Table 3. Comparison of net upstream combined Snake and Clearwater move-
ment (lam/day) above and below the confluence. Only fish with
net upstream movement and tracks of less than six days duration
are represented.

Average net upstream Average net upstream
movement below confluence movement above confluence

1970 km/day 10.71 15.30
95% Confidence
Interval 5 80-22-22 - ~~ 15.62 6 .26---------- 24.34
1971 km/day 16.65 10.32

95% Confidence .
Interval 9. Wy nnnnnnnn-- 23.36 3.06---------- 17.58

54


DEPTH (m)

DEPTH (m)

DEPTH (m)

South
shore

13 August 1970

Figure 10,

[

0
AY T T
ear A248 Wa
1
2b
3b
25 August 1970
° 7
1345

anh ee

10 October 1970

Temperature (C) profiles 6,1 km downstream from the
Snake-Clearwater confluence,

20.


RESEARCH REPORTING SERIES

Research reports of the Office of Research and
Monitoring, Environmental Protection Agency, have
been grouped into five series. These five broad
categories were established to facilitate further
development and application of environmental
technology. Elimination of traditional grouping
was consciously planned to foster technology
transfer and a maximum interface in related
fields. The five series are:

1. Environmental Health Effects Research
2. Environmental Protection Technology
3. Ecological Research

4, Environmental Monitoring

5. Socioeconomic Environmental Studies

This report has been assigned to the ECOLOGICAL
RESEARCH series. This series describes research
on the effects of pollution on humans, plant and
animal species, and materials. Problems are
assessed for their long- and short-term
influences. Investigations include formaticn,
transport, and pathway studies to determine the
fate of pollutants and their effects. This work
provides the technical basis for setting standards
to minimize undesirable changes in living
organisms in the aquatic, terrestrial and
atmospheric environments.


July 1-2

July 22-24

Aug. 11-13

Aug. 26-28

Oct. 14-16

Nov. 11-16

Dec. 16-19

Figure A-la,

Clearwater

River
<+— Fl Directi
Ly pt ow Bareceson / - Arorth
7.32 + 7. “aT 7. 87 7.87
- - - 7.22
7432, ,- 7.41, 8.05 8.05
Snake River South
yp _/.L
- 7.96 7.95
80 498 pag 7
pa hol
8.00 8.13 7.92
8.30 7.83 8.31 8.17 8.41
Ly 6 1 8.38 7.86
a _Ael
- - 8.13
- - - 8.14 -
ay pt 1 -_ 8.25,
1 n 1. 1 Av,
ary) 8.22 7.69
- - 8.13 8.00 68.20
py p 8 OF 1 8,358.27
ty n 4 nl A, rol
* 8.03 7.80 7.41
8.10 8.03 7.74 8.09 8.27
sy p89 . 8,00_ 8.20
Ly pt . hy. WA
7.86 8. aT) 6.48
- - - 8.00 8.21
sy pS 4 1 8.24 8.06
35 10 5 0

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE

shore

shore

Cross-channel pH patterns in the Snake and Clearwater
Rivers during adult steelhead migration, 1969.

63


Clearwater

River
+— Flow Direction J Jr Shore
7) f
“0 0 0
Sept 2-8] 0 iv)
py, 04 ) 1 0 n
a Snake River South Shore
Loy 1 L n / 0 VA
ee O° 0 0
Sept. 8-10] 0 0
py pO it n oO. 1
7b
jo, 1 n too /
“0 . 0 0
Sept. 21-24] 0 0
1, 9 4 0 n 0 n
V/
L 4 L 1 / - VA
“0 0 0
Oct. 8-22 | . -
Ly pO it] 1 0. !
1 aT 1 1 n / - /
(0) 0 (0) :
Nov. 4-H]. -
ni oO. 0) l ie) L
—/
7 | 1 1 hs VA
“0 0 0
Dec. I-11] 0 0
ry, 0 4 id) n i} n
35 10 5 °

Kilometers Below Snake-Clearwater Confluence

Figure A-4c. Cross-channel carbon dioxide patterns (mg/L free C05)
in the Snake and Clearwater Rivers during adult
steelhead migration, 1971.

