Pacific States Marine Fisheries Commission

Smolt Monitoring Program



Revised April 01

Table of Contents

Species Identification
Figure 1. Anatomy of a smolt
Hatchery, Wild, Unknown
Descaling Level (20%)
External Marks
Incidental Species
PIT Tag Data
Detailed Condition Data
Figure 2. Distinguishing characteristics of Chinook
Figure 3. Distinguishing characteristics of Coho
Figure 4. Distinguishing characteristics of Sockeye
Figure 5. Distinguishing characteristics of Steelhead
Figure 6. Distinguishing characteristics of Spring Chinook
Figure 7. Distinguishing characteristics of Fall Chinook


The Smolt Monitoring Program of the Pacific States Marine Fisheries Commission (PSMFC) manages sampling operations at two federal Army Corps of Engineers (COE) hydroelectric projects on the Columbia River. One of these is at Bonneville Dam (river mile 145) and the other is at John Day Dam (river mile 216). These facilities are primarily responsible for reporting flow data and the number and timing of migrating juvenile salmonids (Oncorhynchus spp.) to the Fish Passage Center (FPC). They are secondarily responsible for collecting length and condition data on sub-samples of juvenile salmonids, recording external mark information and time of passage of marked smolts, and recording the number and length of incidental species captured by our sampling system.

The Fish Passage Center (FPC) is a technical office funded by the Bonneville Power Administration (BPA) representing the seven state and federal fisheries agencies and thirteen tribes composing the Columbia Basin Fish and Wildlife Authority (CBFWA). The FPC uses the real time information collected at its 12 monitoring sites to implement flow and spill requests from the hydroelectric projects in order to augment the instream flow of the Snake and Columbia Rivers to reduce the downstream migration travel time of juvenile salmonids. Data are also used for condition monitoring and survival and travel time estimates.

This manual details the knowledge and skills which are needed by personnel within the Smolt Monitoring Program in order to insure the accurate collection of the data utilized by the managers and scientists working in the Columbia basin.


There are some differences between the fish handling procedures at John Day and Bonneville which are detailed in the site-specific handouts. All of the fish identification and handling information in this guide applies to both sites.

Sampled fish are anesthetized with Tricaine (MS-222) prior to handling. When properly anesthetized, fish should be calm and will start to loose their balance (turning on their side) with gills pumping normally to rapidly. They should show reflexes when pressure is applied to the base of the tail. Over-anesthetized fish lose all balance and ability to swim. Reflexes to stimuli will cease and gill activity may notably decrease or completely stop. Fish must not stay in this deeply anesthetized state for more than a few moments, as death is likely to result! If fish are observed in this state, fresh water must be added to the trough and in sever cases, fresh water can be gently flushed over the gills until a stronger gilling response is detected.

Important points to remember while processing fish: Crowd fish slowly and remove any fry (<60mm), or juvenile shad (if possible) before anesthetizing. Never compromise the safety of salmonids to save shad.

Net-transferring fish should not be done unless absolutely necessary, and if done, should be done quickly.
Special care should be taken when using the anesthetic. Read and follow all guidelines and safety requirements. Never leave an anesthetized trough of fish unattended for long.

Closely monitor fish condition while they are anesthetized. Smaller fish are more vulnerable to anesthetic, and the tolerance to anesthetic varies by species.

If possible keep fish underwater throughout the examination process. Always handle them as quickly and gently as possible.

Give the entire operation your undivided attention.


Species Identification

The first step when processing anesthetized fish is species identification. Identifying fish of any kind to the species level requires that one be familiar with fish anatomy (Figure 1).

Figure 1. Anatomy of a smolt.

A working knowledge of correct terminology is essential for quick and efficient identification. The most effective identification techniques used at John Day and Bonneville are based on differences in the shape, size, and location of parr marks; the shape and coloration of fins; and the shape and coloration of the head and body. See Figures 2 through 7 for sketches illustrating the characteristics of the smolts you will encounter. The four salmonid species described in this section and important at these SMP sites are (1) steelhead, (2) chinook, (3) coho, and (4) sockeye salmon.

The first and simplest division should be based on the caudal fin (Figure 1). A fish having a tail which is "squared" off instead of deeply forked is most likely a steelhead (Oncorhynchus mykiss). Other steelhead characteristics include rounded parr marks, a rounded head, and distinct black pigmented spots on the dorsal fin. Overall size and color are highly variable, but steelhead (especially hatchery fish) can be quite large (>230 cm) and tend to be bluish and/or greenish.

