Illustrated Field Guide for Assessing External 

and Internal Anomalies in Fish 

Information and Technology Report 

USGS/BRD/ITR–2002-0007 

U.S. Department of the Interior 

U.S. Geological Survey 
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Illustrated Field Guide for Assessing 

External and Internal Anomalies in Fish 

Information and Technology Report 

USGS/BRD/ITR—2002-0007 

September 2002 

by 

Stephen B. Smith1

Anne P. Donahue2

Robin J. Lipkin2

Vicki S. Blazer3

Christopher J. Schmitt2

Ronald W. Goede4

1

U.S. Geological Survey, Biological Resources Discipline, Office of the Northeast Regional Hydrologist, 12201 Sunrise Valley Drive MS 433, 

Reston, VA, 20192 

2

U.S. Geological Survey, Columbia Environmental Research Center, 4200 New Haven Road, Columbia, MO, 65201 

3

U.S. Geological Survey, Leetown Science Center, National Fish Health Laboratory, 1700 Leetown Road, Kearneysville, WV, 25430 4

Utah Division of Wildlife Resources, Fisheries Experiment Station, 1465 West 200 North, Logan, UT, 84321 
Contents 

Page 

Abstract........................................................................................................................................................................iv

1.0 Introduction.............................................................................................................................................................1

1.1 Background and Development.........................................................................................................................1

1.2 Scope and Intent...............................................................................................................................................1

1.3 Typographic Conventions.................................................................................................................................2

1.4 Animal Welfare.................................................................................................................................................2

2.0 Roles and Responsibilities.......................................................................................................................................2

2.1 Landowner Permission.....................................................................................................................................2

2.2 Shipment of Samples and Records...................................................................................................................2

2.3 Shipment of Equipment and Supplies...............................................................................................................2

2.4 Determining the Age of Fish.............................................................................................................................2

2.5 Photographs and Videotape..............................................................................................................................2

2.6 Communication................................................................................................................................................3

3.0 Equipment and Supplies..........................................................................................................................................3

4.0 Record Keeping and Housekeeping Items...............................................................................................................3

5.0 General Field Procedures.........................................................................................................................................3

5.1 Before Leaving on a Collecting Trip.................................................................................................................3

5.2 Procedures to be Followed Upon Arrival at a Station.......................................................................................3

5.3 Collecting and Holding Fish.............................................................................................................................8

6.0 Processing Fish........................................................................................................................................................8

6.1 Fish Processing Flow Chart..............................................................................................................................8

6.2 Procedures for External Examination.............................................................................................................11

6.2.1 Body Surface........................................................................................................................................11

6.2.2 Head and Oral Cavity............................................................................................................................15

6.2.3 Eyes......................................................................................................................................................18

6.2.4 Opercula...............................................................................................................................................20

6.2.5 Gills......................................................................................................................................................21

6.2.6 Fins.......................................................................................................................................................23

6.3 Procedures for Internal Examination..............................................................................................................25

6.3.1 Liver, Gall Bladder, and Bile................................................................................................................25

6.3.1.1 Liver...........................................................................................................................................25

6.3.1.2 Liver Sample Collection.............................................................................................................26

6.3.1.3 Gall Bladder Fullness and Bile Color.........................................................................................27

6.3.2 Gonads..................................................................................................................................................28

6.3.3 Spleen...................................................................................................................................................30

6.3.4 Kidney(s)..............................................................................................................................................31

6.3.4.1 Posterior (Trunk) Kidney............................................................................................................31

6.3.4.2 Anterior (Head) Kidney..............................................................................................................32

6.4 Scales or Spines..............................................................................................................................................33

6.5 Cleaning Equipment.......................................................................................................................................33

7.0 Post-collection and Processing Procedures...........................................................................................................33

7.1 Complete and Check Fish Health Examination and Station Identification Forms..........................................33

7.2 Clean-up.........................................................................................................................................................33

8.0 Upon Return from the Field...................................................................................................................................33

8.1 Photocopy and Mail Data Forms and Other Records......................................................................................33

8.2 Ship Histopathology Samples.........................................................................................................................33

8.3 Process Film...................................................................................................................................................34

8.4 Age Fish and Mail Age Data...........................................................................................................................34

8.5 Thoroughly Clean Non-Expendable Equipment.............................................................................................34

9.0 Acknowledgements................................................................................................................................................34

10.0 References............................................................................................................................................................34

Appendix A...................................................................................................................................................................37

Appendix B...................................................................................................................................................................43

i 
Table, Boxes and Flow Chart 

Page 

Table 1. Suggested Equipment and Supplies...............................................................................................................4

Box 1. Suggested Housekeeping Activities................................................................................................................6

Box 2. Suggested Quality Assurance and Record Keeping Activities.......................................................................6

Flow Chart......................................................................................................................................................................9

Figures

Figure 1. Tag and scale envelope labeled with a unique fish ID number.................................................................7

Figure 2. Diagnostician and recorder conducting a fish health assessment..............................................................7

Figure 3a. Outdoor work area and equipment setup...................................................................................................7

Figure 3b. Indoor work area and equipment setup.....................................................................................................7

Figure 3c. Outdoor work area and equipment setup, with biologists processing fish.................................................7

Figure 4. Layout of equipment and supplies..........................................................................................................8

Figure 5. Biologists collecting fish using an electrofishing boat............................................................................8

Figure 6a. Length measurements and scale sampling areas for spiny-rayed fish...................................................10

Figure 6b. Length measurements and scale sampling areas for soft-rayed fish......................................................10

Figure 7. Biologists examining the external features of fish.................................................................................11

Figure 8. Normal body surface...............................................................................................................................11

Figure 9a. Raised growths on body surface.............................................................................................................11

Figure 9b. Raised growths on body surface.............................................................................................................12

Figure 10a. Body surface lesion................................................................................................................................12

Figure 10b. Body surface lesion (ulcer).....................................................................................................................12

Figure 11a. Example of normal spine versus deformed.............................................................................................12

Figure 11b. Examples of spine deformities...............................................................................................................12

Figure 12a. An example of hemorrhagic body observation......................................................................................12

Figure 12b. Hemorrhaging within the body surface...................................................................................................13

Figure 13. Example of the presence of abnormal dark spots on the body surface....................................................13

Figure 14a. Example of the appearance of body fungus.............................................................................................13

Figure 14b. Body fungus............................................................................................................................................13

Figure 15. White spots on body surface..................................................................................................................13

Figure 16. Leech attached to the dorsal fin.............................................................................................................13

Figure 17. Black spots..............................................................................................................................................14

Figure 18. Anchor worm..........................................................................................................................................14

Figure 19a. Example of normal versus deformed head..............................................................................................15

Figure 19b. Deformed head.......................................................................................................................................15

Figure 20a. Lower lip growth....................................................................................................................................15

Figure 20b. Lower lip growth....................................................................................................................................15

Figure 20c. Upper and lower lip growth....................................................................................................................15

Figure 21. Swollen nare...........................................................................................................................................16

Figure 22a. Missing barbels.......................................................................................................................................16

Figure 22b. Stubbed barbels.......................................................................................................................................16

Figure 22c. Deformed barbels and lower lip growth.................................................................................................16

Figure 23a. Head lesion.............................................................................................................................................17

Figure 23b. Head lesion.............................................................................................................................................17

Figure 23c. Leech attached to the oral cavity............................................................................................................17

Figure 24. Example of a normal eye........................................................................................................................18

Figure 25a. Example of exopthalmia.........................................................................................................................18

Figure 25b. Example of exopthalmia (also an example of emboli)..........................................................................18

Figure 26a. Opaque or cloudy eye..............................................................................................................................18

Figure 26b. Opaque eye.............................................................................................................................................18

Figure 27a. Missing eye.............................................................................................................................................19

Figure 27b. Missing eye.............................................................................................................................................19

Figure 28. Hemorrhagic eye.....................................................................................................................................19

Figure 29a. Emboli; visible gas bubbles within the eye............................................................................................19

Figure 29b. Emboli or gas bubbles (also an example of popeye)...............................................................................19

ii
Figure 30a. Normal operculum..................................................................................................................................20

Figure 30b. Normal operculum..................................................................................................................................20

Figure 31. Slight shortening of the opercular flap...................................................................................................20

Figure 32. Example of severely shortened opercula with gills clearly exposed.....................................................20

Figure 33. Curled opercular flap..............................................................................................................................20

Figure 34. Normal gill with no apparent aberrations...............................................................................................21

Figure 35. Marginate and frayed gill.......................................................................................................................21

Figure 36. Example of pale gills...............................................................................................................................21

Figure 37a. Parasites on the gills...............................................................................................................................22

Figure 37b. Abnormal discoloration (mottled appearance) of the gills.....................................................................22

Figure 38. Normal fins.............................................................................................................................................23

Figure 39a. Caudal fins displaying active mild erosion............................................................................................23

Figure 39b. Active fin erosion...................................................................................................................................23

Figure 40a. Fins with severe erosion.........................................................................................................................23

Figure 40b. Severe erosion of the caudal fin with a possible secondary infection...................................................23

Figure 41. Caudal fin with frayed or ragged edges.................................................................................................24

Figure 42a. Fins with reddened or hemorrhagic areas..............................................................................................24

Figure 42b. Hemorrhagic and frayed fins..................................................................................................................24

Figure 43. Visible gas bubbles (emboli) within the fins.........................................................................................24

Figure 44a. Fin containing a nodule..........................................................................................................................24

Figure 44b. Dorsal fin with leech...............................................................................................................................24

Figure 45. Viscera removed from the fish for the purpose of conducting the internal examination......................25

Figure 46. Normal liver............................................................................................................................................25

Figure 47. Tan or “coffee with cream” colored liver...............................................................................................25

Figure 48a. Liver with general discoloration............................................................................................................25

Figure 48b. Generally discolored liver......................................................................................................................26

Figure 49. Liver with focal discoloration.................................................................................................................26

Figure 50a. Nodules in the liver.................................................................................................................................26

Figure 50b. Nodules in the liver.................................................................................................................................26

Figure 51. Normal gall bladder................................................................................................................................27

Figure 52a. Empty gall bladder.................................................................................................................................27

Figure 52b. Empty gall bladder.................................................................................................................................27

Figure 53a. Immature male gonads..........................................................................................................................28

Figure 53b. Mature male gonads................................................................................................................................28

Figure 54. Immature female gonads.........................................................................................................................28

Figure 55a. Mature female gonads.............................................................................................................................28

