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Estimating the Capacity of the Klamath Basin to Rear Coho

Technical Memorandum #5

Nicklaus K. AckermanThomas E. Nickelson

Boedicea P. FoxRon Sutton

Steven P. Cramer


Model Reaches


HLFM Version 6.1

Habitat Limiting Factors Model


• Estimate parr and smolt capacity based on aquatic inventory data.

• Determine the life stage habitat that limits smolt production.

Purpose of Model


Coho salmon density by habitat type (fish/m2)

Habitat Type Spring Summer Winter

Cascade 0 0.24 0

Rapid 0.6 0.14 0.01

Riffle 1.2 0.12 0.01

Glide 1.81 0.77 0.12

Trench pool 0.99 1.79 0.15

Plunge pool 0.84 1.51 0.28

Lateral scour pool 1.29 1.74 0.35

Mid-channel scour pool 1.29 1.74 0.35

Dammed pool 2.56 1.84 0.56

Alcove 5.75 0.92 1.84

Beaver pond 2.56 1.84 1.84

Backwater pool 5.75 1.18 0.58

Spawning gravel 2500 eggs/redd / 3 m2/redd = 833 eggs/m2

Seasonal Habitat Use


Table 1. Example of application of the coho salmon habitat limiting factors model (HLFM Version 5.0).Stream: East Fork Lobster Creek

Stream inventories conducted summer 1990 and winter 1990-91.

Stream length: 3.8 km

Seasonal capacity from below Survivlal Potential smolts (Capacity * Survival)

Spawning 1,330,000 eggs 0.32 425,600

Spring 32,373 fry 0.46 14,900

Summer 13,876 parr 0.72 10,000

Winter 4,576 presmolts 0.90 4,118 Limiting habitat and Smolt capacity

Stream area (m2) by habitat

habitat type from inventories Life stage capacity by habitat (Area * Density)

Habitat type Summer Winter Spawning Spring Summer Winter

Cascades 39 296 - 9 -

Rapids 4,398 10,307 6,184 616 103

Riffles 1,847 6,223 7,468 222 62

Glides 2,966 1,911 3,459 2,284 229

Trench pools 62 - - 111 -

Plunge pools 667 1,167 980 1,007 327

Lateral scour pools 4,346 5,526 7,129 7,562 1,934 Mid-channel scour pools - - - - - Dammed pools 168 1,048 2,683 309 587 Alcoves - - - - - Beaver Ponds 671 558 1,428 1,235 1,027 Backwater pools 442 529 3,042 522 307 Spawning gravel 1,596 1,330,000

Total Capacity 1,330,000 32,373 13,876 4,576


Winter Habitat Data Missing

Winter parr/km = 0.19S + 14.51C + 10.47P -1,

Where: W = winter parr/km.

S = summer parr/km as estimated by HLFM.

C = average active channel width of the reach (m).

P = percent of stream area in alcoves and beaver ponds.


Estimating Summer Parr Capacity

EF Lobster Cr. 1988–92 Br.

0

5,000

10,000

15,000

20,000

0 10 20 30 40 50

Female spawners/km

Nu

mb

er

of

sum

me

r p

arr


Estimating Smolt Capacity

EF Lobster 88–92 Broods

0

500

1,000

1,500

2,000

2,500

3,000

3,500

4,000

4,500

0 10 20 30 40 50 60 70 80 90 100 110 120

Female spawners per km

Sm

olt

s p

rod

uce

d


Parr Summer Rearing Densities (parr/m2) in HLFM Version 6.1

Stream segment wetted width (m)

Habitat Type <10 10–<20 20–<30 >30

Cascades 0.24 0 0 0

Rapids 0.14 0.02 0 0

Riffles 0.12 0.01 0 0

Glides 0.77 0.09 0.02 0

Trench Pools 1.79 0.21 0.05 0.01

Plunge Pools 1.51 0.18 0.04 0.01

Lateral Scour Pools 1.74 0.21 0.05 0.01

Mid-channel Scour Pools 1.74 0.21 0.05 0.01

Dam Pools 1.84 0.22 0.05 0.01

Alcoves 0.92 0.92 0.92 0.92

Beaver Ponds 1.84 1.84 1.84 1.84

Backwaters 1.18 1.18 1.18 1.18


Estimating Parr Capacity of the Mainstem


0

5

10

15

20

25

30

35

0102030405060708090100110120130140150160170180190

Mean

Max

Min

0102030405060708090100110120130140150160170180190

5

25

15

10

30

20

35

River mile

Tem

per

atu

re (

°C)

Simulated water temperatures downstream of IGD:

