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Juvenile Chinook salmon assessment of the Nooksack estuary and Bellingham Bay
nearshore
Eric Beamer, Skagit River System CooperativeCorreigh Greene, NOAA Fisheries NWFSC
Alan Chapman and Evelyn Brown, Lummi Natural Resources
January 2015
Talk Outline:
• Some context to understand where this assessment fits with other research
• The system, the fish inputs, our data• The 2014 results• System level density dependence• Bioenergetics• Some preliminary take homes & to do’s
Skagit Chinook Abundance Trend
Recovery Plan adopted 2005
Skagit River Summer Chinookspawner-recruit curve
Doom & gloom!
We’re recovering!(pat ourselves on the back)
The true long-term trend
Example of the MANYthings you need to know
how they work
Example of the MANY thingsthat become “actions”
Recovery Plan Elements:
Example of TOOL thatputs it all together
Emergent Fry
Spawning Adults
Eggs
Juveniles Adults
Juveniles Adults
Redd
Freshwater
Tidal Delta
Nearshore
Ocean
Adults
Example of life stages & some functionsin the Skagit Chinook Recovery Plan Tool
y = 2583.40x + 7013.24R2 = 0.37
0
2000
4000
6000
8000
10000
12000
14000
16000
18000
-1.50 -1.00 -0.50 0.00 0.50 1.00 1.50 2.00
SST PDO Index (2-yrs prior to return)
Stee
lhea
d Re
turn
-1.5
-1.0
-0.5
0.0
0.5
1.0
1.5
2.0
1978
1980
1982
1984
1986
1988
1990
1992
1994
1996
1998
2000
2002
2004
2006
2008
PDO
Inde
x (A
nnua
l Mea
n)
+Fluctuation in ocean survival
Density dependence in FW, Estuary, & some nearshore habitats
y = 0.1284e-0.0446x
R2 = 0.97
0%
4%
8%
12%
16%
20%
0 20 40 60 80
Flood reccurence interval (years)
Eg
g t
o m
igra
nt
fry s
urv
ival
0
20,000
40,000
60,000
80,000
100,000
120,000
140,000
160,000
1970 1980 1990 2000 2010 2020
Peak Q (cfs)
Peak Q (cfs)+Fluctuation in egg to fry survival due to flooding
Skagit Wild PopulationsSkagit Hatchery
Populations
•2014: 24 sites beach seined Feb – Oct•Link 2014 effort to past LNR efforts
Where do (could) the fish come from?
• Nooksack River outmigrants– 100Ks of migrants per
year– LNR smolt trap estimates
• Nearby Rivers– Skagit
• Ind. Tribs in B’ham Bay– Whatcom Creek
• Within system and nearby hatcheries– 4-6 million per year
Where do (could) the fish come from?
Genetic results for wild juveniles 2003 (Rice et al. 2011); 2008-9 (Beamer and Fresh 2012) and 2014 (this project)
In 2014:• Collected 334 fish for genetic
analysis• Waiting for results (Salish Sea
Marine Survival Study, WDFW)
0%
25%
50%
75%
100%
Feb Apr Jun July
% G
enet
ic R
epor
ting
Gro
up
Month in 2008
Unmarked juvenile Chinook salmon in Nooksack Tidal Delta, 2008-9
Whidbey Basin
South Sound / Hood Canal Fall
Nooksack Spring
0
1,000,000
2,000,000
3,000,000
4,000,000
5,000,000
6,000,000
7,000,000
Chinook Hatchery Releases (marked)
Samish River
Nooksack River
Lummi Bay
0100,000200,000300,000400,000500,000600,000700,000800,000
Chinook Hatchery Releases (unmarked)
Samish River
Nooksack River
Lummi Bay
Nooksack Tidal DeltaBellingham Bay
2,0022,0
032,0
042,0
052,0
062,0
072,0
082,0
092,0
102,0
112,0
122,0
132,0
142,0
15
YEAR
0
1
2
3
4
5
6
Log
unm
arke
d Ch
inoo
k de
nsity
Our full dataset• 12 year dataset (2003-2014)
– 2,130 beach seine sets– Over 5,000 Chinook salmon
caught
