Pre-Restoration Habitat Use by Chinook Salmon in the 

Nisqually Estuary Using Otolith Analysis 

By Angela Lind-Null, Kimberly Larsen, and Reginald Reisenbichler 

Open-File Report 2008–1021 

U.S. Department of the Interior 

U.S. Geological Survey 
U.S. Department of the Interior 

DIRK KEMPTHORNE, Secretary 

U.S. Geological Survey 

Mark D. Myers, Director 

U.S. Geological Survey, Reston, Virginia: 2008 

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Suggested citation: 

Lind-Null, Angela, Larsen, Kimberly, and Reisenbichler, Reginald, 2008, Pre-restoration habitat use by 

Chinook Salmon in the Nisqually Estuary using otolith analysis: U.S. Geological Survey Open-File Report 

2008-1021, 13 p. 

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endorsement by the U.S. Government. 

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report. 

ii
iii

Contents 

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

Objectives ............................................................................................................................................................................2

Methods ...............................................................................................................................................................................2

Results ..................................................................................................................................................................................6

Discussion..........................................................................................................................................................................11

Acknowledgments............................................................................................................................................................13

References Cited ..............................................................................................................................................................13

Figures 

Figure 1: Nisqually field sampling sites..........................................................................................................................3

Figure 2: Relationship between fish fork length (mm) and otolith radial distance (microns)................................6

Figure 3: Representative sample of freshwater growth..............................................................................................7

Figure 4: The tidal delta check (TDCK) was seen on samples collected in the tidal delta in mid to late May 

(2004) and mid-June (2005) ...............................................................................................................................................8

Figure 5: The delta-flats check (DFCK) was seen on samples collected in the nearshore beginning in midJune and the delta flats in April.......................................................................................................................................9

Figure 6: Mean Increment width (microns) for freshwater, tidal delta, and delta flats/nearshore residence 

within each habitat...........................................................................................................................................................10

Figure 7: Relationship between the growth rate (mm/day) and the date the fish entered the tidal delta or 

delta flats/nearshore habitat..........................................................................................................................................11

Tables 

Table 1: Number of otoliths from unmarked juvenile Chinook collected in 2004 – 2006 and used for otolith 

analysis.................................................................................................................................................................................3

Table 2: Number of otoliths analyzed / processed.......................................................................................................4

Table 3: Number of unmarked hatchery samples separated from the catch. ........................................................4
Pre-Restoration Habitat Use by Chinook Salmon in 

the Nisqually Estuary Using Otolith Analysis 

By Angela Lind-Null, Kimberly Larsen, and Reginald Reisenbichler 

Introduction 

The Nisqually Fall Chinook population is one of 27 stocks in the Puget Sound 

evolutionarily significant unit listed as threatened under the federal Endangered Species Act. The 

preservation of the Nisqually delta ecosystem coupled with extensive restoration of approximately 

1,000 acres of diked estuarine habitat is identified as the highest priority action for the recovery of 

naturally spawning Nisqually River Fall Chinook salmon (Oncorhynchus tshawytscha) in the 

Nisqually Chinook Recovery Plan. 

In order to evaluate the response of Chinook salmon to restoration, a pre-restoration 

baseline of life history diversity and estuary utilization must be established. Otolith analysis has 

been proposed as a means to measure Chinook salmon life history diversity, growth, and residence 

in the Nisqually estuary. Over time, the information from the otolith analyses will be used to: (1) 

determine if estuary restoration actions cause changes to the population structure (i.e. frequency of 

the different life history trajectories) for Nisqually River Chinook, (2) compare pre and post 

restoration residence times and growth rates, and (3) suggest whether estuary restoration yields 

substantial benefits for Chinook salmon. 

Otoliths are calcium carbonate structures in the inner ear that grow in proportion to the 

overall growth of the fish. Daily growth increments can be measured so date and fish size at various 

habitat transitions can be back-calculated. Careful analysis of otolith microstructure can be used to 

determine the number of days that a fish resided in the estuary as a juvenile (increment counts), size 

at entrance to the estuary, size at egress, and the amount that the fish grew while in the estuary. 

Juvenile Chinook salmon can exhibit a variety of life history trajectories – some enter the sea (or 

Puget Sound) as fry, some rear in the estuary before entering the sea, and some rear in the river and 

then move rapidly through the estuary into the sea as smolts. 