74


SECTION IV
EXPERIMENTAL DESIGN

The fundamental working hypothesis as posed in the initial proposal in

1967 was: (1) “Lower Granite Dam has no effect upon the migrational

behavior of adult steelhead trout." Hypothesis (1) can only be tested

in the post-impoundment phase by study of steelhead behavior through
the slack water of Lower Granite Reservoir.

Comparison with pre-impoundment behavior (the control phase) should

delineate impoundment effects upon steelhead migration. Because of the

addition of dams in the Snake and Clearwater systems, and changes in
amounts and treatments of industrial and sewage effluents into the pool
area since 1967, there is really no true "control" to this pre-post
impoundment comparison, The best available "control" or approximation
to it, is the Lower Granite pool area before impoundment.

We will reject H, after impoundment if:

1. Steelhead travel time through the study area increases or decreases.

2. General migration pathways significantly change.

3. General pathways after impoundment are not significantly different,
but avoidance reactions or temporary stoppages occur at specific
points due to factors such as:

a. low dissolved oxygen

b. high Kraft mill effluent

ce. high or low pH

d, thermal layering

e. presence of hydrogen sulfide
f£. high ammonia levels

g. reverse flows at the Snake-Clearwater confluence

4. Timing of the steelhead run changes, i.e. the peak of the run shifts
forward or backward in time.

If we reject H, for one or more of the above reasons, then the altered
steelhead behavior is a result of impoundment or altered water quality,
or a combination of both. We will compare migration patterns as de-
tailed in Figure 5,

1a


Clearwater

ver
oye —_— Flow Direction / frorth shore
July 1-2 - - - - -
4 1 f- ~ 1 = = 1
Snake River South shore
yp _f L
2 Te 89 112
July 22-24 107 1 117 12
y a fp _ 161 113, 3
aay an 1 1 Irol,
"92 87 99
Aug. 11-13 103 96 91 109 117
py, 97, 1 94 111
7}
ay 1 1 Jol.
"93 89 97
Aug. 26-28 103 94 89 107 110
pig 9 1 96 Jills
Lf p—t i 1 Jor,
82 106 93
Oct. 14-16 85 - 101 90 100
yy 8% 1 100 22 1
yp 1 1 Sol,
99 97 «107
Nov. 11-16 95 104 100 101
v » , 100 j 99101,
| 1 1 /os L
086 88 97
Dec. 16-19 - 37 90 33 97
p/h 1
35 74 — 10 5 o)

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE

Figure A-3a. Cross-channel oxygen saturation patterns (percent
saturation) in the Snake and Clearwater Rivers during
adult steelhead migration, 1969,

69


Mean water quality changes in the Snake River as a result of pollution
inputs, especially the Kraft effluent, in the immediate Lewiston area
were difficult to detect (Figure 14). In terms of toxic effects from
chemical loading, the Snake River was not greatly altered. In the
immediate 3 to 4 km below the confluence on the north shore or Clear-
water River side, gross changes in benthic periphyton and insect com-
munities were evident . . . diversity sharply dropped and "clean water
forms" gave way to chironomids and isopods on a matrix of filamentous
fungi. But none of the chemical parameters routinely measured showed
the free-flowing Snake River, when fully mixed and leaving the steelhead
tracking area, as obviously unsuitable for migrating salmonids. Mean
oxygen percent saturation levels were five percent lower leaving the
tracking area compared to river inflows (97.7% vs 103.7%). As reported
in other work on the lower Snake River (Falter and Funk 1971), this
decline in oxygen was the beginning of a slight oxygen sag which reached
minimum levels 30 to 50 km below the confluence. Any tendency for an
oxygen sag to develop, however, was so slight that on sunny days, the
"spiking" of photosynthesis by pollutants in the Lewiston area caused

a net oxygen increase in the area 5 to 50 km below the confluence.

Carbon dioxide was always low except for an increase to 7.8 mg/l just
below the confluence on the north shore. This increase usually was
found in the Kraft effluent plume before complete mixing occurred.

Total dissolved solids increased slightly in water leaving the tracking
area (mean TDS leaving study area = 169.3 mg/1), mostly because of the
mixing with the Kraft effluent which contained greater than 1000 mg/1
TDS.

