EPA and Hardrock Mining: A Source Book for Industry in the Northwest and Alaska

January 2003

APPENDIX G

AQUATIC RESOURCES
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Appendix G: Aquatic Resources

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TABLE OF CONTENTS

1.0 PURPOSE AND GOALS OF THE APPENDIX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-1

2.0 ISSUES AND TERMINOLOGY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-1

3.0 AFFECTED ENVIRONMENT DESCRIPTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-3

3.1 Fish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-5

3.1.1 Distribution, Abundance, and Composition . . . . . . . . . . . . . . . . . . . . . . . G-5

3.1.2 Adult Spawning Counts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-7

3.1.3 Fish Tissue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-7

3.2 Benthic Macroinvertebrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-9

3.3 Amphibians . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-11

3.4 Aquatic Habitat and Riparian Zone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-13

4.0 IMPACT ASSESSMENT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-14

4.1 Water Quality Impacts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-15

4.1.1 Comparisons to Aquatic Life Water Quality Criteria . . . . . . . . . . . . . . G-15

4.1.2 Toxicity Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-16

4.1.3 Macroinvertebrate Metric Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-17

4.2 Sedimentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-17

4.3 Habitat Alteration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-18

4.4 Hazardous Material Spills . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-18

4.5 Flow Alterations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-19

4.6 Obstruction to Fish Movement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-20

5.0 REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-21

6.0 CONTACTS AND OTHER INFORMATION SOURCES . . . . . . . . . . . . . . . . . . . . G-27

6.1 Contacts for Fish Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-27

6.2 Contacts for Habitat Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-27

6.3 Contacts for Aquatic Life Water Quality Criteria . . . . . . . . . . . . . . . . . . . . . . . G-27

TABLE

Table G-1. Summary of Fish Sampling Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-8
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1.0 PURPOSE AND GOALS OF THE APPENDIX

In the Pacific Northwest and Alaska, freshwater aquatic resources often represent an

important component of the environment that must be considered in impact assessments for

mining projects. Freshwater aquatic resources that typically are addressed in a NEPA document

and baseline studies include fish, benthic macroinvertebrates, and physical parameters that

define habitat for these communities. These aquatic resources, especially fish, often represent

significant issues for the proposed action being evaluated during the NEPA process. 

The purpose of this appendix is to provide a summary of the types of information needed

to characterize freshwater aquatic resources within the project study area and describe methods

that can be used in analyzing impacts of mining projects on freshwater aquatic communities and

their habitat. The remaining portions of this Appendix provide information on Issues and

Terminology (Section 2.0), Affected Environment Description (Section 3.0), Impact Assessment

(Section 4.0), and Literature Cited (Section 5.0). Contacts and other information sources for the

topics discussed in this Appendix are included in Section 6.0. 

When conducting NEPA impact assessments for mining projects, considerable overlap

exists between aquatic resources and surface water and ground water quality and hydrology. 

Descriptions of methods for conducting NEPA impact assessments on hydrology, sedimentation,

and surface and ground water quality are provided in Appendix A, Hydrology, Appendix B,

Receiving Waters, and Appendix H, Erosion and Sedimentation.

This appendix addresses only freshwater aquatic resources. Most of the direct impacts of

mining operations in EPA Region 10 are to freshwater resources, simply because most mines and

mineral deposits are inland, and discharges to marine environments are generally prohibited. In

some cases, including cases where there are effects on anadromous fish, there would be indirect

effects on marine resources. Although not covered in this appendix, NEPA analyses should

address any such impacts to the marine environment and marine aquatic resources, whether

direct or indirect. 

2.0 ISSUES AND TERMINOLOGY

Resident and anadromous fisheries that are located within a mining project study area

represent a concern to the public and governmental agencies such as the National Marine

Fisheries Service (NMFS), the Bureau of Land Management (BLM), the U.S. Fish and Wildlife

Service (USFWS), the U.S. Forest Service (USFS), the U.S. Army Corps of Engineers

(USACE), Tribal Commissions, Tribes, and appropriate state organizations. Fish species,

particularly salmonids (trout and salmon), are important because of their recreational,

commercial, and/or cultural fishery value. Numerous species also are listed as threatened or

endangered (T&E) under the Federal Endangered Species Act or related state statutes. The

USFWS, NMFS, and appropriate state agencies should be contacted as part of the scoping and

issue identification for a particular project to obtain a list of Federal and state listed species. The
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1

 Essential Fish Habitat is defined as ". . . those waters and substrate necessary to fish for spawning, breeding, feeding, or growth

to maturity."

2

 Biological integrity is "a balanced, integrated, adaptive community of organisms having species composition, diversity, and

functional organization comparable to that of natural habitat of the region" (Karr and Dudley 1981).

G-2 January 2003

USFS also uses important fish species (usually salmonids) as Management Indicator Species. 

These species should be included in the NEPA analysis for projects that are located on USFS

land.

In addition, the Magnuson-Stevens Act requires Federal lead agencies to consult on

Essential Fish Habitat1 (EFH) that is established by the appropriate fisheries management

council and NMFS, as identified in their fishery management plans. The Act is a mandate to

conserve marine habitat, but it also includes freshwater habitat for anadromous fish species. In a

regulatory context for conserving fish habitat, the Act requires Federal agencies to consult with

NMFS when any activity proposed to be permitted, funded, or undertaken by a Federal agency

may have adverse impacts on designated EFH. If a project may have adverse effects on EFH,

NMFS is required to develop EFH Conservation Recommendations, which will include

measures to avoid, minimize, mitigate, or otherwise offset adverse effects on EFH. The

consultation process for EFH will be incorporated into interagency procedures previously

established under NEPA, ESA, Clean Water Act, Fish and Wildlife Coordination Act, and any

other applicable statutes.

Benthic macroinvertebrate communities represent an important biological component of

the aquatic environment, since they provide food sources for fish and are indicators of water

quality and habitat conditions. 

The Clean Water Act (CWA) directs the EPA and states to develop and implement

programs that evaluate, restore, and maintain the chemical, physical, and biological integrity2

. 

States adopt water quality standards to protect public health and welfare, enhance the quality of

water, and protect biological integrity. In general terms, a water quality standard defines the

goals of a water body by designating the use or uses to be made of the water, establishing criteria

necessary to protect those uses, and preventing degradation of water quality through

antidegradation provisions. The fish, macroinvertebrate, and periphyton (attached algae)

assemblages are all direct measures of the beneficial use under the CWA. The CWA applies to

all species of aquatic life including, but not limited to, “important” fish species.

