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Water: Bioassessment

Chapter 5 (part B): Habitat Assessment And Physicochemical Parameters

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This Chapter is divided into two parts: Part A and Part B (this file)


Parameters to be evaluated in sampling reach:

 

1

EPIFAUNAL SUBSTRATE/AVAILABLE COVER

high and low gradient streams 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 refugia, feeding, or sites for spawning and nursery functions of aquatic macrofauna. A wide variety and/or abundance of submerged structures in the stream provides 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 refugia 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 refugia in low-gradient streams. However, "new fall" will not yet be suitable for colonization.


Selected References

Wesche et al. 1985, Pearsons et al. 1992, Gorman 1988, Rankin 1991, Barbour and Stribling 1991, Plafkin et al. 1989, Platts et al. 1983, Osborne et al. 1991, Benke et al. 1984, Wallace et al. 1996, Ball 1982, MacDonald et al. 1991, Reice 1980, Clements 1987, Hawkins et al. 1982, Beechie and Sibley 1997.

Habitat Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

1. Epifaunal Substrate/Available Cover

(high and low gradient)

Greater than 70% (50% for low gradient streams) of substrate favorable for epifaunal colonization and fish cover; mix of snags, submerged logs, undercut banks, cobble or other stable habitat and at stage to allow full colonization potential (i.e., logs/snags that are not new fall and not transient). 40-70% (30-50% for low gradient streams) mix of stable habitat; well-suited for full colonization potential; adequate habitat for maintenance of populations; presence of additional substrate in the form of newfall, but not yet prepared for colonization (may rate at high end of scale). 20-40% (10-30% for low gradient streams) mix of stable habitat; habitat availability less than desirable; substrate frequently disturbed or removed. Less than 20% (10% for low gradient streams) stable habitat; lack of habitat is obvious; substrate unstable or lacking.
SCORE ___

20  19  18  17  16

15  14  13  12  11

10   9   8   7   6

 5   4   3   2   1   0

1a.  Epifaunal Substrate/Available Cover--High Gradient

Optimal and Poor Range Photos

1b.  Epifaunal Substrate/Available Cover--Low Gradient

Optimal and Poor Range Photos

2a

EMBEDDEDNESS

high gradient streams

Refers to the extent to which rocks (gravel, cobble, and boulders) and snags are covered or sunken into the silt, sand, or mud of the stream bottom. Generally, as rocks become embedded, the surface area available to macroinvertebrates and fish (shelter, spawning, and egg incubation) is decreased. Embeddedness is a result of large-scale sediment movement and deposition, and is a parameter evaluated in the riffles and runs of high-gradient streams. The rating of this parameter may be variable depending on where the observations are taken. To avoid confusion with sediment deposition (another habitat parameter), observations of embeddedness should be taken in the upstream and central portions of riffles and cobble substrate areas.


Selected References

Ball 1982, Osborne et al. 1991, Barbour and Stribling 1991, Platts et al. 1983, MacDonald et al. 1991, Rankin 1991, Reice 1980, Clements 1987, Benke et al. 1984, Hawkins et al. 1982, Burton and Harvey 1990.

Habitat Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

2.a Embeddedness

(high gradient)

Gravel, cobble, and boulder particles are 0-25% surrounded by fine sediment. Layering of cobble provides diversity of niche space. Gravel, cobble, and boulder particles are 25-50% surrounded by fine sediment. Gravel, cobble, and boulder particles are 50-75% surrounded by fine sediment. Gravel, cobble, and boulder particles are more than 75% surrounded by fine sediment.

SCORE ___

20  19  18  17  16

15  14  13  12  11

10   9   8   7   6

 5   4   3   2   1   0

2a.  Embeddedness--High Gradient

Optimal and Poor Range Photos

2b

POOL SUBSTRATE CHARACTERIZATION

low gradient streams Evaluates the type and condition of bottom substrates found in pools. Firmer sediment types (e.g., gravel, sand) and rooted aquatic plants support a wider variety of organisms than a pool substrate dominated by mud or bedrock and no plants. In addition, a stream that has a uniform substrate in its pools will support far fewer types of organisms than a stream that has a variety of substrate types.