Figure 55b. Mature female gonads.............................................................................................................................28

Figure 55c. Mature female gonads.............................................................................................................................28

Figure 56. Large mass located in gonads..................................................................................................................29

Figure 57a. Normal spleen with no apparent aberrations...........................................................................................30

Figure 57b. Normal spleen.........................................................................................................................................30

Figure 58. Spleen sample containing nodules of various sizes.............................................................................30

Figure 59. Abnormally enlarged spleen...................................................................................................................30

Figure 60. Normal kidney compared to abnormal kidney (mottled in appearance)..................................................31

Figure 61. Swollen kidney........................................................................................................................................31

Figure 62. Various aberrations found in the kidney..................................................................................................31

Figure 63. Abnormal kidney; enlarged and mottled with white nodules..................................................................32

Appendix A-1. Station identification form...................................................................................................................39

Appendix A-2. Fish health examination form...............................................................................................................41

Appendix B-1. External features of a composite fish...................................................................................................44

Appendix B-2. Anatomy of spiny-rayed bony fish.......................................................................................................45

Appendix B-3. Anatomy of soft-rayed bony fish..........................................................................................................46

iii 
ILLUSTRATED FIELD GUIDE FOR ASSESSING EXTERNAL 

AND INTERNAL ANOMALIES IN FISH 

by

Stephen B. Smith

Anne P. Donahue

Robin J. Lipkin

Vicki S. Blazer

Christopher J. Schmitt

Ronald W. Goede

Abstract. Procedures are described for processing fish for examination of external and internal anomalies and 

pathologies indicative of exposure to environmental contaminants and other perturbations. For the procedures 

described here, fish are captured (preferably by electrofishing) and held alive until processing (generally <1 h). 

Fish are weighed, measured, and necropsied, and a scale sample is obtained from for age determination. 

Information is given for the collection and preservation of tissue samples for histopathological analysis. 

Photographs of most abnormalities are included along with normal conditions for easier identification of external 

(oral, head, eye, gill, opercula, and fin) and internal (liver, spleen, gonad, and kidney) anomalies. The report also 

includes recommendations for record keeping, sample labeling, and shipping records, equipment, supplies, and 

samples. A list of suggested equipment and supplies for field processing is included as are instructions for cleaning equipment. 

Keywords: contaminants, fish health, external anomalies, internal anomalies, histopathology. 

Suggested citation: 

Smith, S.B., Donahue, A.P., Lipkin, R.J., Blazer, V.S., Schmitt, C.J., and Goede, R.W., 2002, Illustrated field guide 

for assessing external and internal anomalies in fish: U.S. Geological Survey, Information and Technology 

Report, 2002-0007, 46 p. 

iv 
Conversion Factors 


Multiply By To Obtain 

micron (μm) 

millimeter (mm) 

centimeter (cm) 

meter (m) 

square centimeter (cm2

) 

liter (L) 

milliliter (mL) 

gram (g) 

kilogram (kg) 

Length 

0.00003937 inch 

0.03937 inch 

0.3937 inch 

3.281 foot 

Area 

0.001076 square foot 

Volume 

0.264 gallon 

0.000264 gallon 

Mass 

0.03527 ounce, avoirdupois 

0.453 pound 

v 
1.0 INTRODUCTION 

1.1 Background and Development of this 

Document 

This illustrated field guide was developed from and is 

intended as a companion to an earlier report published 

by the U.S. Geological Survey (USGS) Biomonitoring 

Status and Trends (BEST) Program that described 

field procedures for assessing the exposure of fish to 

environmental contaminants (Schmitt and others, 

1999). The earlier document incorporated information 

and procedures from numerous other sources, including Columbia Environmental Research Center and 

National Water Quality Assessment (NAWQA) 

Program SOPs, and study plans, reports, books, 

manuals, and reports from other studies (Lagler, 1956; 

Lagler and others, 1962; Smith, 1973; Hunn, 1988; 

Meyer and Barclay, 1990; Baker and others, 1997). 

The health assessments based on field observations 

were originally developed from the procedures of 

Goede (1989, 1996) as described by Goede and 

Barton (1990). The earlier document (Schmitt and 

others, 1999) was cross-referenced to Goede’s (1988) 

color atlas of pathologies in salmonid fishes. Here we 

have made the field assessment procedures more generally applicable (that is, for use in a wider geographic 

area and for use by other programs and studies) by 

including photographs of other fishes to aid biologists 

in the identification of various grossly visible external 

and internal anomalies. However, the cross-references 

to Geode (1988) have been retained for use with 

salmonids and for pathologies for which photographs 

in other taxa were not available. 

1.2 Scope and Intent of this Report 

Together with the earlier document (Schmitt and others, 1999), this report describes procedures to be used 

for monitoring and assessing the exposure of fish to 

environmental contaminants and other stressors. We 

describe how to examine and handle freshly captured 

fish, and how to collect, store, and ship the tissues 

necessary for further examination. This report is not 

intended as a guidance document or protocol for 

selecting methods, nor does it contain information for 

interpreting study results based on the use of methods 

in the guide. The rationale for selecting this particular 

suite of methods, as well as information on the interpretation of findings, is presented elsewhere 

(Biomonitoring of Environmental Status and Trends, 

1996; Schmitt and Dethloff, 2000; Meador and others, 

1993). The procedures we describe are primarily 

post-fish collection; although information on preparing for and organizing a study and suggested methods 

for documenting the date, time, and location of collection are included, most of the actual procedures begin 

after fish have been collected. Procedures are specified for making observations by using photographs 

and collecting information and tissues; preserving, 

wrapping and packaging samples; numbering samples 

and recording data; and storing and shipping samples 

and records. We also provide instructions for documenting (see Appendix A-1) the type of equipment 

used to collect the fish, the duration of the fishing 

effort, and the location of the collection site. A list of 

suggested equipment and supplies is also provided. 

To the extent possible, the procedures conform to 

Good Laboratory Practices (U.S. Environmental 

Protection Agency, 1989); however, quality assurance 

and quality control issues are beyond the scope of this 

document. Depending on the purpose and design of 

the study, it may be necessary to utilize or develop 

additional project-specific protocols and standard 

operating procedures (SOPs) conforming to this guide, 

as well as a quality assurance plan. Collection locations and times, preferred taxa, exact numbers of 

samples, modifications or additions to standard procedures, and field and laboratory cooperators should be 

identified in the work/study plan or protocol under 

which the procedures described in this guide are used. 

This guide and its sample data forms may be photocopied or otherwise reproduced on waterproof paper 

for field use. 

Fish collections conducted under the auspices of 

USGS monitoring programs (BEST and NAWQA) 

include observations of external anomalies. The 

BEST program, as well many smaller-scale research 

projects, also examine internal organs. Fish are often 

collected from areas where contaminants are present 

at concentrations that may affect the health of individual fish. Contaminants of concern include polycylcic 

aromatic hydrocarbons (PAHs), such as chrysene and 

phenantherene; organochlorine pesticides (DDT, 

toxaphene); industrial compounds (polychlorinated 

biphenyls - PCBs, and polychlorinated dibenzo-pdioxins); metals (mercury, lead); metalloids (arsenic, 

selenium); currently used pesticides (atrazine, 

propanil, chlorpyriphos); and pharmaceuticals. 

Nevertheless, it is important to note that this guide 

does not include specific diagnoses; rather, it provides 

more generic identifications of observable conditions. 

Diagnosis can only be accomplished through 

histopathology and other laboratory expertise. 

The methods described in this report and in the previous document (Schmitt and others, 1999) have been 

used extensively by the authors. Nevertheless, the 

procedures may need to be altered by investigators 

using this guide to collect tissue types and quantities 

that meet the needs of different work/study plans or 

protocols. Corresponding changes may also need to 

be made in the lists of required equipment and supplies. 
2 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

1.3 Typographic Conventions 

Within this document, the following typographic conventions are used: 

• Important actions, notes, and reminders 

are indicated in bold or italics. 

• Information to be recorded is also indicated in bold. 

• The cross symbol ([) indicates a healthor safety-related item. 

1.4 Animal Welfare 

The procedures described in this guide conform to the 

American Society of Ichthyologists and Herpetologists 

(ASIH), American Fisheries Society (AFS), and 

American Institute of Fishery Research Biologists 

(AIFRB) “Guidelines for Use of Fishes in Field 

Research” (ASIH and others, 1988); and with all 

known SOPs and guidelines for the humane treatment 

and disposal of test organisms during culture and 

experimentation. 

2.0 ROLES AND RESPONSIBILITIES 

Generally, studies based on this illustrated field guide 

will have field and laboratory components; we 

describe only the field portions. Conducting or otherwise arranging for necessary laboratory analyses is 

usually the responsibility of the principal investigator, 

project chief, or study manager. Activities and 

responsibilities of field cooperators and personnel 

include: coordinating and conducting sample collections; ensuring that personnel are trained in the operation of electrofishing, global positioning system 

(GPS), and photographic equipment (which are all 

beyond the scope of this guide); conforming to all pertinent health, safety, certification (watercraft operation, electrofishing, and so forth); collection permit 

requirements (both state and federal collection permits 

and their required reporting and pre-notification); 

securing prior written permission to enter private 

lands; ensuring that boats, motors, trailers, and other 

equipment are properly cleaned after sampling (to 

thwart the transport of living organisms between 

waterways); and shipping samples and records to 

cooperators and laboratories. Consult the work/study 

plan to determine the species and number of specimens required; this information is necessary under the 

terms of many collection permits. Walsh and Meador 

(1998) present additional information that may be useful in the collection of fishes. 

Note: The health and safety items presented here conformed to all regulations at the time this guide was 

prepared. However, regulations governing the handing and shipment of chemicals and samples and the 

use of certain types of equipment are subject to 

change. It is the responsibility of the parties using 

this guide to ascertain and conform to these regulations. 

Note: At least one representative of each field team 

should have documented firsthand experience in the 

conduct of the procedures described in this guide. 

2.1 Landowner Permission 

If travel across or sampling on private property is necessary, obtain permission from the landowner or a representative of the landowner, and have them sign and 

date a form prepared for that station (referred to as a 

Station Identification Form; see Appendix A-1 for an 

example) to indicate landowner consent in advance of 

each entry. 

Note: If prior written permission cannot be obtained, 

do not enter! 

2.2 Shipment of Samples and Records 

Restrictions on shipping histopathology samples will 

depend on the fixative used. Check with shipping 

companies about samples in fixative—shipping by 

ground transport in properly labeled boxes will likely 

be required. Project participants may consider using 

Chain-of-Custody (COC) Forms when shipping or 

mailing samples and data, even if it is not required. 