The purpose of this study is to evaluate and use analysis of otolith microstructure as a tool 

for characterizing the importance of the estuary to Chinook salmon in the Nisqually River before 

and after restoration efforts at the Nisqually National Wildlife Refuge (NNWR). This tool is used to 

quantify changes in habitat use and help assess restoration benefits to the federally threatened 

Nisqually River Chinook salmon population. 

Analysis of otolith microstructure typically is superior to the alternative of traditional markrecapture methods. The latter are extremely expensive or inadequate in estuary habitats, typically 

are biased and substantially underestimate use, and do not directly reveal the importance or 

contribution to adult recruitment (i.e., they do not account for differential survival afterward in 

Puget Sound or the ocean). Analysis of otolith microstructure for these purposes, while new, is 

proving highly successful in a similar study that USGS and partners are conducting in the Skagit 

River estuary system located in northern Puget Sound. This work has been based on research by 

Neilson et al. (1985). We expect to use the Skagit River data as a reference for the before/after 

restoration comparison in the Nisqually River. 

1
Objectives 

Objective #1: Develop a Nisqually-specific signature of otolith microstructure growth patterns and 

checks that allow us to distinguish growth and residence of juvenile salmon in the estuary from 

growth in the river (upstream) and in Puget Sound (seaward). Evaluate between-year variation in 

these characters by comparing otoliths collected in 2004 with those collected in 2005. 

Objective #2: Determine whether distinct growth patterns on the otoliths of hatchery and wild 

salmon in the Nisqually River allow us to recognize unmarked hatchery fish and separate them 

from wild fish. 

Objective #3: Analyze the otoliths of returning adults in order to catalog the juvenile life-history 

trajectories of these “successful” fish and provide a preliminary estimate for the proportions and 

numbers of wild and hatchery adults that reared in the delta and estuary as juveniles. 

Objective #4: Describe the relationship between juvenile salmon size or date of entry to the estuary 

with the fish’s growth rate or residence time in the estuary. 

Methods 

Unmarked and marked juvenile Chinook salmon were collected by the Nisqually tribe and 

U.S. Fish and Wildlife Service – NNWR in March through October of 2004 and February through 

October of 2005 from various sites within the Nisqually River mainstem, tidal delta, nearshore, and 

associated habitats (Table 1). No Chinook were caught in the nearshore or EEM (Animal fyke trap) 

catch during February of 2005. The fish were collected by beach seining in the following distinct 

habitat zones (Cowardin et al. 1979; Figure 1): 

1. Freshwater (FW) – forested slow water habitat on the mainstem Nisqually River without tidal 

influence. 

2. Forested Riverine Tidal (FRT) – riparian forest, mud/silt substrate, and tidal influence. 

3. Emergent Forested Transition (EFT) – scrub/shrub and marsh vegetation, mud/silt substrate, 

and tidal influence. 

4. Estuarine Emergent Marsh (EEM) – low and high salt marsh vegetation, mud substrate, and full 

tidal influence. 

5. Delta Flats (DF) – sparse to no vegetation, mud and/or gravel/cobble substrate, and large tidal 

fluctuations. 

6. Nearshore (NS) – areas outside of Nisqually tidal delta, vegetation and substrate variable. 

7. Pocket Estuary (PE) – sand spit enclosed estuary with salt marsh vegetation, sand and mud 

substrate, and forested bluffs. 

A few sites within the EEM habitat were sampled with fyke nets. Each fish was euthanized and 

measured for length and weight. The fish were preserved in alcohol and sent to USGS where the 

sagittal otoliths of unmarked fish were extracted, sectioned, and polished according to the Western 

Fisheries Research Center’s (WFRC) standard protocols. 

2
Table 1: Number of otoliths from unmarked juvenile Chinook collected in 2004 – 2006 and used for 

otolith analysis. Additional fish were collected in 2005 and 2006 but not listed here. March April May June July August September October TOTAL

2004 FRESHWATER 10 20 10 11 0 0 6 1 58

FRT 17 18 3 7 0 1 0 0 46

EFT 2 1 9 9 0 0 0 0 21

EEM 7 0 40 44 17 0 0 0 108

NEARSHORE 000200 0 02

DELTA FLATS 0 13 3 17 3 0 0 0 36

POCKET ESTUARY 030000 0 03

2005 EEM (Animal Fyke Trap) 1 10 12 11 10 4 0 0 48

NEARSHORE 002510 0 08

2006 NEARSHORE 0 1 13 1 2 2 0 0 19

TOTAL 37 66 92 107 33 7 6 1 349

3

 Figure 1: Nisqually field sampling sites. 
A total of 167 juvenile Chinook salmon were collected in 2004 directly from the various 

