substrate size and type
  4. Habitat complexity and cover
  5. Vegetation cover and structure in the riparian zone
  6. Channel-riparian interactions
photo of healthy stream
Figure 1. Stable channel-riparian interactions in Clifton Gorge, Ohio, as evident by the deposition of cobble bars and vegetated boulders in the center of the channel.

Although habitat includes all the physical, chemical, and biological attributes that affect or sustain the organisms within an ecosystem, this section deals with only the structural attributes of habitat (Kaufmann et al. 1993, 1999). Physical habitat does not include the physicochemical attributes of the stream water (e.g., water chemistry, water temperature, water clarity, water quantity, and light intensity), but, instead, it includes geomorphologic characteristics and biological attributes that determine habitat structure and affect energy inputs (e.g., presence of macrophytes and riparian vegetation).

photo of channelized tributary
Figure 2. Channelized tributary to Little Miami River, Ohio. Shallow root structure is insufficient to stabilize stream channel and artificial stream path alters gradient and development of habitat complexity.

The difference between relatively unimpaired physical habitat for aquatic life (see Figure 1) and a degraded habitat (see Figure 2) can be aesthetically obvious, but we recommend that in all cases the six attributes listed in this module should be considered before making a decision to include or defer physical habitat as a candidate cause of stream impairments.  Physical habitat attributes vary naturally with physiographic and climatic setting and watershed size.  Thus, anthropogenic alterations of these attributes from conditions expected naturally for a stream, given its physiographic and climatic setting and watershed size, represents the stressor gradient for stream biota.  Therefore, having a clear idea about what is natural for the region, lithology, soil type, and climate is particularly important when evaluating physical habitat.

Although there are exceptions, most natural streams are characterized by sequences of faster water (i.e., riffles) and slower water (i.e., pools) habitats that provide cover and diversity of substrate and hydraulic conditions to meet the various life history requirements of important biota such as macroinvertebrates and fish.  For example, large fish may require pools of sufficient depth to provide refugia during low flow periods, and both small and large fish require refuges from predators.  Lithophilic spawning fish and sprawling macroinvertebrates require interstitial spaces within stable, coarse gravel, cobble, or boulder substrata unembedded by fine substrates.

Exceptions to this pattern most often occur in regions characterized by low stream gradients where bedrock may be buried by unconsolidated, fine materials (i.e., sand or silt). For example, streams in the Mississippi Alluvial and Southeast USA Coastal Plains ecoregion may be sand-bottomed with little or no coarse inorganic substrates; most coarse substrates in these streams are woody debris (Wallace and Benke 1984).

simple conceptual diagram for physical habitat
Figure 3. A simple conceptual diagram illustrating causal pathways, from sources to impairments, related to physical habitat. Click on the diagram to go to the Conceptual Diagrams tab and view a larger version.

The conceptual diagram in Figure 3 shows how sources and activities lead to altered physical habitat and subsequently to biological effects. If you are still deciding what aspects of physical habitat are of greatest interest, we recommend reading through the conceptual diagram and this entire page. If you already know the attribute of interest, you may skip to Ways to Measure to review how these attributes may be measured.

Stream size and channel dimensions strongly define the potential amount of habitat available to organisms. (Kaufmann et al. 1999). Within a region, the general size class of a stream in terms of its drainage area, stream order, and annual runoff is relatively consistent, but these relationships can vary among climatic regions with differing precipitation and evapotranspiration regimes.  Anthropogenic activities can alter channel dimensions by changing the frequency of high discharges (i.e., bankfull or floods) or the discharge at low flow.  However, flow alteration is also treated as a distinct candidate cause.

Channel gradient (i.e., the slope or downstream change in elevation of the stream bed) determines the potential energy in a stream channel affecting water velocity and water's ability to move bed and bank material in the stream channel. Stream power, the capacity of a stream to move materials, is a function of channel gradient, cross-sectional area, shape, hydraulic roughness, and discharge. Channel gradient interacts with these other variables to influence the diversity of microhabitats for organisms within the stream reach, particularly in terms of water velocity. Moreover, these hydraulic characteristics interact with bed particle size to affect stream bed stability (Kaufmann et al. 1999). Generally, channel gradient is determined by the geomorphologic setting of a stream. However, anthropogenic activities that change bedload, or one of the other factors affecting stream power, can, in turn, alter channel gradients.  In addition, anthropogenic activities such as channelization may directly alter the effective channel gradient.

