United States

Department

of Agriculture

Forest Service

Intermountain

Research Station

General Technical

Report INT-GTR-307

July 1994

Underwater Methods for

Study of Salmonids in

the Intermountain West

Russell F. Thurow
Intermountain Research Station

324 25th Street

Ogden, UT 84401

THE AUTHOR

RUSSELL F. THUROW is a Fisheries Research Biologist with the Intermountain Research Station, Forestry

Sciences Laboratory, Boise, ID. He received an undergraduate degree in fisheries from the University of

Wisconsin-Stevens Point and a master’s degree in

fisheries resources from the University of Idaho. He

has been using underwater techniques to study resident and anadromous fish populations since 1973.

After 15 years of research with the Idaho Department

of Fish and Game, he joined the Intermountain Station’s

Fisheries Research Work Unit in 1990. His current research focuses on the biology of salmonid populations

and the interaction between various salmonid life

stages and their habitats.

RESEARCH SUMMARY

Underwater observation using snorkeling gear is an

accepted technique for censusing fish populations in

flowing waters. Several factors, including the behavior

of the target fish species and attributes of the physical

habitat, can bias underwater counts. This paper describes the use of underwater observation and outlines

procedures for estimating fish abundance, the size

structure of populations, and habitat use. It also provides criteria for identifying fish underwater.

ACKNOWLEDGMENTS

Earlier versions of this manuscript were reviewed by

J. Griffith, T. Hillman, J. McIntyre, K. Overton, D. Schill,

and B. Rieman. Cover photo by Susan Adams. Figure

15 by Ray Beamesderfer, Oregon Department of Fish

and Wildlife. Figures 13 and 14 by Ken Bouc, reprinted

with permission of NEBRASKAland Magazine and the

Nebraska Game and Parks Commission. Figures 9, 12,

and 17 by Paul Valcarce, Limnophoto. Figures 6, 8, 10,

and 16 by John Woodling, reprinted with permission of

the Colorado Division of Wildlife. All other photos by the

author. Rodger Nelson built the cutthroat trout distribution map. The illustration in appendix C was adapted

from Simpson and Wallace (1978). The illustrations in

appendix D were drawn by Eric Stansbury of the Idaho

Department of Fish and Game.

CONTENTS

Page

Introduction ............................................................... 1

Considerations Before the Survey ............................ 1

Objectives .............................................................. 1

Safety .................................................................... 2

Equipment ............................................................. 2

Training.................................................................. 2

Ethics ..................................................................... 3

Recommended Snorkeling Protocols ........................ 4

Timing .................................................................... 4

Minimum Criteria ................................................... 4

Selecting Appropriate Sampling Units ................... 5

Snorkeling Procedures .......................................... 6

Precision and Accuracy ......................................... 9

Species Identification and Habitats ......................... 11

Anadromous Salmonids ...................................... 12

Resident Salmonids............................................. 14

Species Other Than Salmonids ........................... 18

Research Needs ..................................................... 18

References .............................................................. 19

Appendixes:

A: Example of a Sampling Unit Map .................... 23

B: Example of a Snorkel Data Sheet ................... 24

C: External Characteristics of a

Typical Salmonid ............................................. 25

D: Diagnostic External Features of Juvenile

Salmonids Found in the Intermountain West.... 26

E: Distribution of Interior Races of Cutthroat

Trout in the Western United States ................. 28

The use of trade or firm names in this publication is for reader information and does not

imply endorsement by the U.S. Department of Agriculture of any product or service.
1

INTRODUCTION

Underwater observation with snorkeling gear is

a valuable tool for studying fish populations and assessing how fish use habitat in flowing waters. Precise estimates of fish abundance can be obtained

using underwater counts (Griffith 1981; Northcote

and Wilkie 1963; Schill and Griffith 1984; Zubik and

Fraley 1988). However, several factors, including the

behavior of the target fish species and attributes of the

physical habitat (stream size, water clarity, temperature, and cover), can bias results.

This guide was developed to assist biologists in

identifying and accounting for potential biases and

to encourage a standardized procedure for the use

of underwater techniques to survey salmonids in

streams. The guide addresses the principal resident

and anadromous salmonids found in the Intermountain West (Idaho, Montana, Nevada, Utah, and western Wyoming).

CONSIDERATIONS BEFORE THE

SURVEY

Before using underwater techniques several factors

need to be considered, including study objectives,

safety, equipment, training, and ethics.

Objectives

Biologists should carefully consider the objectives

of the study before deciding whether underwater

observation is the appropriate sampling technique.

Underwater observation can provide quantitative

information on the abundance (Schill and Griffith

1984), distribution (Hankin and Reeves 1988), size

structure (Griffith 1981), and habitat use (Fausch

and White 1981) of salmonids. Underwater techniques may also be useful for capturing salmonids

in small streams (Bonneau and others, in preparation). Biases can result, however, unless certain conditions of depth, water clarity, and temperature are

met (see Recommended Snorkeling Protocols, Minimum Criteria).

Underwater Methods for Study of

Salmonids in the Intermountain

West

Russell F. Thurow

If minimum criteria are met, underwater observation has advantages for sampling fish populations.

Snorkeling is feasible where environmental conditions such as deep, clear water of low conductivity

may limit the effectiveness of electrofishing (Schill

and Griffith 1984). Because of the small amount

of equipment required for snorkeling, the technique

can be used in remote locations where it may be difficult to use other sampling apparatus such as traps,

nets, and electrofishing gear. Snorkeling is especially

applicable for censusing fish populations in roadless

areas (Thurow 1985). Because fish are not handled

and disturbance is minimized, snorkeling is useful

for sampling stocks of fish that are protected or rare.

Less time is required to complete snorkel surveys,

and the technique is more cost effective than markrecapture or removal methods typically used to estimate abundance (Hankin and Reeves 1988; Schill

and Griffith 1984).

Snorkeling is a relatively unbiased method for observing fish in their natural environments (Heggenes

and others 1990). Snorkelers can observe spawning,

feeding, movements, and other behaviors without

disturbing the fish (Helfman 1983). Snorkelers can

also measure environmental variables such as temperature, velocity, and depth in precise locations.

Underwater observation also has disadvantages.

Fish are not handled, so snorkelers must estimate

fish size (Grunder and Corsi 1988). Snorkelers may

fail to detect fish, count fish more than once, incorrectly estimate fish size, and misidentify fish (Griffith

and others 1984). Counting fish accurately in a dense

population is difficult (Heggenes and others 1990).

Some species and sizes of fish are more easily seen

than others (Hillman and others 1992). Small fish

and species that remain near the substrate may be

more difficult to see than larger, more mobile species

(Helfman 1983). Differences in fish behavior during

different times of the day or year also may bias observations (Rodgers and others 1992). Instream cover can

limit the accuracy of underwater counts if fish are

concealed. Counts completed in habitat lacking cover

may be more accurate than those completed in complex habitat with abundant cover (Rodgers and others

1992).
2

Safety

Although underwater observation avoids the hazards of electrofishing, safety should be emphasized

(Griffith and others 1984). Snorkelers should always

have a partner, either on shore or in the water. Never

attach ropes or survey tapes to a snorkeler. Assess

the hazards of the site before entering the water.

Avoid areas of extreme water velocity and turbulence,

especially those immediately upstream from debris

jams or bedrock outcrops. If it becomes necessary

to survey turbulent stream reaches, attempt to complete surveys from the channel margins and avoid

entering the most turbulent locations. Use extreme

caution when snorkeling under and within debris jams

to avoid entrapment. Stay alert for rattlesnakes,

since they often live in riparian zones. Recognize the

symptoms of hypothermia and know how to treat it.

Exercise extreme caution when conducting surveys

at night and during the winter when snorkelers may

be exposed to additional hazards. Require all crew

members to complete cardiopulmonary resuscitation

(CPR) and first aid training. Carry a first aid kit

that includes a cardiopulmonary resuscitation mask

and a device for extracting poison.

Equipment

Daytime snorkeling in water warmer than 8 °C requires only a minimum of equipment: full neoprene

wetsuit (6.4 mm thick), hood, gloves, mask, snorkel,

and data recorders. Suits should be of black or dark

blue, rather than of bright colors that may startle

fish. In turbulent streams, knee and elbow pads provide added protection. Pads can be ordered on the

suit, purchased separately, or cut from surplus suits

and glued on. Masks may be worn directly over contact lenses, or prescription masks can be purchased

for snorkelers who wear glasses. Masks with front

and side lenses increase the observer’s field of view.

