to: sue madsen, skagit fisheries enhancement group...

To: Sue Madsen, Skagit Fisheries Enhancement Group

From: Eric Beamer, Skagit River System Cooperative

Date: December 18, 2014

Subject: McElroy Slough beach seine summary results for unmarked juvenile Chinook

salmon: 2014

Sites and Effort

Fifty-four beach seine sets were made in McElroy Slough from February through June, 2014

(Table 1). Sites up- and downstream of the tidegate site were sampled (Figure 1) and are

consistent with sites sampled in previous years. Sampling frequency was once in February and

twice per month in March through June. The sampling period is designed to capture the entire

period when juvenile Chinook salmon use estuarine habitats in Puget Sound.

In 2014, per a recommendation after the 2011 beach seining effort, we installed data loggers up

and downstream of the tidegate in order to measure variables influenced by tidegate operation:

Water surface elevation (WSE) when the tidegate doors close,

WSE up and downstream of the tidegate,

water temperature up and downstream of the tidegate, and

water salinity up and downstream of the tidegate.

Table 1. Number of beach seine sets made by sampling date and position relative to the tidegate in

McElroy Slough, 2014.

Sampling Date downstream of tidegate upstream of tidegate

26-Feb-14 3 3

10-Mar-14 3 3

26-Mar-14 3 3

08-Apr-14 3 3

23-Apr-14 3 3

06-May-14 3 3

22-May-14 3 3

04-Jun-14 3 3

20-Jun-14 3 3

Grand Total 27 27

Figure 1. Location of beach seine sampling sites in McElroy Slough. Yellow dots are located downstream

of the tidegate site. White triangles are located upstream of the tidegate site.

Fish Assemblage

We caught over 5,000 fish representing eleven different species in 2014 (Table 2).

Table 2. Total catch by species at McElroy Slough sites February 26 through June 20, 2014. Mean catch

per unit effort is in parentheses.

Strata:

Downstream

of tidegate

Upstream

of tidegate

Salmonid species: Chinook salmon, unmarked subyearling

Oncorhynchus tshawytscha 19 (0.70) 1 (0.04)

Coho salmon, unmarked subyearling

Oncorhynchus kisutch 155 (5.74) 1,279 (47.37)

Coho salmon, unmarked yearling

Oncorhynchus kisutch 7 (0.26) 6 (0.26)

Pink salmon, subyearling

Oncorhynchus gorbuscha 1 (0.04) 1 (0.04)

Chum salmon, subyearling

Oncorhynchus keta 401 (14.85) 206 (7.36)

Cutthroat trout, yearling

Oncorhynchus clarki 2 (0.08) 30 (1.11)

Total salmonids: 585 1,523

Other fish species:

Three-spine stickleback

Gasterosteus aculeatus 1,453 (53.81) 934 (34.59)

Prickly sculpin

Cottus asper 3 (0.11) 86 (3.19)

Pacific staghorn sculpin

Leptocottus armatus 734 (27.19) 57(2.11)

Other or unknown cottid 0 (0.00) 2 (0.07)

Starry flounder

Platichthys stellatus 4 (0.15) 0 (0.00)

Shiner surf perch

Cymatogaster aggregata 2 (0.07) 1 (0.04)

Total other fish species: 2,196 1,080

Total fish catch: 2,781 2,603

Unmarked Juvenile Chinook Salmon

Results

1. Juvenile Chinook salmon were caught up- and downstream of the tidegate each of the

five years of sampling at McElroy Slough (Figures 2 and 3).

2. Juvenile Chinook abundance varied by year. Years 2006 and 2007 were low compared to

years 2009 and 2011. Year 2014 is in between the low (2006 & 2007) and high (2009 &

2011) years (Figures 2 and 3).

3. Juvenile Chinook use of McElroy Slough in 2014 was seasonal, peaking in March

(Figure 2), which was earlier than the April or May of previous years (Figure 3).

4. Timing of unmarked juvenile Chinook is best shown in 2011 and 2014, years with a

longer season of sampling. The February though June sampling period is more certain to

capture the entire seasonal use period of juvenile Chinook salmon.

5. Based on the graphical results shown in Figures 2 and 3, juvenile unmarked Chinook

density is consistently lower upstream of the tidegate than downstream.

6. Juvenile unmarked Chinook salmon cumulative density upstream of the tidegate over the

sampling seasons ranged from less than one-tenth up to one-third of the seasonal

cumulative Chinook density downstream of the tidegate. Year specific results are:

22% Year 2006

31% Year 2007

11% Year 2009

33% Year 2011

6% Year 2014

Figure 2. Monthly average unmarked juvenile Chinook salmon density up- and downstream of the

tidegate site within McElroy Slough, 2014. Error bars are standard error. No sampling was done in the

months of January and July. Juvenile Chinook salmon were caught upstream of the tidegate only in May.