Channel substrate size and type determine the variety of habitats and the overall surface area for habitation by epilithic and interstitial aquatic animals (Pugsley and Hynes 1986).  For benthic organisms, substrate size and packing influence the stability of the substrate for attachment in varying flows (Biggs et al. 1997, Downes et al. 1997, Matthaei et al. 2000). This includes not only the characteristics of the geological substrates forming the stream bottom but, also, the presence of aquatic macrophytes or other organic materials—such as woody debris.  Substrate size and bedform (e.g., the presence of riffles or pools) influence the hydraulic roughness of the stream bed and the variation in current velocities in a stream channel. Substrate size and sorting (e.g., the variation in particle sizes within a substrate) also affect the size of spaces within substrates that provide cover for smaller fish, salamanders, and macroinvertebrates. Human activities, which disturb stream banks or increase upland erosion, increase the supply of sediments to stream channels. Increases in fine sediments decrease mean substrate size and increase the percentage of fine sediments. Suspended and fine bedded sediments are treated as a distinct candidate cause. Increases in bedload can destabilize channels,leading to channel aggradation  and accelerate channel migration.

Habitat complexity and cover are attributes that supply refugia from predation and sites for other biotic interactions. Habitat complexity and cover also modulate the constant force of flow under normal conditions and during periods of high flows and are refugia from lack of water at low flows. Components of habitat complexity (Kaufmann et al. 1999) include

  • The extent and distribution of geomorphological units, such as pools and riffles
  • The presence, size, and amount of large woody debris
  • The presence, extent, and diversity of other in-channel cover (e.g., undercut banks, boulders, macrophytes, algae, etc.)
  • Residual pool depth and channel complexity
  • Channel sinuosity

Geomorphologic units (i.e., pools-riffle or step-pool sequences), channel sinuosity, and hydraulic roughness result from and contribute to geomorphological processes that dissipate the energy of flowing water in stream channels.  Woody debris and living plants along stream banks also contribute to this dissipation of energy.

For fish that live in the water column, pools or other low-velocity areas are flow refugia (e.g., eddies, backwaters, and wake areas immediately downstream of rocks or woody debris in the stream channels) (Negishi et al. 2002). Pools also act as refuges when water depths become too low elsewhere in the channel at low discharges. Residual pool depth is a measure of the pool depth that would be remaining if discharge were reduced to 0. For many macroinvertebrates and some benthic fish, riffles represent turbulent, highly oxygenated areas of the stream that also have coarse sediments that resist movement during both normal and high flows (Matthaei et al. 1999, 2000). Therefore, channel complexity, which, at minimum, suggests a mixture of both low-velocity and high-velocity habitats, contributes to the diversity of animals residing in a stream (Jenkins et al. 1984, Tockner et al. 2003).

Any type of in-channel cover or water depths that shield fish or macroinvertebrates from observation by predators or competitors act as refuges from these biotic interactions.

Vegetation in the riparian zone plays many important roles in streams. Most of these roles will be dealt with in other candidate cause modules because the riparian zone generally affects the delivery of stressors to the stream channel and is not the point of exposure for stream organisms. Riparian woody vegetation is a primary source of woody debris in the channel. Riparian vegetation shades streams and provides leaf litter, an important food resource for stream organisms. Riparian vegetation growing immediately along stream banks stabilizes those banks, supplies cover and benthic substrates along the channel edge, and increases habitat complexity (Sweeney 1992, Trimble 1997, Sweeney et al. 2004). When flows exceed bankfull discharge, vegetation on the floodplain contributes to hydraulic roughness and moderates erosion (see also Temperature).