It is advisable to carry an extra mask and snorkel for

each team on backcountry trips. Neoprene socks worn

inside canvas tennis shoes or wading shoes are more

durable than neoprene booties and protect the feet

better. Fins are useful in large rivers where counts

must be conducted while floating downstream. A can

of black neoprene wetsuit cement should be carried for

patching holes; the cement dries in 10 minutes, forming a durable bond. Wetsuit zippers should be well

lubricated with wax or graphite.

Data can be recorded on a slate or cuff carried by

the snorkeler. I prefer a cuff cut from a piece of PVC

plastic pipe 10 cm in diameter and 20 cm long, modified from the design described by Helfman (1983). The

pipe is cut in half, producing two halves each 20 cm

long. Four holes are drilled at the corners of each

cuff, and a loop of surgical tubing is threaded through

each pair of holes. The cuff slides over the snorkeler’s

arm and is secured by tightening the surgical tubing.

Pencils may be stored inside the lengths of surgical

tubing. The cuff fits comfortably on the snorkeler’s

forearm; both hands remain free. Hand tally counters

are useful if large concentrations of fish of several

sizes or species are encountered.

Underwater observation in cold water or at night

may require specialized equipment. If water temperatures are consistently below 8 °C, a drysuit should

be worn. It allows snorkelers to complete counts

comfortably, even in water near 0°C. Two types of

drysuits are widely available, neoprene and nylon.

Both types are durable, but the nylon suit is more

lightweight and compact. Various layers of undergarments can be worn inside, enabling a snorkeler

to work comfortably in a broad range of water temperatures. Unless the suit will be used for scuba

diving, it should be purchased without valves and

with attached latex socks. Layers of wool or pile

should be worn inside and over the latex socks. Knee

and elbow pads protect the snorkeler and the suit.

Several excellent hand-held halogen lights are

available for night snorkeling. When a beam of light

is focused on fish, they typically maintain their position for 2 to 3 seconds before swimming away. Most

species will hold their position longer if underwater

lights with red filters are used (Hillman 1993). A filter

can be made from red Plexiglass. No other specialized

equipment is needed for night snorkeling.

Training

Although snorkeling is easy to learn, training and

practice are required to correctly identify species of

fish underwater, estimate fish sizes accurately, and

complete precise counts. All snorkelers, whether novice or experienced, will improve their abilities with

annual training. Snorkelers should review available

literature describing snorkeling techniques before

beginning practice sessions (see References). Experienced snorkelers should conduct training sessions,

administer tests, and review the results with individual snorkelers. The objectives of the study should

be clearly stated at the start of the training.

Training should be structured to address equipment,

safety, ethics, techniques, and data collection. Select

locations for training where snorkelers can practice

the selected technique under field conditions simulating those of actual surveys. Have snorkelers practice

identifying, counting, and estimating the size of target species.

Identifying Species—Snorkelers may familiarize

themselves with the species to be surveyed by reviewing

drawings, color plates, and photos; viewing videotapes;

visiting aquaria; and snorkeling with experienced
3

snorkelers. See Sigler and Miller (1963), Scott and

Crossman (1973), Simpson and Wallace (1978), or

Behnke (1992) for detailed species descriptions, drawings, and color plates. Carl and others (1959) and

McConnell and Snyder (1972) presented keys and

illustrations to identify juvenile resident and anadromous salmonids. Martinez (1984) provided detailed

comparative descriptions of trout larvae. The species

included in this guide (see Species Identification and

Habitats) represent the principal salmonids in the

Intermountain West. If available, underwater videotapes are excellent tools to assist snorkelers in identifying species under field conditions. Aquaria, or

other fish facilities with observation windows, offer

an opportunity to observe salmonids underwater.

There are several ways to test snorkelers’ abilities

to identify species underwater. One method is to capture several species of fish and place them in temporary live cages. Snorkelers independently view each

fish and report their results to an instructor. Or, an

instructor in the water points out fish for a snorkeler

to identify and record. In both cases, results are reviewed with the snorkeler; training continues until

all snorkelers identify target species accurately. The

stream reach to be surveyed on a given sampling trip

offers the best location to practice species identification. Snorkelers should practice throughout the field

season.

Estimating Fish Size—Accurately estimating

the size of fish underwater requires practice. Objects

viewed underwater are magnified about 1.3 times.

One way to estimate a fish’s size is to approach it

underwater, align its snout and tail with adjacent objects, and measure that distance with a ruler (Cunjak

and Power 1986). Snorkelers can carry a ruler, mark

one on their counting sleeve, or use a known distance

(index finger to thumb, for example). Swenson and

others (1988) described a method for estimating fish

size underwater by using a dive mask with a calibrated bar attached to it.

Snorkelers can practice estimating fish sizes by

viewing objects and fish of known sizes underwater.

Calibrated wooden dowels or floating cutouts of fish

of various sizes can be attached to weights and distributed throughout a stream channel. Snorkelers

approach each object and estimate its size. Live fish

of known size can also be used. One method is to individually mark fish of known sizes in a stream reach.

Snorkelers approach each marked fish and estimate

its size. Another method is to capture fish of several

size classes and place them in temporary live cages

(Rich 1993). Snorkelers independently view each fish

and report their results to an instructor.

Training improves snorkelers’ abilities to estimate

fish sizes accurately. Griffith (1981) reported that

five observers were tested on their ability to estimate

lengths of 15 fish underwater. Before training, from

52 to 72 percent of the estimates were within 25 mm

of the true length. After 1 hour of practice, the most

experienced observers estimated fish size within

25 mm of the true length in 90 percent of the trials.

Rich (1993) trained snorkelers with no previous experience, using live cages in a hatchery raceway. After

1 day of training, the novice group was able to estimate fish size within 25 mm of the true length in more

than 90 percent of the tests. Snorkelers should continually check their size estimates throughout the field

season.

Estimating Fish Abundance—Snorkelers should

be familiar with the size of sampling units they will

survey and the method they will use to estimate fish

abundance. The selection of sampling units depends

on the objectives of the study and the physical characteristics of the stream (see Selecting Appropriate

Sampling Units). Select a stream reach with physical characteristics similar to those that crews will

actually survey, and train snorkelers to duplicate the

proposed snorkeling method. For example, if the survey will be in small streams and a lone snorkeler will

proceed upstream while counting all fish in individual

habitat units, duplicate those conditions in training.

Provide snorkelers with an opportunity to count the

total number of target salmonids, recording them by

species and size class in several sampling units. Test

snorkelers’ ability to make precise counts of fish by

comparing the counts of several observers in a stream

reach. If feasible, establish sampling units that contain a known number of fish of known sizes for testing snorkelers’ abilities to complete precise and accurate counts.

Ethics

Biologists have an incomplete understanding of the

distribution and abundance of many native salmonids.

Snorkelers surveying streams in the Intermountain

area may encounter several protected native fish species that warrant special consideration. Snake River

spring/summer and fall chinook salmon (Oncorhynchus

tshawytscha) are protected as threatened species and

sockeye salmon (O. nerka) are protected as an endangered species under Section 7 of the Endangered Species Act. At the request of the National Marine Fisheries Service, the Forest Service and other agencies

are establishing protocols to minimize any potential

effects snorkel counts may have on these species.

Snorkelers and survey crews should avoid areas where

adult salmon spawn.

Lahontan cutthroat (O. clarki henshawi) and Paiute

cutthroat trout (O.c. seleniris) are federally protected

as threatened species. Bull trout (Salvelinus confluentus), Bonneville cutthroat (O.c. utah), Colorado River
4

cutthroat (O.c. pleuriticus), finespotted cutthroat

(undescribed), redband trout (O. mykiss ssp.), and

Montana grayling (Thymallus arcticus montanus)

are listed as Category 2 candidates under the Endangered Species Act and are undergoing a status review.

Westslope cutthroat (O.c. lewisi) and Yellowstone cutthroat trout (O.c. bouvieri) are listed as sensitive species by the Forest Service, U.S. Department of Agriculture, and the States of Idaho and Montana. Steelhead

(O. mykiss) are listed as a sensitive species by the Forest Service and the State of Idaho. Some States have

legislation making it illegal to harass any fish. Under

Title 36 Idaho Code, it is illegal to “harass any fish by

striking it...or chasing it up or downstream in any

manner.” Crew members should not touch or in any

way disturb protected fish while conducting snorkel

surveys. If the study objectives require capturing

federally protected species, a National Marine Fisheries Service or U.S. Fish and Wildlife Service permit

will be required in addition to a State collecting permit.

Fish population surveys provide information that

is used to sustain and enhance fisheries resources.

Snorkelers may encounter concentrations of fish and

large individuals of some species. These fish may be

highly vulnerable to angling. Considering the sensitive status of many native fish in the Intermountain

West, crew members should not harvest fish from

streams they survey or pass survey results to other

anglers.