After reviewing the proposed mining plan for a particular project, the potentially disturbed

or impacted areas should be related to the presence of fish species, macroinvertebrate

communities, and habitat conditions (including riparian and hyporheic zones) within the project

study area. Potential aquatic resource issues for mining projects include:

C Potential adverse effects on water quality and aquatic communities and habitat due

to sedimentation, metals, acid generating materials, and other toxic chemical

loadings.
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3

Riparian is a term that refers to “plant communities contiguous to and affected by surface and subsurface hydrologic

features of perennial or intermittent lotic and lentic water bodies (rivers, streams, lakes, or drainage ways). Riparian areas have

one or both of the following characteristics: 1) distinctly different vegetative species than adjacent areas, and 2) species similar

to adjacent areas but exhibiting more vigorous or robust growth forms. Riparian areas are usually transitional between wetland

and upland” (USFWS, 1997). Riparian areas also often include wetlands. 

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C Potential effects of transporting and storing fuel and other toxic chemicals that could

pose risk of spills and adversely affect aquatic communities and their habitat.

C Potential water use by mining operations that may affect flows in project area water

bodies, which could adversely affect habitat for important fish species and

macroinvertebrate communities. 

C Potential direct disturbance to habitat used by important fish species during life

history events such as spawning, rearing, and adult movements.

These issues are discussed in more detail in Section 4.0.

3.0 AFFECTED ENVIRONMENT DESCRIPTION

The initial steps in describing an affected environment include: (1) define the study area

and (2) collect and review available information on aquatic resources that are located within the

project study area. Information in this appendix focuses on specific aspects of the data collection

and review task for aquatic resources and a summary of methods that can be used in conducting

additional baseline studies.

The affected environment description should characterize important information on fish

communities, macroinvertebrate communities, amphibians and other aquatic and semi-aquatic

vertebrates, and aquatic habitat, including the adjacent riparian3

 zone, within the project study

area. Fish and macroinvertebrate assemblages are defined as an associations of organisms in a

given water body (EPA 1996). The study area for aquatic resources should include potentially

affected watersheds. The study area should encompass on-site (project area boundary) and offsite (both upstream and downstream) water bodies and adjacent riparian zones that receive both

direct and indirect impacts. The level of detail and analyses need to be commensurate with the

importance of the impact (Council on Environmental Quality, 1986). The following types of

information are typically needed to characterize aquatic resource topics for the Affected

Environment Section of a NEPA document:

Fish (Aquatic Vertebrates) Assemblage Information

C Species list (all species included). This includes any other aquatic vertebrate species

(e.g., amphibians) that might be collected in conjunction with the fish.

C Distribution, abundance, and composition of game fish and T&E and candidate

species.

C Distribution, abundance, and composition of amphibians and other aquatic and semiaquatic vertebrates (including aquatic mammals and reptiles)

C List of any critical habitat designations for T&E species, as established by the
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USFWS and/or state agencies.

C List of any Essential Fish Habitat established by regional fisheries management

council.

C Seasonal timing of spawning for game and T&E and candidate species.

C Habitat requirements of game and T&E and candidate species.

Fish Tissue Contamination Information

C Species, type of sample (i.e. whole fish, fillet), and number of samples; and

C Metal concentration in sample.

Macroinvertebrate Assemblages Information

C Enumeration and identification of benthic invertebrates to the lowest taxonomic

level (Plotnikoff and White 1996).

C Community metric data (e.g., total number of taxa, percent dominance, number of

Plecoptera taxa, number of Ephemeroptera taxa, and number of Trichoptera taxa.).

Information on Other Aquatic Organisms (Amphibians and Aquatic/Semi-Aquatic

Mammals)

C Species composition and abundance.

C Habitat requirements and seasonal timing of breeding. 

Habitat Information

C Streams - Gradient, widths and depths, pool frequency, substrate composition,

streambank erosion, existing barriers and/or road crossings, culvert characteristics,

large woody debris, percent undercut banks, surface fins, flow characteristics,

temperature, and dissolved oxygen.

C Lakes and Reservoirs - Depth, surface area, littoral zone area, presence of aquatic

vegetation, and substrate composition.

C Riparian Zone - Width, percent cover and composition of vegetation by strata, and

estimated shaded area by seasons.

Project scoping and discussions with Federal and state agency biologists should be used to

define the specific list of topics to be covered as part of the Affected Environment Description. 

Sources of information for the aquatic resource topics can be obtained by searching published

literature, unpublished agency file information, and contacts with relevant Federal and state

agencies. 

Summaries of recommended methodologies to collect baseline data, if needed, are

provided below. The summaries focus on field studies for fish, benthic macroinvertebrates, and

habitat characterization. For topics such as the life history and habitat requirements of fish,

sufficient information is usually available in published literature. Prior to initiating any baseline
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studies, the proposed methods should be discussed and approved by appropriate Federal and

state agency fishery biologists and/or aquatic ecologists.

3.1 Fish

3.1.1 Distribution, Abundance, and Composition 

The timing and frequency of fish surveys largely depend upon the extent of migration or

movements exhibited by the important fish species. If the important species are resident (i.e.,

minimal movement or migrations), one sampling effort in the summer or fall should be adequate

to characterize composition and abundance. Additional sampling efforts may be needed to

characterize composition and abundance information for more mobile species. If spawning

information is needed, one survey should be scheduled to coincide with the peak spawning

period for the important species. It also is important to note that surveys of downstream, and in

some instances upstream, areas may be appropriate. This is true even if no fish reside within or

migrate through the project boundary. Final decisions on the timing and frequency of surveys

should be made through discussions with the appropriate agency biologists. 

The selection of a sampling method to collect data on the distribution, abundance, and

composition of fish communities depends mainly upon the type of water body. Each sampling

technique has limitations in terms of its effectiveness in particular types of habitat and behavior

and life stages of fish species. In streams and shallow rivers, sampling methods include

backpack or shoreline electrofishing, snorkeling, weirs, minnow traps, and seining. Of these

methods, electrofishing is the most commonly used technique due to the time efficiency in

completing the survey. However, electrofishing has been restricted in some watersheds within

the Pacific Northwest that contain federally threatened or endangered salmon or trout species. In

deeper rivers, boat electrofishing and hoop nets can be used to collect fish. Possible types of

collecting methods for lakes or reservoirs include boat electrofishing, gill nets, fyke nets, and

seine nets. Collection permits are required from the USFWS, NMFS, and/or state fish and

wildlife agencies for all of these methods except snorkeling. Applications of the various fish

sampling methods in terms of general type of habitat and life stage are listed in Table G-1. Brief

summaries of these sampling methods are provided below; refer to literature citations in Table

G-1 for more detailed descriptions of the sampling methods.

Backpack Electrofishing. In streams and rivers with depths less than about 3 feet,

backpack electrofishing is a common method used to collect adult and juvenile fish by producing

an electrical field in the water. In addition, some amphibians may be collected along with the

fish; they should be enumerated and identified as well. The method is not effective in capturing

small-sized fish (i.e. young-of-the-year) because of their relatively small surface area. Prior to

initiating the survey, the sampling effort is quantified in terms of linear distance, stream area

sampled, or duration of sampling in minutes. The crew moves in an upstream direction and

electrofishes all habitat within the reach. All fish species are netted and then processed in the

field by identifying and enumerating each fish by species. Species identifications should be

made by a qualified fisheries biologist and/or voucher specimens checked by a fish taxonomist at

a university, college, or museum. If population studies are required, the upper and lower ends of
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the sampling reach are blocked off with nets. Multiple passes through the reach are usually

required for estimating fish population numbers. 