Fish with forked tails are one of the three other species of salmon (chinook, coho, or sockeye). At this point you need to look at other features such as parr marks, back spotting, and anal fin shape for specific identification (Figure 1).

Chinook salmon (O. tshawytscha) are characterized by large, football shaped parr marks centered on their lateral line which are wider than the spaces separating them. Chinook usually have large black spots on their backs (above the lateral line), caudal fins usually tipped with black, and wedge shaped anal fins. In addition, a distinction is made between spring (yearling) and fall (subyearling) runs of chinook smolts (Figure 3, 6, and 7). Spring chinook have large eyes, large pupils, and large blunt heads. They also have a leaner, more torpedo-like body shape with a longer, narrower caudal peduncle.

Fall chinook have smaller eyes that tend to turn down, a football shaped body, and a silvery appearance (typically signaling advanced smoltification). In general, spring chinook are larger than fall chinook, but their fork length measurements will overlap so size should not be used as a primary indicator for identification.

Coho salmon (O. kisutch) usually have thin bar-like parr marks centered on the lateral line. The parr marks are narrower than the spaces separating them and this is the main characteristic used when separating them from chinook. Coho also have a longer, sickle shaped anal fin which usually has a white leading edge, small black spots on their backs (above the lateral line), and caudal fins often tipped in black.

Sockeye salmon (O. nerka) have very faint narrow parr marks centered above the lateral line. They are generally small, silvery, fragile looking fish with a wedge shaped anal fin, and little or no pigment in the fins or spots on the back.

Parr marks can be difficult to see so hold the fish just under the water and tilt it to get the best light. If they are still not visible, or not distinct enough for you to decide what kind of fish you are handling; you must determine the species based on other characteristics. This is extremely important for coho and chinook salmon which sometimes hybridize and have mixed spotting and parr mark characteristics. In this case, the best indicator is the anal fin. On chinook it is wedge shaped and on coho it is sickle shaped with a white leading edge (Figure 2).

Your ability to quickly and correctly identify salmonid species will increase as you become more practiced. If you are not sure of a fish after considering all of its characteristics consult with the other person on your shift. Remember that this is not a contest and one should not hesitate to ask the opinion of your co-workers. The goal is to always identify sampled fishes correctly. Accurate identification and proper recording are the very foundation of our work (see the Shift Catch and 24 Hour Summary sheets for recording species data).

Hatchery, Wild, Unknown

A second distinction is made between hatchery and wild or unclipped (unknown) fish. Fish lacking adipose fins and/or a ventral fin are categorized as hatchery for chinook yearlings, steelhead, coho, and sockeye, while those with all their fins are wild for steelhead and sockeye, or unknown for all unclipped chinook and coho. Unclipped chinook and coho are of unknown origin, i.e. they may be from hatcheries or from wild stock.

The exceptions to this generalization are steelhead. All hatchery steelhead in the Columbia basin are supposed to be adipose (ad) or ventrally clipped. Any steelhead retaining all of its fins should be designated as a wild fish. However, some hatchery fish always escape without being clipped and are released into the river. If a steelhead is encountered in our sampling operation which has an intact adipose fin but obvious hatchery characteristics (frayed or missing fins, large size, and/or distinctive coloration) it should be designated as a hatchery fish.

Descaling Level (20%)

Another important piece of data SMP personnel are required to determine is whether or not individual fish are descaled. If a fish is missing 20% or more of its scales on either side (NOT both sides cumulatively) it is recorded as being "descaled". If less than 20% of its scales are missing it is recorded as a "good". The shaded area on the fish to the right constitutes 20% of that side of the fish.

Note: Areas of scale regeneration are NOT considered descaled. Isolated patches of descaling must be mentally "added" together. The 20% descaling does not need to be contiguous. In addition to the "descaled" or "good" designation made for every fish, a subsample is taken three times a week for more detailed condition data (See the Subsample Data section below). Mortalities

All fish, even those that have recently died, which are captured by the bypass system are included on the data sheets. Dead fish are identified to species and are included in the total as "Morts". Descaling information is not collected for mortalities. Any fish that enter the sample holding tank already dead are considered facility mortalities. Any fish that is killed after it enters the sample holding tank or dies in the recovery tank is a sample mortality. Any fish that dies after we place that fish in a research holding tank is a research mort as long as that fish didn't die due to over anesthetization on our part.