Tannins, sulfates, and ammonia were sometimes good indicators of the
effluent plume, but once mixed with the river flow, these increases
were usually undetectable (Figure 14), Ammonia levels were higher above
than below the confluence because of ammonia inputs from cattle feed-
lots in the 15 miles upstream (Falter and Funk 1973).

Net increases were shown in the Pearl-Benson Index and total volatile
solids even after complete mixing and dilution (Figure 14), The chemi-
cal station 2.4 km below the confluence had the highest Pearl-Benson
Indexes and total volatile solids, indicating a major deflection of the
Clearwater River flow and effluent plume closer to the north shore at
this station.

STEELHEAD MIGRATION PATHS AND BEHAVIOR

General Patterns

The Snake River run of steelhead consists of two overlapping groups:
Group A (destined for the Salmon, Imaha, and Grand Ronde Rivers) enters

a7


Giea irwater
River

+— Flow Ore /. Los Shore

| 7 ae
“1.0 i 0
Sept.2-8 | -
1, fo, 10.0 \ 7.0
ad Snake River South Shore
bee 1 7, L
"7.0 2.0
Sept. 8-10 } -
L p.0 4 5.5 1 3.0 1
T}
1 Tf i n ARYA
"8.0 9.0 8.0
Sept. 21-24 | ~ 1.5
1,90 , 14.0 1 9.0 L
7 #
Loy pd 1 1 / VA
“4.0 5.0 - 14.0
Oct.8-22 | . 1.0
! ay fd. n 8.0 it 7.0 l
ya n 1 / VA
“10.0 6.0 7.0
Nov. 4-11] — -
Ly, 5.01 4.0 1 1.5 1
pol
Jy pal 1 L
2.0 6.0 23.0
Dec. ltl] _ .
y fr 04 5.0 1 6.0 n
7h 10 5 0

Kilometers Below Snake-Clearwater Confluence

Figure A-12c, Cross-channel Pearl-Benson Index patterns (mg/L Standard
Calcium Spent Sulfite Liquor Solids) in the Snake and
Clearwater Rivers during adult steelhead migration, 1971.

98


Fish No. 70-9 Aug.26-Aug.28 <4— Flow Direction

North Shore

Fish No. 70-10 Aug.26-Aug.28

© South Shore

VJ VL

Fish No. 70-11 Sept.9-Sept.14

I"

Fish No. 70-12 Sept.9-Sept.17

Man, |

Fish No. 70-13 Sept.10-Sept.12

ar

Fish No. 70-14 Sept.JO-Sept.I1

V 7 ON ee aw

Fish No, 70-15 Sept.26-Oct.4
Ey

N 7
n SN = = art n

\ 7 V

Kilometers Below Snake-Clearwater Confluence

Figure 16 (Continued). Adult steelhead migration paths in the Snake

River, Lower Granite pool area, 1970.

34


No.

A-la

A-1b

A-lc

A-2a

A-2b

A-2e

A-3a

A-3b

A-3c

A-4a

A-4b

SECTION IX

APPENDIX

Cross-channel pH patterns in the Snake and
Clearwater Rivers during adult steelhead
migration, 1969

Cross-channel pH patterns in the Snake and
Clearwater Rivers during adult steelhead
migration, 1970

Cross-channel pH patterns in the Snake and
Clearwater Rivers during adult steelhead
migration, 1971,

Cross-channel oxygen patterns (mg/1) in the Snake

and Clearwater Rivers during adult steelhead
migration, 1969

Cross-channel oxygen patterns (mg/1) in the Snake
and Clearwater Rivers during adult steelhead
migration, 1970

Cross~channel oxygen patterns (mg/1) in the Snake
and Clearwater Rivers during adult steelhead

migration, 1971

Cross~-channel oxygen saturation patterns (percent
saturation) in the Snake and Clearwater Rivers
during adult steelhead migration, 1969

Cross-channel oxygen saturation patterns (percent
saturation) in the Snake and Clearwater Rivers
during adult steelhead migration, 1970

Cross-channel oxygen saturation patterns (percent
saturation) in the Snake and Clearwater Rivers
during adult steelhead migration, 1971