Shoreline Electrofishing. Shore-based electrofishing can be used in larger wadeable

streams and rivers, where backpack electrofishing produces an electrical field that is too small

and weak to be effective. In shore-based electrofishing, all equipment (electrical unit and

generator) is located on land, except for the lead electrode. A two or three-person crew

electrofishes the sampling reach in the manner as described above for backpack electrofishing. 

Boat Electrofishing. A flat-bottomed boat equipped with electrofishing equipment can be

used to collect fish in slow-moving rivers and standing water environments. The boat design

consists of a forward deck that can accommodate two standing adults as dip-netters and one or

two booms that extend forward from the bow with an electrode. The sampling procedure

involves slow operation of the boat in an upstream direction along shoreline areas with depths

less than approximately five feet. Fish are netted as they are stunned and then placed in

collecting containers. Field processing is similar to backpack electrofishing.

Snorkeling. As part of the R1/R4 Fish Habitat Inventory procedures that are used on

USFS land in the Pacific Northwest, direct counts of game and T&E fish are made by snorkeling

(Overton et al., 1997). This technique is not recommended for fish assemblage characterization

since some of the small non-game species can be difficult to observe. Typically, one or two

snorkelers count all fish in a single pass within the study reach. Sampling criteria required for

this technique include: (1) stable flow periods between late June and September; (2) direct

sunlight conditions between late morning and early afternoon; (3) water temperatures should

exceed 9 B

C; and (4) visibility should be greater than 3 to 4 meters. All fish are counted in the

entire habitat unit or a portion of the unit using one of the following approaches: (1) proceed up

the center of the unit and count fish by zigzagging outward to both banks; (2) proceed up one

bank and count all fish towards the other bank if the water is too deep or turbulent to zigzag; or

(3) float downstream along the center of the stream in deep water.

Weir. This technique involves the construction of a temporary or permanent barrier across

the entire width of the stream to divert fish into a trap. Weirs are best suited for capturing

migratory adult and juvenile fish as they move up or down streams. The use of weirs is limited

to streams and small rivers because of construction expense, formation of navigation barriers,

and tendency to clog with debris and ice.

Minnow Traps. This portable trap captures juvenile fish as they enter through a

conical-shaped funnel at both ends. The traps are usually baited with fish eggs when they are

used to collect juvenile salmon. Typically, the traps are scattered along a stream or river

segment and fished for at least 12 to 24 hours.

Seining. Appropriate-sized seine nets also can be used in slow-moving sections of

streams or shallow rivers to collect young-of-the-year and juvenile fish, if bottom substrate is

relatively smooth and free of debris and other snags. Beach or haul seines are constructed of
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mesh panels hung from a float line with a weighted leadline attached to the lower edge. A mesh

bag is often attached to the middle of the net, which collects fish as the seine is dragged along

the bottom by two people.

Hoop Nets. This entrapment device is a cylindrical or conical net distended by a series of

hoops or frames. The net has one or more internal funnel-shaped throats whose tapered ends are

directed inward from the mouth. In riverine habitats, hoop nets are set with the mouth opening

downstream and sufficient depths to cover the net. Hoop nets are usually baited and fished for at

least 24 hours. This method is selective for bottom-feeding species such as carp, catfish, and

suckers.

Fyke Nets. This entrapment device is a modified hoop net with one or two wings or

leaders of webbing attached to the mouth to guide fish into the enclosure. Generally, fyke nets

are set in shallow areas of ponds, lakes, or reservoirs, with sufficient depths to cover the top f the

net. Fyke nets are selective for certain mobile, cover-seeking species such as sunfishes and pike.

Gill Nets. This entanglement gear consists of vertical walls of netting that are typically

set out in a straight line in lakes, reservoirs, and ponds. Fish are captured as they swim into the

netting and become entangled in the mesh. Gill nets can be set in many different ways,

depending on the species desired and types of habitats in the water body. A variety of species

can be captured by gill nets, but the gear is most effective for species that exhibit substantial

daily movements. This collecting method usually targets adult fish, although juveniles can be

captured if smaller mesh sizes are used.

3.1.2 Adult Spawning Counts 

The number of spawning salmon that return to freshwater streams or rivers can be estimated by

ground counts or aerial helicopter flyovers. These methods are applicable in clear streams with

depths less than about six to eight feet. Helicopter surveys are conducted by flying just above

tree height along the stream. An observer records the number and location of salmon. A

sufficient number of surveys should be conducted to cover the peak spawning period for each of

the salmon species. For effective counting, weather conditions should be mostly sunny and

clear. Ground counts of spawning salmon can be used to census the number of salmon that reach

their spawning areas in a drainage. One or more observers walk along the stream and count the

number of spawning salmon. The survey needs to occur during the peak spawning period when

most of the salmon have returned to their spawning areas.

3.1.3 Fish Tissue 

Definition of metal concentrations in fish tissue can provide important baseline information

concerning the background levels in the project study area. If metal contamination in fish tissue

is identified as an impact issue, it is important to determine concentrations in the study area prior

to the initiation of a new or modified monitoring activity. Numerous problems are typically
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Table G-1. Summary of Fish Sampling Techniques

General Type of Water Body/

Sampling Gear

Types of Information Salmonid Life

Stages

Refere

Descriptions of S

Species List

Distribution

Abundance/Composition

Population

Adult Spawning Counts

Adults

Juvenile

Young of the Year

Streams/Shallow Rivers

Backpack electroshocker, shore-basedelectroshocker

x x x x x x Nielsen and Johnson (19

Snorkeling x x Overton et al. (1997)

Seine net x x x x x x Nielsen and Johnson (19Minnow trap x x x x x Nielsen and Johnson (19Weir x x x x x Nielsen and Johnson(198Ground survey x x See Section 3.1.2Aerial (helicopter) flyover x x See Section 3.1.2

Deep Rivers (Moderate Velocities)

Hoop net x x x x x Nielsen and Johnson (19

Deep Rivers (Low Velocities)

Boat or raft electroshocker x x x x x Nielsen and Johnson (19

Lakes, Reservoirs, and Ponds

Boat electroshocker x x x x x Nielsen and Johnson (19Fyke net x x x x x Nielsen and Johnson (19Gill net x x x x x Nielsen and Johnson (19Seine net x x Nielsen and Johnson (19
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encountered during the design and implementation of a baseline sampling program for fish tissue

analyses. Problem areas include definition of the most meaningful tissue(s) and metals for study,

difficulties in collecting the desired samples (i.e., species, numbers, and sizes), proper handling

and preparation of samples without contamination, and the interpretation of results. Metals are

not evenly distributed among different specimens or within different organs or tissues. Natural

variation in metal concentrations also typically exists in fish populations due to a variety of

reasons such as movements, feeding habits, and physiological differences. Therefore, a

relatively large number of replicates should be collected, if possible, to statistically differentiate

various fish populations inhabiting the study area.