South Sound hatcheries less than two weeks prior to hatchery releases for determination of unique 

patterns specific to individual hatcheries. An average of 15 fish per hatchery were sacrificed and 

the otoliths of at least 8 fish from select hatcheries were processed. These particular hatcheries 

corresponded to “high incidence” hatchery populations composing at least 5% of the CWT catch 

for this study in 2004 (shown in italics): Clear Creek 44.6%, Kalama 28.0%, White River 6.5%, 

Garrison/Chambers Creek 5.8%, Voights Creek 5.8%, Lost CWT 5.0%, Soos Creek 1.4%, 

Tumwater 2.2%, and Clark’s Creek 0.7%. 

In 2004, a total of 274 pairs of otoliths were collected from unmarked fish. All fish otoliths 

(one from each pair) were processed and sorted as “high incidence” hatchery or wild fish (Tables 2 

and 3). Samples identified as “high incidence” were not analyzed. If the sample was not obviously 

hatchery or wild, the fish was categorized as “unknown origin” and was not analyzed further. Fish 

from the pocket estuary also were not analyzed due to small sample size (n=3). A total of 97 fish 

were identified as hatchery, 119 as wild, and 58 as unknown origin. A total of 97 samples were 

analyzed out of the 119 available wild fish. Some samples were not suitable for analysis because 

of: (i) presence of vaterite (a morph of the calcium carbonate structure), (ii) poor initial quality, (iii) 

uneven microstructural growth along the radial axis or (iv) processing error. 

Table 2: Number of otoliths analyzed / processed. With the exception of the 2005 Animal fyke trap, 

the number analyzed does not include unmarked hatchery fish separated from the catch. 

March April May June July August September October TOTAL

2004 FRESHWATER 4 / 10 12 / 19 4 / 10 2 / 10 0 / 0 0 / 0 0 / 6 0 / 1 22 / 56

FRT 8 / 17 10 / 17 1 / 3 2 / 7 0 / 0 1 / 1 0 / 0 0 / 0 22 / 45

EFT 1 / 1 1 / 1 2 / 9 1 / 9 0 / 0 0 / 0 0 / 0 0 / 0 5 / 20

EEM 5 / 7 0 / 0 11 / 36 10 / 44 9 / 17 0 / 0 0 / 0 0 / 0 35 / 104

NEARSHORE 0 / 0 0 / 0 0 / 0 1 / 2 0 / 0 0 / 0 0 / 0 0 / 0 1 / 2

DELTA FLATS 0 / 0 5 / 13 1 / 3 6 / 17 0 / 3 0 / 0 0 / 0 0 / 0 12 / 36

POCKET ESTUARY 0 / 0 0 / 3 0 / 0 0 / 0 0 / 0 0 / 0 0 / 0 0 / 0 0 / 3

2005 EEM (Animal Fyke Trap) 1 / 1 7 / 10 11 / 11 7 / 9 7 / 10 4 / 4 0 / 0 0 / 0 37 / 45

NEARSHORE 0 / 0 0 / 0 0 / 2 1 / 5 1 / 1 0 / 0 0 / 0 0 / 0 2 / 8

2006 NEARSHORE 0 / 0 0 / 1 4 / 13 1 / 1 0 / 2 0 / 2 0 / 0 0 / 0 5 / 19

TOTAL 19 / 36 30 / 64 33 / 87 25 / 104 17 / 33 5 / 7 0 / 6 0 / 1 141 / 338

Table 3: Number of unmarked hatchery samples separated from the catch. 