An example of a COC form can be found in Schmitt 

and others (1999). 

2.3 Shipment of Equipment and Supplies 

When sampling multiple sites with multiple teams, the 

use of non-expendable equipment (that is, coolers, 

balances, and so forth) should be coordinated among 

cooperators. To expedite the flow of non-expendable 

equipment, it is important to plan schedules as far in 

advance as possible. This will help to ensure that the 

equipment reaches each team when they need it! 

2.4 Determining the Age of Fish 

Information on the age of each fish is important for 

interpreting the results of certain anomalies. This document does not specify procedures for determining the 

age of specimens collected, but does provide information on structures for age determination and their collection procedures. Techniques for aging fish are 

described by Tesch (1971), Jearld (1983), Blouin and 

Hall (1990), Frie (1982), Weisburg and Frie (1987) 

and in most fishery biology texts (for example, Lagler 

1956; Neilson and Johnson, 1983; Kocovsky, personal 

communication). 

2.5 Photographs and Videotape 

Photographs or color slides of sampling sites and 

operations are desirable, both for presentations and as 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 3 

a record. It is also advantageous to photographically 

record any lesions or other anomalies identified during 

the fish health assessment, as noted in the instructions. 

Note: It is generally better (in terms of quality and 

expense) to take multiple photos than to duplicate 

slides. Videotape is an acceptable alternative to film. 

2.6 Communication 

Field biologists should have access to project coordinators/study directors in the event they need assistance. Pertinent telephone (including cellular telephone), FAX numbers and email addresses should be 

provided. 

3.0 EQUIPMENT AND SUPPLIES 

The equipment and supplies needed to conduct the 

procedures outlined in this guide are listed in Table 1. 

The number needed per station or per fish is indicated 

unless that number must be determined from the study 

plan. The size of sample containers may also need to 

be determined from the study plan. Meador and others (1993), and Walsh and Meador (1998) present 

additional useful information on the collection of fish; 

the latter also provide a list of suppliers and vendors 

of equipment and supplies. 

4.0 RECORD KEEPING AND HOUSEKEEPING 

ITEMS 

Housekeeping activities that should be performed 

throughout the sampling day are outlined in Box 1. 

Quality assurance measures, including activities to 

ensure proper record keeping, are outlined in Box 2. 

5.0 GENERAL FIELD PROCEDURES 

5.1 Before Leaving on a Collecting Trip 

a) If time permits, pre-label enough labels, envelopes 

(Figure 1), and containers for the number of specimens you will be collecting given the specifications of 

the study plan. Bring extra, unlabeled supplies. 

Note: It is also advantageous to label, group, and 

package the expendables needed for each fish prior to 

arrival on site. The identification numbers may vary 

with study plan; consult plan before packaging. 

b) Pre-fill the 125-mL bottles with about 85 mL of fixative. 

Note: The volumes suggested here are for 10% neutral 

buffered formalin. For other preservatives, different 

tissue: preservative ratios may be necessary. 

[ 10% neutral-buffered formalin is the 

preferred fixative because it can be 

shipped via ground transport. The 

fixative; however, may vary with the 

project; therefore, consult the study 

plan. Regardless of the fixative used, 

it should be handled safely (that is, in 

accordance with the MSDS). Fill containers under a hood or outdoors, and 

wear protective clothing (lab coat or 

long sleeves and pants; latex or vinyl 

gloves; and safety glasses, goggles, or 

face shield) to prevent eye and skin 

contact. 

[ Some preservatives and fixatives are 

also flammable, as are acetone and 

ethanol. Consult the MSDS for these 

materials, and avoid extreme heat and 

ignition sources (that is, sparks and 

flames). 

c) Check the equipment and supplies list (Table 1) to 

be certain all materials and equipment are present, and 

check the operation of all equipment (for example, 

balance) to ensure that it is functioning properly. 

d) All equipment should be clean when it is taken into 

the field. Any material that will come in contact with 

specimens should be cleaned with cleaning agents that 

will not affect later analyses. 

5.2 Procedures to be Followed Upon Arrival 

at a Station 

The preferred minimum size of a sampling team is six 

individuals. Once at the station, do the following 

before you start sampling: 

Divide the team into two groups (of at least three), 

if possible. It is suggested that one person in the fishprocessing group be designated as the recorder for the 

duration of the sampling at any site. Remember the 

person recording has a critical job to assure all portions of the examination and data form(s) (see 

Appendix A-1 and A-2) are completed correctly. 

Group 1, which includes the trained diagnostician and 

the recorder (Figure 2), should: 

a) Initiate the Station Identification Form (see 

Appendix A-1) for the day’s sampling by recording 

the station number, date, station description, start 

time, and the names of the team members. 

Measure and record on the Station Identification Form 
4 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007 

Table 1. Suggested Equipment and Supplies. 

Safety and Other Apparel 

Gloves 

Disposible latex or vinyl (for fish processors) 

Long-sleeved or rubber (for fish collectors) 

Work (for general use) 

Raingear, boots, etc. 

Safety Glasses 

Data Collection and Recording Supplies 

Camera and film, or camcorder and tape 


Clipboards


Forms 


Fish Health Examination Form 

Station Identification Form 

Pens 

Ball-point 

Waterproof (fine-tipped) 

Field Guide, study plan, field notebook 

Waterproof paper with pre-printed labels 

Cleaning Supplies 

Acetone (preferably reagent grade, not crude) 

Acetone squirt bottle w/extra 28 mm lid for shipping 

and transporting 

Alcohol wipes 

Beaker 

De-ionized water 

Garden sprayer or pump spray bottle 

Plastic trash bags 

Fish Processing Supplies 

Aluminum foil 

Blunt instrument 

Optional: Anesthetic [MS-222 (Finquel

), CO2, 

clove oil] depending upon protocol 

Bottles, 125-mL polyethylene w/leak-proof tops 

Ethanol, 100% 

Fixative (10% buffered formalin) 

Scale envelopes 

Small towels or cloth diapers 

Stainless steel pan for weighing fish < 2000 g 

Collecting and Processing Equipment and Related Materials 

120V AC power source (>1 amp) 


Calibration weights 


Dissecting tools 


Electrofishing boat, backpack shocker, or electric seine 


and related equipment 

Ground-Fault Interrupting (GFI) extension cord 

GPS unit 

Hand lens 

Hanging balance, for large fish 

Measuring board, mm 

Portable electric balances (preferably DC) 

Tubs or live boxes 

assorted sizes


3 pr. 


3 pr. 


enough for all


3 pr. 


1 


2 


1 per fish


1 per station


3 


3 


1 each


0.5 L, for rinsing instruments 


1 


50, for hand cleaning 


1, 100-mL, for acetone rinse 


4 L, for rinsing instruments


optional, for dispensing DI water 


number varies, for waste disposal 


300 ft, heavy duty


1 


1 per fish, for histopathology samples


1.5 L; 95% may be used if necessary


85 mL per fish, for histopathology samples


1 per fish, for scales or spines


1 per fish


optional 


1 inverter, generator, or outlet (optional) 


1 of appropriate mass for each balance 


1 kit 


1 optional, depending on balance(s) 


1 


1 


1 


1 


capacity varies with target taxa 


total no. varies with study plan and when


boat has no livewell 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 5 

Table 1. Suggested Equipment and Supplies--Continued. 

Fish and Tissue Packaging 

Coolers 

Cloth tags 


Ice (wet, cubes or block) 


Mailing labels for samples 


Shipping labels for samples


Miscellaneous Equipment and Supplies 

Cell phone 


Conductivity meter


Duct tape 


Field guide(s) or other reference(s) for identifying fish 


Fire extinguisher (dry chemical, type A, B, and C)


First-aid kit 


Flashlights and other lights 


Kitchen (poultry) shears or scissors


Material Safety Data Sheets for all chemicals (fixative, 


acetone, ethanol, etc.) 

Paper towels 

Pliers 

Portable table and chairs 

Shade canopy 

Thermometer or other instrument for measuring water 

temperature 

large (total no. varies with study plan, for 

cooling fish composite samples, etc.) 

1 per fish 

50 lb 

1 sheet 

total no. varies with study plan 

optional but recommended 


for electrofishing


1 roll, for securing sharps containers, etc. 


1 


1 


optional 


1 pr. 


1 each


1-2 rolls


1 pr. 


optional 


optional 


1 


the water temperature (°C) in the general area from 

which fish were collected. 

b) If AC-powered equipment is to be used, provide 

120-V AC, 60-cycle power for the electronic balance 

[that is, inverter and 12-V DC boat, vehicle, or trolling 

motor (1 amp minimum) battery; portable generator; 

electrofishing boat; or a grounded 120-V AC outlet] 

(Figures 3a–3c) or use a battery operated portable balance. 

Portable work surfaces (for example, folding table, 

tailgate, cooler top) or indoor work areas should be set 

up to facilitate a dry, comfortable work area (Figures 

3a–3c). 

[ Important! The use of 120-V AC electrical power outdoors, especially 

around water, is potentially hazardous. 

The grounding requirements of 

portable power devices (that is, generators and inverters) vary; read and 

follow the instructions supplied with 

whatever device you use. Many 

portable generators are now equipped 

with ground-fault interrupting (GFI) 

outlets; if yours is so equipped, use 

them. If it is not, use an extension 

cord equipped with a GFI. In 

addition, use this type of extension 

cord whenever working with electrical 

power in the field. 

[ The use of portable, engine-powered 

generators presents additional safety 

hazards - fire, burns, and fumes. 

Carry fuel only in approved containers, and allow the generator to cool 

before re-fueling to minimize fire hazards. In addition, an approved sparkarresting muffler may be required in 

some locales. To avoid fume hazards, 

do not use portable generators in 

buildings, vehicles, or other enclosed 

places. 

d) Set up and level the balances. 

Note: Setting the balances up inside an empty cooler 

on a level spot works well. If it is windy or raining, 

close the lid between operations. 

e) Power up the balance(s) and ascertain that it (they) 

is (are) operating properly by weighing the 
appropriate calibration mass. Record the make,

model, and ID or serial number of the balance(s)

and the “before” calibration weight(s) on the

Station Identification Form (Appendix A-1). 