Selected References

Beschta and Platts 1986, U.S. EPA 1983.
Habitat Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

2b. Pool Substrate Characterization

(low gradient)

Mixture of substrate materials, with gravel and firm sand prevalent; root mats and submerged vegetation common. Mixture of soft sand, mud, or clay; mud may be dominant; some root mats and submerged vegetation present. All mud or clay or sand bottom; little or no root mat; no submerged vegetation. Hard-pan clay or bedrock; no root mat or submerged vegetation.
SCORE ___

20  19  18  17  16

15  14  13  12  11

10   9   8   7   6

 5   4   3   2   1   0

2b.  Pool Substrate Characterization--Low Gradient

Optimal and Poor Range Photos

3a

VELOCITY/DEPTH COMBINATIONS

high gradient streams 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 4 patterns present: (1) slow-deep, (2) slow-shallow, (3) fast-deep, and (4) fast-shallow. The general guidelines are 0.5 m depth to separate shallow from deep, and 0.3 m/sec to separate fast from slow. The occurrence of these 4 patterns relates to the stream's ability to provide and maintain a stable aquatic environment.


Selected References

Ball 1982, Brown and Brussock 1991, Gore and Judy 1981, Oswood and Barber 1982.

Habitat Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

3a. Velocity/ Depth Regimes

(high gradient)

All 4 velocity/depth regimes present (slow-deep, slow-shallow, fast-deep, fast-shallow). (slow is <0.3 m/s, deep is >0.5 m). Only 3 of the 4 regimes present (if fast-shallow is missing, score lower than if missing other regimes). Only 2 of the 4 habitat regimes present (if fast-shallow or slow-shallow are missing, score low). Dominated by 1 velocity/ depth regime (usually slow-deep).

SCORE ___

20  19  18  17  16

15  14  13  12  11

10   9   8   7   6

 5   4   3   2   1   0

3a.  Velocity/Depth Regimes--High Gradient

Optimal and Poor Range Photos

3b

POOL VARIABILITY

low gradient streams Rates the overall mixture of pool types found in streams, according to size and depth. The 4 basic types of pools are large-shallow, large-deep, small-shallow, and small-deep. A stream with many pool types will support a wide variety of aquatic species. Rivers with low sinuosity (few bends) and monotonous pool characteristics do not have sufficient quantities and types of habitat to support a diverse aquatic community. General guidelines are any pool dimension (i.e., length, width, oblique) greater than half the cross-section of the stream for separating large from small and 1 m depth separating shallow and deep.


Selected References

Beschta and Platts 1986, USEPA 1983.
Habitat Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

3b. Pool Variability

(low gradient)

Even mix of large-shallow, large-deep, small-shallow, small-deep pools present. Majority of pools large-deep; very few shallow. Shallow pools much more prevalent than deep pools. Majority of pools small-shallow or pools absent.
SCORE ___

20  19  18  17  16

15  14  13  12  11

10   9   8   7   6

 5   4   3   2   1   0

3b.  Pool Variability--Low Gradient

Optimal and Poor Range Photos

4

SEDIMENT DEPOSITION

high and low gradient streams Measures the amount of sediment that has accumulated in pools and the changes that have occurred to the stream bottom 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.