The final design for a fish tissue sampling study should be determined through discussions

with the appropriate Federal and state agencies. Decisions need to be made regarding the

sampling locations, target species, number of replicate samples, composite or individual samples, 

and tissues or organs to be analyzed. The types of tissues that are typically analyzed for metals

include liver, gills, muscle, and whole body. Fish can be collected using any of the methods

discussed above. Hook-and line method also is sometimes used to collect fish for tissue

analyses.

Specific field and laboratory procedures have been developed to analyze metal

concentrations in fish tissue. Field processing techniques, which are described in EPA (1980),

involve decontamination of the sampling equipment, double wrapping the fish or tissue in 5

percent nitric acid-rinsed aluminum foil, and then placing the samples on ice during the time of

sampling. At a minimum, samples should be kept on ice for no more than 24 hours. Fish or

tissues should be frozen prior to shipment to a commercial laboratory for chemical analyses. The

procedure for decontaminating sampling equipment consists of the following steps: (1) initial

rinse with tap water; (2) wash with biodegradable detergent; (3) rinse with deionized water; (4)

rinse with 5 percent nitric acid; and (5) final rinse with analyte-free water. Tissue can be

removed from the whole fish in the field or in the laboratory. Latex gloves should be used for

each decontamination procedure and field processing of each sample and then discarded.

Additional field data that are recommended for each fish sample include measurements of

weight (in grams), length (in millimeters), and the removal of scales for age determination. It is

important that the laboratory selected to perform the tissue analyses follows these procedures,

including Quality Control/Quality Assurance measures.

3.2 Benthic Macroinvertebrates

Both quantitative and semi-quantitative methods are used to obtain abundance and

composition data for macroinvertebrates. Sampling methods should be selected based on the

scope and purpose of the overall study. Methods and data should be reviewed for accuracy and

their appropriateness for meeting the study’s specific objectives. The design of any additional or

new studies must decide on whether semi-quantitative or quantitative methods are appropriate,

given the purpose of the study and the nature of data from previous investigations (for example,

to identify any trends, it might be appropriate to use the same methods as earlier studies even if

other methods would provide more complete information). 
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Semi-quantitative methods typically consist of kick net samplers in streams. After placing

the net in a riffle or run, the substrate material in front of the net is rubbed or agitated to remove

any macroinvertebrates. The organisms in the sampled area drift into the net. The sampled area

is estimated rather than measured. Data analyses usually consist of relative abundance of the

various macroinvertebrate taxa present in the sample. Many state environmental agencies and

the U.S. Geological Survey use this method in their National Water Quality Assessment

Program. The existence of semi-quantitative data from previous surveys make the use of such

methods more appropriate than would otherwise be the case. 

Quantitative methods are used to provide abundance and composition data per unit area

sampled. The sampling methodology depends upon the type of water body. In riffle areas of

streams or rivers with depths less than about 18 inches, sieve-type samplers (either Surber or

Hess) are the most common devices used to collect macroinvertebrates. The Surber sampler

consists of a 1 square foot frame (0.09 square meter) with an attached net and bucket (0.5

millimeter mesh). The Hess sampler is a circular frame with an attached net (0.5 millimeter

mesh) that encloses a surface area of approximately 1 square foot or 0.1 square meter. Both

methods involve the removal of macroinvertebrates on substrate surfaces by hand. All collected

material then is washed and concentrated into the bucket and placed into a labeled sample jar and

preserved with formalin and ethanol. Field collection techniques for these methods are described

by the following authors: Surber sampler (Surber, 1937; Hughes, 1975, Klemm et al., 1990) and

Hess sampler (Hess, 1941; Waters and Knapp, 1961; Jacobi, 1978).

Quantitative sampling in deeper rivers, lakes, reservoirs, or ponds is accomplished using a

grab-type device such as a petite Ponar, Peterson, or Eckman. These grab samplers are designed

to penetrate the substrate and then enclose bottom substrate material with either spring- or

gravity-operated mechanisms. The Eckman grab is relatively light and designed for soft bottoms

consisting of sand, clay, silt, and organic material. For clay hardpan and coarse sands, heavier

grabs such as the petite Ponar or Petersen are used. The most important criterion in effective

grab sampling is to penetrate the bottom material and obtain complete closure of the sides of the

sampler. The surface area sampled ranges from 0.25 square foot (0.02 square meter) with the

petite Ponar to approximately 1 square foot (0.09 square meter) with the Peterson sampler. 

Descriptions of sampling techniques for these grab samplers are provided by Weber (1973),

Elliott and Drake (1981), Lewis et al. (1982), and Klemm et al. (1990).

The design of a macroinvertebrate sampling program needs to select sampling sites that

encompass areas potentially affected by past or future mining operations. If possible, a reference

site, which is located outside the influence of the mining activities, should be selected that

exhibits similar habitat conditions compared to downstream sites. By comparing sites with

similar habitat conditions, the identification of possible causes for differences in

macroinvertebrate communities often focuses on water quality. Two to four replicate samples

also should be collected at each sampling site to provide sufficient data for statistical analyses, if

required. At a minimum, one sampling effort should be conducted in the summer or early fall. 

Two sampling efforts (spring, summer, or fall) would account for seasonal changes in

macroinvertebrate communities that result from developing young and adult hatching. If
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previous sampling has been conducted, additional sampling should be scheduled to coincide with

the dates as much as possible.

Laboratory processing for all samples consists of sorting and picking all macroinvertebrates into a vial, followed by identification and enumeration of all organisms. If the

sample contains a large number of macroinvertebrates, subsampling of 500 organisms can be

used (Hayslip, 1993). Identifications should be taken to the lowest possible taxonomic level to

provide information on the composition and diversity of macroinvertebrates inhabiting the water

body. 

Data analyses recommended for a baseline study of macroinvertebrates varies depending

upon whether issues were identified during scoping. At a minimum, the number of taxa,

abundance, and composition data should be analyzed. However, data analyses are recommended

only if at least 50 organisms are present in the sample. Densities are presented as the number of

individuals of each taxon per square foot or square meter; composition is presented as percent of

each taxon total macroinvertebrate densities at a sampling location. If a more detailed evaluation

of sedimentation or metal toxicity are required, the following additional metrics can be analyzed.

C Number of Ephemeroptera (mayflies) taxa.

C Number of Plecoptera (stoneflies) taxa.

C Number of Trichoptera (caddisflies) taxa, whose absence may indicate metals

contamination.

C Percent Dominant Taxon - Percent composition of the most abundant taxon in the

macroinvertebrate community at a sampling location.

C Percent Baetidae - Percent composition of baetid mayflies (metal sensitive group).

C Species Diversity - Index that indicates taxonomic richness and abundance among

the various taxa.

C Metal Tolerance Index - Rating system representing relative sensitivity or tolerance

to metals developed by McGuire (1994) for western montane streams.