RECOMMENDED SNORKELING

PROTOCOLS

In this section I recommend procedures for measuring fish distribution, abundance, habitat use, and

size structure. The protocols outline sampling designs

and procedures, illustrate the principal sources of

error, and suggest approaches for reducing the error

of estimates.

Timing

Seasonal timing of snorkel surveys depends on the

objectives of the study and the behavior of the target

species. If the objective is to estimate the abundance

of fish or the habitat use by a certain life stage of a

species, the investigator must have some knowledge

of fish behavior. For example, if the objective is to

estimate the abundance of juvenile steelhead, the survey might be conducted in summer rearing areas. If

the objective is to characterize habitat used by adult

bull trout before spawning, the survey might be conducted before August. Underwater counts of fish are

most reliable if conducted when emigration and immigration are minimal. Resident and anadromous salmonids migrate, and their behavior and habitat use

vary by season. Most species maintain relatively static

summer ranges between the stabilization of streamflows in late June or July and the onset of cooler

water temperatures in early September (Bjornn 1971;

Edmundson and others 1968). Streams are generally

suitable for summer estimates of population density

between early July and late August.

Daytime underwater visibility is generally best

between late morning and early afternoon when the

sun is directly overhead. Cloudy or overcast days

may be most suitable for sampling sites with abundant overhead cover. On clear days, dark shadows

may form beneath cover, and the snorkeler must

swim into the shadows to observe fish. A small halogen light may be used to search for fish in shaded locations. On overcast days, the contrast between light

and shadow is reduced; fish beneath cover, such as

undercut banks, can be observed farther away. If

minimum depth, velocity, and temperature criteria

are met, the presence of direct sunlight or the time of

day may not be critical. Hillman and others (1992)

found no significant relationship between the time of

day and the accuracy of counts. Time of day will influence water temperature, however, and snorkelers

may need to schedule surveys carefully to meet temperature criteria.

Nighttime surveys may be more effective for studying salmonids than daytime surveys under some

conditions. Fish that remain concealed during daylight often move out of cover and are visible at night

(Campbell and Neuner 1985; Goetz 1990; Griffith

and Smith 1993).

Ambient light levels influence the behavior and distribution of fish at night. Robinson and Barraclough

(1978) observed differences in the behavior of sockeye salmon during dark moon phases compared to

full moon phases. If underwater surveys are done

at night, they should be completed during the same

moon phase to avoid additional bias.

Minimum Criteria

Before developing the study design and selecting

the appropriate sampling units, certain minimum

criteria for water depth, temperature, and visibility

must be met in the proposed study stream.

Depth—The area to be surveyed must be deep

enough to enable observers to submerge a mask. Shallower water limits the snorkelers’ ability to view fish

hiding beneath and behind obstructions. Snorkelers

can count fish in water that is deep enough to submerge a mask, but too shallow to float the snorkeler,

provided the observer can crawl through the unit.

Shallow water along stream margins makes it difficult for a team of divers to maintain an organized line

while floating downstream (Schill and Griffith 1984).
5

Temperature—Water temperature influences fish

behavior and may bias underwater counts. As temperatures decline, stream-dwelling salmonids in the

Intermountain West typically migrate or seek concealment cover. Salmonids may migrate from summer habitat into other portions of the watershed as

temperatures decline below 10 °C (Bjornn 1971).

Movement into concealment cover at reduced water

temperatures is well documented for a variety of resident and anadromous salmonids, including juvenile

chinook salmon (Edmundson and others 1968; Hillman

and others 1987), juvenile steelhead (Bustard and

Narver 1975; Edmundson and others 1968; Everest

and Chapman 1972), cutthroat trout (Bustard and

Narver 1975; Griffith and Smith 1993), and rainbow

trout (Campbell and Neuner 1985). The accuracy of

underwater counts of juvenile salmonids declines

with decreased water temperatures (Angradi and

Contor 1989; Hillman and others 1992; Riehle 1990;

Shepard and others 1982). At water temperatures

below 9 °C, most juvenile salmonids hide during the

daytime, and counts underestimate the true population. Accuracy of counts improves as temperatures

increase above 9 °C (Hillman and others 1992).

The effects of temperature may be both species and

stream specific. Bull trout are uncommon where water

temperatures exceed 15 °C (Fraley and Shepard 1989;

Goetz 1990). Lahontan cutthroat trout frequently

occur in waters with temperatures up to 26 °C (Nelson

and others 1992). In streams that rarely exceed 10 °C,

it may be possible to accurately count fish, even at

temperatures lower than 9 °C. In streams that commonly exceed 20 °C, salmonids may migrate or seek

cover at temperatures warmer than 9 °C.

In general, daytime surveys of fish in summer rearing habitat should be conducted when stream temperatures exceed 9 °C. Observers should carry an accurate thermometer to measure water temperatures in

each sampling unit. However, because the effects of

temperature may be species and stream specific, investigators may need to adapt their survey to local

temperature regimes.

Visibility—Water clarity can severely limit an

observer’s ability to count fish reliably. Palmer and

Graybill (1986) observed a significant positive correlation between visibility and numbers of fish observed

as visibility increased above 2 m. Researchers working in a variety of streams have recommended minimum visibilities ranging from 1.5 to 4 m for underwater counts (Gardiner 1984; Griffith and others 1984;

Hillman and others 1992; Zubik and Fraley 1988).

Researchers agree that the minimum acceptable visibility depends on the target species, the nature of the

physical habitat, and the experience of the snorkeler.

The water must be clear enough to allow snorkelers

to see the stream bottom in the deepest sampling

unit, identify fish by species, and detect fish trying

to avoid the snorkeler. Within most small streams

of the Intermountain West, visibility of 3 to 4 m will

meet the listed criteria. Larger, deeper streams will

require greater water clarity. In most cases, abundance estimates should not be made in units where

water clarity does not exceed maximum water depth.

As visibility increases, fewer snorkelers are needed

to survey an entire unit.

The parent geology of a watershed can provide clues

about the potential clarity of its waters and the suitability of snorkeling for sampling salmonid populations. Most streams draining granitic rock have low

suspended sediments, are unproductive (have low dissolved solids), and have high visibility. In contrast,

streams draining sedimentary or volcanic rock often

have high levels of suspended sediment, are very productive, and have low visibility.

Observers should periodically measure the visibility

of a known object in stream reaches to be surveyed.

Do not assume underwater visibility is adequate without measuring it. A suitable object for measuring

visibility is a silhouette of a salmonid drawn with

parr marks and spots. Estimate visibility by averaging measurements of the minimum distance at which

the marks on a silhouette are visible to the snorkeler.

To locate the minimum distance, the snorkeler moves

away from the object and notes the distance at which

it disappears, then moves toward the object and notes

the minimum distance at which it reappears clearly.

Storms and other events can periodically reduce visibility in streams that are otherwise suitable for snorkeling. If this occurs, stop snorkeling and resume after

conditions improve.

In some portions of some sampling units, turbulence will reduce local visibility, even though water

clarity in the unit is adequate. Snorkelers should

survey areas surrounding the turbulence first and

then attempt to survey the turbulent areas. Salmonids typically maintain territories outside areas of

extreme turbulence although they may seek cover

in turbulent areas if disturbed.

Selecting Appropriate Sampling Units

The selection of sampling units is controlled by the

objectives and design of the study, physical characteristics of the stream environment, and the investigator’s

budget. Good experimental design is crucial to distinguish among different hypotheses (Hurlbert 1984).

Design of experiments is beyond the scope of this

guide. The reader is urged to review texts on the subject and papers by Hurlbert (1984), McAllister and

Peterman (1992), and Romesburg (1981).

Underwater survey techniques are flexible; sampling

units can be adapted to the investigators’ needs. A

variety of sampling units may be selected.
6

salmonids face the current, a snorkeler moving upstream is less likely to startle fish. As Heggenes and

others (1990) reported, a snorkeler who moves slowly

can nearly touch fish before they are frightened.

Fish are counted as the snorkeler passes them so

duplicate counts are avoided. Any fish that reenter

the observer’s view can be seen moving upstream.

When it is impractical to move upstream, snorkelers

may enter the water upstream from the sampling

unit and float downstream with the current, remaining as motionless as possible. Fish are counted by

species and size class. Sizes can be estimated by approaching fish, aligning their snout and tail with adjacent objects, and measuring that distance with a

rule or marked glove (see Training, Estimating Fish

Size).

Water clarity, physical obstructions, and the type

of estimate will determine the number of observers

needed to complete the survey. As a general rule,

enough snorkelers are needed to complete the survey

in a single pass. The following section describes various types of estimates and considerations for the

number of observers required.