Selected References

MacDonald et al. 1991, Platts et al. 1983, Ball 1982, Armour et al. 1991, Barbour and Stribling 1991, Rosgen 1985.
Habitat Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

4. Sediment Deposition

(high and low gradient)

Little or no enlargement of islands or point bars and less than 5% (<20% for low-gradient streams) of the bottom affected by sediment deposition. Some new increase in bar formation, mostly from gravel, sand or fine sediment; 5-30% (20-50% for low-gradient) of the bottom affected; slight deposition in pools. Moderate deposition of new gravel, sand or fine sediment on old and new bars; 30-50% (50-80% for low-gradient) of the bottom affected; sediment deposits at obstructions, constrictions, and bends; moderate deposition of pools prevalent. Heavy deposits of fine material, increased bar development; more than 50% (80% for low-gradient) of the bottom changing frequently; pools almost absent due to substantial sediment deposition.
SCORE ___

20  19  18  17  16

15  14  13  12  11

10   9   8   7   6

 5   4   3   2   1   0

4a.  Sediment Deposition--High Gradient

Optimal and Poor Range Photos

4b.  Sediment Deposition--Low Gradient

Optimal and Poor Range Photos

5

CHANNEL FLOW STATUS

high and low gradient streams The degree to which the channel is filled with water. 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.


Selected References

Rankin 1991, Rosgen 1985, Hupp and Simon 1986, MacDonald et al. 1991, Ball 1982, Hicks et al. 1991
Habitat Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor
5. Channel Flow Status

(high and low gradient)

Water reaches base of both lower banks, and minimal amount of channel substrate is exposed. Water fills >75% of the available channel; or <25% of channel substrate is exposed. Water fills 25-75% of the available channel, and/or riffle substrates are mostly exposed. Very little water in channel and mostly present as standing pools.

SCORE ___

20  19  18  17  16

15  14  13  12  11

10   9   8   7   6

 5   4   3   2   1   0

5a.  Channel Flow Status--High Gradient

Optimal and Poor Range Photos

5b.  Channel Flow Status--Low Gradient

Optimal and Poor Range Photos

Parameters to be evaluated broader than sampling reach:

 

6

CHANNEL ALTERATION

high and low gradient streams 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.


Selected References

Barbour and Stribling 1991, Simon 1989a, b, Simon and Hupp 1987, Hupp and Simon 1986, Hupp 1992, Rosgen 1985, Rankin 1991, MacDonald et al. 1991.
Habitat Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

6. Channel Alteration

(high and low gradient)

Channelization or dredging absent or minimal; stream with normal pattern. Some channelization present, usually in areas of bridge abutments; evidence of past channelization, i.e., dredging, (greater than past 20 yr) may be present, but recent channelization is not present. Channelization may be extensive; embankments or shoring structures present on both banks; and 40 to 80% of stream reach channelized and disrupted. Banks shored with gabion or cement; over 80% of the stream reach channelized and disrupted. Instream habitat greatly altered or removed entirely.

SCORE ___

20  19  18  17  16

15  14  13  12  11

10   9   8   7   6

 5   4   3   2   1   0

6a.  Channel Alteration--High Gradient

Optimal and Poor Range Photos

6b.  Channel Alteration--Low Gradient

Optimal and Poor Range Photos

7a

FREQUENCY OF RIFFLES (OR BENDS)

high gradient streams Is a way to measure 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 (see 7b). 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 refugia 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 (Gordon et al. 1992).


Selected References

Hupp and Simon 1991, Brussock and Brown 1991, Platts et al. 1983, Rankin 1991, Rosgen 1985, 1994, 1996, Osborne and Hendricks 1983, Hughes and Omernik 1983, Cushman 1985, Bain and Boltz 1989, Gislason 1985, Hawkins et al. 1982, Statzner et al. 1988.
Habitat Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

7a. Frequency of Riffles (or bends)

(high gradient)

Occurrence of riffles relatively frequent; ratio of distance between riffles divided by width of the stream <7:1 (generally 5 to 7); variety of habitat is key. In streams where riffles are continuous, placement of boulders or other large, natural obstruction is important. Occurrence of riffles infrequent; distance between riffles divided by the width of the stream is between 7 to 15. Occasional riffle or bend; bottom contours provide some habitat; distance between riffles divided by the width of the stream is between 15 to 25. Generally all flat water or shallow riffles; poor habitat; distance between riffles divided by the width of the stream is a ratio of >25.