All weights should be recorded in grams and the

recorder should confirm that the balance is in the correct mode at all times. Also, personnel working with

the balances should ensure that any weigh boats or

other equipment being used to hold fish are resting

completely and solely on the weighing platform of the

balance. 

adjust if necessary using the thumb screw at the top of

the cylinder. 

f) Unpack the expendables (bags, tags, labels, and so

forth; Figure 4), and label the containers (if not done

already).

g) Fill a container (tub, bucket, cooler) with ambient

water and pre-soak the diapers or towels to be used to

handle the fish (to remove any detergents or other

chemicals).

6 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

Box 2. Suggested Quality Assurance and Record Keeping Activities.

• Keep a logbook of the team’s activities (when the team left, 

who was present and what each person did, etc.)

• Make all entries in INK. Use a ballpoint pen that will write

under all conditions on data-entry and other forms. 

FORMS SHOULD BE PRINTED ON WATERPROOF

PAPER.

• PRINT legibly.

• Do not use ditto marks (“) for observations that repeat on a

series of lines. Instead, write the entry on the first and last

applicable lines, and connect the observations with a single

vertical line. 

• If you do not obtain a measurement (equipment broken, 

etc.), write an explanation in the comment field on the data

sheet.

• If you make a mistake, draw a SINGLE line through the

incorrect entry (e.g. CARP), and initial and date the

correction. Then, indicate the nature of the error in the 

appropriate comment field on the data sheet.

• Number sampling sites in accordance with the study plan 

under which an investigation is conducted. Each sampling

site should have a unique identifier. Initiate a new Station

Identification Sheet for each day that you sample at a site. 

• Number fish collected at a sampling site as instructed by

the study plan. If no numbering system is detailed, fish

should be numbered with a unique identifier (referred to as

the fish identification number) that indicates the ID of the

individual specimen, the sampling site from which it was

collected, and the date of the collection. That same number

will be used an all envelopes and containers used for that

fish.

• Initiate a new Fish Health Examination Form (see

Appendix A-2 for an example) for each specimen. 

Record the species, sex, length, weight, results of the 

field health assessment procedures, numbers of tissue

collected, and any further remarks or comments 

pertaining to that individual fish. 

• To eliminate possible bias in subsequent analyses, all 

samples bear the fish identification numbers, but no

other markings.

• If you photograph (or videotape) any anomalies (i.e.

raised growths, lesions, parasites, etc.), use a previously

prepared tag or scale envelope as a specimen identifier

in each frame. There are spaces for recording the 

number of photos taken or the video footage shot in each

section of the Fish Health Examination Form; filling

them in will make it easier to annotate slides or tape

later. It is easier for the recorder if you follow the order

of the Fish Health Examination Form, which follows the

order of this document.

Note: If specimens that are designated as juvenile or

indeterminant are collected, and gender identification 

will be made histologically at a later date, group and 

bag these specimens separately. 

• Check and initial each Fish Health Examination

Form to be certain that all observations have been

made and recorded before proceeding to the next 

fish. Do not leave any blank fields on the data sheets

unless specified by the study plan. 

Box 1. Suggested Housekeeping Activities, to be Performed as Needed.

• Cap the acetone squirt bottle and the marking pens when

they are not in use.

• After each fish is processed, thoroughly wash all contact

instruments and dissecting tools with de-ionized water

and rinse them with acetone. 

Check the zero of the hanging balance, and
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 7 

Figure 1. Tag and scale envelope labeled with a unique fish ID 

number. 

[ For protection against pathogens and 

parasites associated with either the 

fish or water, team members handling 

the fish and collecting tissues should 

wear disposable latex or vinyl gloves. 

The gloves should be replaced as necessary if they become torn or punctured, and disposed of properly. 

Hands should be washed with disposable alcohol wipes. In waters known 

or suspected to harbor Pfiesteria sp. or 

other pathogens, fish collectors and 

handlers should take extra precautions 

by wearing long gloves or sleeve protectors. 

Figure 2. Diagnostician and recorder conducting a fish health 

assessment. 

Figure 3a. An outdoor work area and equipment setup. 

Figure 3b. An indoor work area and equipment setup. 

Figure 3c. An outdoor work area and equipment setup, with biologists processing fish. 
°

8 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

Figure 4. Layout of equipment and supplies. 

Group 2 (fish collectors) should: 

Obtain the Station Identification Form (Appendix A-1) 

and record settings for the electrofishing equipment 

(in the General Comments) and location coordinates. Then, initiate sampling (Figure 5). Record 

the range of latitude and longitude sampled in 

degrees (000°) and decimal minutes (00.0000), the 

map datum (WGS84, NAD83, and so forth) and 

the stop time when finished. 

5.3 Collecting and Holding Fish 

The target taxa and desired number of specimens 

should be found in the study plan for the specific project. The collection of larger, adult fish is encouraged 

because; 1) obtaining the necessary amounts of tissues 

for histopathology may be difficult with smaller fish; 

2) the observations may be difficult to perform with 

small fish; and 3) older fish are exposed for longer 

periods of time and anomalies are more prevalent. 

The preferred collection methods are DC electrofishing (Figure 5), seining, or DC electric seining (the 

methods of capture that are least injurious to the fish); 

however, be certain that nets have not been chemically 

treated or used previously in heavily contaminated 

waters. Hook-and-line capture is also permissible. 

Trap-, gill-, or trammel-netting, and AC electrofishing 

Figure 5. Biologists collecting fish using an electrofishing boat. 

are not recommended because these methods are more 

injurious to the fish and can bias the quantitative 

health assessments. To complete the procedures 

described, fish should be held alive. 

Note: Holding fish for prolonged periods in tanks or 

live wells with abrasive surfaces or in net pens can 

cause external lesions. 

6.0 PROCESSING FISH 

The actual processing of the fish begins here. The 

order in which the procedures are performed is important to ensure that activities conducted in one step do 

not compromise observations or tissues obtained in 

subsequent steps and that tissues with short holding 

times are collected as rapidly as possible. 

Consequently, the procedures that are described in the 

following sections and diagrammed in the accompanying flow chart should be performed in the order in 

which they are presented, which also conforms to the 

organization of the Fish Health Examination form 

upon which the observations are recorded. 

6.1 Fish Processing (Flow Chart) 

[ This is a reminder that personnel handling and dissecting the fish should 

wear gloves. 

a) Prepare the work surface by covering it with a piece 

of foil (dull side up/shiny side down) large enough to 

wrap the fish you will be processing. 

b) Secure a towel or diaper (from the soaking container) or use a disposable pad. Wring it dry, then tare it 

on the large balance. It may be useful to perform the 

necropsy using a diaper or pad to absorb fluids 

released from fish. 

c) Secure a fish from the holding tank. Ascertain its 

condition and identify it to species. Make a reasonably positive identification at this time, using a 

guide to species names and abbreviations. Initiate a 

Fish Health Examination Form (Appendix A-2) for the 

fish by assigning the fish a unique ID number or use 

the pre-labeled number. Record the Station ID 

number, date, fish ID number, and species on the 

Fish Health Examination Form (Appendix A-2). If 

you are not sure of the fish species identification, note 

on the data form that you will confirm it at a later 

time. 

Note: For fish nomenclature see Robins and others 

(1991). 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 9 

d) Place the fish, in its towel, on the previously tared Health Examination Form.

electronic balance. If the fish is too heavy for the balance, unwrap it and weigh it on the hanging balance. Note: Check the zero and the operational mode of the

A tared holding container (such as a stainless steel, balance between each fish, and re-adjust or tare as

plastic, or aluminum pan) can be used to weigh fish necessary.

<2000 g on the larger capacity electronic balances.

f) Unwrap the fish and measure it on the measuring 

e) Record the weight of the fish (±1 g) on the Fish board (total length, in millimeters; squeeze the caudal 

Start 

Secure fish 

Anesthetize/Subdue fish 

Conduct remaining external examination See Section 6.2, Procedures 

for External Examination 

Flow Chart 

Discard carcass* 

Collect scales/spines from left side of fish 

Conduct internal examination 

Weigh & measure fish 

Collect normal and abnormal 

external tissue in fixative 

See Section 6.3, Procedures 

for Internal Examination 

*Carcass may be frozen for residue analysis (see Schmitt and others, 1999) 
10 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

fins together – Figures 6a and 6b). 

g) Record the total length (mm) on the Fish Health 

Examination Form (See Figure 6a). 

Figure 6a. Length measurements and scale sampling areas for 

spiny-rayed fish. From Lagler, Freshwater Fishery Biology, (1956) 

Wm. C. Brown Publishers, used with permission from the McGrawHill Companies. 

h) Conduct the external examination of the head surface and the eyes at this time (per instructions under 

Section 6.2). DO NOT remove anomalies at this 

time - the fish has not been subdued. 

i) To subdue fish, expose the anterior dorsal surface of 

the specimen and, with a blunt instrument, subdue the 

fish with a sharp blow to the rear of its head. 

Alternatively, and although these procedures are not 

descibed here, the fish may be anesthetized with tricaine methanesulfonate (MS-222; Finquel

), carbon 

dioxide, or clove oil at recommended concentrations 

depending upon study plan or protocol. 

j) If you have not already done so, label a tag and a 

scale envelope (fish identification number; Figure 

1); use a permanent, waterproof felt-tipped pen and 

write in large, block letters. Use this label in any photographs or video footage taken. 

soft-rayed fish. 

Figure 6b. 

From Lagler (1956). 

Length measurements and scale sampling areas for 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 11 

6.2 Procedures for External Examination 

Begin the external observation (Figure 7) using photos 

and Fish Health External Examination Form 

(Appendix A-2). Within each section, be sure to 

record all observations by marking (X) in all boxes 

on the data form that apply. Recorded examinations 

of eyes, opercula, gills, and fins (if necessary, refer to 

the diagram of the external features of a fish located in 

Appendix B-1) may include marking both “normal” 

and deteriorated conditions since more than one structure is involved. 

Note: Aesthetic observations are unnecessary. 

Make a clear, precise mark for each data entry for 

the external examination. Provide a brief description of the anomaly (that is, size, color, and so 

forth) in the spaces located in each section. If the 

observation does not seem to fit any of the listed categories, check “other” and describe your observations in the indicated areas. Record further remarks 

about listed categories in the General Comments 

section. The general procedure during the external 

examination is to record all observations that apply, 

and to collect and preserve a sample of anything that 

appears abnormal. If an abnormal sample is collected, 

it is very helpful to the histopathologist to also collect 

and preserve some normal tissue of the same type. To 

ensure proper preservation, no piece of preserved tissue should be larger than 1-cm3

; cut larger pieces to 

this size if necessary. 