Direct Enumeration—Direct enumeration procedures can be used to count the total number of fish

within a given sampling unit. Typically, either one

observer or multiple observers count all fish in a single pass. This method assumes the counts of fish are

accurate.

In small streams with excellent visibility, one snorkeler may be able to see from bank to bank. The observer counts all fish in the entire sampling unit using

one of three approaches. Depending on the characteristics of the unit, the snorkeler can proceed up the center of the unit and count fish by zigzagging outward

One investigator may select sample units that

include several habitat types (pools, runs, riffles,

glides) and that represent large segments of the

stream. Schill and Griffith (1984) estimated the seasonal abundance of Yellowstone cutthroat trout in

the Yellowstone River. They selected four sampling

units ranging from 350 to 1,316 m long, composed of

several habitat types.

Another investigator may stratify a large watershed into sections and sample units within each section. Thurow (1985) monitored the abundance of

juvenile steelhead in a 160-km section of the Middle

Fork Salmon River. He systematically selected 20

sampling units spaced about 8 km apart. To maximize the number of fish counted, he selected units in

optimal steelhead rearing areas consisting of pocketwater habitat.

Other investigators may stratify small streams into

habitat units, count fish in a random or systematic

sample of the units, and extrapolate abundance estimates from the sampled units to a total estimate for

each stream. Hankin and Reeves (1988) estimated

the total abundance of fish in small coastal streams.

The authors estimated the total area of each habitat

type. After the starting point was randomly selected,

sampling units consisted of systematically selected

habitats of each type. Total numbers of fish were estimated in each unit and averaged. A total estimate

of fish abundance in each habitat type was derived

by multiplying the mean abundance per habitat type

by the area of the respective habitat type and summing across all habitat types. Sampling by habitat

type reduces the variance of the expanded estimate

by accounting for the influence of habitat type on fish

abundance.

If sampling units will be resurveyed in the future,

they should be recorded permanently so other investigators can relocate them. Some useful techniques are

to mark the units on a topographic map; photograph

them, taking care to include permanent landmarks

in the photo; and sketch a detailed map of the unit

illustrating access, physical features, starting and

ending points of the survey, and the point from which

the photo was taken (see appendix A).

Snorkeling Procedures

When selecting an appropriate snorkeling procedure,

the investigator must consider the direction of the

survey, the number of snorkelers required, and the

type of estimate desired.

Where feasible, moving upstream against the current is the most effective snorkeling technique. Snorkelers should enter the water downstream from the

unit to be surveyed and proceed upstream slowly while

avoiding sudden movements (fig. 1). Because most

Figure 1—In small streams, one snorkeler enters the water downstream from

the sampling unit and proceeds slowly

upstream.
7

to both banks (fig. 2). Care should be taken to search

for fish throughout the unit, including the margins,

and to inspect all cover components (such as undercut banks, substrate, organic debris). If the water

is too deep or turbulent to zigzag and visibility is adequate, the observer moves up one bank of the unit

and counts all fish to the other bank. In water too

deep to count upstream, the observer floats down the

center of the unit and counts all fish from bank to

bank, remaining as motionless as possible.

Although water clarity may allow one observer to

see across the width of the channel, another snorkeler

may be needed to count fish concealed by visual obstructions such as boulders, ledges, and organic debris

if all fish are to be counted in a single pass. Shallow

habitats (pocket water, riffles) typically require more

observers than deep-water habitats. To avoid recounting fish, observers should stay adjacent to each

other, move at the same speed, and only count fish

that pass them.

If two snorkelers are used, the unit is divided, and

snorkelers use one of three techniques. Where feasible,

the unit is divided in half. Snorkelers begin in the

center of the unit, move upstream shoulder to shoulder, and count all fish between themselves and the

bank (fig. 3). If the unit is too deep or turbulent to

allow that approach, snorkelers can use natural breaks

and features such as boulders to divide the unit. Snorkelers count all fish in their portion of the unit. In

water too deep to move upstream, two snorkelers lock

hands and float down the center of the unit, counting

all fish from their shoulders to the bank.

With three or more snorkelers, the unit is divided

into equal corridors. Snorkelers proceed upstream

and count all fish in one direction between themselves

and the adjacent snorkeler. Snorkelers nearest the

shore also count all fish between themselves and the

nearest bank. Fish are not counted until they pass

snorkelers. In water too deep to proceed upstream,

snorkelers hold onto lengths of PVC pipe to maintain a

straight counting line (Schill and Griffith 1984) (fig. 4).

The distance between observers should always be less

than the maximum underwater visibility. For example, if the visibility is 6 m, snorkelers should be stationed less than 6 m apart during the survey.

When it is not feasible to count all fish from bank to

bank, snorkelers may count fish within a subunit of

the stream channel. Snorkelers measure the underwater visibility and count all fish within their range

of vision. The area surveyed is estimated by multiplying the length snorkeled by the visible corridor.

With either one or several observers, fish are counted

by species and size class. Counts are recorded on a

PVC cuff or slate and later transferred to a data sheet

(appendix B). After completing counts, observers or

other crew members measure the surface area of the

snorkeled unit. Record the total length of the unit

and measure the width at three or more equally

spaced intervals. The surface area can be estimated

either by multiplying the length times a mean width

or by calculating the area of individual segments and

pooling them for a total area estimate. The density

of fish is typically expressed as the number of fish

Figure 2—A snorkeler counting fish in a

single pass zigzags through an entire unit

while moving upstream. The dashed line

represents the approximate path of the

snorkeler who counts fish left and right.

Flow
8

Flow

Figure 3—Two snorkelers counting fish

in a unit while moving upstream. Observer 1 counts all fish to the left of center and observer 2 counts the remainder.

Flow

Figure 4—Several snorkelers maintaining a

line with a pole as they move downstream in a

large river. The unit has been equally divided,

and fish are counted as the snorkelers pass

them. The arrows indicate the directions each

snorkeler counts fish. The dashed lines represent the approximate paths of the snorkelers.

1

2
9

marked and unmarked fish are randomly mixed and

have equal chances of being seen. When sample sizes

are sufficient, population estimates are calculated for

each size class using Chapman’s modification of the

Peterson mark-recapture technique (Ricker 1975):

(M + 1) (C + 1)

 (R + 1)

where

M = number marked

C = number captured (observed)

R = number of marked fish recaptured (observed)

N = population estimate.

A total population estimate is derived by pooling the

estimates for each size class. Ricker (1975) lists formulas for calculating confidence intervals around the

estimate.

Habitat-Use Estimates—Direct underwater observation has become increasingly popular for observing

fish in their natural environments (Heggenes and

others 1990). Underwater observation is generally

considered unbiased for studying fish habitat use,

particularly because fish can be observed without

disturbing them. Researchers have used snorkeling

techniques to study habitat use of different salmonid

life stages (Cunjak 1988; Cunjak and Power 1986;

Fausch and White 1981; Rimmer and others 1984).

Snorkelers typically move upstream through the sampling unit, searching for fish. Upon encountering a

fish, the observer carefully notes the species and its

focal point (the location of the fish’s snout). The fish

is approached and its size estimated. If more accurate

estimates of fish size, weight, or food habits are required, fish can be collected underwater using several

techniques. Lethal methods of capture include explosive charges (Everest 1978) and spear guns (Helfman

1983). Nonlethal capture methods include slurp guns

(Morantz and others 1987), nets (Bonneau and others,

in preparation), and electrofishing (James and others

1987). A weight and float can be used to mark the

fish’s focal point or a measurement can be taken at

the focal point immediately after the fish is observed.

A series of macrohabitat and microhabitat measurements can be made to describe the habitat used by

the fish. This method assumes that fish are undisturbed when first sighted, so their position reflects

conditions selected by the fish.

Precision and Accuracy

Precision is a measure of the repeatability of measurements. Precise estimates tend to have small variance. The statistical precision of underwater estimates

of fish abundance is derived by replicating counts.

Counts may be replicated temporally within the same

per 100 m2

 or the number of fish per hectare. By

converting fish counts to densities, the investigator

standardizes the data, making it possible to compare

counts spatially and temporally, both within a watershed and among watersheds.

If counts within individual units are replicated, average density and variance can be calculated, and confidence limits can be placed around the mean (Schill

and Griffith 1984). Hankin and Reeves (1988) list formulas for estimating total fish abundance and calculating confidence limits around the estimates.