• Annual variability– Habitat– Outmigrants– Floods– Connectivity (logjam)
• 2014 has the best spatial and temporal coverage
– 856 beach seine sets– 1,010 Chinook caught– > 60,000 fish caught– 58 different taxa
0
50
100
150
200
250
300
2 3 4 5 6 7 8 9 10
Fish
/hec
tare
bea
ch se
ined
Month
Unmarked juvenile Chinook 2014
Bellingham Bay Shoreline
Nooksack tidal delta
0
50
100
150
200
250
300
2 3 4 5 6 7 8 9 10
Fish
/hec
tare
bea
ch se
ined
Month
Marked juvenile Chinook 2014
Bellingham Bay Shoreline
Nooksack tidal delta
• Seasonal curve present
• Wild fish arrive earlier than hatchery fish
• B’ham Bay shoreline sites had more fish the Nooksack estuary sites in 2014
050
100150200250300350400450500
2 3 4 5 6 7 8 9 10
Fish
/hec
tare
bea
ch se
ined
Month
Unmarked juvenile Chinook, Bellingham Bay Shoreline 2014
Lagoons & FW inputs
Other shorelines
050
100150200250300350400450500
2 3 4 5 6 7 8 9 10
Fish
/hec
tare
bea
ch se
ined
Month
Marked juvenile Chinook, Bellingham Bay Shoreline 2014
Lagoons & FW inputs
Other shorelines
Within B’ham Bay:• Shoreline sites
that are protected from wave energy and have freshwater inputs had more wild fish the in 2014
1 2 3 4 5 6 7 8 9MONTH
0
50
100
150Fo
rk len
gth
(mm
)
Bellingham Bay, Marked
1 2 3 4 5 6 7 8 9MONTH
0
50
100
150
Fork
lengt
h (m
m)
Bellingham Bay, Unmarked
1 2 3 4 5 6 7 8 9MONTH
0
50
100
150
Fork
lengt
h (m
m)
Nooksack Tidal Delta, Marked
1 2 3 4 5 6 7 8 9MONTH
0
50
100
150
Fork
lengt
h (m
m)
Nooksack Tidal Delta, Unmarked
Arrive small and earlyArrive large and late
1 2 3 4 5 6 7 8 9MONTH
0
50
100
150
Fork
leng
th (m
m)
Lagoon & FW input, Marked
1 2 3 4 5 6 7 8 9MONTH
0
50
100
150
Fork
leng
th (m
m)
Lagoon & FW input, Unmarked
1 2 3 4 5 6 7 8 9MONTH
0
50
100
150
Fork
leng
th (m
m)
Other shorelines, Marked
1 2 3 4 5 6 7 8 9MONTH
0
50
100
150
Fork
leng
th (m
m)
Other shorelines, Unmarked
Arrive large and late Arrive small and early
1
3
4
3
2
24
Habitat Connectivity (how easily can fish find available habitat?)
•Landscape scale•Function of distance traveled and complexity of pathway
– delta channel branching– in bay – current direction
Nooksack Estuary & Bellingham Bay Shoreline:pathways & connectivity
0.1
1
10
100
1000
0 0.02 0.04 0.06 0.08 0.1 0.12
Aver
age
dens
ity (f
ish/h
a)
Landscape Connectivity
Nooksack Estuary & Bellingham Bay Shoreline:influence of connectivity on unmarked juvenile Chinook
R² = 0.907
0.1
1
10
100
1000
0 0.02 0.04 0.06 0.08 0.1 0.12
Aver
age
dens
ity (f
ish/h
a)
Landscape Connectivity
Connected EstuaryDisconnected EstuaryUpper Silver Creek
1
10
100
1000
0 0.01 0.02 0.03 0.04 0.05 0.06
Aver
age
Dens
ity (f
ish/h
a)
Landscape Connectivity
Open nearshoreOpen nearshore w FWProtected/Lagoon w FW
Nooksack Estuary & Bellingham Bay Shoreline:influence of connectivity on unmarked juvenile Chinook
Low DO; few fish overall;mostly low DO tolerant species
Difference in unmarked juvenile Chinook density in 2014 when you account for season and connectivity
Significant Pairings p-Value
Connected Estuary < Open nearshore 0.007
Connected Estuary < Open nearshore w FW 0.001
Connected Estuary < Protected/Lagoon w FW 0.000
Disconnected Estuary < Protected/Lagoon w FW 0.000
Open nearshore < Protected/Lagoon w FW 0.000
Avg.