Cross-channel carbon dioxide patterns (mg/1 free C09)

in the Snake and Clearwater Rivers during adult
steelhead migration, 1969

Cross-channel carbon dioxide patterns (mg/l free C02)

in the Snake and Clearwater Rivers during adult
steelhead migration, 1970

59

Page
63

64

65

66

67

68

69

70

71

72

73


Fish No. 69-1 Aug.20 4—Flow Direction North Shore

\ Release Point
n 1

4
15 10 5 © South Shore

Fish No. 69-2 Aug.2l

Fish No. 69-3 Sept.25
Ve

Fish No. 69-4 Sept.25
a

Fish No. 69-5 Oct.3-Oct.30

Fish No. 69-6 Oct.4-Oct.5

v\

Fish No. 69-7 Oct.7-Nov.25

Kilometers Below Snake-Clearwater Confluence

Figure 15. Adult steelhead migration paths in the Snake River, Lower
Granite pool area, 1369.

30


No.

A-12a

A-12b

A-12c

A-13a

A-13b

A-13c

APPENDIX - (Continued)

Cross-~channel Pearl-Benson Index patterns (mg/1
Standard Calcium Spent Sulfite Liquor Solids) in
the Snake and Clearwater Rivers during adult
steelhead migration, 1969

Cross-channel Pearl-Benson Index patterns (mg/l
Standard Calcium Spent Sulfite Liquor Solids) in
the Snake and Clearwater Rivers during adult
steelhead migration, 1970

Cross-channel Pearl-Benson Index patterns (mg/1
Standard Calcium Spent Sulfite Liquor Solids) in
the Snake and Clearwater Rivers during adult
steelhead migration, 1971

Cross-channel total volatile matter patterns (mg/1
total volatile matter) in the Snake and Clearwater
Rivers during adult steelhead migration, 1969

Cross-channel total volatile matter patterns (mg/1
total volatile matter) in the Snake and Clearwater
Rivers during adult steelhead migration, 1970

Cross-channel total volatile matter patterns (mg/1

total volatile matter) in the Snake and Clearwater
Rivers during adult steelhead migration, 1971

42

97

98

99

100

101


Clearwater

ver
: 4—\ Flow Direction /- orth shore
July 1-2 - - - - -
4 of b- = 1 = =~ L
Snake River South shore
yp . _/.L
- - 33
July 22-24 29 22 - 32 22
typ 1 = 37 4
pa Sil
"51 61 44
Aug. 11-13 - 40 38 52 41
yp 53 3150 4
yy 1 1 1 Jal
"35 42 30
Aug. 26-28 - 33 41 39 48
ay p50 ! 26 504
Oct, 14-16 - - - -
ay) . 1 J's /
98 77 «68
Nov. 11-16 169 «6114 109 52 100
12/9 1 126 95 4
typ \ 1 ts VA
7" 82 83 37
Dec, 16-19 90 - - 79 48
i, 78 9 1 82.102 4
35° 10 5 0

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE

Figure A-13a. Cross-channel Total Volatile Matter patterns (mg/L Total
Volatile Matter) in the Snake and Clearwater Rivers
during adult steelhead migration, 1969.

99


Fish No. 7!-22 Oct.8-Oct.lO — Flow Direction North Shore
—T Release Point

1 1
15 10 5 0 South Shore

Fish No. 71-23 Oct.9

Fish No. 71-24 Oct.10-Oct.l!

Fish No. 71-25 Oct.l0-Oct.l4

== ~ ----
mA Ueeeeoot
x _——--"
n ~s= n 1

Fish No. 71-26 Oct.16-Oct.24

AA NZ ne

Fish No. 71-27 Oct.16-Oct.23

Fish No. 71-28 Oct.I7-Octl9 .
n 1 1 n

Kilometers Below Snake-Clearwater Confluence

Figure 17 (Continued), Adult steelhead migration paths in the
Snake River, Lower Granite pool area, 1971.