SCORE ___

20  19  18  17  16

15  14  13  12  11

10   9   8   7   6

 5   4   3   2   1   0

7a.  Frequency of Riffles (or bends)--High Gradient

Optimal and Poor Range Photos

 

7b

CHANNEL SINUOSITY

low gradient streams Evaluates the meandering or sinuosity of the stream. 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 refugia for benthic invertebrates and fish during storm events. To gain an appreciation of this parameter in low gradient streams, a longer segment or reach than that designated for sampling may 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 "oxbow" streams of coastal areas and deltas, meanders are highly exaggerated and transient. Natural conditions in these streams are shifting channels and bends, and alteration is usually in the form of flow regulation and diversion. A stable channel is one that does not exhibit progressive changes in slope, shape, or dimensions, although short-term variations may occur during floods (Gordon et al. 1992).


Selected References

Hupp and Simon 1991, Brussock and Brown 1991, Platts et al. 1983, Rankin 1991, Rosgen 1985, 1994, 1996, Osborne and Hendricks 1983, Hughes and Omernik 1983, Cushman 1985, Bain and Boltz 1989, Gislason 1985, Hawkins et al. 1982, Statzner et al. 1988.
Habitat Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

7b. Channel Sinuosity

(low gradient)

The bends in the stream increase the stream length 3 to 4 times longer than if it was in a straight line. (Note - channel braiding is considered normal in coastal plains and other low-lying areas. This parameter is not easily rated in these areas.) The bends in the stream increase the stream length 2 to 3 times longer than if it was in a straight line. The bends in the stream increase the stream length 1 to 2 times longer than if it was in a straight line. Channel straight; waterway has been channelized for a long distance.
SCORE ___

20  19  18  17  16

15  14  13  12  11

10   9   8   7   6

 5   4   3   2   1   0

7b.  Channel Sinuosity--Low Gradient

Optimal and Poor Range Photos

8

BANK STABILITY (condition of banks)

high and low gradient streams Measures whether the stream banks are eroded (or have the potential for erosion). Steep banks are more likely to collapse and suffer from erosion than are gently sloping banks, and are therefore considered to be unstable. Signs of erosion include crumbling, unvegetated banks, exposed tree roots, and exposed soil. Eroded banks indicate a problem of sediment movement and deposition, and suggest a scarcity of cover and organic input to streams. Each bank is evaluated separately and the cumulative score (right and left) is used for this parameter.


Selected References

Ball 1982, MacDonald et al. 1991, Armour et al. 1991, Barbour and Stribling 1991, Hupp and Simon 1986, 1991, Simon 1989a, Hupp 1992, Hicks et al. 1991, Osborne et al. 1991, Rosgen 1994, 1996.
Habitat
Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

8. Bank Stability
(score each bank)

Note: determine left or right side by facing downstream

(high and low gradient)

Banks stable; evidence of erosion or bank failure absent or minimal; little potential for future problems. <5% of bank affected. Moderately stable; infrequent, small areas of erosion mostly healed over. 5-30% of bank in reach has areas of erosion. Moderately unstable; 30-60% of bank in reach has areas of erosion; high erosion potential during floods. Unstable; many eroded areas; "raw" areas frequent along straight sections and bends; obvious bank sloughing; 60-100% of bank has erosional scars.
SCORE ___ (LB) Left Bank      10     9
8          7          6
5          4          3
2          1          0

SCORE ___ (RB)

Right Bank   10     9
8          7          6
5          4          3
2          1          0