Figure 3. Monthly average unmarked juvenile Chinook salmon density up- and downstream of the

tidegate site within McElroy Slough in previous years. Error bars are standard error. Where “0.0” is

shown, beach seining occurred but no unmarked juvenile Chinook salmon was caught (graph from 2011

McElroy Fish Monitoring Technical Memo from Eric Beamer to Skagit Fisheries Enhancement Group).

McElroy Slough, 2007

0.0 0.00.0 0.00

10

20

30

40

50

2 3 4 5 6

Month

Un

mark

ed

ju

ven

ile C

hin

oo

k

per

hecta

re

Downstream TG

Upstream TG

no sampling

in Feb & Mar


0.00

100

200

300

400

500

2 3 4 5 6

Month

Un

mark

ed

ju

ven

ile C

hin

oo

k

per

hecta

re

Downstream TG

Upstream TG

no sampling

in Feb & Mar


0.0 0.0 0.0

0

100

200

300

400

500

2 3 4 5 6

Month

Un

mark

ed

ju

ven

ile C

hin

oo

k

per

hecta

re

Downstream TG

Upstream TG


0.00.0 0.00

10

20

30

40

50

2 3 4 5 6

Month

Un

mark

ed

ju

ven

ile C

hin

oo

k

per

hecta

re

Downstream TG

Upstream TG

no sampling

in Feb & Mar

Discussion

1. We are assuming juvenile Chinook salmon are not natal to watersheds associated with

McElroy Slough, thus any juvenile Chinook found upstream of the tidegate must have

traveled upstream through the tidegate as a juvenile. This is a reasonable assumption

based on spawner survey data and spot electrofishing results for freshwater areas

upstream of the tidegate, which have not documented juvenile Chinook (but have

documented other species). This assumption is also supported by previous years’ beach

seine data, which found marked Chinook salmon present (at low levels) upstream of the

tidegate. Hatchery Chinook salmon are not reared or released in watersheds associated

with McElroy Slough.

2. Accepting the assumption above, it is good to know that juvenile Chinook are able to

move upstream through the tidegate and occupy tidal habitat upstream. We can conclude

the tidegate does allow for upstream passage of juvenile Chinook salmon. However, it is

unknown whether results observed from 2006 through 2014 represent an improvement

over the old tidegate because there are no “before tidegate replacement” fish monitoring

data.

3. Without “before tidegate replacement” and “reference site” monitoring data, it is difficult

to determine whether cumulative seasonal juvenile Chinook densities of one-tenth to one-

third (bullet 6 in Results) are “good” or “bad” juvenile Chinook salmon results for this

tidegate site. Juvenile Chinook density is clearly lower upstream of the tidegate (Figures

2 and 3) than downstream. Reference site tidal channels show the reverse relationship

(i.e., more juvenile Chinook salmon upstream than downstream) (Figure 11 from Greene

et al. 2012), so it is reasonable to conclude the tidegate, as currently installed and

operated, is a partial impediment to upstream juvenile Chinook salmon movement.

4. Tidegate operations that increase the time doors are open on flooding tide stage would

likely improve juvenile Chinook salmon access to habitat upstream of the tidegate.

Tidegate door closure results (below) could be used to determine whether the self-

regulating tidegate setting could be changed so the doors closed at a higher WSE, thus

leaving the doors open longer on flood tides.

Water surface elevation and tidegate door closures

The tidegate doors closed 184 times during the period when data loggers were present. Door

closures occurred at downstream water elevations ranging from 3.5 to 7.5 ft NAVD88 (Figure 4).

Doors closed most often at elevations of 5 to 6 ft NAVD88.

Figure 4. Histogram of the number of tidegate door closures by water surface elevation (WSE) on the

downstream side of the McElroy Slough tidegate.

Temperature, salinity, and WSE

Water temperature in McElroy Slough increased steadily from February through June and was

warmer downstream than upstream of the tidegate starting in March and continuing through June

(the end of our sampling) (Figure 5). Water salinity in McElroy Slough was low and stable from

February through April and then increased steadily through June (Figure 6). Salinity was

consistently higher downstream of the tidegate than upstream. Water surface elevation did not

fluctuate seasonally and averaged higher downstream of the tidegate than upstream (Figure 7).

Figure 8 (a, b & c) illustrates that tides and tidegate operation (whether or not the doors are

closed) influence water temperature, salinity, and WSE up- and downstream of the tidegate.