40


q— Flow Direction
1

i j~

Clearwater

River
Irs Iroren shore

1 1
154 142 138
Sept. 4-18 114 125
rp 124, 122 1 163 A
‘ Snake River South
bgt 1 1 Js /
Oct. 15 “230 215 190
to 182 217
Nov. 7 ty sla 188 1 150 1
Loyd 1 1 /s [
790 111 52 .
Nov. 1-25 182 240
fay) 140, 165 ‘i 178 1
35 10 5 0

Figure A-7b,

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE

shore

Cross-channel total dissolved solids patterns (mg/L NaCl)
in the Snake and Clearwater Rivers during adult steelhead

migration, 1970,

82


SECTION IIL
INTRODUCTION

This report summarizes the three-year pre-impoundment phase of a proposed
two-part study relating adult summer steelhead migrational behavior to
water quality changes associated with the impoundment of Lower Granite
Dam on the lower Snake River, Idaho-Washington. Lower Granite Dam is a
low-head dam at river kilometer (RK) 172 currently under construction
and scheduled for completion in 1975, It will convert a free-flowing
stretch of the Snake River that now receives urban sewage and Kraft
pulping mill wastes to an impoundment.

The chief objective of the two-part study is to assess migrational
behavior of adult summer steelhead before and after limnological condi-
tions in the lower Snake River are altered by filling of Lower Granite
Reservoir. The study situation offers an opportunity to observe organ-
ism response to changing environmental conditions in an uncontrolled
field situation. We then propose to relate pre- and post-impoundment
behavior with pre- and post-limnology of the lower Snake River study
section. This comparison will help describe the impact of Lower Granite
Dam on the Snake and Clearwater River steelhead runs. In the first
study phase, reported here, we described steelhead travel paths, migra-
tion rates, and other general characteristics of upstream movement
during peak migration times in 1969, 1970, and 1971.

STUDY AREA

The Snake River flows north out of Hell's Canyon for 160 km, then turns
west at RK 224 to join the Columbia River in southeastern Washington
(Figure 1). The two largest tributaries of the lower Snake are the
Salmon and the Clearwater Rivers at RK 290 and RK 225, respectively.
Asotin Creek at RK 233 and Alpowa Creek at RK 211 also flow into the
Snake River in the study area.

Width of the Snake River in the study area ranged from 140 to 260 m
(200 m average). Stream depth was 2.0 to 8.5 m (4.0 m average) during
the study period, Mean minimum flows in the study area approximated
570 m/sec, occurring near September 1 (U.S. Geological Survey 1970).
Mean maximum flows approximated 5700 m3/sec around June 1, Hydropower
peaking at Hell's Canyon and Brownlee Dams on the middle Snake River
(RK 397 and RK 459) cause daily flow fluctuations of up to 150 m/sec
during summer months.

Widely spaced rapids separate long pools of moderate velocity and great-
er depth in the study area. Rubble 8 to 20 cm in diameter dominates
the substrate, and many sandbars are formed in the study area by annual
high water.


CONTENTS

Abstract

List of Figures

List of Tables

Acknowledgments

Sections

rt Conclusions

Ir Recommendations

IIL Introduction

Iv Experimental Design

Vv Methods

VI Results
Mixing Patterns
Water Quality
Steelhead Migration Paths and Behavior

VII Discussion

VIII Literature Cited

Kx Appendix

Ait

di
iv
vi

vi

10

12

15
24
27
55
57
59


Fish No. 7I-1_ July22-July23,

4— Flow Direction

North Shore

Release / f
Point |

1S 10

Fish No. 71-2 Aug.3

1
© South Shore

[7

Fish No. 7!-3 Aug.|O-Aug. Il

AN.

Fish No. 71-4 Aug.10
v

Fish No. 71-5 Aug.!t

mwang

Fish No. 71-6 Aug.18-Aug.I9

45

Fish No. 71-7 Aug.18

= a)

Kilometers Below Snake-Clearwater Confluence

Figure 17, Adult steelhead migration paths in the Snake River,
Lower Granite pool area, 1971.