8a.  Bank Stability (condition of banks)--High Gradient

Optimal and Poor Range Photos

8b.  Bank Stability (condition of banks)--Low Gradient

Optimal and Poor Range Photos

9

BANK VEGETATIVE PROTECTION

high and low gradient streams Measures the amount of vegetative protection afforded to the stream bank and the near-stream portion of the riparian zone. The root systems of plants growing on stream banks help hold soil in place, thereby reducing the amount of erosion that is likely to occur. This parameter supplies information on the ability of the bank to resist erosion as well as some additional information on the uptake of nutrients by the plants, the control of instream scouring, and stream shading. Banks that have full, natural plant growth are better for fish and macroinvertebrates than are banks without vegetative protection or those shored up with concrete or riprap. This parameter is made more effective by defining the native vegetation for the region and stream type (i.e., shrubs, trees, etc.). In some regions, the introduction of exotics has virtually replaced all native vegetation. The value of exotic vegetation to the quality of the habitat structure and contribution to the stream ecosystem must be considered in this parameter. In areas of high grazing pressure from livestock or where residential and urban development activities disrupt the riparian zone, the growth of a natural plant community is impeded and can extend to the bank vegetative protection zone. Each bank is evaluated separately and the cumulative score (right and left) is used for this parameter.


Selected References

Platts et al. 1983, Hupp and Simon 1986, 1991, Simon and Hupp 1987, Ball 1982, Osborne et al. 1991, Rankin 1991, Barbour and Stribling 1991, MacDonald et al. 1991, Armour et al. 1991, Myers and Swanson 1991, Bauer and Burton 1993.
Habitat
Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

9. Vegetative Protection
(score each bank)

Note: determine left or right side by facing downstream

(high and low gradient)

More than 90% of the streambank surfaces and immediate riparian zones covered by native vegetation, including trees, understory shrubs, or nonwoody macrophytes; vegetative disruption through grazing or mowing minimal or not evident; almost all plants allowed to grow naturally. 70-90% of the streambank surfaces covered by native vegetation, but one class of plants is not well-represented; disruption evident but not affecting full plant growth potential to any great extent; more than one-half of the potential plant stubble height remaining. 50-70% of the streambank surfaces covered by vegetation; disruption obvious; patches of bare soil or closely cropped vegetation common; less than one-half of the potential plant stubble height remaining. Less than 50% of the streambank surfaces covered by vegetation; disruption of streambank vegetation is very high; vegetation has been removed to 5 centimeters or less in average stubble height.

SCORE ___ (LB)

Left Bank      10     9
8          7          6
5          4          3
2          1          0
SCORE ___ (RB) Right Bank   10     9
8          7          6
5          4          3
2          1          0

9a.  Bank Vegetative Protection--High Gradient

Optimal and Poor Range Photos

9b.  Bank Vegetative Protection--Low Gradient

Optimal and Poor Range Photos

10

RIPARIAN VEGETATIVE ZONE WIDTH

high and low gradient streams Measures the width of natural vegetation from the edge of the stream bank out through the riparian zone. The vegetative zone serves as a buffer to pollutants entering a stream from runoff, controls erosion, and provides habitat and nutrient input into the stream. A relatively undisturbed riparian zone supports a robust stream system; narrow riparian zones occur when roads, parking lots, fields, lawns, bare soil, rocks, or buildings are near the stream bank. Residential developments, urban centers, golf courses, and rangeland are the common causes of anthropogenic degradation of the riparian zone. Conversely, the presence of "old field" (i.e., a previously developed field not currently in use), paths, and walkways in an otherwise undisturbed riparian zone may be judged to be inconsequential to altering the riparian zone and may be given relatively high scores. For variable size streams, the specified width of a desirable riparian zone may also be variable and may be best determined by some multiple of stream width (e.g., 4 x wetted stream width). Each bank is evaluated separately and the cumulative score (right and left) is used for this parameter.


Selected References

Barton et al. 1985, Naiman et al. 1993, Hupp 1992, Gregory et al. 1991, Platts et al. 1983, Rankin 1991, Barbour and Stribling 1991, Bauer and Burton 1993.
Habitat
Parameter
Condition Category
Optimal
Suboptimal
Marginal
Poor

10. Riparian Vegetative Zone Width
(score each bank riparian zone)

(high and low gradient)

Width of riparian zone >18 meters; human activities (i.e., parking lots, roadbeds, clear-cuts, lawns, or crops) have not impacted zone. Width of riparian zone 12-18 meters; human activities have impacted zone only minimally. Width of riparian zone 6-12 meters; human activities have impacted zone a great deal. Width of riparian zone <6 meters: little or no riparian vegetation due to human activities.