External Marks

After determining the species, clip designation, and condition category (good, descaled, or mort), all fish must be carefully examined for freeze brands and other external marks. A short description of each follows.

Brands are applied by placing fish against a super cooled brand tool which freeze burns the brand (usually letters or numbers) on their skin. While holding the fish just under water, tilt it to get the best light and look along its back on both sides for a brand.

Brands are applied above the lateral line in the anterior or dorsal positions and can be on the right or left side of the fish (Figure 1). (NOTE: Left and right are determined as if YOU were the fish.) In addition, each brand can be orientated in one of four rotations, with 1 being vertical (12 o'clock), 2 at 900 (3 o'clock), 3 at 1800 (6 o'clock), and 4 at 270 0 (9 o'clock). If you detect a mark that might be a brand, place the fish in the partitioned section of the sorting trough. Make certain that the species and descaling condition information is recorded (as is done with all fish) at this time. Finish working the remaining fish in the sorting trough and then re-examine the fish (or fishes) that are suspected of being branded.

Common problems with reading brands include, confusing 2nd and 4th rotations and the left and right side of the fish. Brands can be tough to spot and read but with practice and preparation, it will become routine.

Another type of tag or mark we will encounter is the elastomer tag. This is a small piece of plastic that is injected into the clear tissue posterior of the eye. Besides the typical species, clip, and condition of the fish, we need to record color and location (left or right eye) of the tag.

There are two other types of tags that we could possibly see. One is a Visual Implant (VI) tag. This is very similar to the elastomer tag, except that it has a number printed on it that needs to be recorded. The other tag would be the Floy tag. Floy tags are spaghetti like pieces of plastic anchored just behind the dorsal fin. They are 2-3 inches long and have a number printed on them. Record the number and color along with the typical fish information for both of these tags.

A current "Mark and Brand Release" sheet will be available throughout the season. Study this list to familiarize yourself with the marks currently being released. This list is also very helpful in determining the true identity of partial or unrecognizable brands as it lists all brands (including possible positions and orientations) that are currently in the river for each salmonid species. There will also be a branding tool imprint sheet posted which shows what many brands should look like. This may also help in identifying smudged or partial brands (which have been quite common).

Mark recovery information is used to calculate travel time, estimate survival, evaluate accelerated growth programs, etc. Brands must be properly read and recorded to be of any value, so please, pay attention and always get the confirmation of co-workers if a brand is difficult to identify, or if the brand is not listed on the Mark and Brand Release sheet.

Incidental Species

A variety of incidental (non-salmonid or adult salmonid) species are encountered while monitoring the out-migration at John Day and Bonneville. The most abundant of these incidentals are juvenile American Shad (Alosa sapidissima) and juvenile and adult Pacific Lamprey (Entosphenus tridentatus). The demand for information concerning these species in the Columbia River system is increasing steadily due to the incredibly high numbers of shad and the steady decline of lamprey in the system. Multi-season information regarding other non-targeted species is also becoming increasingly important.

During peak periods of juvenile shad passage (>2,000/ sample), their sample number can be estimated using weight (n=500). Crowd the sample towards the PA chamber until the shad density increases sufficiently. Fill a bucket with about 4 liters of water and record the weight. Juvenile shad tend to school and mill in the upper water column. They should be carefully netted, drained for a moment, and transferred into the bucket of water. Use the net slowly and try not to unnecessarily disturb or stress juvenile salmonids. If a smolt is accidentally netted, release all fish in the net and start over. Weigh the bucket with the juvenile shad, record, and release shad behind perforated plate on the north side of holding tank. Subtract the start weight from the end weight to obtain the total weight of the shad. Repeat this process until the majority of the juvenile shad are removed from the sample. The total weight is then divided by the average weight, giving the total number of shad. A new average is to be figured daily to account for variation in juvenile shad growth. All hand counted shad should be added to this total number. The demand for information concerning these species in the Columbia River system is increasing steadily due to the incredibly high numbers of shad and the steady decline of lamprey in the system. Multi-season information regarding other non-targeted species is also becoming increasingly important.

PIT Tag Data

An increasingly important research tool is the PIT tag, which stands for Passive Integrated Transponder (PIT). A PIT tag is an integrated circuit chip attached to a copper wire antenna coil encapsulated in glass. Each uniquely coded tag is 2.1 mm in diameter by 12.0 mm in length. This tag is injected into the body cavity of a juvenile or adult fish where it remains throughout the life of the fish. PIT tags rely upon an outside power supply for detection. PIT tag detectors energize a tag as a fish travels through or over them. The energized tag immediately emits its code back to the interrogation equipment, which then processes the code through a computer interface. The new facility at JDA interrogates all guided fish for a PIT tag as does the retrofit equipment at Bonneville first powerhouse and the new equipment at the new outfall site for the second powerhouse.