Expansion Estimates—The expansion method

may be used to estimate the total population of fish

in sampling units where total enumeration is not feasible. Expansion methods may be needed in large

rivers where too few observers are available to survey

the entire channel width in a single pass. This method

assumes counts are accurate and the density of fish

in each snorkeler’s lane represents the unsampled

area. The investigator typically stratifies the sampling unit into relatively homogeneous sections (such

as bank and midchannel) (Grunder and Corsi 1988).

Within each stratified area, counting lanes are selected randomly with widths less than or equal to

the underwater visibility. One snorkeler counts the

number of fish within each counting lane. Several

snorkelers can count adjacent lanes simultaneously

(see Snorkeling Procedures, Direct Enumeration).

Observers are randomly assigned counting lanes, and

counts are replicated (Zubik and Fraley 1988). The

total population within the unit is estimated by dividing the total number of fish counted in each homogeneous section by the percent of the section that was

surveyed. For example, a total of 500 cutthroat trout

are counted in lanes representing 60 percent of the

sampling unit. Five hundred is divided by 0.6 to derive a total population estimate of 833 cutthroat trout.

If the unit encompassed 1.5 ha, the population density equals 556 fish per hectare. If counts within individual lanes are replicated, the mean density, variance, and confidence limits can be calculated (Slaney

and Martin 1987).

Mark-Recapture Estimates—Underwater observation can also be used in concert with other techniques to derive mark-recapture population estimates.

Researchers have captured fish with angling gear and

marked them with brightly colored tags that are visible underwater (Slaney and Martin 1987; Vore 1993;

Zubik and Fraley 1988). Colored tags can be used

to differentially mark each size class of fish. After

the marked fish redistribute in the sampling unit,

a snorkeler or team of snorkelers record the number

of marked and unmarked fish by species and size class.

This method assumes no immigration or emigration

occurs from the time of marking until the recovery

survey, marking does not affect mortality, and both

= N
10

unit (Slaney and Martin 1987) or spatially by replicating multiple units in the same strata (Hankin and

Reeves 1988). For example, observers make three

counts in the same unit, calculate the mean and variance, and place confidence limits around the mean

value. As another example, observers count fish in

several systematically selected units of the same

strata. Fish are counted in every 10th pool in a 30-km

reach of stream. Two counts are completed in each of

20 pools. The means and variances of the 20 counts are

calculated and used to place confidence limits around

the mean value. Replicate counts require independence and may be completed by individual snorkelers

or teams of snorkelers. Bias between snorkelers can

be reduced by using trained observers.

When trained snorkelers are used, precise estimates

of fish abundance can be obtained with underwater

counts (Griffith 1981; Northcote and Wilkie 1963;

Schill and Griffith 1984; Zubik and Fraley 1988). The

variation between counts by experienced observers is

typically small (fig. 5). Thurow and Schill (in preparation) replicated counts of age-1+ bull trout in 42

habitat units including pools, runs, riffles, and pocket

water in a small (4- to 6-m-wide) stream. Mean counts

ranged from one to six fish per habitat unit. Of the

replicate counts, 85 percent were within one fish of

the mean and 98 percent of the counts were within

two fish of the mean. Hankin and Reeves (1988) replicated counts of age-1+ steelhead in 30 pools in a small

(2- to 16-m-wide) stream. Mean counts ranged from

1 to 60 steelhead. Of the replicate counts, 87 percent

were within 15 percent of the mean count. Regardless of the size of the stream and sampling unit, most

replicate counts by trained snorkelers are precise.

Biologists counted trout in eight reaches of large (22-

to 38-m wide) New Zealand streams; coefficients of

variation between repeated counts ranged from 2 to

11 percent (Teirney and Jowett 1990). Schill and

Griffith (1984) made 28 replicate counts in 10 reaches

of a large (77- to 99-m-wide) river; 93 percent of the

replicate counts were within 15 percent of the average

count.

Although variation in replicate counts is typically

small, the accuracy of underwater estimates has been

difficult to assess because the true population density is usually unknown (Hillman and others 1992).

Rodgers and others (1992) concluded that because

the relative accuracy of snorkel estimates varies

from stream to stream, snorkel counts should be

regularly calibrated with other methods of estimating population size. The accuracy of underwater estimates has been estimated by comparing snorkel

counts with abundance estimates derived from electrofishing (Griffith 1981; Hankin and Reeves 1988),

seining (Goldstein 1978), and toxicants (Hillman and

others 1992; Northcote and Wilkie 1963). Slaney and

Martin (1987) and Zubik and Fraley (1988) reported

a technique that combines snorkeling and markrecapture estimates and can be used to calibrate snorkel counts in remote streams (see Snorkeling Procedures, Mark-Recapture Estimates).

Of 13 studies I reviewed in which population estimates were compared with snorkeling estimates of

fish abundance, the snorkeling estimates were within

70 percent of the actual population estimates in all

but two cases (table 1). Snorkelers observed from 75

to 78 percent of the bull trout estimated by electrofishing. Snorkelers observed from 74 to 105 percent

of the cutthroat trout estimated by electrofishing and

mark-recapture estimates based on snorkeling. Estimates larger than 100 percent suggest that either

the comparison method underestimated the actual

population size, or snorkelers counted some fish more

than once. Snorkelers observed 96 percent of the steelhead and 102 percent of the brook trout estimated by

electrofishing. Hillman and others (1992) observed an

average of 22 percent of the age-1+ steelhead collected

with sodium cyanide. One factor that may have contributed to the inaccuracy of Hillman and others’ (1992)

underwater estimates was that fish concealed themselves in the substrate, even at water temperatures

warmer than 10 °C.

Investigators do not have enough information to

calibrate snorkeling estimates with more accurate

estimates of fish abundance for all species and life

stages under all habitat conditions. In the absence

of more complete information, investigators can standardize snorkeling procedures in an attempt to increase precision and periodically compare their fish

abundance estimates with estimates derived from

other methods.

Figure 5—Comparison of independent counts

of age-1+ steelhead by two snorkelers (1, 2)

in 22 sampling units of the South Fork Salmon

River, 1984 (Thurow 1987).

Snorkeler 1 Count

Snorkeler 2 Count 80

70

60

50

40

30

20

10

0

0 10 20 30 40 50 60 70 80
11

Table 1—Comparisons of salmonid population estimates made by daytime snorkeling and other techniques at water temperatures warmer

than 10 °C

Percent of actual population

Stream observed by snorkeling Means of

Size size, width, Standard estimating

Species class flow Mean deviation (Range) N actual population Source

mm - - - - - - - - Percent - - - - - - - - -

Brook trout >100 Small, 4-6 m wide, 101.7 0.8 (101 - 103) 3 Electrofishing Griffith 1981

 0.06-0.10 m3/s

>75 Small, 5 m wide 110.0 — — 1 Electrofishing Hillman and Chapman 1993

Brown trout >75 Small-medium, 105.8 12.9 (94 - 126) 5 Electrofishing Hillman and Chapman 1993

 9-18 m wide

Bull trout >75 Small, 3-10 m wide 78.3 35.6 (47 - 117) 3 Electrofishing Shepard and Graham 1983

>100 Small, 4-6 m wide 74.9 15.3 (48 - 86) 14 Electrofishing Thurow and Schill,

 0.71 m3/s in preparation

Cutthroat trout >75 Small, 3-10 m wide 94.8 17.1 (71 - 117) 5 Electrofishing Shepard and Graham 1983

>200 Large, 40+ m wide 74.1 17.3 (51 - 92) 4 Mark-recapture Slaney and Martin 1987

 19-22 m3/s by angling and

 snorkeling

110-430 Large, 30-45 m wide 105.4 3.8 (102 - 110) 3 Mark-recapture Zubik and Fraley 1988

 12-14 m3/s by angling and

 snorkeling

>75 Small, 4-6 m wide 102.4 2.8 (100 - 104) 4 Electrofishing Griffith 1981

 0.06-0.10 m3/s

Rainbow trout >100 Large, 14 m3/s 59.0 — (36 - 86) 12 Rotenone Northcote and Wilkie 1963

>75 Small, 5-9 m wide 90.8 19.7 (77 - 105) 2 Electrofishing Hillman and Chapman 1993

Steelhead >100 Small, 2-16 m wide 96.3 44.8 (50 - 209) 14 Electrofishing Hankin and Reeves 1988

 0.8 m3/s

>100 Small-medium 21.8 25.4 (0 - 42) 15 Mark-recapture with Hillman and others 1992

 sodium cyanide

SPECIES IDENTIFICATION AND

HABITATS

As discussed earlier (see Training), snorkelers must

practice before conducting surveys if they are to identify species accurately. The following descriptions are

intended to help snorkelers identify species by observing size, coloration, morphology, and behavior. Appendix C illustrates the external characteristics of a typical salmonid. Appendix D illustrates the diagnostic

external features of eight species of juvenile salmonids.