Information on how to use metric data in evaluating the impacts of mining or other

stresses within a water body are discussed in Section 4.0 (Impact Assessment). For the purposes

of including these metrics in baseline characterizations of macroinvertebrate communities,

procedures are discussed in Plafkin et al. (1989), (Klemm et al. (1990), Wisseman (1996), and

Barbour et al. (1997). 

3.3 Amphibians

Amphibians are another group of organisms that inhabit aquatic environments. Due to

widespread declines of amphibian populations, conservation planning and monitoring efforts

have been implemented by Pacific Northwest Federal and state agencies. In the Pacific

Northwest, numerous native amphibian species are listed as state "sensitive" or "special concern"

species. Federal agencies such as the Forest Service also have targeted certain amphibian

species as Forest "sensitive" species. 
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In general, two groups of amphibian assemblages are associated with aquatic habitats in

the Pacific Northwest: (1) stream-dependent species which live in or adjacent to water during

all or part of their life cycle (e.g., tailed frogs, Ascaphus truei, and giant salamanders,

Dicamptodon spp.); and (2) pond-breeders which require standing water or lentic habitats for

egg-laying and larval development (Olson et al., 1997). The following information describes the

more common methods that can be used to collect data on species presence and relative

abundance for stream and lentic environments. Detailed descriptions of these and other

sampling methods can be found in Heyer et al. (1994) and Olson et al. (1997).

Visual Observations and Dipnetting. The most common method in determining the

presence and relative abundance of amphibians in both stream and lentic environments involve

visual observations and dipnetting. Species presence and relative abundance can be made by

walking and counting amphibians within defined sections of the study area. If relatively large

numbers of amphibians are encountered, subsampling can be used. Dipnetting can be used to

collect egg masses, larvae, and adults in shallow aquatic areas by making sweeps in front and to

the sides at designated stops. Each scoop should include the upper 2 to 3 centimeters of bottom

from a sweep approximately 1 meter (3 feet) in length. After each scoop, water and fine

sediment should be strained from the net by gently sloshing it back and forth in the surface

water. The contents should be examined for adult and larval amphibians. If relative abundance

is a study objective, it is important to standardize the distance between stops, as well as the

number and length of sweeps. In this situation, abundance data are presented as the number of

amphibians per area sampled. 

A systematic approach in obtaining relative abundance data can be achieved by using

quadrate or transect sampling methods. Quadrate sampling consists of laying out a series of

small squares at randomly selected sites within a habitat type and thoroughly searching those

squares for amphibians. In the transect method, narrow strip transects are randomly layed out

and surveyed for amphibians. Patch sampling, which is a modified form of quadrate sampling,

can be used to determine the presence and abundance of amphibians in discrete subunits of an

area (i.e, logs, debris jams, etc.). Detailed descriptions of these methods are provided by Heyer

et al. (1994).

Funnel Traps. For nocturnal or cryptic species, and habitats that are difficult to sample

due to depth or abundance of vegetation, funnel trapping is a useful method. Funnel traps

consist of a holding chamber with one or two tapered mouths that channel organisms toward a

small entrance to the trap interior. One type of funnel trap that can be used is the commercially

available minnow trap, which is constructed of 0.25-inch plastic or galvanized hardware cloth. 

Other commercial traps are available that are constructed of nylon webbing wrapped around a

wire-frame. Traps are sometimes baited to attract amphibians. 

Night Surveys. Since some amphibians are more active at night, visual surveys can be

conducted using a flashlight. The reflective shine of amphibian eyes are used to record larvae

and adults (Olson et al. 1997).
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Snorkeling. Visual surveys conducted by snorkeling are useful in deep portions of lakes

and wetlands. Visual counts are made along snorkeled transects or defined areas. The number

of amphibians also can be recorded per unit of time surveyed.

Electrofishing. Generally, this method is used for fish surveys, but incidental observations

of amphibians can be included as part of the fish survey. Pools and backwater areas represent

the areas where amphibians may be encountered.

The design and selection of study sites for amphibian surveys are discussed in detail by

Olson et al. (1997). Surveys should consider all aquatic habitats within a study area that could

be inhabited by amphibians such as streams, rivers, ponds, lakes, meadows, and other wetland

areas. If larvae and egg surveys are required, the surveys must be timed to coincide with the

breeding and early development of the species (spring and summer).

3.4 Aquatic Habitat and Riparian Zone

The level of detail required for characterizing aquatic habitat within water bodies depends

upon numerous factors such as the presence of game fish or T&E fish species, presence of

critical habitat for Federally listed fish species, management goals for aquatic resources

established by Federal and state agencies, types of potential impacts that could result from the

mining project, and the level of concern for habitat impacts as identified during the scoping

process. In some instances, existing habitat information may be available for watersheds that

support game or T&E fish species. The data should be reviewed and determined whether it

would be sufficient to characterize aquatic habitat for the NEPA document. If additional field

surveys are required, methods should be used to allow comparisons to future monitoring

programs or other watersheds. Examples of methods that are currently being used in the Pacific

Northwest are summarized below.

Mining projects that are located on USFS land should use their preferred methods. The

USFS Columbia Basin Anadromous Fish Policy and Implementation guidelines directed

Columbia Basin Forests to have comparable data within basins to identify existing habitat

conditions. The Salmon Conservation Strategy (PACFISH) use habitat variables for monitoring

goals and objectives that help protect, maintain, and restore important fish habitat. As a result of

these requirements, the R1/R4 habitat procedures were developed by Overton et al. (1997). The

following parameters are covered in the R1/R4 manual: general type of habitat designation,

discharge, gradient, stream width, stream depth, type and frequency of pools, percent surface

fines, substrate composition, percent undercut bank, number of large woody debris, bank

stability, vegetative cover, and Rosgen channel classification. The riparian zone provides

important habitat values for the aquatic environment. Riparian surveys should include

information on width of the zone, percent cover and composition of vegetation, and estimated

shaded area. Methods for collecting these data are described by Platts et al. (1983), MacDonald

(1991), and Hansen et al. (1995). When designing baseline habitat surveys for a mining project,

these parameters should be considered. The final study design should be developed through

discussions with the USFS and state agency biologists or habitat specialists.
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Specific habitat procedures also may be recommended by state agencies. The appropriate

state agency should be contacted prior to designing aquatic habitat studies to determine whether

specific procedures are required. Standardized methods for characterizing habitat in western

U.S. streams/rivers also are described by Binns (1982), Platts et al. (1983), Hamilton and Bergen

(1984), and Rosgen (1985).