Note: This line is 1 cm long. ______ 

6.2.1 BODY SURFACE: Examine all surfaces for 

any anomalies (Figures 8–18). Remove them and 

place them in the labeled bottle of fixative. Record 

anomaly type(s) found by checking the appropriate 

blocks. Describe any anomalies noted as “other”. 

Note the general location of all anomaly type(s) in 

the “other” field and record the number of pieces 

in fixative. 

Normal (Figure 8): No aberrations present on the 

body surface. 

Figure 8. Normal body surface. 

Raised growth (Figures 9a and 9b): On body surface; 

may be tumor but must be verified histopathologically. 

Figure 9a. Raised growths present on body surface. 

Figure 7. Biologists examining the external features of the fish. 
12 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

Figure 9b. Raised growths on body surface. 

Reddened lesions (Figures 10a and 10b): Ulcers, 

abrasions, cuts, sores, and so forth. 

Figure 10a. Body surface lesion. 

Figure10b. Body surface lesion (ulcer). 

Spinal Deformities (Figures 11a and 11b): Abnormal 

shape of the spine, backbone is not straight. 

Figure 11a. Example of normal spine versus deformed. 

Figure 11b. Examples of spine deformities. 

Hemorrhagic Body (Figures 12a and 12b): 

Reddened (that is, bloody) area visible on the body 

surface. 

Figure 12a. An example of hemorrhagic body observation. 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 13 

Figure 12b. Hemorrhaging within the body surface. 

Focal Discoloration (Figure 13): Abnormally darkened areas (dark spots, possible melanoma) present on 

the body surface. 

Figure 13. Example of the presence of abnormal dark spots on the 

body surface. 

Body Fungus (Figures 14a and 14b): Fungal growth 

on various parts of the body surface. 

Figure 14b. Body Fungus. 

Parasites: The presence of white spots, leeches, 

black spots, or worms: 

White Spots (Figure 15): Small white, 

raised areas on the fins and body surface, 

often protozoan parasites. 

Figure 15. White spots on body surface. 

Leeches (Figure 16): Visibly attached to 

body surface. 

Figure 16. Leech attached to the dorsal fin. 

Figure 14a. Example of the appearance of body fungus. 
14 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

Black spots (Figure 17): Small black spots 

distributed throughout the body surface. 

Figure 17. Black spots. 

Anchor Worm (Figure 18): Copepod 

Figure 18. Anchor worm. 

Other: Any observation that does not fit in the 

above; describe in spaces provided. Record the condition of the Body Surface and the number of 

pieces in fixative. 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 15 

6.2.2 HEAD AND ORAL CAVITY: Anomalies 

associated with the anterior region of the fish including the head and oral cavity (lips), and barbels 

(Figures 19a–23c). Check all that apply: 

Deformed Head (Figures 19a and 19b): Abnormal 

shape of the anterior portion of the fish (do not mistaken these malformations with those that may have 

been caused if the specimen was subdued with a blunt 

instrument). 

Deformed 

Normal 

Figure 19a. Example of normal versus deformed head in rainbow 

trout (Oncorhynchus mykiss). 

Figure 19b. Deformed head. 

Upper and Lower Lip Growths (Figures 20a–20c): 

Raised growth on lateral or dorsal region of the lip or 

oral cavity (possible papilloma). 

Figure 20a. Lower lip growth. 

Figure 20b. Lower lip growth. 

Figure 20c. Upper and lower lip growth. 
16 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

Swollen Nare (Figure 21): Nostril with swelling or 

abnormal enlargement of the opening. 

Figure 21. Swollen nare. 

Barbels (Figures 20a–20c): 

Missing Barbels: Any number of barbels 

not present. 

Figure 22a. Missing barbels. 

Stubbed Barbels: Barbels are clubbed, 

stubbed or shortened. 

Figure 22b. Stubbed barbels. 

Deformed Barbels: Growth of abnormally 

shaped barbels, possibly being forked or 

fused. 

Figure 22c. Deformed barbels and lower lip growth. 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 17 

Other (Figures 23a–23c): Abnormalities that do not 

fit any of the previous categories, that is, lesions, parasites, and so forth. Describe. Record the condition 

of the Head/Oral Cavity and the number of pieces 

in fixative. 

Figure 23c. Leech attached to the oral cavity. 

Figure 23a. Head lesion. 

Figure 23b. Head lesion. 
18 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

6.2.3 EYES: The left and right eyes should be examined (Figures 24–29b) and scored separately, as follows (check all that apply): 

Normal (Figure 24): No aberrations evident; eyes 

“clear”, not protruding, milky, opaque, or bloody. 

Figure 25b. An example of exopthalmia. Also an example of 

emboli (see Figure 29b). 

Opaque (Figures 26a and 26b): Generally refers to 

opaque or cloudy eyes, or the appearance of cataracts. 

The nature of the opacity is not important here. 

Figure 24. Example of a normal eye. 

Exopthalmia (Figures 25a and 25b): Swollen, protruding eye (also known as popeye). 

Figure 26a. Opaque or cloudy eye. 

Figure 25a. Example of exopthalmia; eye is protruding (otherwise 

known as popeye). 

Figure 26b. Opaque eye. 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 19 

Missing (Figures 27a and 27b): An eye appears to be 

missing from the fish. (Note: It may be actually 

scarred over). 

Figure 27a. Missing eye. 

Figure 27b. Missing eye. 

Hemorrhagic eye (Figure 28): Characterized by the 

presence of blood in the eye(s). 

Emboli (Figures 29a and 29b): Gas bubbles visible 

within the eye. 

Figure 29a. Emboli; visible gas bubbles within the eye. 

Figure 29b. Emboli, or gas bubbles present in the upper most 

(left) eye. This is also an example of popeye, both conditions 

should be marked on the Fish Health Examination Form. 

Other: Any manifestations that do not “fit” the above 

(that is, parasites, spots, cuts, abrasions); describe. 

Record the condition and number of pieces in fixative for each eye on the Fish Health Examination 

Form. 

Figure 28. Hemorrhagic eye. 
20 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

6.2.4 OPERCULA: It is necessary to only observe 

the degree of shortening of the opercular flaps 

(Figures 30a–33). Score the opercula according to the 

following criteria (check all that apply): 

Normal (Figure 30a and 30b): No shortening of the 

opercular flaps; gills are completely covered. 

Figure 30a. Normal operculum. 

Slight shortening (Figure 31): Slight shortening of 

the operculum with a very small portion of the gill 

exposed. 

Figure 31. Slight shortening of the opercular flap. 

Severe Shortening (Figure 32): Severe shortening of 

the opercula with a considerable portion of the gill 

exposed. 

Figure 32. Example of severely shortened opercula, gills are 

clearly exposed. 

Other (Figure 33): Any observation that does not fit 

above; describe. Record the condition of the opercula and the number of pieces in fixative. 

Figure 30b. Normal operculum. 

Figure 33. Curled opercular flap, categorized as “other”. 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 21 

6.2.5 GILLS: The right and left gills are examined 

and evaluated separately (Figures 34–37b). Be careful 

when examining the gills. Gill structure and tissue 

can easily be affected by the manner in which the fish 

is handled during and after collection. Evaluate the 

gills as follows (check all that apply): 

Normal (Figure 34): No apparent aberrations. 

Figure 34. Normal gill; bright red with no apparent aberrations. 

Frayed: This generally refers to actual erosion of the 

tips of the gill lamellae resulting in “ragged” appearing gills (Figure 35). Mere separation of gill lamellae 

can be interpreted as “frayed” but the condition may 

have caused by something as simple as the manner in 

which the gill was exposed by the investigator. 

Marginate (Figure 35): A graphic description of a 

gill with a light discolored margin along the distal end 

or tips of the lamellae or filaments. 

Figure 35. Marginate and frayed gill: discolored margin with 

ragged gill lamellae. 

Pale (Figure 36): This refers to gills that are very 

light in color. Extreme anemia can discolor the gills 

to the point of being white. Severe bleeding can also 

result in somewhat pale gills. Gills begin to pale after 

death, which is common in fish taken from nets. All 

of this should be considered in making the observation. 

Figure 36. Example of pale gills. 
22 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

Other (Figures 37a and 37b): Any observation that 

does not fit the above (that is, parasites, abnormal discoloration, and so forth); describe. Record the condition and number of pieces in fixative for each gill. 

Figure 37a. Other (parasites); obvious parasites on the gills. 

Figure 37b. Other; abnormal discoloration (mottled appearance) 

of the gills. 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 23 

6.2.6 FINS: Eroded or “ragged” fins are a departure 

from normal condition and health. Previously eroded 

fins that are healed over and show no evidence of 

active erosion are considered normal in this assessment. The evaluation of fins is relative to the degree 

of active erosion in evidence. Fins are observed collectively. If only one fin is actively eroding or has 

other abnormalities, record the observation and fin 

location. If several fins are eroding with unequal 

severity, check all that apply and note in the fin 

comments which fins are abnormal (Figures 38–44b). 

Note: Erosion usually involves both the fin membrane 

and rays, whereas fraying involves only the membrane. 

Normal (Figure 38): No active erosion, fraying, or 

hemorrhage. This includes previously eroded fins that 

are completely healed over. 

Figure 38. Normal fins, no abnormalities present such as fraying, 

erosion, or hemorrhaging. 

Mild Erosion (Figures 39a and 39b): Active erosion 

but no evidence of hemorrhage or secondary infection. 

Figure 39a. Caudal fins displaying active mild erosion. 

Figure 39b. Active fin erosion. 

Severe Erosion (Figures 40a and 40b): Active erosion with hemorrhage and/or evidence of secondary 

erosion. 

Figure 40a. Fins with severe erosion. 

Figure 40b. Severe erosion of the caudal fin with a possible secondary infection. 
24 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

Frayed (Figure 41): Margins of fins ragged or torn. 

Figure 41. Caudal fin with frayed or ragged edges. 

Hemorrhagic (Figures 42a and 42b): Reddened 

(that is, bloody) area visible within the intact fin. 

Figure 42a. Fins with reddened or hemorrhagic areas. 

Figure 42b. Hemorrhagic and frayed fins. 

Emboli (Figure 43): Gas bubbles visible within the 

fin. 

Figure 43. Visible gas bubbles (emboli) within the fins. 

Other (Figures 44a and 44b): Any observation that 

does not fit above (that is, parasites, lesions, and so 

forth); describe. 

Figure 44a. Fin containing a nodule, categorized as “other”. 

Figure 44b. Dorsal fin with leech, categorized as “other”. 