1 3

17

74

46

28

13

2

0

10

20

30

40

50

60

70

80

Nu

mb

er o

f O

bse

rvat

ion

s

WSE NAVD88 feet

Water Surface Elevation at Downstream of Tidegate

when doors close

Downstream of Tidegate

Figure 5. Monthly average water temperature up- and downstream of the McElroy Slough tidegate in

2014. DSTG = downstream of tidegate, USTG = upstream of tidegate. Error bars are standard error.

Figure 6. Monthly average water salinity up- and downstream of the McElroy Slough tidegate in 2014.

DSTG = downstream of tidegate, USTG = upstream of tidegate. Error bars are standard error.

USTG water tempDSTG water temp

1 2 3 4 5 6 7 8

MONTH

-10

0

10

20

30D

egre

es C

USTG salinityDSTG salinity

1 2 3 4 5 6 7 8

MONTH

0

10

20

30

PP

T

Figure 7. Monthly average water surface elevation (WSE) up and downstream of the McElroy Slough

tidegate in 2014. DSTG = downstream of tidegate, USTG = upstream of tidegate. Error bars are standard

error.

USTG WSEDSTG WSE

1 2 3 4 5 6 7 8

MONTH

3

4

5

6

7

8

9

10W

SE

in ft (N

AV

D88)

Figure 8a. Water temperature (left panels), salinity (middle panels), and elevation (right panels) results from data loggers located up- and

downstream of the McElroy Slough tidegate in 2014. Each row of graphs represents a one-month period. Units are: temperature – degrees C;

salinity – PPT; water surface elevation – NAVD88 ft. DSTG = downstream of tidegate, USTG = upstream of tidegate. Graphs on this page are for

the months of February and March.

-1

0

1

2

3

4

5

6

7

8

9

Water Bottom Tempearature at McElroy Slough, February 2014

DSTG water temp

USTG water temp

3

5

7

9

11

13

15

17

Water Bottom Tempearature at McElroy Slough, March 2014

DSTG water temp

USTG water temp

0

5

10

15

20

25

30

Water Bottom Salinity at McElroy Slough, February 2014

DSTG salinity

USTG salinity

0

5

10

15

20

25

30Water Bottom Salinity at McElroy Slough, March 2014

DSTG salinity

USTG salinity

3

4

5

6

7

8

9

10

Water Surace Elevation at McElroy Slough, March 2014

DSTG WSE NAVD88 ft

USTG WSE NAVD88 ft

3

4

5

6

7

8

9

10

Water Surace Elevation at McElroy Slough, February 2014

DSTG WSE NAVD88 ft

USTG WSE NAVD88 ft

Figure 8b. Water temperature (left panels), salinity (middle panels), and elevation (right panels) results from data loggers located up- and



the months of April and May.

4

9

14

19

24

29

Water Bottom Tempearature at McElroy Slough, April 2014

DSTG water temp

USTG water temp

4

9

14

19

24

29

Water Bottom Tempearature at McElroy Slough, May 2014

DSTG water temp

USTG water temp

logger buried 5/5 to 5/22

0

5

10

15

20

25

30

35

Water Bottom Salinity at McElroy Slough, April 2014

DSTG salinity

USTG salinity

0

5

10

15

20

25

30

Water Bottom Salinity at McElroy Slough, May 2014

DSTG salinity

USTG salinity

logger buried 5/5 to 5/22

2

3

4

5

6

7

8

9

10

Water Surace Elevation at McElroy Slough, May 2014

(logger/WSE corrected on 5/22)

DSTG WSE NAVD88 ft

USTG WSE NAVD88 ft

3

4

5

6

7

8

9

10

Water Surace Elevation at McElroy Slough, April 2014

DSTG WSE NAVD88 ft

USTG WSE NAVD88 ft

Figure 8c. Water temperature (left panels), salinity (middle panels), and elevation (right panels) results from data loggers located up- and



the month of June.

4

9

14

19

24

29

Water Bottom Tempearature at McElroy Slough June 2014

DSTG water temp

USTG water temp

0

5

10

15

20

25

30

Water Bottom Salinity at McElroy Slough, June 2014

DSTG salinity

USTG salinity

3

4

5

6

7

8

9

10

Water Surace Elevation at McElroy Slough, June 2014

(logger/WSE corrected on 5/22)

DSTG WSE NAVD88 ft

USTG WSE NAVD88 ft

References

Greene, C., J. Hall, E. Beamer, R. Henderson, and B. Brown. 2012. Biological and physical

effects of "fish-friendly" tide gates: Final report for the Washington State Recreation and

Conservation Office, January 2012. National Marine Fisheries Service, Northwest Fisheries

Science Center, Seattle.

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