4.0 IMPACT ASSESSMENT

Numerous reviews of the effects of mining on aquatic resources are useful in identifying

potential issues for a mining project (e.g., Martin and Platts, 1981; Meehan, 1991; Ripley et al.,

1995; Waters, 1995; and Starnes and Gasper, 1996). Environmental impact statements (EIS) or

environmental assessments (EA) that have been completed for similar mining projects also

should be used in the issue identification task. This type of information available from published

literature sources in conjunction with the scoping process are used in identifying specific impact

issues for a project. Potential aquatic resource issues for a mining project may include the

following topics:

C Potential effects of water quality changes on aquatic and semi-aquatic (mammals,

amphibians, birds) communities and their habitat that may result from mine

operation. Parameters of concern may include heavy metals, pH, and

acid-generation materials.

C Potential effects of sedimentation on aquatic and semi-aquatic communities and their

habitat due to construction and operation activities.

C Potential effects of physical disturbance or removal of habitat on aquatic and semiaquatic biota.

C Potential effects of spills on aquatic and semi-aquatic biota that may result from fuel

transportation and use (i.e., leaking equipment and refueling) and use of other

hazardous materials.

C Potential effects of flow changes on aquatic habitat and riparian zones and their

respective biota due to water withdrawals.

C Potential effects of physical blockages or barriers created by mining construction or

operation activities on fish movements.

The analysis should encompass potential effects on riparian areas, which can in turn affect

aquatic ecosystem health, and on aquatic and semi-aquatic organisms and ecosystems. As

required under NEPA regulations, the impact assessment must analyze both direct and indirect

impacts (Council on Environmental Quality, 1986). The analyses used in the environmental

impact assessment must be scientifically accurate and exhibit scientific integrity. Specific

methods used in analyzing impacts and making conclusions must be referenced in the NEPA

document. The following information describes methods that can be used in analyzing impacts

for the various issues listed above. 
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3

Acute toxicity is defined as concentrations that cause mortality or immobilization during a short-term period (usually 48 to 96

hours) of exposure.

4

Chronic toxicity is defined as concentrations that cause reproductive impairment or other sublethal effects during a long-term

period (seven days to greater than one year) of exposure.

G-15 January 2003

4.1 Water Quality Impacts

4.1.1 Comparisons to Aquatic Life Water Quality Criteria 

Water quality issues associated with mine exploration, operation and abandonment activities

involve the potential discharge of mine water and process solutions; increased loads of metals

and other toxic pollutants; and the generation of acid from waste rock, spent ore, and mine

workings. If these pollutants reach surface waters, toxic conditions could affect important

aquatic species. Potential analytes of concern for mining projects generally include pH, cyanide

and associated chemical species, and metals.

Actions and/or measures that can be taken to avoid or reduce water quality impacts from

mining activities are discussed in Appendix B, Receiving Waters; Appendix C, Characterization

of Ore, Waste Rock, and Tailings; Appendix D, Effluent Quality; Appendix E, Wastewater

Treatment; and Appendix F, Solid Waste Management.

The most common approach used to analyze the effects of water quality changes on

aquatic communities is to compare projected post-mining water quality to applicable standards

intended to protect aquatic life. Water quality standards are based on three components:

(1) designated beneficial use or uses of water (i.e., aquatic life use)

(2) criteria designed to protect those uses (e.g., pH)

(3) an antidegradation provision. 

The fish, macroinvertebrate, and/or periphyton assemblages are all direct measures of the

aquatic life beneficial use under the CWA. For many metals, criteria are used to protect aquatic

organisms from both acute4

 and chronic5 toxicity. Standards for metals such as cadmium,

chromium III, copper, lead, nickel, and zinc are dependent upon hardness (mg/L as CaCO3),

which is reflected in equations that are used to calculate the criterion for each metal. Toxicity is

inversely related to hardness and EPA typically uses a conservative hardness (5th or 10th

percentile) in determining applicable criteria. It is essential to have representative hardness data

for the receiving water. The standards for metals also are based on either total recoverable or

dissolved concentrations. The standards used (i.e., total recoverable or dissolved) should be

incorporated into a baseline surface water sampling program.

The analysis requires close coordination between the surface water and aquatic resource

analyses. The first step in the analysis is to characterize natural background concentrations using

available data. Second, water quality conditions during mining and post-closure are projected. 

The final step in the analysis is to compare the pre-mining and post-mining water quality
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G-16 January 2003

concentrations to state water quality standards. It is important to estimate water quality during

and after mining for both the proposed operation and alternatives; this would involve analyses 

both qualitative and quantitative) including various combinations of best management practices

and other mitigation measures. 

If analytes of concern are identified for the project study area, a qualitative discussion of

impacts can be made using available published literature. The discussion should describe the

types of effects that the analytes of concern may have on fish and macroinvertebrate

communities. If possible, affected water bodies that may exhibit toxic conditions should be

identified in terms of their length or surface area. 

The issue of sediment water quality effects on aquatic biota is more difficult to evaluate,

since standards are not available. The best approach in analyzing this issue is to compare natural

background and post-mining sediment quality to benchmark values available in the published

literature. These comparisons help identify whether the sediment quality is within background

levels reported for areas with no known metal contamination. Examples of information sources

for metal concentrations in sediment include Washington State Department of Ecology (1991);

EPA (1994a; 1995); and Jones et al. (1996). 

4.1.2 Toxicity Studies 

Additional site-specific information can be obtained by conducting toxicity studies using surface

water or sediment from the project study area. These tests can be used to confirm potential water

quality concerns identified as part of the water quality comparisons between post-mining

conditions and applicable water quality standards. Typically, microcrustaceans (Dapnia or

Ceriodaphnia species) and fish species are used as test organisms, although test procedures exist

for a variety of macroinvertebrates such as midges, mayflies, annelid worms, and amphipods. If

additional testing is required, decisions need to be made concerning the test organisms, type of

test (acute or chronic), static or flow-through conditions, test medium (surface water or

sediment), and concentrations to be tested. Mining companies (or their representatives) are

strongly encouraged to consult with the EPA and the appropriate state agency before designing

and conducting toxicity tests. The following test procedures should be followed for designing

and conducting the tests:

C Acute Toxicity - Methods for Measuring the Acute Toxicity of Effluents and

Receiving Waters to Freshwater and Marine Organisms (Weber, 1993).

C Chronic Toxicity - Short-Term Methods for Estimating the Chronic Toxicity of

Effluents and Receiving Waters to Freshwater Organisms (Lewis et al., 1994).

C Sediment Toxicity and Bioaccumulation - Methods for Measuring the Toxicity and

Bioaccumulation of Sediment-Associated Contaminants with Freshwater

Invertebrates (EPA, 1994b) and Standard Test Methods for Measuring the Toxicity

of Sediment-Associated Contaminants with Freshwater Invertebrates (American

Society for Testing Materials, 1998).

Additional guidance in designing and conducting toxicity testing is provided in Standard
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G-17 January 2003

Methods for the Examination of Water and Wastewater (American Public Health Association et

al., 1989).

4.1.3 Macroinvertebrate Metric Analysis 

Macroinvertebrate communities are useful indicators for assessing the effects of various types of

environmental stress, as reflected in degraded water quality conditions or habitat. Many benthic

macroinvertebrates have limited migration patterns or a sessile mode of life, which makes them

well-suited to assess site-specific impacts. Macroinvertebrate assemblages are comprised of a

broad range or organisms that exhibit varying levels of tolerance to pollution sources such as

sedimentation and metals (Barbour et al., 1997). 