Mean of July 3–9, 2001


0

5

10

15

20

25

30

35

0102030405060708090100110120130140150160170180190

Mean

Max

Min

0102030405060708090100110120130140150160170180190

5

25

15

10

30

20

35

River mile

Tem

per

atu

re (

°C)

Refuge Dependent

HabitatFlow

TemperatureDependent


Estimating Capacity in IGD–Shasta ReachHypothetical Scenario

Week Mean Q Mean T Q Scalar T Scalar K

1-Jul 2,200 18.0 1.98 0.88 13,447

8-Jul 2,000 19.0 1.96 0.73 11,045

15-Jul 1,800 19.5 1.88 0.63 9,061

22-Jul 1,600 20.0 1.79 0.51 7,002

29-Jul 1,400 20.5 1.67 0.39 4,979

5-Aug 1,200 21.0 1.48 0.28 3,182

12-Aug 1,000 22.0 1.19 0.13 1,159

19-Aug 950 21.0 1.11 0.28 2,391

26-Aug 900 21.0 1.04 0.28 2,235

2-Sep 850 20.0 0.97 0.51 3,776

9-Sep 800 20.0 0.89 0.51 3,493

16-Sep 750 19.0 0.82 0.73 4,625

23-Sep 800 18.0 0.89 0.88 6,055

K = min (Base*ScalarQ*ScalarT)


Habitat and Capacity IGD–Shasta Reach at ~830cfs

ChannelUnit Type Length

Sum of Unit Capacity Parr/m Parr/m2

PRIMARY POOL 23,053 3,180 0.14 0.01

RAPID 2,308 31 0.01 0.00

RIFFLE 33,010 303 0.01 0.00

SIDE CHANNEL GLIDE 214 14 0.07 0.77

POOL 4,246 3,623 0.85 0.12

RIFFLE 8,920 252 0.03 0.00

SPLIT POOL 474 235 0.50 0.08

RIFFLE 3,465 68 0.02 0.00

TOTAL 75,690 7,705 0.13 0.01


Effect of Temperature on Capacity:Insect Drift Related to Velocity,Uvas Creek (Smith & Li 1982)

50

30

25

10 50 80

Velocity (cm sec-1)

Re

lati

ve

ins

ect

dri

ft (M

ayfl

y eq

uiv

alen

ts h

-1)

20 40 60 70 90


Effect of Temperature on Capacity:Focal Velocity vs. Temperature,Rainbow Trout (Smith & Li 1982)

50

40

30

20

10

10 15 20

Water temperature (oC)

Fo

cal p

oin

t v

elo

cit

y (

cm

se

c-1)


Effect of Temperature on Capacity:Juvenile Coho Rearing and Temperature

– Oregon Coast

MWAT (oC)

12-14 14.1-16 16.1-18 18.1-20 20.1-22 22.1-24 24.1+

Mea

n c

oh

o d

ensi

ty (

no

. / m

2 )

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

1

5

11

12

10

4 1


Effect of Temperature on Capacity:Capacity Scaling Function

0.0

0.2

0.4

0.6

0.8

1.0

12 14 16 18 20 22 24 26

Mean Weekly Temperature(oC)

Cap

acit

yC

ap

acit

y S

ca

lar


Effect of Flow on Capacity:USGS/USFWS Study Sites


Effect of Flow on Capacity:Velocity Suitability Curve

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0

Velocity (ft/s)

Hab

itat

su

itab

ilit

y in

dex

'

Trinity River

Klamath ThermalRefugia

IMF Composite


Effect of Flow on Capacity:Depth Suitability Curve

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

0.0 1.0 2.0 3.0 4.0 5.0 6.0

Depth (ft)

Hab

itat

Su

itab

ilit

y In

dex

' Trinity River

Klamath ThermalRefugia

IMF Composite


Effect of Flow on Capacity:Suitability indices by cover type

Cover Type WDF Study Trinity Coho IMFNo cover — — 0.05

Filamentous Algae — — 0.05

Non-emergent rooted aquatic vegetation 1.00a 0.38b 0.70

Grass/sedge/herbaceous plant 0.10c — 0.10

aTermed in this study: submerged vegetation.bTermed in this study: aquatic vegetation.c Termed in this study: grasses/bushes on bank.