The sizes of salmonids surveyed will depend on

the objectives of the study and the reliability with

which different size and age groups can be identified.

Summer estimates of salmonid abundance should be

limited to age-1+ fish for all species except chinook

salmon. Young-of-the-year (YOY) chinook salmon

typically emerge in April or May. By early summer,

YOY chinook salmon are large enough for snorkelers

to identify accurately. In contrast, summer counts

of YOY brook (Salvelinus fontinalis), bull, and cutthroat trout and steelhead are typically unreliable.

Young-of-the-year fish of these four species are similar in size and color in summer; they may be indistinguishable to all but the most experienced snorkelers.

Most will be smaller than 80 mm during surveys in

July and perhaps as late as August. Small fish typically occupy the shallow stream margins where snorkeling is less effective. Griffith (1981) counted only

20 percent of the YOY brook trout estimated by electrofishing, compared to 102 percent of the age-1+ brook

trout. Timing of emergence varies depending on water

temperatures, and YOY fish may be present during

surveys one year and not the next. In 1984, YOY steelhead in a reach of the South Fork Salmon River began

emerging on July 14; 98 percent of the fry emerged

by August 10 from redds that were capped with a net

(Thurow 1987). In 1985, lower stream discharge and

warmer water temperatures accelerated emergence;

steelhead fry began emerging from redds on July 3;

98 percent of the fry had emerged by July 17 from

capped redds. Although abundance estimates of YOY

fish may be unreliable, observers should record the

presence of YOY salmonids to indicate that adults

may have spawned in the vicinity of the sampled unit.

In order to assess size and age groups of fish accurately, the observer must understand the structure

of the population (Griffith 1981). When information

is lacking, the observer should collect a representative sample of the different size groups in the survey
12

area. The size groups suggested in this document are

intended as a guide. The timing of emergence and

growth rates vary among watersheds, and observers

need to adjust their size classes accordingly. This is

particularly true for estimating age classes of steelhead and other trout.

Anadromous Salmonids

Historically, anadromous salmonids in the Intermountain West were widely distributed in tributaries

to the Snake River in Idaho. Current populations are

confined to the Snake River basin downstream from

Hells Canyon Dam, including the Clearwater and

Salmon River drainages. Species include steelhead,

three races of chinook salmon (spring, summer, and

fall), and sockeye salmon. Snake River coho salmon

(O. kisutch) are extinct.

The abundance of wild anadromous stocks has declined severely and, as described earlier (see Considerations Before the Survey, Ethics), all stocks of salmon are protected under Section 7 of the Endangered

Species Act. Wild steelhead are listed as a sensitive

species, and adults are protected from angler harvest.

Hatchery-reared anadromous fish have been widely

introduced in attempts to supplement declining wild

stocks.

Investigators should evaluate the stocking history

of the drainage to be surveyed. If hatchery-reared

fish have been introduced, it may be desirable to distinguish wild from hatchery fish during the survey.

The adipose fin has been removed from all hatcheryreared steelhead and some chinook salmon parr or

smolts, and a ventral fin has been removed from all

chinook salmon parr or smolts stocked in Idaho waters (Kiefer 1993). Hatchery-reared parr or smolts

may also be larger than wild fish of similar age. Fish

stocked as fry may not be distinguishable from wild

fish.

Steelhead—Juvenile steelhead use most areas of

a watershed; they typically represent the most abundant salmonid in Intermountain streams that are

accessible to anadromous fish. Three distinct size

classes are usually present: age 1 (70 to 130 mm),

age 2 (130 to 200 mm), and age 3 (200 to 250 mm)

(Everest 1969; Thurow 1985). Age classes may vary

among drainages. Steelhead color varies; fish are

typically bluish to olive green on the back. Their sides

are a lighter color, silver with a faint horizontal reddish band and oval parr marks (fig. 6). The ventral

surface is white or silver. Steelhead have irregular

black spots on the back, sides, head, and dorsal and

caudal fins. Pelvic and anal fins have a distinct white

tip. The anal fin is taller than it is long. The maxillary

of juvenile fish is short and does not usually extend

past the posterior margin of the eye.

Steelhead usually maintain daytime stations closely

associated with submerged cover. They tend to prefer

rubble-boulder substrates and fast water. Steelhead

are territorial; they maintain some space between

themselves and other fish.

Chinook Salmon—Formerly abundant, chinook

salmon populations have declined rapidly since the

1960’s; wild stocks in several tributaries are approaching extinction. Juvenile chinook will be of two discrete

size classes: age 0 (50 to 80 mm) and age 1 (longer than

100 mm).

Young salmon are typically greenish blue to black

on the back. Their lower sides are silver, and the ventral surface is white (fig. 7). The back, top of head,

and upper sides are spotted. The dorsal fin is not

spotted, and the adipose fin is partially pigmented.

The caudal fin is distinctly forked, and the eyes are

large, relative to the head, compared to other species

described here. Parr marks are large, broad, vertical

bars centered on the lateral line. The anal fin is longer

than it is tall.

While juvenile chinook salmon tend to occupy C-type

channels (low-gradient, low-velocity, meadow reaches)

(Rosgen 1985), they may use a variety of habitats.

They usually associate with organic debris and overhead cover. Juvenile fish generally feed in groups in

the water column, in side channels, or along stream

margins. Adult chinook typically stage in large pools

(deeper than 1 m) when returning to natal spawning

areas.

Sockeye Salmon/Kokanee—Within the Intermountain West, sockeye salmon and their resident

form, kokanee, were indigenous to tributaries of the

Salmon and Payette River drainages in Idaho. Remnant populations of sockeye salmon remain in waters

of the Salmon River drainage. Kokanee remain in

their historic range and have been introduced widely

throughout the Intermountain West.

Kokanee and sockeye salmon differ little in coloration. The dorsal surface of the head and back is steel

blue to green blue with few spots. Sides are silver with

the ventral surface white to silver. Breeding males

have red-gray to bright red sides and olive-to-green

heads (fig. 8). Breeding females have red-gray sides

and olive heads. The body is elongated, streamlined,

and compressed laterally. The head is conical, and

the snout and mouth are large. The dorsal fin is not

spotted, and the adipose fin is not pigmented. The

caudal fin is distinctly forked. Parr marks on juvenile fish are narrow, vertical bars that do not extend

below the lateral line. Sockeye salmon/kokanee rear

in lakes and typically school.
13

Figure 6—Juvenile steelhead/

rainbow trout. Note the oval

parr marks, prevalent spotting,

and white tips on the pelvic

and anal fins.

Figure 8—Adult kokanee/

sockeye salmon approaching

breeding coloration. Note the

elongated body, unspotted

dorsal fin, forked tail, and lack

of spots.

Figure 7—Juvenile chinook

salmon. Note the broad, vertical parr marks, large eye, unspotted dorsal fin, forked tail,

and dorsal spotting. The adipose fin has been clipped from

these hatchery-reared fish.
14

Resident Salmonids

The Intermountain West historically supported a

diverse population of indigenous resident salmonids.

Stream-dwelling species included rainbow or redband

trout, bull trout, mountain whitefish (Prosopium williamsoni), grayling, and nine subspecies of cutthroat

trout. A combination of factors including habitat

degradation, genetic introgression, and exploitation

have contributed to the decline of native salmonid

populations (Rieman and McIntyre 1993; Thurow

and others 1988).

Several species of resident salmonids have been

propagated in hatcheries and introduced in the Intermountain West. Since the 1870’s, stocks of rainbow

trout have been mixed and reared in hatcheries with

little regard to their ancestry (Behnke 1992). These

hatchery rainbow trout stocks have been widely introduced to waters containing native salmonid populations. Similarly, cutthroat trout, especially the

Yellowstone subspecies, have been introduced into

Intermountain streams outside their original range

(Varley and Gresswell 1988). Exotic species including

brook (Salvelinus fontinalis) and brown trout (Salmo

trutta) have been widely introduced.

Before conducting underwater surveys, investigators

should evaluate the stocking history of target drainages to determine the species that may be present. If

hatchery-reared fish have recently been introduced,

it may be desirable to distinguish them from wild fish.

The dorsal or pectoral fin rays will be bent or appear

clipped on most fish that have been reared in hatcheries for more than 3 months.