March April May June July August September October TOTAL

2004 FRESHWATER 0 0 6 7 0 0 5 1 19

FRT 111500 0 08

EFT 0 0 5 5 0 0 0 0 10

EEM 1 0 14 24 5 0 0 0 44

DELTA FLATS 0 5 1 8 2 0 0 0 16

NEARSHORE 000000 0 00

2005 NEARSHORE 002400 0 06

EEM (Animal Fyke Trap) 003230 0 08

2006 NEARSHORE 0 1 7 0 0 2 0 0 10

TOTAL 2 2 38 47 8 2 5 1 121 

4
In 2005, a total of 333 pairs of otoliths were collected from unmarked fish. The majority of 

samples from the 2005 collection were not analyzed due to limited funding in the current funding 

contract. At the request of our cooperators and project officer we processed otoliths from one 

particular site in the EEM habitat (Animal fyke trap) (Table 2). A total of 48 pairs of otoliths were 

collected from unmarked fish at the Animal fyke site. One otolith from each pair was processed 

and sorted as to hatchery or wild. A total of 8 fish were identified as hatchery, 32 as wild, and 8 as 

unknown origin. Both hatchery and wild fish were analyzed for a total of 37 out of 45 suitable 

otoliths, however only wild fish were included in the analyses. 

The nearshore collection was supplemented with samples collected in 2005 (n=8) and 2006 

(n=19) due to small sample size in 2004 (n=2) (Table 1). A total of 16 fish were identified as 

hatchery, 10 as wild, and 3 as unknown origin. A total of 8 samples were analyzed out of the 10 

available wild fish. 

Adult samples were collected from the fishery and spawning grounds by the Nisqually tribe 

in 2005 and 2006. In 2005, a total of 176 samples were collected from the fishery and 125 were 

collected from the spawning grounds. In 2006, a total of 189 samples were collected from the 

fishery and 34 were collected from the spawning grounds. No adult samples were processed or 

analyzed due to limited funding under the current funding contract. Collections are archived for 

future funding opportunities.

Fish collected from freshwater showed a pattern which was used as a reference pattern on 

the otoliths. This reference pattern did not have any “checks” beyond the recognizable emergence 

and first feed checks. Checks are generally referred to as a consistently prominent mark or pattern 

on the otolith which interrupts the normal sequence of otolith deposition (Campana 1983). Each 

increment was interpreted as daily growth for the fish. Otoliths from fish collected in all other 

habitat types were visually analyzed for additional patterns, checks, or increased growth beyond the 

identifiers observed on the freshwater residence portion of the otoliths. 

Daily growth increments and checks in the otolith microstructure were measured with the 

aid of a digital imaging system, Image-Pro. We selected a standardized radial axis for 

measurements at 85 ± 5 degrees ventral of the longitudinal axis passing through an identifiable and 

preferred nucleus. Distances along the radial axis and individual increment widths between checks 

or increase in growth representing change in habitat, were recorded for each fish. 

Growth rates (mm/day) in the tidal delta were calculated from lengths based on the FraserLee method (Murphy and Willis 1996): 

aS

S

aL

L i

c

c

i + − =

where 

Li is the back-calculated length of the fish at the beginning of the tidal delta check, 

Lc is the length of the fish at capture, is the radius of the otolith at capture, Sc

Si is the radius of the otolith at the beginning of the tidal delta check, and 

a is the intercept from the overall regression of capture fork length verses otolith radius 

 (Figure 2). 

Average growth rate and mean increment widths (MIW) were determined for all habitat types. 

Residence time and fork lengths upon entry to the tidal delta and delta flats/nearshore habitat zones 

were also calculated. 

5
y = 154.56x - 0.3533

R2

 = 0.802

20

40

60

80

100

120

0.2 0.3 0.4 0.5 0.6 0.7

Otolith Radius (mm)

Fish FL at capture (mm)

Figure 2: Relationship between fish fork length (mm) and otolith radial distance (microns). 

Results 

Otolith microstructure pattern varied little over the years in 2004 – 2006; however the 

timing (i.e. month) of check formation did vary. After first feed, the increments on all otoliths 

became more legible and consistent across the radial axis (Figure 3). An interruption in the 

microstructure pattern, designated as a tidal delta check (TDCK), was detected on samples 

collected within tidal delta habitats EFT and EEM, indicating the fish’s transition from freshwater 

to the estuarine habitats (Figure 4). Increments were consistently narrow across the radial axis until 

the tidal delta check appeared where consistently wider increments indicated increased growth. No 

tidal delta check or increased growth was seen on otoliths from fish collected in the freshwater or 

the upper most tidal delta habitat (FRT). 