The evaluation of impacts on macroinvertebrates typically uses relevant literature

pertaining to the effects of sedimentation and metals contamination on macroinvertebrate

communities. Previous studies have found that macroinvertebrates often respond to

sedimentation or metals contamination by exhibiting reduced densities, reduced taxa richness,

and a shift from sensitive to tolerant taxa (Winner et al., 1980; Clements, 1994; Waters, 1995). 

The absence or low numbers of Ephemeroptera, Plecoptera, and Trichoptera may indicate metal

contamination. Predictions of potential impacts can be made using the results of these relevant

studies. 

Additional analysis of macroinvertebrate data from a project study area can be used to

monitor or confirm the projected impacts of mining projects. Numerous types of information or

metrics have been used to evaluate the effects of various types of environmental stresses on

macroinvertebrate communities. Examples of metrics that have been used to evaluate the effects

of metals and sediment on macroinvertebrate communities include total abundance, total number

of taxa, number of Ephemeroptera taxa, number of Plecoptera taxa, number of Trichoptera taxa,

percent dominant taxon, percent Baetidae, and Metal Tolerance Index (Plafkin et al., 1989; Resh

and Jackson, 1993; Wisseman, 1996; Fore et al., 1996; and Barbour et al., 1997). Refer to

Section 3.2 for definitions of these metric terms. The final selection of the metric data should be

made through discussions with appropriate Federal and state agency biologists. After

completing the metric data analyses, comparisons should be made between the reference and

downstream sites. Procedures for conducting macroinvertebrate metric data analyses are

described by Plafkin et al. (1989), Wisseman (1996), and Barbour et al. (1997).

4.2 Sedimentation

Several types of analyses can be used to evaluate the potential effects of sedimentation on

aquatic communities and their habitat. Indicators that can be used to discuss potential

sediment-related impacts in streams include change in percent fines or cobble embeddedness. 

For all types of water bodies, aquatic life water quality standards also may exist for

sediment-related parameters such as turbidity or total suspended solids (TSS). Baseline data

should be used to characterize the range in values for one or more of these parameters. If

possible, percent increases in these values that could occur as a result of project activities should

be estimated (see Appendix H, Erosion and Sedimentation for a detailed discussion of methods
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G-18 January 2003

to quantify sediment loadings). The predicted increase in the sediment-related indicators should

then be related to levels that have been reported as limiting fish or macroinvertebrate

development. For example, percent fines of 40 percent or greater have been reported to

adversely affect salmonid fry development and emergence (Bjornn et al., 1977; McCuddin,

1977). Burton et al. (1991) proposed that no statistically significant increase in natural baseline

percent embeddedness should occur in Idaho salmonid rearing habitats.

If quantitative predictions are not possible for the sediment indicators, then a qualitative

analysis should be used to discuss potential adverse effects on aquatic communities using

published literature. The duration of impacts that have resulted from similar mining projects

should be included in the impact discussion. The impact analysis also should estimate the linear

length of streams, surface area of lakes/reservoirs that could potentially exhibit increased

sediment yield as a result of mining activities. The analysis should focus on the affected aquatic

environments that support aquatic communities and habitat.

4.3 Habitat Alteration

The types of information that are needed to evaluate the potential effects of removing or

altering habitat for important game and T&E fish species and other aquatic and semi-aquatic

species include: (1) identify stream segments or water bodies affected by mining activities; (2)

quantify the area of disturbance in square feet or acres; (3) determine list of fish species that

utilize the affected areas; (4) characterize the general types of habitat affected; and (5) describe

the fish life stages (i.e., spawning, young-of-the-year rearing, etc.) that potentially use the

affected areas. The impact discussion should evaluate the significance of altering or removing

the habitat for the important species by considering the magnitude (square feet or acres affected)

and duration of impacts. The use of the impacted area should be related to the amount of similar

types of habitat that are available within the project study area.

Mining activities also may involve the loss of aquatic habitat by physical placement of

materials in a portion of a drainage, which may itself need a permit. In this situation, flows are

usually diverted from the "affected stream segment" into a newly constructed channel. The

impacts of removing and replacing stream segments should be quantified in square feet or acres

in relation to the important fish and macroinvertebrate taxa that occur in the affected areas. The

recovery of aquatic communities in the newly constructed channels needs to be discussed using

published studies that have monitored aquatic biota after flow was returned to a stream. 

4.4 Hazardous Material Spills

Transportation of fuel and other toxic chemicals to and from the mine site present

potential risks to aquatic communities from spills that enter water bodies. At a minimum, the

impact discussion should describe the effects of potential spills on aquatic communities using

available literature on toxicity of fuel and the various chemicals being transported and/or stored

on-site. The analysis should focus on stream segments or water bodies that are located adjacent

to and downstream of the transportation route and project area---all areas where spills may

occur. The discussion also should explain that the magnitude and duration of impacts would
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Appendix G: Aquatic Resources

G-19 January 2003

depend upon the chemical spilled, volume spilled, toxicity to aquatic species, time of year,

weather conditions, and physical characteristics of the water body. Reference should be made to

any relevant published studies that have conducted after similar types of spills. 

A risk assessment may be used to analyze the impacts from potential spills, if this topic is

identified as a significant issue. The following types of information are typically included in a

risk assessment:

C Identify the types and volumes of toxic chemicals that are transported to and from,

and/or are stored at the mine site;

C Determine the frequency and schedule of transporting toxic chemicals;

C Identify the transportation route;

C Define the spill scenarios to be analyzed;

C Determine the presence of important fish species in water bodies located adjacent to

the transportation route;

C Characterize the condition of roads used in transporting toxic chemicals; 

C Describe the effects of fuel or chemical spills on aquatic species using available

published literature; 

C Describe spill risks in terms of probabilities using vehicle accident data; and

C Describe methods (BMPs) for reducing the risk of spills from transport and/or

storage of fuels and toxic chemicals.

The contents and methodology to be used in the risk assessment analysis should be

discussed with the appropriate Federal and state agencies prior to commencing the work. 

Guidance documents that can be used in designing the risk assessment include EPA (1992; 1997;

1998).

4.5 Flow Alterations

Water use for mine operations could affect flows in streams that contain important game

and T&E fish species. Stream flow and water volumes represent an important aspect of fish

habitat. These parameters in combination with other factors such as substrate, depth, and

overhanging cover define habitat conditions in a stream.