SCORE ___ (LB)

Left Bank      10     9
8          7          6
5          4          3
2          1          0

SCORE ___ (RB)

Right Bank   10     9
8          7          6
5          4          3
2          1          0

10a.  Riparian Vegetative Zone Width--High Gradient

Optimal and Poor Range Photos

10b.  Riparian Vegetative Zone Width--Low Gradient

Optimal and Poor Range Photos

5.3 ADDITIONS OF QUANTITATIVE MEASURES TO THE HABITAT ASSESSMENT

Kaufmann (1993) identified 7 general physical habitat attributes important in influencing stream ecology. These include:

  • channel dimensions
  • channel gradient
  • channel substrate size and type
  • habitat complexity and cover
  • riparian vegetation cover and structure
  • anthropogenic alterations
  • channel-riparian interaction.

All of these attributes vary naturally, as do biological characteristics; thus expectations differ even in the absence of anthropogenic disturbances. Within a given physiographic-climatic region, stream drainage area and overall stream gradient are likely to be strong natural determinants of many aspects of stream habitat, because of their influence on discharge, flood stage, and stream power (the product of discharge times gradient). In addition, all of these attributes may be directly or indirectly altered by anthropogenic activities.

In Section 5.2, an approach is described whereby habitat quality is interpreted directly in the field by biologists while sampling the stream reach. This Level 1 approach is observational and requires only one person (although a team approach is recommended) and takes about 15 to 20 minutes per stream reach. This approach more quickly yields a habitat quality assessment. However, it depends upon the knowledge and experience of the field biologist to make the proper interpretation of observed of both the natural expectations (potentials) and the biological consequences (quality) that can be attributed to the observed physical attributes. Hannaford et al. (1997) found that training in habitat assessment was necessary to reduce the subjectivity in a visual-based approach. The authors also stated that training on different types of streams may be necessary to adequately prepare investigators.

The second conceptual approach described here confines observations to habitat characteristics themselves (whether they are quantitative or qualitative), then later ascribing quality scoring to these measurements as part of the data analysis process. Typically, this second type of habitat assessment approach employs more quantitative data collection, as exemplified by field methods described by Kaufmann and Robison (1997) for EMAP, Simonson et al. (1994), Meador et al. (1993) for NAWQA, and others cited by Gurtz and Muir (1994). These field approaches typically define a reach length proportional to stream width and employ transect measurements that are systematically spaced (Simonson et al. 1994, Kaufmann and Robison (1997)) or spaced by judgement to be representative (Meador et al. 1993). They usually include measurement of substrate, channel and bank dimensions, riparian canopy cover, discharge, gradient, sinuosity, in-channel cover features, and counts of large woody debris and riparian human disturbances. They may employ systematic visual estimates of substrate embeddedness, fish cover features, habitat types, and riparian vegetation structure. The time commitment in the field to these more quantitative habitat assessment methods is usually 1.5 to 3 hours with a crew of two people. Because of the greater amount of data collected, they also require more time for data summarization, analysis, and interpretation. On the other hand, the more quantitative methods and less ambiguous field parameters result in considerably greater precision. The USEPA applied both quantitative and visual-based (RBPs) methods in a stream survey undertaken over 4 years in the mid-Atlantic region of the Appalachian Mountains. An earlier version of the RBP techniques were applied on 301 streams with repeat visits to 29 streams; signal-to-noise ratios varied from 0.1 to 3.0 for the twelve RBP metrics and averaged (1.1 for the RBP total habitat quality score). The quantitative methods produced a higher level of precision; signal-to-noise ratios were typically between 10 and 50, and sometimes in excess of 100 for quantitative measurements of channel morphology, substrate, and canopy densiometer measurements made on a random subset of 186 streams with 27 repeat visits in the same survey. Similarly, semi-quantitative estimates of fish cover and riparian human disturbance estimates obtained from multiple, systematic visual observations of otherwise measurable features had signal:noise ratios from 5 to 50. Many riparian vegetation cover and structure metrics were moderately precise (signal:noise ranging from 2 to 30). Commonly used flow dependent measures (e.g., riffle/pool and width/depth ratios), and some visual riparian cover estimates were less precise, with signal:noise ratios more in the range of those observed for metrics of the EPA's RBP habitat score (<2).