In 2004, a tidal delta check was not observed on samples collected in March from EFT and 

EEM habitats. Insufficient sample sizes in April precluded analysis of the tidal delta check. In mid 

to late May, the tidal delta check appeared on samples from EFT and EEM habitats. In 2005, the 

tidal delta check first appeared on samples collected in the EFT and EEM in early June, but was 

barely detectable on some samples in late May (2 out of 8). 

6
In addition to the tidal delta check, an additional interruption was seen on otoliths collected 

in the nearshore habitat beginning in June and in the delta flats habitat in April. We called this 

check a delta-flats check (DFCK). It indicated the fish’s transition from estuarine habitat to the 

nearshore habitat (Figure 5). This check looked identical to the nearshore check located on Chinook 

in the Skagit River system (Beamer et al. 2000). Due to classification of sites, we called this check 

a delta-flats check instead of a nearshore check. The check was abbreviated in 

some samples (3 out of 11), possibly due to the fish being caught immediately upon entrance into 

the habitat. Insufficient samples were available to determine whether a delta-flats check was visible 

on samples collected in the nearshore in March or April. The number of samples containing a deltaflats check that were collected in the nearshore habitat were considerably low (1 out of 8). 

With samples analyzed from multiple years, a one-way ANOVA was run to test for 

differences between years among tidal delta and freshwater MIW and growth rates. A significant 

difference occurred for MIW in the freshwater portion of the otolith for Animal fyke samples 

(P<.05). Therefore, the 2005 Animal fyke trap samples were excluded from the freshwater portion 

of the analysis. 

No difference was visually observed in the microstructure pattern between EFT and EEM. 

To further validate this observation, a one-way ANOVA was run to test for significant differences 

between EFT and EEM. No significant differences occurred in growth rate or MIW (P>0.05) and 

therefore the data were combined and classified as “tidal delta.” FRT was not included as part of 

the tidal delta habitat for analysis because visually the microstructure pattern did not differ from 

freshwater samples nor was an additional check or increased growth ever observed. 

 

 40x objective 

Figure 3: Representative sample of freshwater growth. The letters below represent: 

H = hatch, E = emergence, FF = first feed, FW = freshwater residence. 

7
 

 20x objective

 

 

 40x objective 

Figure 4: The tidal delta check (TDCK) was seen on samples collected in the tidal delta in mid to late 

May (2004) and mid-June (2005). The check was bold and prominent consisting of two thin dark 

bands encompassing two wide bright bands containing a thick dark band between them. This 

sequence was then repeated following approximately 1 increment. Beyond the tidal delta check, 

increments were consistently wider indicating increased growth. The letters below represent: 

H = hatch, E = emergence, FF = first feed, FW = freshwater residence, TDCK = tidal delta check, and 

D = tidal delta residence. 

 

8
 

 10x objective

 

 40x objective 

Figure 5: The delta-flats check (DFCK) was seen on samples collected in the nearshore beginning in 

mid-June and the delta flats in April. The check was bold and prominent consisting of two thin dark 

bands encompassing two wide bright bands containing a thick dark band between them. Beyond 

the delta-flats check, increments were consistently wider indicating increased growth. The letters 

below represent: H = hatch, E = emergence, FF = first feed, FW = freshwater residence, TDCK = tidal 

delta check, D = tidal delta residence, DFCK = delta-flats check, and N = delta flats/nearshore 

residence. 

9
We tested for differences in MIW in freshwater and tidal delta portions of the otoliths 

(Figure 6). One-way ANOVA showed a significant difference (P<0.05) across habitats. On 

average, delta flats habitat had the lowest freshwater and tidal delta MIW. Overall, the MIW of the 

freshwater portion of all otolith samples was lowest followed by the tidal delta and nearshore 

habitats, respectively. 

The equivalent results for growth rate were that the freshwater growth rates (mean= 0.42 

mm/day) were lower compared to the tidal delta growth rates for fish residing in the tidal delta 

(mean = 0.57 mm/day), nearshore (mean = 0.57 mm/day), and delta flats (mean = 0.66 mm/day) 

habitats, with a 36% increase in growth from freshwater habitat to tidal delta habitat. The delta 

flats/nearshore growth rate for fish caught in the delta flats was the same as the tidal delta growth 

rate. No significant difference was found between tidal delta and delta flat/nearshore growth rates 

(one-way ANOVA, P>0.05). 

The average fork length upon entry to the tidal delta was 72.8 mm. Fish caught in the tidal 

delta spent an average of 16 days with a minimum residence time of 10 days and a maximum of 35. 