Detailed Condition Data

Detailed condition data is collected from each species three times per week. A sample size of 100 individuals per species is targeted and the data is entered into a spreadsheet and saved for later evaluation.

Important: all of the fish used in subsample evaluations must also be recorded on the normal sample sheets.

Categories found on the Detailed Condition data sheet and their definitions:

Fork Length: (to the nearest millimeter). Measure from the tip of the nose to the fork in the tail.

Clip: Record the appropriate clip code (be sure to check for both adipose and ventral fin clips).
  1. Adipose (AD)
  2. Left Ventral (LV)
  3. Right Ventral (RV)
  4. Adipose and Left Ventral (AL)
  5. Adipose and Right Ventral (AR)
Injury: physical injuries.
  1. Head - injury on the head or in the eye.
  2. Operculum - torn or folded gill cover.
  3. Popeye - eye protruding from socket.
  4. Body - injury on the rest of the body.
  5. Hemorrhage - blood present in fins or body tissues.
Disease: evidence of infections or parasites.

  1. Parasites - visible external parasites (leeches, Argulus, trematodes, etc.).
  2. Columnaris - yellow rimmed sores, ulcers, or open lesions on the body or fins.
  3. Fungus - fungal infection on the body surface (usually head or caudal fin).
  4. Bacterial Kidney Disease (BKD) - swollen belly usually most prevalent on subyearling (Fall) chinook.

  1. Bird: an injury inflicted by a bird (usually paired vertical scrapes).
  2. Other: an injury inflicted by a fish or mammal (punctures or abrasions caused by mouths, teeth, or claws).
  1. Partial Descaling: between 3 and 20% descaling on either (not both cumulatively) side of the fish. Areas of scale regeneration are NOT considered descaled.
  2. Descaled: >20% descaling on either side (as described in the normal sampling protocol).

Figure 2. Distinguishing characteristics of Chinook salmon (Oncorhynchus tshawytscha).
  1. Caudal fin forked, usually tipped in black.
  2. Parr marks are large, vertically oblong, wider then the intervening spaces, and
  3. centered on the lateral line.
  4. Anal fin wedge shaped, and usually not pigmented.
  5. Large, oblong spots on the back.
Figure 3. Distinguishing characteristics of Coho salmon (Oncorhynchus kisutch).
  1. Caudal fin forked, usually tipped in black.
  2. Parr marks are thin, vertical bars, narrower than the intervening spaces, and centered on the lateral line.
  3. The anal fin is sickle shaped, formed by anterior rays being longer than the rest and usually pigmented white.
  4. Small, round spots on the back, smaller than those on chinook.
Figure 4. Distinguishing characteristics of Sockeye salmon (Oncorhynchus nerka).
  1. Caudal fin forked, an generally clear or colorless.
  2. Parr marks are short, narrow bars located mostly above the lateral line.
  3. The body is delicate with a small head and silvery sides.
  4. Usually no spots on the back or fins.
Figure 5. Distinguishing characteristics of Steelhead (Oncorhynchus mykiss).
  1. Caudal fin not forked, with rounded lobes.
  2. Parr marks nearly round, centered on lateral line.
  3. Head more rounded than salmon when viewed from the top.
  4. Dorsal fin has distinct black pigmented spots. In general, more spotting on fish.
Similar physical characteristics of Spring and Fall Chinook
  1. Caudal fin forked, usually tipped in black.
  2. Parr marks are large, vertically oblong, wider then the intervening spaces, and centered on the lateral line.
  3. Anal fin rays are short, wedge shaped, and usually not pigmented.
  4. Large, oblong spots on the back.
Figure 6. Distinguishing characteristics of Spring Chinook (Oncorhynchus tshawytscha).
  1. Large eye and pupil.
  2. Larger, more blunt head.
  3. Leaner body shape.
  4. Longer, narrower caudal peduncle.
Figure 7. Distinguishing characteristics of Fall Chinook (Oncorhynchus tshawytscha).
  1. Smaller eye that tends to turn down in head.
  2. Deeper body, "football shape".
  3. Usually more silvery in appearance.