Flow/WUA RelationshipIGD–Shasta River

0

20

40

60

80

100

0 1,000 2,000 3,000 4,000

Mainstem flow (cfs)

% M

axim

um

WU

A

Main Channel

Split Channel

Side Channel

QSc = 0.46*QSMc+0.50*QSSc+0.04*QSSp


Flow Scalar for Capacity

Mainstem flow (cfs)

500 1000 1500 2000 2500 3000 3500 4000

Cap

acit

y sc

alar

0.8

0.9

1.0

1.1

1.2

1.3

1.4

1.5


Hypothetical Scenario—Flow and Temperature Combined Effect

Week

July 1July 8

July 15

July 22

July 29Aug 5

Aug 12Aug 19

Aug 26Sep 2

Sep 9Sep 16

Sep 23

Cap

acit

y

0

2000

4000

6000

8000

10000

12000

14000

16000

Flo

w (

CF

S)

600

800

1000

1200

1400

1600

1800

2000

2200

2400 Capacity Mean Q

Tem

per

atu

re (

oC

)

17

18

19

20

21

22

23

Mean Temp


Estimating Smolt Capacity of the Mainstem

Below the Shasta


• Identify location of tributary confluence

Estimating Refuge Capacity

• If tributary enters at transition between 2 units (i.e. the top or bottom of a unit) sum capacity of each unit.

• If tributary enters a riffle/rapid, include unit below, unless unit below is a riffle/rapid and unit above is a pool, then include the pool.

• If tributary enters a pool, include unit above unless another pool is below.


Estimating Refuge Capacity


Summer Capacity of Thermal Refugia by Reach and Population

Population Model reach # Refugia Parr capacityUpper Klamath Klamath

Mainstem 10 0

Klamath Mainstem 2

3 186

Klamath Mainstem 3

6 659

Subtotal 9 845

Mid Klamath Klamath Mainstem 4

33 7,834

Klamath Mainstem 5

12 2,302

Subtotal 45 10,136

Lower Klamath Klamath Mainstem 6

7 1,761

Subtotal 7 1,761

Total 61 12,742


Estimating Smolt Capacity of Tributaries


Km

of

Hab

itat

0

100

200

300

400

500

600

700

800

Lower Klamath Middle

Klamath

Upper Klamath

MS

Trib MS

Trib MS

Trib

Lower

Trin

ity

SF Trin

ity

Upper T

rinity

Salm

onSco

tt

Shasta

W/out To Mask

W/To Mask

Length of Habitat by Historic Population & Percentage with the 21.5°C Temperature Mask


Mid Klamath

Distribution &Temperature Mask


Lower

Kla

mat

h

Mid

dle K

lam

ath

Upper K

lam

ath

Lower

Trin

ity

SF Trin

ity

Upper T

rinity

Salm

onSco

tt

Shasta

Km

of

hab

itat

0

100

200

300

400

500

600

700

800

Surveyed

Unsurveyed

Habitat Length Surveyed by Historic Population Compared to Total Habitat Available

without the 21.5°C Mask


Estimating Stream Smolt Capacity

• Estimate summer parr capacity and winter smolt capacity for surveyed reaches using HLFM.

• Extrapolate capacities from surveyed reaches to unsurveyed reaches.

• Where possible, identify streams with high temperatures and apply temperature scalar and 45% survival to summer parr capacity to reduce smolt capacity.


Extrapolation from Surveyed Reaches to Unsurveyed Reaches

Survey data available & ACW of surveyed and unsurveyed reaches similar (> or < 10m):

–Apply the capacity of the surveyed reach to the unsurveyed reaches.

–If multiple reaches surveyed, apply average capacities of surveyed reaches.


Extrapolation from Surveyed Reaches to Unsurveyed Reaches

Survey data unavailable or ACW of surveyed and unsurveyed reaches dissimilar:

–Apply average capacity of surveyed reaches of similar size for the historic population.


Average Capacities of Surveyed Reaches by Historic Population

ACW <10m ACW >10m

Population Parr/km Smolts/km Parr/km Smolts/km

Lower Klamath 3,200 580 3,200 850

Middle Klamath 3,050 490 3,050 820

Upper Klamath 1,250 350 3,650 800

Trinity 2,500 530 4,250 850

Salmon 2,650 550 2,650 840

Scott 1,400 320 2,800 780


Mid Klamath

Distribution &Surveyed Reaches


Predicted Smolt Capacity by Historic Population

Sm

olt

ca

pa

cit

y (

in t

ho

us

an

ds

)

0

100

200

300

400

500

600

700

800


• Capacity in most of mainstem is limited to thermal refugia.

Conclusions:

• Between IGD and Shasta River, capacity can be influenced by flow management.

• Juvenile capacity of the entire basin is roughly 1.7 million smolts.

• IP Database used to define distribution appears liberal in assigning potential habitat.

• Capacity estimates of tributaries could be improved with:– Better understanding of potential distribution

– Updated stream surveys with a regionally consistent protocol

– Winter stream habitat surveys

– Expanded temperature monitoring


Flow Scalar for Capacity

Mainstem Flow (cfs)

0 1000 2000 3000 4000 5000

Cap

acity

Sca

lar

0.6

0.8

1.0

1.2

1.4

1.6

CFS ApproachHardy and Addley 2006 - Reach Level at R-Ranch

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