These fish samples provided a minimum estimate of residence because the fish were sacrificed 

prior to entering the Sound. Evaluation of those fish caught in the delta flats and nearshore habitats 

exhibited an average residence time of 21 days in the tidal delta (n = 10). This value represents a 

truer estimate of residence time in the tidal delta, however the sample size was quite small. Fish 

caught in the delta flats were on average 60.2 mm when they entered the tidal delta and 69.5 mm 

upon exit, whereas fish caught in the nearshore were 73.1 mm upon entrance to the tidal delta. A 

positive relationship existed between the growth rate and the date the fish entered the tidal delta or 

nearshore (Figure 7). This could not be explained by a difference in size at entrance into the tidal 

delta and nearshore habitats. 

2.00

2.50

3.00

3.50

4.00

4.50

5.00

012 3 4 5 6

Location of Capture 

Mean Increment Width (microns)

Freshwater

Tidal Delta

Delta Flats/Nearshore

(22) (22)

(46)

(40)

(7)

(12)

(12)

(8)

(8)

(1)

FW FRT Tidal 

Delta

Delta 

Flats 

Nearshore 

Figure 6: Mean Increment width (microns) for freshwater, tidal delta, and delta flats/nearshore 

residence within each habitat. Two samples collected in the delta flats were excluded from the 

delta flats/nearshore portion of the MIW analysis because residence time was only one day. The 

number of samples are represented in parentheses. Error bars represent ±1 standard deviation. 

10
0.25

0.40

0.55

0.70

0.85

1.00

19-Mar 8-Apr 28-Apr 18-May 7-Jun 27-Jun 17-Jul 6-Aug 26-Aug

Date Entered Tidal Delta or Nearshore

 Growth Rate (mm/day)

Tidal Delta

Delta Flats/Nearshore

R2 = 0.325

Figure 7: Relationship between the growth rate (mm/day) and the date the fish entered the tidal 

delta or delta flats/nearshore habitat. 

Discussion 

Hatchery Chinook salmon vastly outnumber wild salmon in the Nisqually River; however 

distinct microstructure patterns unique to each hatchery allowed us to recognize and separate 

unmarked hatchery fish from wild. The majority of unmarked hatchery fish were seen in natural 

habitats during May and June subsequent to hatchery release. Few hatchery strays were seen in 

March and April prior to release. 

We characterized a Nisqually-specific signature of otolith microstructure growth patterns 

and checks for wild fish that allowed us to distinguish entry into the tidal delta and nearshore 

habitats. However, we were not able to distinguish between all habitat types prior to mid-May 

(2004) or early-June (2005) when the tidal delta check first appeared. The tidal delta check was not 

visible on freshwater or FRT samples regardless of when they were caught nor on samples 

collected in March in the EEM and EFT. We do not know whether a tidal delta check occurs in 

April because we had an insufficient sample size (n=1). Samples collected in March displayed few 

(x = 7) increments following the freshwater pattern which indicated that the fish were collected at 

or very early after entrance to the habitat and may not have had sufficient time to develop a visible 

check. This could be clarified by substantially increasing early season (March) sample size or by 

the addition of otolith microchemical analysis of Sr:Ca ratios (Fowler et al. 1995) in the 

hypothesized freshwater/tidal delta transition zone. 

The delta-flats check first appeared in early June in nearshore samples and in April in delta 

flats samples. It is unclear whether a delta-flats check appeared in nearshore samples in April due 

to limited sample size (n=1). 

11
We saw no visual difference in the microstructure pattern between otoliths collected in 

2004, 2005, and 2006. However, analysis revealed differences in MIW for freshwater residence and 

when the tidal delta check first appeared between the 2004 and 2005 Animal fyke samples. 

The majority of samples from the 2005 collection have not been analyzed to date due to limited 

funding. We focused our efforts for this reporting period on one sampling year (2004) rather than 

divide the effort across two years, lowering the sample size further and possibly missing potential 

characterization of some life history types. 

Mean increment widths generally increased as the fish moved from freshwater to the 

nearshore habitats. The magnitude of the difference in MIW between the tidal delta and nearshore 

habitats probably is underestimated and may be an artifact of low sample size compounded by the 

brief time spent in the nearshore habitat for a large proportion of the fish. 