Record the condition or conditions that apply if one 

or more fins are affected. Note the location of any 

conditon in the General Comments and the number 

of pieces in fixative. 
±

ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 25 

6.3 PROCEDURES FOR INTERNAL EXAMINATION 

Lay the subdued fish on the foil and open the abdominal cavity with a cut from the vent forward to the pectoral girdle; cut through or closely to one side of the 

pelvic girdle. Do NOT insert the scissors so far that 

the internal organs are damaged. 

Reach into the anterior end of the abdominal cavity 

with one gloved finger and find the esophagus. Cut 

the esophagus with the scissors, and remove the entire 

viscera except for the kidneys, which will remain in 

the carcass (Figure 45). Use only gloved fingers and a 

blunt probe to free the internal organs from the carcass. Put the carcass aside (on the foil) while working 

with the excised internal organs (if necessary, refer to 

the diagrams of the internal features of spiny-rayed or 

soft-rayed fish located in Appendices B-2 and B-3). 

Figure 45. Viscera removed from the fish for the purpose of conducting the internal examination. 

6.3.1 LIVER, GALL BLADDER, AND BILE: 

Although treated separately here and on the Fish 

Health Examination Form (Appendix A-2), the 

liver, gall bladder, and bile are examined and 

sampled together. If obtaining organ weight is part 

of the study plan, record the liver weight (± 0.1 g or 

less) on the Fish Health Examination Form. 

6.3.1.1 LIVER: The appearance of the liver may be an 

artifact of the sampling; the observer should take that 

into consideration. Note that the appearance of the 

intact liver and gall bladder may, for example, vary 

with the length of time from collection to observation. 

It also depends on the extent of blood loss during 

sampling. Check all that apply (Figures 46–50b). 

Normal Liver; Dark- to light-red color (Figure 46): 

Dark red is the normal color. However, the liver is a 

blood storage organ, and it may be a lighter red color 

after bleeding, but not so pale as to be classified as 

general discoloration or as tan. Color may also vary 

among species and taxa. 

Figure 46. Normal liver, dark red in color. 

Tan or “coffee with cream color” liver (Figure 47): 

Fatty liver; (that is, more or less uniformly light tan 

color). 

Figure 47. A tan, or “coffee with cream” color liver. 

General discoloration (Figures 48a and 48b): 

Uniform color other than the above (gray is common); 

describe. 

Figure 48a. Liver with general discoloration. 
26 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

Figure 48b. Generally discolored liver. 

Focal discoloration (Figure 49): Color change in part 

of the liver, giving it a mottled appearance; describe. 

Figure 49. Liver with focal discoloration. 

Nodules in liver (Figures 50a and 50b): Nodules 

(that is, white parasitic cysts or bacterial granulomas) 

and incipient nodules, such as those in hepatoma (dark 

blotches) or cholangioma (“popcorn” look); swollen 

areas. 

Figure 50a. Nodules in the liver. 

Figure 50b. Nodules in the liver. 

Other: Aberration or deviation in the liver that does

not fit into above scheme; describe.

Record the liver condition on the Fish Health

Examination Form.

6.3.1.2 Liver Sample Collection: For fish with a discrete liver, use acetone-rinsed scissors to cut any

grossly observable foci or lesions from the liver and

put them into the fixative. If bile is not collected, try

not to puncture the gall bladder. 

For fish without a discrete liver, such as common carp

(Cyprinus carpio) or sucker (Catostomidae), the procedure is analogous, but the liver is usually not

removed. Upon completion of the visual observation,

locate and inspect as many of the dispersed hepatic

lobes as possible.

Note: Here, nodule refers to the dispersed liver organ, 

not to a pathological condition. 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 27 

6.3.1.3 GALL BLADDER FULLNESS AND BILE COLOR: 

The bile is observed indirectly through the observation 

of the gall bladder. The ranking scheme considers 

“fullness” of the bladder and degree of “green-ness” 

as follows (Figures 51–52b): 

Bile color should be classified as: 

Yellow or straw color; 

Light green to grass green; or 

Dark green or dark blue-green (Figure 51). 

Figure 52b. Empty gall bladder. 

Record the color of the bile and the fullness of the 

gall bladder on the Fish Health Examination Form. 

Note: If bile color can be determined, bile is present 

and the gall bladder should be described as either 

“partly full” or “full”. If the gall bladder is empty, 

Figure 51. A normal gall bladder, which is full with dark green do not check a color. 

bile. 

Gall Bladder fullness may be either: 

Empty (Figures 52a and 52b) or nearly so; 

Partly full; or 

Full (Figure 51) or distended. 

Figure 52a. Empty gall bladder. 
±

28 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

6.3.2 GONADS: Locate the gonads (Figures 53–56) 

and determine the gender of the fish, if possible. 

Note: The gross visible appearance of the gonads 

varies greatly among taxa and over the life of the fish. 

Generally, ovaries have a granular appearance and are 

yellow, orange, or pink; in contrast, testes are lighter 

in color (that is, whitish to yellow) and have a less 

granular appearance. An intersex condition (both) 

may also be observed. Some local experience with 

the species to be collected will be required before gender and reproductive stage can be accurately determined in the field. 

Record the gender on both the front page of the Fish 

Health Examination Form (Appendix A-2) and within 

the Gonads section. Dissect the gonads from the viscera. 

Record the gonadal stage (that is, ripe, spent, 

intermediate) on the Fish Health Examination Form. 

Ripe female fish frequently have distended abdomens 

and large, full gonads; ovaries contain many large 

eggs. If obtaining organ weight is part of the study 

plan, record the gonad weight (± 0.1 g or less) on 

the Fish Health Examination Form. Observe the condition of the gonads as follows: 

Male (Figures 53a and 53b): 

Figure 53a. Immature male gonads. 

Female (Figures 54, 55a–55c) 

Figure 54. Immature female gonads. 

Figure 55a. Mature female gonads (salmonid). 

Figure 55b. Mature female gonads (common carp). 

Figure 53b. Mature male gonads. Figure 55c. Mature female gonads (Micropterus sp.) 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 29 

Other-Gonads (Figure 56): 

Figure 56. Large mass located in gonads, categorized as “other”. 

Note any lesions, parasites, and so forth by checking “other” (preserve a sample), and describe. 

Cut 1-cm pieces from the posterior end (bottom tips) 

of the gonads, and place a maximum of five gonad 

pieces in the fixative. If the gonad is small, preserve 

the entire organ. 

Record the number of pieces in fixative. 
±

30 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

6.3.3 SPLEEN: Locate the spleen and dissect it 

whole from the viscera. If obtaining organ weight is 

part of the study plan, record the spleen weight (± 

0.002 g) on the Fish Health Examination Form 

(Appendix A-2). Observe the condition of the spleen 

(Figures 57a–59) as follows (check all that apply): 

Normal: 

Red to Black (Figure 57a and 57b): “Black” is actually a very dark red color; both conditions are considered normal. 

Figure 57a. Normal spleen, dark red in color with no apparent 

aberrations. 

Figure 57b. Normal spleen. 

Abnormal: 

Granular (see Goede, 1988: photo 32): “Rough” 

appearance of the spleen. 

Nodular (Figure 58): Manifests fistulas or nodules of 

varying sizes. These are often cysts, such as those 

caused by parasites or chronic mycobacterial infections. 

Figure 58. Spleen sample containing nodules of various sizes. 

Enlarged (Figure 59): The spleen can be significantly 

and noticeably enlarged or swollen. 

Figure 59. Example of an abnormally enlarged spleen. 

Other: Occasionally there are grossly visible aberrations that do not fit any of the classes above. The 

spleen may be mottled gray, and some fishes may 

have very small spleens. These should be classified as 

“other” and described. 

Record the spleen condition on the Fish Health 

Examination Form. 

If the spleen is large (>0.8 g), cut it in half, and place 

one half in the fixative, and retain the other with the 

carcass. Otherwise, place the entire spleen in the fixative. Record that the spleen in fixative was 

collected on the Fish Health Examination Form. 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 31 

6.3.4 KIDNEY(S): In some fishes (common carp, 

centrarchids), the anterior (head) and posterior (trunk) 

kidney are separate; in others (salmonids, ictalurids), 

they are continuous. We treat them as being together 

for examination, but separate for sample collection. 

Observe and sample both (Figures 60–63). 

6.3.4.1 Posterior (Trunk) Kidney: 

The trunk kidney is exposed by removing the layer of 

mesentery at the posterior dorsal border of the abdominal cavity, dorsal to the gas bladder. Observe its condition as follows (check all that apply on the Fish 

Health Examination Form, Appendix A-2). 

Normal (Figure 60): Firm, dark red color lying relatively flat dorsally in the visceral cavity along the 

length of the ventral surface of the vertebral column. 

A B 

Figure 60. (A) normal kidney; (B) abnormal kidney which is mottled in appearance. 

Abnormal: 

Swollen (Figures 61–63): Wholly or partly enlarged 

or swollen; 

Mottled (Figures 62 and 63): Gray discoloration, 

mottled or “patchy” appearance, ranging from 

scattered patches of gray to mostly or totally gray discoloration; 

Figure 62. Examples of various aberrations found in the kidney. 

Granular (Figures 61 and 62): The kidney has a 

“granular” or irregular surface which may be due to 

the presence of granulomas, hemorrhages, congestion 

or other causes. These areas are generally not hard 

and “gritty”; 

Urolithiasis (see Goede, 1998: photos 38-40): 

Urolithic deposits are hard and “gritty”. This condition is also known as nephrocalcinosis and involves 

deposition of white or “cream-colored” amorphous 

mineral material in the tubules of the kidney. It can 

range in appearance from very small white spots to 

severe conditions with very large “serpentine” 

deposits. 

Note: These sites of deposition are not to be confused 

with the Stannius bodies (corpora of Stannius), which 

are the white nodular tissues present in salmonid kidneys and which have an endocrine function. The 

Stannius bodies are generally not associated with the 

tubules and usually occur at the “edges” in an area 

about midway along the kidney. They appear more 

globular than do urolithic deposits. 

Figure 61. Swollen kidney. 
32 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

Other (Figure 63): This is used to classify any aberrations that do not fit into the above scheme; describe. 

Figure 63. Abnormal kidney; enlarged, mottled, and “other” 

(white nodules). 

Record the trunk kidney appearance on the Fish 

Health Examination Form. 

Place at least one 1-cm piece of the trunk kidney in 

the fixative, and record the number of pieces preserved (if possible—fish kidney tends to fall apart) on 

the Fish Health Examination Form. 