Den
sity
(fish
/ha)
Fork
Len
gth
(mm
)
40
45
50
55
60
0 1 2 3 4 5 6 7
0
10
20
30
0 500 1000 1500 2000 2500 3000Delta density (fish/ha)
(fi
shda
ys/h
a/10
00)
Outmigrants (millions)
0
1,000
2,000
3,000
0 1 2 3 4 5 6 7
A
B
C
System Level Density
Dependence:
Wild Skagit Chinook Example
Photo by Todd Bennett
How are the fish doing?
Using bioenergetics to evaluate potential benefits of different habitats
Assumption: All types of estuarine environments are equally beneficial to fish
Reality: estuarine environments vary in• Temperature patterns over time• Prey abundance patterns• Prey energetic quality• Predator density
Goal: test the assumption using bioenergetics models
Jan Feb Mar Apr May Jun
Weight at estuary entry
Weight when leaving estuary
Size
of f
ish
(g)
What bioenergetics modeling can tell us
FW-influencedlagoons
Forestedriverine tidal
Estuarineemergent
marsh
Month
WARNING: RESULTS ARE HIGHLY PRELIMINARY
Preliminary Take Homes:• Nooksack delta and Bellingham Bay shoreline habitats are
consistently used by juvenile Chinook salmon• Within system (Nooksack) and out of System (Whidbey Basin)
juvenile Chinook are present. • In B’ham Bay, protected nearshore and lagoon habitats with
freshwater are important early in the year– Fish are present long enough to be influenced by good and bad (food,
toxins, etc)• Progeny from local spawners (Whatcom Creek) likely have a (minor
but detectable) influence on juvenile Chinook distribution within B’ham Bay.
• Within the system, landscape Connectivity is important– Linkage between estuary connectivity and WRIA 1 nearshore projects
ideas beyond B’ham Bay (north). Likely not any value to Nooksack Chinook, but might be valuable if connectivity is improved
• Silver Creek and upper estuary connected to Silver Creek– Investigate DO further– Improve river and tidal flushing; improve watershed inputs
Some Major To Do’s:• Update Nooksack River juvenile Chinook
outmigration estimates by life history type (migrating fry, parr, & yearling)
• Update system density dependence analyses with better outmigration results & include effects of Whatcom Creek
• Update bioenergetics with better density (outmigrant) data
• Update with 2014 genetic origin result• Incorporate results into “tool”• Apply results to salmon recovery planning
efforts in WRIA 1
AcknowledgementsPeople Involved• City of Bellingham: Renee LaCroix and Sara Brooke Benjamin• WCC: Liz Anderson, Andy Wargo, Lyle Skaar, Erin Thorson,
Catherine Harris, Nicole Masurat, Brett Wilson, Nelson Lee, Magnus Borsini, Maggie Counihan, Ben Kunesh, & Michael Vaughan
• Lummi Tribe Natural Resources: Mike MacKay, Ralph Phair, Jesse Cooper, Michael Williams, Ben LaClair, Tony George, Rudy Adams, & Guy Jones,
• Skagit River System Cooperative: Bruce Brown, Josh Demma, Rich Henderson, Karen Wolf, & Greg Hood
Funding and Collaboration• Primary funding from City of Bellingham• Collaboration and inkind services: Salish Sea Marine Survival
Project (LLTK, UW, NOAA, WDFW, others) and ESRP Learning Objective Project: Chinook Density Dependence (SRSC & NOAA)