Overall, the growth rate increased as the fish migrated from one habitat to another. Fish 

were growing faster (36%) in the tidal delta compared to freshwater, but this increase is 

significantly less than that seen in the Skagit River (U.S. Geological Survey, unpublished data). 

Our analysis revealed that fish grew at the same rate in the nearshore as in the tidal delta. This may 

be due to small sample size or that the majority of fish were caught soon after arrival (mean number 

of days residing before capture = 8; 8 out of 10 residing less than 10 days) in the nearshore habitat. 

Funds and allocated time were insufficient to accomplish the analysis of adults during the 

current funding period. As previously mentioned, it is important to establish baseline information 

of life history trajectories from the juveniles, and then proceed to examining that portion of the 

adult otolith corresponding to the juvenile stage. Our resources were exhausted in working with the 

juveniles so we were not able to proceed to the adult samples. Otoliths collected from carcasses in 

Fall of 2006 were the first adult collections to correspond to the 2004 collection of juvenile 

outmigrants (i.e. 2003 brood year) in the estuary. Sampling will be attempted through 2010 to 

exhaust possible adult returns from 2003 – 2006 brood years. 

Our results suggest that otolith microstructure analysis can be a valuable tool to establishing 

a baseline for use of the Nisqually River estuary habitats by juvenile Chinook salmon under 

existing conditions. However, this study provides limited information due to small samples sizes in 

some months, and only looks at contributions of wild-origin fish. The sample sizes contributed to 

uncertainty about whether Nisqually salmon deposit various habitat transition checks on the otoliths 

in all months. This uncertainty occurs for both tidal delta checks and delta-flats checks. Collection 

and analysis of additional fish especially in tidal delta and nearshore habitat zones should be 

addressed. Furthermore, these collections should occur over several years to allow adequate 

evaluation of inter-annual variation in microstructure growth patterns and checks, and may reveal 

additional life history types. Analysis of otolith microchemistry in conjunction with microstructure 

would provide an additional avenue for identifying early entry (March and April) into the tidal 

delta and perhaps the nearshore. Of course, further work should include analysis of adults because 

they show the proportions and numbers of adults that reared in the estuary as juveniles. 

12
13

Acknowledgments 

This research was a collaborative effort between the U.S. Fish and Wildlife Service –

Nisqually National Wildlife Refuge (NNWR), Ducks Unlimited, Nisqually Indian Tribe, and the 

U.S. Geological Survey. A special thanks to Sayre Hodgson, Chris Ellings, Jeanette Dorner, Jean 

Takekawa, Marian Bailey, Jennifer Cutler, Nano Perez, Craig Smith, John Kerwin, Bill St. Jean, 

NNWR volunteers, and various South Sound hatcheries. 

The use of trade, firm, or corporation names in this publication is for the information and 

convenience of the reader. Such use does not constitute an official endorsement or approval by the 

United States Department of Interior or the United States Geological Survey of any product or 

service to the exclusion of others that may be suitable. 

References Cited 

Beamer, E.M., J.C. Sartori, and K.A. Larsen. 2000. Skagit Chinook life history study progress 

report number 3 [online]. Available from http://www.skagitcoop.org/documents.html [accessed 

18 September 2007]. 

Campana, S.E. 1983. Calcium deposition and otolith check formation during periods of stress in 

coho salmon, Oncorhynchus kisutch. Comp. Biochem. Physiol. 75A(2): 215-220 

Cowardin, L.M., V. Carter, F.C. Golet, and E.T. LaRoe. 1979. Classification of wetlands and 

deepwater habitat of the United States. Department of the Interior, Fish and Wildlife Service, 

Washington, D.C. 79 pp. 

Fowler, A.J., S.E. Campana, and S.R. Thorrold. 1995. Experimental assessment of the effect of 

temperature and salinity on elemental composition of otoliths using solution-based ICPMS. Can. 

J. Fish. Aquat. Sci. 52: 1421-1430. 

Murphy, B.R., and D.W. Willis, editors. 1996. Fisheries techniques, 2nd edition. American 

Fisheries Society, Bethesda, Maryland. 

Neilson, J.D., G.H. Geen, and D. Bottom. 1985. Estuarine growth of juvenile Chinook salmon 

(Oncorhynchus tshawytscha) as inferred from otolith microstructure. Can. J. Fish. Aquat. Sci. 42: 

899-908.