The type of analysis required to evaluate this issue depends upon the magnitude of flow

change and the presence of important species in the affected water bodies. If flow data are

lacking, studies may be required to obtain the necessary data. In general, key aspects of the data

set (including sources of data, periods of time covered, definitions and descriptions of of data

elements) that is used should be fully described. Mining companies (or their representative)

should contact hydrologists with the lead Federal agency and appropriate state agency prior to

designing flow studies. The simplest approach is to estimate the percent change in flow for the

affected streams compared to pre-project or base flow conditions. If possible, the flow data

should be summarized on a monthly basis to reflect any seasonal aspects of fish distribution,

movements, or life history information. Using the percent flow changes, a qualitative discussion

should be made to identify the types of impacts on fish species. For example, a 40 percent
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Appendix G: Aquatic Resources

G-20 January 2003

reduction in flows during the spring would reduce available wetted habitat for rainbow trout

spawning. Relevant published literature should be used to identify the types of impacts that

could result from flow changes. This qualitative approach is appropriate for projects that would

result in relatively small flow changes or study areas that do not support important game or T&E

species.

If flow alteration is a controversial issue for a project, a quantitative method such as the

Instream Flow Incremental Methodology (IFIM) should be used to quantify the effects of flow

regimes on fish habitat (Bovee, 1982). IFIM utilizes a hydraulic-simulation technique to predict

depths, velocities, and substrates within a stream reach at different flows. Results from the

simulation are then combined with microhabitat preferences for the fish species of interest to

estimate the amount of suitable habitat. Microhabitat preferences are expressed in the form of

habitat-suitability curves for the various life stages for each fish species of interest. Studies have

been conducted to develop habitat-suitability curves for a variety of fish species (e.g., Bovee,

1978; Raleigh, 1982; McMahon, 1983; Raleigh et al., 1984; Raleigh and Nelson, 1985; Raleigh

et al., 1986a; 1986b). These curves can be used in the habitat simulation analysis. If curves are

lacking for the species of interest, curves should be developed for the project study area

following techniques described by Bovee and Cochnauer (1977).

Implementation of the IFIM requires the use of a system of computer programs called

PHABSIM (Physical Habitat Simulation) (Milhous et al., 1981). The PHABSIM programs

simulate the physical habitat of fish as a function of stream flow and transform the hydraulic

information (depth, velocity, substrate) into a measure of useable habitat. Field surveys are

required to collect flow, depth, and substrate data along transects established in the streams

affected by flow changes. After the hydraulic simulation is completed, suitability curves for the

target species are used as input to a habitat program, which computes the amount of physical

habitat that is available for each target species at a range of flows. This analysis should be

completed for both pre- and post-project scenarios. The end product is a quantitative estimate of

the change in available habitat in square feet for each target species. A significance level should

be established through discussions with appropriate agency biologists or IFIM specialists to

interpret the results. For example, a 25 percent reduction in spawning habitat for brown trout

could represent a significant impact.

4.6 Obstruction to Fish Movement 

If mining activities place materials or structures in a drainage on a temporary or

permanent basis, the effects on fish movements need to be addressed. The initial step in the

analysis is to identify whether important game or T&E fish species exhibit wide range

movements in the affected stream segment. The period of movement then needs to be identified

for each species. A particularly important period for trout and anadromous salmon species is

spawning, when fish migrate to specific areas to lay eggs. Another critical period for salmon is

out-migration of juveniles from their nursery streams to the ocean. Blockages or obstructions to

these movements need to be identified in the impact assessment. In most instances, project

mitigation is required to eliminate potential blockages to fish movement. 
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G-21 January 2003

5.0 REFERENCES

American Public Health Association, American Water Works Association, and Water Pollution

Control Federation, 1989. Standard Methods for the Examination of Water and

Wastewater, Seventeenth Edition, American Public Health Association, Washington,

D.C.

American Society for Testing Materials, 1998. Standard Test Methods for Measuring the

Toxicity of Sediment-Associated Contaminants with Freshwater Invertebrates, Method E

1706-95b. In: 1998 Annual Book of ASTM Standards, ASTM, West Conshohocken,

Pennsylvania.

Barbour, M.T., Gerritsen, J., Snyder, B.D., and Stribling, J.B., 1997. Revision to Rapid

Bioassessment Protocol for Use in Streams and Rivers: Periphyton, Benthic

Macroinvertebrates, and Fish, U.S. Environmental Protection Agency Report

EPA/841-D-97-002, Washington, D.C.

Binns, N.A., 1982. Habitat Quality Index Procedures Manual, Wyoming Game and Fish

Department, Cheyenne, Wyoming, 209 pp.

Bjornn, T.C., Brusven, M.A., Molnau, M.P., Milligan, J.H., Klamt, C.E., and Schaye, C., 1977. 

Transport of Granitic Sediment in Streams and its Effects on Insects and Fish, Bulletin

17, University of Idaho, Moscow, Idaho, 43 pp.

Bovee, K.D, 1978. Probability of Use Criteria for the Family Salmonidae, Instream Flow

Information Paper No. 4, U.S. Fish and Wildlife Service, FWS/OBS-78-07, 53 pp.

Bovee, K.D, 1982. A Guide to Stream Habitat Analysis Using the Instream Flow Incremental

Methodology, Instream Flow Information Paper No. 12, U.S. Fish and Wildlife Service,

FWS/OBS-82-86, 235 pp.

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Management, vol. 5, pp. 55-68.

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Lewis, P.A., Mason, W.T., and Weber, C.I., 1982. Evaluation of Three Bottom Grab Samplers for

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EPA and Hardrock Mining: A Source Book for Industry in the Northwest and Alaska

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EPA and Hardrock Mining: A Source Book for Industry in the Northwest and Alaska

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Appendix G: Aquatic Resources

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Appendix G: Aquatic Resources

G-27 January 2003

6.0 CONTACTS AND OTHER INFORMATION SOURCES

6.1 Contacts for Fish Information

Alaska Department of Fish and Game, Juneau, AK and appropriate Regional Office

C Commercial Fisheries Management and Development Division

C Division of Subsistence

C Division of Sports Fish

Washington Department of Fish and Wildlife, Olympia, WA and Regional Office

C Fish Management Program

Oregon Department of Fish and Wildlife, Portland, OR and Regional Office

C Fisheries Division

Idaho Department of Fish and Game, Boise, ID and Regional Office

C Fisheries Division

6.2 Contacts for Habitat Information

Alaska Department of Fish and Game, Juneau, AK and appropriate Regional Office

C Habitat and Restoration Division

Washington Department of Fish and Wildlife, Olympia, WA and Regional Office

C Habitat Program

Oregon Department of Fish and Wildlife, Portland, OR and Regional Office

C Habitat Conservation Division

Idaho Department of Fish and Game, Boise, ID and Regional Office

C Fisheries Division

6.3 Contacts for Aquatic Life Water Quality Criteria

Alaska Department of Environmental Conservation, Juneau, AK and appropriate Regional Office

C Division of Environmental Quality

Washington Department of Ecology, Olympia, WA and Regional Office

C Water & Shorelands Division

Oregon Department of Environmental Quality, Portland, OR and Regional Office

C Water Quality Division

Idaho Division of Environmental Quality, Department of Health and Welfare, Boise, ID

C Division of Environmental Quality