Rainbow Trout—In drainages where steelhead are

present, nonanadromous rainbow trout may be distinguished from steelhead by their size. It is unlikely

that steelhead parr larger than 250 mm will migrate

(Thurow 1985). It is reasonable to assume that all

steelhead/rainbow larger than 250 mm are nonsmolting steelhead or resident rainbow trout. Below migration barriers, steelhead/rainbow less than 250 mm

should be considered steelhead because they are indistinguishable from resident rainbow trout. Rainbow

trout larger than 250 mm are usually seen in deepwater habitats. They seldom use habitats preferred

by juvenile steelhead.

In drainages where steelhead are not present, resident rainbow or redband trout may be distinguished

from other resident species by their coloration and parr

marks. Although rainbow trout may vary in appearance among drainages, they will retain characteristics

similar to steelhead (see Anadromous Salmonids,

Steelhead).

Cutthroat Trout Subspecies—Cutthroat trout

have the broadest distribution of any species of trout

in North America (Behnke 1992). Within the Intermountain West, cutthroat trout were the most widely distributed trout in Idaho, Montana, and Nevada,

and were the only native trout in Utah and Wyoming.

Nine subspecies of cutthroat trout exist in the Intermountain area (appendix E): westslope, Yellowstone,

Bonneville, Colorado River, finespotted, Lahontan,

Paiute, Alvord (undescribed), and Humboldt

(undescribed).

It is beyond the scope of this guide to describe each

form. Each subspecies exhibits different coloration

and spotting patterns. Snorkelers should be familiar with the distribution of cutthroat trout in their

locality before conducting surveys. Behnke (1992)

cites more detailed taxonomic information that can

assist in identifying subspecies.

Cutthroat trout are often the most common resident

trout in streams. Resident and migratory populations

may be present. Fish of several age classes are usually

present. It is not feasible to estimate age classes visually because age and size classes overlap. Cutthroat

trout can be recorded to the nearest 100-mm length

group. Most YOY fish are smaller than 70 mm.

Color and spotting pattern vary by subspecies.

Most westslope cutthroat trout are greenish blue to

steel gray on the back and upper sides. Their lower

sides are yellow green to copper, and their belly is

silver. Large fish may be distinctively red orange on

the lower sides. The spotting pattern is distinct and

is a good diagnostic feature: spots are irregular in

shape with more spots concentrated above the lateral line and posterior to the anal fin (fig. 9). An

arch drawn from the pectoral fin to the anal fin has

few spots below it and several spots above it. Few

spots are found on the head or anal fin.

Finespotted Snake River cutthroat trout also have

a unique color and spotting pattern. This subspecies

has the smallest spots of any trout native to the Intermountain West (fig. 10). The spots are profuse

and resemble a heavy sprinkling of ground pepper

(Behnke 1992). The color of finespotted cutthroat

trout resembles that of the Yellowstone cutthroat

trout. However, the finespotted subspecies has red

ventral fins, and its sides may be yellower than the

Yellowstone subspecies.

Juvenile cutthroat trout of several subspecies have

oval parr marks and white fin margins; they appear

similar to juvenile steelhead/rainbow trout. Both the

spotting pattern and coloration should be used to

identify cutthroat trout. The maxillary is longer than

a steelhead’s, extending past the posterior margin of

the eye. The red/orange slash underneath the jaw

may not be visible.

Cutthroat trout subspecies use all habitat types,

but tend to be most abundant in pools and habitats

with low water velocity. Larger fish generally use
15

deep pools and maintain stations in the water column

or move through the pool. Juvenile fish associate

closely with overhead and instream cover.

Bull Trout—Bull trout are the only char native

to the Intermountain West and are perhaps the least

understood salmonid. Resident and migratory populations exist. Fish of several age classes may be observed; some may be longer than 600 mm. Like cutthroat trout, bull trout can be recorded to the nearest

100 mm. Most YOY fish are smaller than 80 mm.

Their backs are normally olive green to brown with

white or pale yellow spots (fig. 11). Their sides are

pale in color with orange or red spots visible on adults

and white or pale yellow spots on juveniles. Fins are

tinged with yellow orange; the pectoral, pelvic, and

anal fins have white borders. The dorsal fin is typically unpigmented or of a solid color. Bull trout may

have vermiculations (wormlike markings) on their

back, although they are not as distinctive as those

of brook trout. Small fish have irregular parr marks

that appear as dark blotches. Compared to other species, the head is long with a large mouth and long,

blunt snout. Eyes are sloped toward the top of the

head more prominently than other salmonids.

Their cryptic coloration makes bull trout difficult

to see. They typically reside on or just above the substrate. Some researchers suggest that daytime counts

underestimate the true abundance of bull trout and

are less accurate than nighttime counts (Fraley and

Shepard 1987; Goetz 1990). Schill (1991) found no

significant difference in day and night counts. Bull

trout appear to prefer cold water (less than 15 °C),

coarse substrate, and organic debris. Because bull

trout may seek cover before other species do, snorkelers

Figure 9—Adult westslope cutthroat trout cruising through a

pool. Note the distinctive spotting pattern, copper-colored

sides, and orange slash underneath the jaw.

Figure 10—Adult finespotted

Snake River cutthroat trout.

Note the distinctive, small,

pepperlike spots, reddish color

of the ventral fin margins, and

orange slash underneath the

jaw.
16

should scan the substrate and underwater cover immediately when entering sampling units. Snorkelers

should carefully search for bull trout in potential hiding places such as debris jams, undercut banks, and

crevices under boulders.

Mountain Whitefish—Mountain whitefish are

abundant in many waters of the Intermountain West,

and several age classes may be observed. Since most

investigators do not collect information about mountain whitefish, information on their abundance, size

structure, and habitat use is incomplete. Investigators

are encouraged to collect such information. Age and

size classes overlap; mountain whitefish can be recorded in 100-mm size groups.

Mountain whitefish are light gray blue on the back

and silver on the sides, with a white belly. Their body

is slender with a pointed head and small, terminal

mouth (fig. 12). Scales are large relative to other salmonids and may reflect light. The adipose fin is large.

Juvenile whitefish have two rows of small, round parr

marks that seldom extend below the lateral line.

Whitefish use all habitat types, but they tend to

be most abundant in pools and areas with low water

velocity. Adults typically aggregate and forage near

the substrate in deep pools.

Brook Trout—Brook trout have been introduced

widely to waters in the Intermountain West. Brook

trout can be recorded in 100-mm groups. Most YOY

fish are less than 80 mm. Their backs are olive green

to dark brown with numerous distinctive vermiculations (fig. 13). Their sides are covered with red spots

encircled with blue halos. The belly is white. Anal,

pelvic, and pectoral fins are black and red with a distinctive white border. The nostril has a band of dark

pigment across it.

Brook trout typically live in low-gradient, C-type

channels (Rosgen 1985) and pools behind beaver

dams. Although they tend to be most abundant in

low-velocity meadow streams, brook trout also use

steeper gradient stream reaches.

Bull trout will hybridize with brook trout (Markle

1992), and the potential for hybridization exists if

adults of both species are present. Hybrids may be

difficult to identify. Markle (1992) suggested using

the coloration of the dorsal fin as a diagnostic feature.

Hybrids typically have a spotted or faintly banded

dorsal fin; bull trout have an unpigmented or solidcolored dorsal fin (fig. 11); and brook trout have a

banded dorsal fin (fig. 13). Adams (1994) compared

visual identification of 63 fish with electrophoretic

analysis of fin clips. She correctly identified 86 percent of the hybrids, 96 percent of the bull trout, and

100 percent of the brook trout. Hybrids exhibited

highly variable coloration and markings; some hybrids looked like brook trout but either lacked or had

only faint vermiculations, faint black or red bands on

the paired fins, or faint halos around spots. Other

hybrids looked like bull trout but had a spotted dorsal fin, dark bands on the paired fins, or a dark band

across the nostril.

Brown Trout—Brown trout have been introduced

widely in waters of the Intermountain West. Brown

trout tolerate disturbances in watersheds, such as increased water temperature and turbidity, more than

native salmonids.

They are olive brown on the back. Their light brown

or yellowish sides have numerous brown, black, and

red spots surrounded by halos of pink or gray (fig. 14).

The belly is white or yellow. The adipose fin is orange.

Figure 11—Adult bull trout

hiding on the substrate of a

pool. Note the large mouth,

pale yellow spots, white fin

margins, and unpigmented

dorsal fin.
17

Figure 12—Adult mountain

whitefish near the bottom of

a pool. Note its slender body,

small terminal mouth, silver

color, large scales reflecting

light, and forked tail.

Figure 14—Adult brown

trout. Note the brown and

yellow coloration and spots

with gray halos.

Figure 13—Adult brook trout.