The USEPA's EMAP habitat assessment field methods are presented as an option for a second level (II) of habitat assessment. These methods have been applied in numerous streams throughout the Mid-Atlantic region, the Midwest, Colorado, California, and the Pacific Northwest. Table 5-1 is a summary of these field methods; more detail is presented in the field manual by Kaufmann and Robison (1997).

Table 5-1. Components of EMAP physical habitat protocol.

Component Description
  1. Thalweg Profile
Measure maximum depth, classify habitat, determine presence of soft/small sediment at 10-15 equally spaced intervals between each of 11 channel cross-sections (100-150 along entire reach). Measure wetted width at 11 channel cross-sections and mid-way between cross-sections (21 measurements).
  1. Woody Debris
Between each of the channel cross sections, tally large woody debris numbers within and above the bankfull channel according to size classes.
  1. Channel and Riparian Cross-Sections
At 11 cross-section stations placed at equal intervals along reach length:
  • Measure: channel cross section dimensions, bank height, undercut, angle (with rod and clinometer); gradient (clinometer), sinuosity (compass backsite), riparian canopy cover (densiometer).
  • Visually Estimate*: substrate size class and embeddedness; areal cover class and type (e.g., woody) of riparian vegetation in Canopy, Mid-Layer and Ground Cover; areal cover class of fish concealment features, aquatic macrophytes and filamentous algae.
  • Observe & Record*: human disturbances and their proximity to the channel.
  1. Discharge
In medium and large streams (defines later) measure water depth and velocity @ 0.6 depth (with electromagnetic or impeller-type flow meter) at 15 to 20 equally spaced intervals across one carefully chosen channel cross-section. In very small streams, measure discharge with a portable weir or time the filling of a bucket.
* Substrate size class and embeddedness are estimated, and depth is measured for 55 particles taken at 5 equally-spaced points on each of 11 cross-sections. The cross-section is defined by laying the surveyor's rod or tape to span the wetted channel. Woody debris is tallied over the distance between each cross-section and the next cross-section upstream. Riparian vegetation and human disturbances are observed 5 m upstream and 5 m downstream from the cross section station. They extend shoreward 10 m from left and right banks. Fish cover types, aquatic macrophytes, and algae are observed within channel 5 m upstream and 5 m downstream from the cross section stations. These boundaries for visual observations are estimated by eye.

Table 5-2 lists the physical habitat metrics that can be derived from applying these field methods. Once these habitat metrics are calculated from the available physical habitat data, an assessment would be obtained from comparing these metric values to those of known reference sites. A strong deviation from the reference expectations would indicate a habitat alteration of the particular parameter. The close connectivity of the various attributes would most likely result in an impact on multiple metrics if habitat alteration was occurring. The actual process for interpreting a habitat assessment using this approach is still under development.

Table 5-2. Example of habitat metrics that can be calculated from the EMAP physical habitat data.

Channel mean width and depth
Channel volume and Residual Pool volume
Mean channel slope and sinuosity
Channel incision, bankfull dimensions, and bank characteristics
Substrate mean diameter, % fines, % embeddedness
Substrate stability
Fish concealment features (areal cover of various types, e.g., undercut banks, brush)
Large woody debris (volume and number of pieces per 100 m)
Channel habitat types (e.g., % of reach composed of pools, riffles, etc.)
Canopy cover
Riparian vegetation structure and complexity
Riparian disturbance measure (proximity-weighted tally of human disturbances)

 

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