Channel-riparian interactions play an important—but variable—role in stream structure and function. Depending on the stream setting and hydrographic regime, natural overbank flows may vary from periodic (i.e., ≈ 1 per year) that inundate small areas of the adjacent riparian zone, to more infrequent flooding of large portions of the floodplain, to seasonal inundation of adjacent riparian wetlands. Overbank flows during periods of high discharge are important for stream geomorphology, and they can transport inorganic and organic materials between the channel and its floodplain. Anthropogenic alterations along the stream banks (i.e., floodwalls, levees, channelization) or upstream (i.e., flow-control dams) are intended to contain such flooding to reduce property damage but also change natural processes in the stream.

When describing altered physical habitat as a candidate cause, anthropogenic structural alterations in the stream channel  [e.g., walls, rip-rap and other revetments (i.e., bank armoring structures), culverts, bridge abutments, and channelization] are obvious. They alter flow, erosion, and deposition patterns, resulting in habitat alteration. Therefore, if the stream segment is a concrete channel or a reservoir, that attribute can be listed as a candidate cause. In addition to such anthropogenic alterations of the stream channel, anthropogenic alterations in the riparian zone or elsewhere in the stream catchment can be sources or indicators of potential changes to stream physical habitat.

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Checklist of sources, site evidence and biological effects

This module addresses changes in physical habitat as proximate stressors. Candidate causes associated with altered physical habitat should be considered when observations support portions of the source-to-impairment pathways in the conceptual diagram for physical habitat (Figure 3). The conceptual diagram and some of the other information also are useful for Step 3: Evaluate Data from the Case.

Below is a checklist of observations that can assist in discerning cases where altered physical habitat should be among the candidate causes of impairment. The list is intended to guide you in collecting evidence to support, weaken, or eliminate physical habitat as a candidate cause, but it is not exhaustive. For more information on specific sources and activities, site evidence, and biological effects listed in the checklist, click on checklist headings or go to the When to List tab of this module.

Consider listing candidate causes associated with altered physical habitat when the following sources, site evidence, and biological effects are present:

Sources and Activities
  • Presence of a low-head dam or weir downstream that submerges channel features
  • Presence of levees, walls, or other structures that confine high flows to the channel
  • Residential, commercial, or urban development that increases impervious surfaces
  • Agricultural activities designed to move water quickly off the land (e.g., drainage ditches or swales, tile drainage)
  • Removal or alteration of riparian vegetation
  • Activities that directly alter the channel, such as channelization, dredging, pipeline crossings, and gravel mining
  • Presence of a dam or weir upstream
  • Historical presence of a dam
  • Historical or current activities that directly disturb benthic substrates, such as dredge mining of placers for minerals such as gold
Site Evidence
  • Concrete structures, rip-rap or other revetments lining the channel
  • Coarse substrates (i.e., boulder, cobble, and woody debris) embedded by finer substrates (i.e., sand, silt, and clay)
  • Stream flow passing between abutments of a bridge or through a culvert or pipe
  • Straightening or deepening (i.e., channelization) of stream channel; materials previously removed from the channel mounded adjacent to channel
  • Predominance of runs, glides, or pools instead of alternating pools and riffles or other fast-water habitats
  • Presence of bare, eroded banks lacking vegetation
  • Lack or alteration of riparian vegetation
  • Head-cut and incision of stream channel
  • Extreme width:depth ratios
  • Lack of other habitat forming features (i.e., filamentous algae, aquatic macrophytes, large woody debris, brush and small woody debris, overhanging vegetation, undercut banks, or artificial structures)
  • Trampling of stream banks and  bank vegetation by livestock
Biological Effects
  • Reduced abundance, for example, of sunfish or bass (Centrarchidae) or salmon, trout or whitefishes (Salmonidae)
  • Reduced abundance of piscivorous fish
  • Reduced abundance of darters (Etheostoma or Percina), sculpins (Cottus), or madtoms (Noturus)
  • Reduced abundance of young-of-year fish
  • Reduced fish taxonomic richness
  • Reduced relative abundance of clinging and sprawling invertebrates
  • Changes in relative abundance of invertebrate functional feeding groups (e.g., grazers)
  • Changes in periphyton biomass and species composition

Consider these commonly associated candidate causes when listing altered physical habitats:

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