Note the vermiculations on the

back, distinctive red spots encircled in halos, white borders

on the fins, and banded dorsal

fin.
18

Species Other Than Salmonids

Several species other than salmonids may be encountered during snorkel surveys. Three common

species can be confused with trout or salmon: northern squawfish (Ptychocheilus oregonensis), redside

shiners (Richardsonius balteatus), and suckers

(Catostomus spp.). Although the lack of an adipose

fin is a diagnostic characteristic, snorkelers should

be familiar with the distribution of nonsalmonids to

avoid confusion.

Northern squawfish can exceed 500 mm in length.

Their body is elongate, with a long, tapered head. The

snout is long, and the mouth is large. Their back is

dark olive green, the sides are gray silver, and the

belly is yellow white (fig. 15). The caudal fin is deeply

forked. Squawfish tend to reside at lower elevations

in slow-moving stream reaches. They are typically

observed near the bottom of large pools.

Redside shiners generally cluster together; they

rarely exceed 100 mm in length. The body is deep and

compressed laterally with a long caudal peduncle and

forked tail. Their back is steel blue, dark olive, or

brown; the sides and belly are silver (fig. 16). Their

eyes are large relative to their head, similar to chinook

salmon. They can be distinguished from chinook

salmon by the lack of an adipose fin and spots, and

by the dark lateral stripe extending from the snout to

the base of the tail. In adults, a reddish coloration is

often present from the opercle to the anal fin. Redside

shiners typically use slow-moving reaches of streams

with warmer temperatures.

Suckers are usually observed in aggregations; they

can exceed 400 mm in length. Their bodies are long,

with an oval cross section. Their head is large with

small eyes and a long, blunt snout (fig. 17). The mouth

is ventral with thick, fleshy lips. Suckers tend to be

sedentary and reside near the substrate.

Snorkelers may encounter other nonsalmonid species, including dace (Rhinichthys spp.) and sculpin

(Cottus spp.). These species are typically small (less

than 100 mm) and sedentary; they are not likely to

be confused with age-1+ salmonids.

RESEARCH NEEDS

The accuracy and precision of underwater surveys

of salmonids is strongly influenced by biological factors (behavior of the target species) and by physical

conditions (environmental attributes of the sampling

Figure 15—Adult northern

squawfish. Note the large

mouth, forked tail, lack of

spots, and absence of an

adipose fin.

Figure 16—Juvenile redside

shiner. Note the lack of parr

marks, lack of spots, and absence of an adipose fin.
19

unit). Underwater surveys may be biased by the behavior of different life stages within the same species

and by the behavior of various species within the same

life stage. Each species and life stage may respond

differently to changing environmental conditions.

Biologists do not have enough information to develop

protocols for sampling the distribution and abundance

of most species and life stages across the full range

of existing habitat conditions. There is a need to continue comparing the accuracy of underwater surveys

with other techniques. The feasibility of using underwater techniques to assess the presence or absence

of fish populations that are fragmented and in low

abundance has not been adequately assessed. For

most species and life stages, the variability in abundance estimates across a range of habitat conditions

is largely unknown. The influence of physical conditions including stream size, temperature, light intensity, cover abundance and quality, and water clarity

on sampling efficiency has not been adequately described. For most species, the sampling effort required

to achieve a desired level of accuracy and precision

in estimating abundance is unknown.

As additional native salmonids receive protected

status, underwater surveys could become more widely

used as a nonlethal sampling method. Additional

work on the biological and physical factors influencing

underwater surveys is necessary to enable biologists

to better evaluate and account for the associated bias.

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20

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21

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23

APPENDIX A: EXAMPLE OF A SAMPLING UNIT MAP

Direction of

flow

Stop on riffle

Boulders

Start

on

riffle

Point

of photo

Trail

Bridge

Sign

on

tree

14.5

Sulphur Creek —Site L1

14.5
24

APPENDIX B: EXAMPLE OF A SNORKEL DATA SHEET

Date__________________ page_______ of_______

Diver 1_______________

Location________________________________________

Diver 2_______________

Time__________________ H2O temp________________

Diver 3_______________

 Unit

 No. Diver 1 Diver 2 Diver 3

_____ chin 0 ______ ______ ______ Cover:

chin 1 ______ ______ ______ UC______% (undercut)

ST1+ ______ ______ ______ OC______% (overhead)

ST2+ ______ ______ ______ SC______% (submerged)

ST3+ ______ ______ ______ LS______% (large substrate)

RB>250 ______ ______ ______

CT<100 ______ ______ ______

CT 100-199 ______ ______ ______

CT 200-299 ______ ______ ______

CT>300 ______ ______ ______

BT<100 ______ ______ ______ Max Depth

BT 100-199 ______ ______ ______ (pools only)

BT 200-299 ______ ______ ______ ________M

BT 300-399 ______ ______ ______

BT 400-499 ______ ______ ______

BT>500 ______ ______ ______

YOY ______ ______ ______

chin = chinook salmon

ST = steelhead/rainbow

RB = rainbow trout

CT = cutthroat trout

BT = bull trout

 Comments:

 underwater visibility

 weather conditions
25

APPENDIX C: EXTERNAL CHARACTERISTICS OF A TYPICAL SALMONID

(Adapted from Simpson and Wallace 1978)

Nostril

Anus

Fin rays

Caudal

peduncle

Adipose

fin

Lateral

line

Dorsal

fin

Premaxillary

Maxillary

Branchiostegal

rays Pectoral

fin

Accessory

pelvic

appendage

Pelvic

fin

Anal

fin

Eye

Caudal

fin
26

APPENDIX D: DIAGNOSTIC EXTERNAL FEATURES OF JUVENILE SALMONIDS

FOUND IN THE INTERMOUNTAIN WEST

(Illustrations by Eric Stansbury, Idaho Department of Fish and Game)

Steelhead/Rainbow Trout (O. mykiss)

Cutthroat Trout (O. clarki subspecies)

Chinook Salmon (O. tshawytscha)

Kokanee/Sockeye Salmon (O. nerka)

(con.)

1. Abundant spots on head and body. 2. Maxillary short, does not extend past eye. 3. Dorsal fin spotted, white tip.

4. White tips on pelvic and anal fins. 5. Oval parr marks.

1. Few spots on head. 2. Maxillary long, typically extends past eye. 3. Red/orange mark beneath jaw. 4. Spots

concentrated near caudal peduncle. 5. White tips on pelvic and anal fins. 6. Oval parr marks.

1. Large eye. 2. Abundant spots on back. 3. Broad vertical parr marks. 4. Trailing edge of adipose fin black.

5. Deeply forked tail. 6. Anal fin longer than tall.

1. Narrow, alternating parr marks above lateral line. 2. Unpigmented dorsal and adipose fin. 3. Deeply forked tail.

4. Sides silver. 5. Anal fin longer than tall.
27

APPENDIX D (Con.)

Bull Trout (Salvelinus confluentus)

Brook Trout (Salvelinus fontinalis)

Brown Trout (Salmo trutta)

Mountain Whitefish (Prosopium williamsoni)

1. Large mouth and long snout. 2. Eyes sloped toward top of head. 3. White or pale yellow spots on back and

sides. 4. Parr marks appear as dark blotches. 5. Unpigmented or solid colored dorsal and adipose fins. 6. White

borders on ventral fins.

1. Dark band through nostril. 2. Vermiculations on back. 3. Banded dorsal fin. 4. Large, oval parr marks.

5. Square tail. 6. White borders followed by black and red bands on ventral fins.

1. Brown, black, and red spots with gray and pink halos. 2. Bar-shaped parr marks. 3. Trailing edge of adipose fin

orange.

1. Pointed head. 2. Small, subterminal mouth. 3. Two rows of oval parr marks above lateral line. 4. Large, coarse,

scales. 5. Deeply forked tail.
28

APPENDIX E: DISTRIBUTION OF INTERIOR RACES OF CUTTHROAT TROUT

IN THE WESTERN UNITED STATES

(Adapted from Behnke 1992)

Colorado

River

Alvord

Paiute

Westslope

Finespotted

Yellowstone

Bonneville

Humboldt

Lahontan
Federal Recycling Program Printed on Recycled Paper

Thurow, Russell F. 1994. Underwater methods for study of salmonids in the Intermountain

West. Gen. Tech. Rep. INT-GTR-307. Ogden, UT: U.S. Department of Agriculture,

Forest Service, Intermountain Research Station. 28 p.

This guide describes underwater methods using snorkeling gear to study fish populations in flowing waters of the Intermountain West. It outlines procedures for estimating

salmonid abundance and habitat use and provides criteria for identifying and estimating

the size of fish underwater.

KEYWORDS: snorkeling, underwater equipment, population estimates, habitat,

Salmonidae, species identification, anadromous fishes
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