6.3.4.2 Anterior (Head) Kidney: In fishes with separate 

kidneys, the head kidney is located dorsal to the liver 

and may be viewed after the latter has been removed. 

Record the head kidney appearance according to 

the criteria above; record observations in the anterior 

head kidney section of the Fish Health Examination 

Form (Appendix A-2). 

Remove as much of the head kidney as you can (at 

least one 1-cm piece) and place it in fixative. Record 

the number of pieces in fixative (if possible) on the 

Fish Health Examination Form. 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 33 

6.4 Scales or Spines 

Collect a scale sample (most fishes) or pectoral fin 

spine (ictalurids) from the left side of the fish. If the 

left side is damaged (that is, scales or pectoral fin not 

present), collect from the right side. 

Spiny-rayed fishes (bass, walleye, and so forth) – 

from the area of the appressed pectoral fin (Figure 6a). 

Soft-rayed fishes (common carp, suckers, and so 

forth) – beneath the anterior portion of the dorsal fin, 

above the lateral line (Figure 6b). 

Ictalurids (that is, catfishes) – entire disarticulated 

pectoral spine; cut away as much fin and flesh as possible. Be sure to get the base of the spine (that is, 

twist off like a chicken leg). 

Note: These structures are included as representative 

because most fishery biologists have the training, 

experience, and equipment necessary to read them. 

Other hard structures (otoliths, opercular bones, vertebrae, and so forth) may be used if these structures 

are known to be valid indicators of age in the species 

you are working with and you have the capability to 

read them. 

Place the scale or spine sample in a labeled scale 

envelope (Figure 1) and allow to air-dry. Store it 

until it can be read. If scale envelopes are stored in 

a plastic bag, do not seal the bag. Record that the 

sample was collected and the side of the fish from 

which it was collected on the Fish Health 

Examination Form (Appendix A-2). 

6.5 Cleaning Equipment 

Thoroughly rinse all contact surfaces (measuring 

board, table, and so forth) with tap or ambient water. 

Wash all dissecting equipment with de-ionized water, 

and follow with an acetone rinse. 

Reminder: Acetone is flammable. 

7.0 POST-COLLECTION AND PROCESSING 

PROCEDURES 

7.1 Complete and Check Fish Health 

Examination and Station Identification 

Forms 

Post-calibrate the balances by re-weighing the calibration masses, and record the “After” calibration 

readings on the Station Identification Form 

(Appendix A-1). Turn off the balance(s) and re-pack 

them in their case(s). 

Important: The team leader checks the Fish Health 

Examination Forms and the Station Identification 

Forms again to be certain that all information has 

been recorded and is legible. Make sure each 

section (i.e. liver, gonad, spleen, etc.) has a box 

marked. Do not leave blanks within the examination form, mark ‘normal’ if no anomalies were 

found. Otherwise be sure that all observed anomalies are completely identified and appropriate 

boxes are marked. After each form has been 

reviewed and approved, it should be initialed in the 

“Reviewer’s Initials” box. 

7.2 Clean-up 

Properly dispose of used expendables. Thoroughly 

clean all work surfaces. Thoroughly clean and inspect 

all equipment used in the field to protect against the 

transportation of living organisms among waterways. 

Note: Procedures for cleaning equipment are beyond 

the scope of this document and may vary among agencies, regions, states, and water bodies. 

Pay particularly close attention to boats (including live 

wells), motors, trailers, and tubs used to hold fish. A 

stop at a car wash may be advantageous (be sure to 

rinse thoroughly with clean water). A garden sprayer 

or pump spray bottle containing a weak bleach solution can be used for a final rinse of all equipment. 

Tap water is sufficient for cleaning smaller equipment 

(pans, measuring boards, coolers, live boxes), followed by the bleach solution. Water should be used to 

rinse dissecting equipment and the weighing pans of 

electronic balances (be careful!). Give dissecting 

equipment a final acetone rinse. 

8.0 UPON RETURN FROM THE FIELD 

8.1 Photocopy and Mail Data Forms and 

Other Records 

Field teams should make two copies of all data forms 

and field notes. The team leader should retain one set 

of copies and the notebook. The second set of copies 

and the original data forms should be sent to the project coordinator/study director and if needed, a completed COC form (see Schmitt and others, 1999). If 

the project coordinator/study director is a member of 

the field team, retain both the original data forms and 

field notes and at least one set of photocopies. For 

additional security, store the originals and copies in 

separate locations. 

8.2 Ship Histopathology Samples 

Before you ship these samples, top off the fixative and 
34 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

check each bottle to be certain that the tops are tightly

fastened. If needed, samples should be shipped with a

completed COC form. Check transport restrictions

for your given fixative to determine the method of

transportation and packaging instructions.

8.3 Process Film


As soon as possible, annotate your slides, photographs or videotape – mark the station number, fish

identification number (if applicable), and date.

8.4 Age Fish and Mail Age Data 

Fish should be aged using the techniques developed 

for the structure (for example, scale, spine, otolith) 

that was collected. These techniques may vary with 

species. If the original data must be sent to a cooperating laboratory, original data forms should be shipped 

with a completed COC form. COC is optional if photocopied data forms are being shipped. 

8.5 Thoroughly Clean Non-Expendable 

Equipment 

Equipment and supplies should be cleaned as soon as 

possible after returning from the field. Do not use 

detergents or other cleaning agents that could damage 

specimens or bias laboratory analyses during the next 

sampling trip. 

Reminder: Special care should be taken when cleaning equipment to ensure that no living organisms are 

transported from one waterway to the next. 

9.0 ACKNOWLEDGMENTS 

The authors wish to thank R. Goldstein, T. Bartish, 

and P. Baumann for their review of the document; P. 

Greene for assistance with data forms; M. Mac, D. 

Hardesty, B. Poulton, J. Morrison, C. Smith, B. 

Wissel, and Leetown Science Center for providing 

photographs and assisting with photographs. The photographs in this guide came from sources of known 

and in some cases unknown origin. We thank and 

acknowledge the efforts of all that contributed these 

photographs, which are the heart of this guide. 

10.0 REFERENCES 

[ASIH] American Society of Ichthyologists and 

Herpetologists, [AFS] American Fisheries 

Society, [AIFRB] American Institute of 

Fishery Research Biologists, 1988, 

Guidelines for use of fishes in field research: 

Fisheries, v. 13, p. 16-23. 

Baker, J.R., Peck, D.V., and Sutton, D.W., 1997, 

Environmental Monitoring and Assessment 

Program Surface Waters, Field operations 

manual for lakes: U.S. Environmental 

Protection Agency, Report EPA/620/R97/001. 

Biomonitoring of Environmental Status and Trends 

Program, 1996, Summary report from a 

workshop on selection of tier 1 bioassessment methods: U.S. Department of the 

Interior, National Biological Service, 

Information and Technology Report 7, 55 p. 

Blouin, M.A., and Hall, G.R., 1990, Improved method 

for sectioning pectoral spines of catfish for 

age determination: Journal of Freshwater 

Ecology, v. 5, p. 489-490. 

Frie, R.V., 1982, Measurement of fish scales and 

back-calculation of body lengths using a digitizing pad and microcomputer: Fisheries, v. 7, 

no. 6, p. 5-8. 

Goede, R.W., 1989, Fish health/condition assessment 

procedures: Utah Division of Wildlife 

Resources, Fisheries Experiment Station. 

— 1996, Fish health/condition assessment procedures. Part 1 -- procedures manual: Utah 

Division of Wildlife Resources, Fisheries 

Experiment Station, 31 p. 

— 1988, Fish health/condition assessment procedures. Part 2 -- a color atlas of necropsy 

classification categories: Utah Division of 

Wildlife Resources, Fisheries Experiment 

Station. 

Goede, R.W., and Barton, B.A., 1990, Organismic 

indices and an autopsy-based assessment as 

indicators of health and condition of fish, in 

Adams, S.M., ed., Biological indicators of 

stress in fish. American Fisheries Society 

Symposium 8: Bethesda, MD, American 

Fisheries Society, p. 93-108. 

Hunn, J.B., 1988, Field assessment of the effects of 

contaminants on fishes: U.S. Fish and 

Wildlife Service, Biological Report 18(19), 

25 p. 

Jearld, A., Jr., 1983, Age determination, in Nielsen, 

L.A., and Johnson, D.L., eds., Fisheries techniques: Bethesda, MD, American Fisheries 

Society, p. 301-324. 

Lagler, K.F., 1956, Freshwater fishery biology: 

Dubuque, IA, Wm. C. Brown Company 421 

p. 

Lagler, K.F., Bardach, J.E., and Miller, R.R., 1962, 

Ichthyology: New York, John Wiley & Sons, 

545 p. 

Meador, M.R., Cuffney, T.F., and Gurtz, M.E., 1993, 

Methods for sampling fish communities as 

part of the National Water-Quality 

Assessment Program: U.S. Geological 

Survey, Open-File Report 93-104, 40 p. 

Meyer, F.P., and Barclay, L.A., 1990, Field manual for 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 35 

the investigation of fish kills: U.S. Fish and 

Wildlife Service, Resource Publication 177, 

120 p. 

Nielson, L.A., and Johnson, D.L., 1983, Fisheries 

techniques: Bethesda, MD, American 

Fisheries Society, 468 p. 

Robins, C.R., Bond, C.E., Brooker. J. R., Lachner, 

E.A., Lea, R.N., and Scott, W.B., 1991, 

Common and scientific names of fishes from 

the United States and Canada: Bethesda, MD, 

American Fisheries Society, 183 p. 

Schmitt, C.J., Blazer, V.S., Dethloff, G.M., Tillitt, 

D.E., Gross, T.S., Bryant, W.L., Jr., DeWeese, 

L.R., Smith, S.B., Goede, R.W., Bartish, 

T.M., and Kubiak, T.J., 1999, Biomonitoring 

of Environmental Status and Trends (BEST) 

Program: field procedures for assessing the 

exposure of fish to environmental 

contaminants: U.S. Geological Survey, 

Biological Resources Division, Information 

and Technology Report 1999-0007, 68 p. 

Schmitt, C.J., and Dethloff, G.M., eds.2000, 

Biomonitoring of Environmental Status and 

Trends (BEST) program: selected methods 

for monitoring chemical contaminants and 

their effects in aquatic ecosystems: U.S. 

Geological Survey, Information and 

Technology Report 2000-0005, 81 p. 

Smith, L.S., 1973, Introductory anatomy and biology 

of selected fish and shellfish: Seattle, WA, 

University of Washington, College of 

Fisheries 128 p. 

Tesch, F.W., 1971, Age and growth, in Ricker, W.E., 

ed, Methods for assessment of fish production in fresh waters (2nd ed.): Oxford, 

England, Blackwell Scientific Publications, p. 

98-130. 

U.S. Environmental Protection Agency, 1989, Toxic 

Substances Control Act (TSCA); good laboratory practice standards; final rule: EPA 40 

CFR, Part 792. 

Walsh, S.J., and Meador, M.R., 1998, Guidelines for 

quality assurance and quality control of fish 

taxonomic data collected as part of the 

National Water-Quality Assessment Program: 

U.S. Geological Survey, Water-Resources 

Investigations Report 98-4239, 33 p. 

Wiesburg, S.G., and Frie, R.V., 1987, Linear models 

for the growth of fish, in Summerfelt, R.C., 

and Hall, G.E., eds., Age and growth of fish: 

Ames, IA, Iowa State University Press, p. 

127-143. 

ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 37 

Appendix A


Data Forms


ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 39 

Appendix A-1 

STATION IDENTIFICATION FORM STATION ID # ___________ DATE _____/_____/_____ 

STATION DESCRIPTION (River and Location): _____________________________________________ 

Water TEMPERATURE (°C): Sampling START Time: Sampling STOP Time: 

LANDOWNER’S PERMISSION: ____________________________________ Date: ________ 

____________________________________ Date: ________ 

Team Leader: ___________________________ 

Other Personnel: ____________________ ____________________ 

____________________ ____________________ 

____________________ ____________________ 

____________________ ____________________ 

GPS COORDINATES: (Degrees – Minutes) 

LATITUDE LONGITUDE 

(D) (M) (D) (M) 

MAXIMUM: _____ - _____._______ _____ - _____._______ 

MINIMUM: _____ - _____._______ _____ - _____._______ 

MAP DATUM: 

_____________ 

BALANCE: 

(make and serial #) MASS: 

CALIBRATION: 

Before After 

RECORDER’S INITIALS: ______________________________________ 
40 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007 

Appendix A-1--Continued 

GENERAL COMMENTS 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 41 

Appendix A-2 

FISH HEALTH EXAMINATION FORM DATE: ___/___/___ STATION ID# ______ FISH ID# __________ 

SPECIES: _________________ Weight: _______(g) Length: _______(mm) Sex: ____________ 

EXTERNAL EXAMINATION: (check all that apply) 

BODY SURFACE: HEAD and ORAL CAVITY: EYES: 

normal 

raised growth(s) 

reddened lesion(s) 

spinal deformities 

hemorrhagic body 

focal discoloration 

body fungus 

parasite(s) specify: 

white spots 

leech(es) 

black spot(s) 

Anchor worm(s) 

OTHER specify: 

___________________________ 

___________________________ 

___________________________ 

# in fixative ____ # of photos ____ 

normal head 

deformed head 

upper lip growth 

lower lip growth 

swollen nare 

BARBELS: 

normal 

missing 

stubbed 

deformed 

OTHER specify: 

___________________________ 

___________________________ 

___________________________ 

# in fixative ____ # of photos ____ 

Left: 

normal 

exopthalmic 

opaque 

missing 

hemorrhagic 

emboli 

OTHER specify: 

______________ 

______________ 

______________ 

______________ 

# in fixative ____ 

# of photos ____ 

Right: 

normal 

exopthalmic 

opaque 

missing 

hemorrhagic 

emboli 

OTHER specify: 

______________ 

______________ 

______________ 

______________ 

# in fixative ____ 

# of photos ____ 

OPERCULA: 

normal OTHER specify: ____________________________________________________ 

slight shortening ____________________________________________________ 

severe shortening ____________________________________________________ 

# in fixative ____ # of photos____ 

GILLS: 

Left: 

normal 

frayed 

marginate 

pale 

OTHER specify: ______________ # in fixative ____ 

______________ 

______________ # of photos ____ 

Right: 

normal 

frayed 

marginate 

pale 

OTHER specify: ______________ # in fixative ____ 

______________ 

______________ # of photos ____ 

FINS: 

normal 

mild erosion 

severe erosion 

frayed 

hemorrhagic 

emboli 

OTHER specify: __________________________ # in fixative ____ 

_______________________________________ 

_______________________________________ # of photos ____ 
42 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007 

Appendix A-2--Continued 


INTERNAL EXAMINATION: (check all that apply)


LIVER: 

normal (dark to light red) 

tan (coffee with cream) 

general discoloration 

focal discoloration 

nodules 

OTHER specify: ________________ 

_____________________________ 

_____________________________ 

Weight_____(0.1g) with gallbladder intact 

# in fixative ____ # of photos____ 

GALL BLADDER and BILE: 

Color: 

yellow 

light-grass green 

dark green to blue-green 

Fullness: 

empty 

partly full 

full or distended 

OTHER specify: 

_______________________________ 

_______________________________ 

_______________________________ 

_______________________________ 

_______________________________ 

# in fixative ____ # of photos____ 

GONADS: 

Gender: 

male 

female 

indeterminate 

Stage: 

ripe 

spent 

intermediate 

OTHER specify: _______________________________________ 

_______________________________________ 

Weight _____(0.1g) # in fixative ____ # of photos____ 

SPLEEN: 

normal granular OTHER specify: ________________________________________________ 

(red to black) nodular ________________________________________________ 

enlarged 

Weight_____(0.002g) # in fixative ____ # of photos____ 

POSTERIOR (Trunk) KIDNEY: ANTERIOR (Head) KIDNEY: 

normal 

swollen 

mottled 

granular 

urolithiasis 

OTHER specify: __________________ 

_______________________________ 

_______________________________ 

# in fixative ____ # of photos____ 

normal 

swollen 

mottled 

granular 

urolithiasis 

OTHER specify: ___________________ 

________________________________ 

________________________________ 

# in fixative ____ # of photos____ 

GENERAL COMMENTS: 

_________________________________________________________________________________________ 

_________________________________________________________________________________________ 

_________________________________________________________________________________________ 

_________________________________________________________________________________________ 

_________________________________________________________________________________________ 

_________________________________________________________________________________________ 

_________________________________________________________________________________________ 

_________________________________________________________________________________________ 

SCALES: 

side sampled: 

left 

right 

SPINES: 

specify: _______________________ 

_______________________ 

OTHER:______________________ 

INITIALS: 

RECORDER: ______________________ 

DISSECTOR: __________________ 

REVIEWER: __________________ 

____

____
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 43 

Appendix B


External and Internal Diagrams of Fish Anatomy

44 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

B-1. From Hunn (1988) External features of a composite fish. 
ILLUSTRATED FIELD GUIDE FOR ASSESSING ANOMALIES IN FISH 45 From Hunn (1988). . B-2. Anatomy of a spiny-rayed bony fish, the largemouth bass, Micropterus salmoides
46 INFORMATION AND TECHNOLOGY REPORT USGS/BRD/ITR–2002-0007

From Hunn (1988). . B-3. Anatomy of a soft-rayed bony fish, the brook trout, Salvelinus fontinalis
REPORT DOCUMENTATION PAGE Form Approved 

OMB No. 0704-0188 

Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering 

and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or any other aspect of this collection of 

information, including suggestions for reducing this burden, to Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 

1204, Arlington, VA 22202-4302, and to the Office of Management and Budget. Paperwork Reduction Project (0704-0188), Washington, DC 20503. 

1. AGENCY USE ONLY (Leave Blank) 2. REPORT DATE 

September 2002 

3. REPORT TYPE AND DATES COVERED 

Information and Technology Report 

4. TITLE AND SUBTITLE 

Illustrated Field Guide for Assessing External and Internal Anomalies in Fish 5. FUNDING NUMBERS 

6.AUTHOR(S) 

Stephen B. Smith, Anne P. Donahue, Robin Lipkin, Vicki S. Blazer, Christopher J. Schmitt, 

and Ronald W. Goede 

7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 

U.S. Department of the Interior 

U.S. Geological Survey, Biological Resources Division 

Columbia Environmental Research Center 

Columbia, MO 65201 

8. PERFORMING ORGANIZATION 

REPORT NUMBER 

USGS/BRD/ITR--2002-0007 

9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 

U.S. Department of the Interior 

U.S. Geological Survey 

Biological Resources Division 

Reston, VA 20192 

10. SPONSORING/MONITORING 

AGENCY REPORT NUMBER 

11. SUPPLEMENTARY NOTES 

12a. DISTRIBUTION/AVAILABILITY STATEMENT 

Release unlimited. ailable from the National Technical Information Service, 5285 Port Royal 

Road, Springfield, VA 22161 (1-800-553-6847 or 703-487-4650). ailable to registered users 

from the Defense Technical Information Center, Attn: Help Desk, 8722 Kingman Road, Suite 

0944, Fort Belvoir, VA 22060-2618 (1-800-225-3842 or 703-767-9050). 

12b. DISTRIBUTION CODE 

13. ABSTRACT (Maximum 200 words) Procedures are described for processing fish for examination of external and internal anomalies and 

pathologies indicative of exposure to environmental contaminants and other perturbations. For the procedures described here, fish are 

captured (preferably by electrofishing) and held alive until processing (generally <1 h). Fish are weighed, measured, and necropsied, and a 

scale sample is obtained from for age determination. Information is given for the collection and preservation of tissue samples for 

histopathological analysis. Photographs of most abnormalities are included along with normal conditions for easier identification of external 

(oral, head, eye, gill, opercula, and fin) and internal (liver, spleen, gonad, and kidney) anomalies. The report also includes recommendations 

for record keeping, sample labeling, and shipping records, equipment, supplies, and samples. A list of suggested equipment and supplies for 

field processing is included as are instructions for cleaning equipment. 

14. SUBJECT TERMS: contaminants, fish health, external anomalies, internal anomalies, histopathology. 15. NUMBER OF PAGES 

35 pages +appendices 

16. PRICE CODE 

17. SECURITY CLASSIFICATION 

OF REPORT 

Unclassified 

18. SECURITY CLASSIFICATION 

OF THIS PAGE 

Unclassified 

19. SECURITY CLASSIFICATION 

OF ABSTRACT 

Unclassified 

20. LIMITATION OF ABSTRACT 

Unlimited 

Av

Av

NSN 7540-01-280-5500 	 Standard Form 298 (Rev. 2-89) 

Prescribed by ANSI Std 239-18