37


Sept. 2-8

Sept. 8-10

Sept. 21-24

Oct. 8-22

Nov. 4~I1

Dec. I-11

Ri
+— Flow Direction fp :

Clearwater
iver

48h,
North Shore

1 _, 13.23 13.434
35 fe)

i Sh 1
7*9.40 9.00 8.98
7.90 8.68
L900, 9.10 4 9.45 1
oe Snake River South Shore
fof
7 1 ml l
9.54 9.68 9.50
7. 8.68
1 he 9.56 4 9.69 4 >
pf
1 Sb 1 L 1
“"10.30 10.30 10.20
10.23 9.73
i _, 10.39 10.20 4 10.50 4
L / £ 1 1 iz S- [
“10.48 10.35 10.06
10.26 -
1 ~y 720.23 10.50 4 10.46 1
1 “Aa 1 lL L /
11.57 11.77 11.72
1, 11.73 11.72 4 11.76 4 :
TS
pif
ae of b- lL L L
13.47 12.70 13.30
14,58 14.30
13.90 1

5

fe)

Kilometers Below Snake-Clearwater Confluence

Figure A-2c, Cross-channel oxygen patterns (mg/L) in the Snake and
Clearwater Rivers during adult steelhead migration,

1971.

68


Sept.2-8

Sept. 8-10

Sept. 21-24

Oct. 6-22

Nov. 4~1t

Dec. I-11

Figure A-5c.

Ri
— Flow Direction | Jn

Clearwater
ver

ree Shore
101

hore

86 80 69
100
fs 78 Lt 89 1
oe Snake River South SI
Ly pt n t VEUA
“96 99 86
100 101
2 7 PL n 95 1 99 1
VEWA
L af fn L —_ L
“97 95 85
93 111
1,27 4 92 1 97 t
+ /
yee n n /- [
“104 113 107
1 Al6_1 113 1 113 1
oe _/-L
“136 144 139
ty A48_ 148 A 143 1
Lye ' 1 / vA
V6 89 103
125 125
py Al? 1 122 n 119 n :
35 7Al 10 5 ro)

Kilometers Below Snake-Clearwater Confluence

Cross-channel bicarbonates patterns (mg/L Cac03)
in the Snake and Clearwater Rivers during adult
steelhead migration, 1971.

77


EPA-660/3-73-017
February 1974

Ecological Research Series



ABSTRACT

A three-year field study was conducted from 1969-1971 to assess the
relationship of Kraft mill effluent and pre-impoundment limnological
conditions to adult steelhead trout (Salmo gairdneri Richardson) behavior
in the Snake River near Lewiston, Idaho. Steelhead were tagged with an
ultrasonic transmitter and followed through a 25 km section of the pro-
posed Lower Granite Reservoir. Limnological parameters were measured in
the Clearwater and Snake Rivers and then compared with fish behavior.
Mixing patterns of the Clearwater River with the Snake River were also
assessed,

Mean water quality changes in the Snake River as a result of pollution
inputs in the Lewiston area are very subtle. In terms of toxic effects
from chemical loading, the Snake River water quality is not greatly
altered except in the immediate area of pollution input; we did not
observe steelhead avoidance of these localized problem areas.

No significant correlation could be made between any chemical water
quality parameter and steelhead behavior. However, as the temperature
dropped below 15 C fish movement slowed, fish generally stopped moving
at night, and resting periods increased in length and number. Steel-
head generally showed a preference to move in water with off-bottom
current velocities of 0.2 to 0.5 m/sec and showed a definite pattern of
crossover and resting points in the river.

This report was submitted in fulfillment of Project Number 18050 DMB

under the sponsorship of the Environmental Protection Agency. Work
was completed as of December, 1971.

ai


Clearwater

. iver
yp Flow Direction 09 /iorth shore
8.02 7.98 8.04 7.64
pH 8.15 7.97
pp—Si2 8,11 1 8.19 8.13
Snake River South shore
yp . Ar.08
“10.08 10.46 9.96 10.35
Oxygen (mg/1) | 9.64 10.30
wy AO) oars 10,1 10,94
A __for.7/
"102.5 105.2 99,1 100.8
Oxygen Percent | 97.7 103.7
Saturation 1 y 7200, 105.7 1 102.1 104.0
Vp 1 . / 3.2.
“0.7 0.3 2.7. 7.8
Carbon dioxide | 0.9 . 1.6
(mg/1 C02) Y pOrk, 0,2 ‘ 1,8 3.4)
VL : 1 fil
"107.6 100.0 94.0 35.2
Bicarbonates 103,1 114.8
(mg/1 caC0,) 7 j138 109.4 1 118.5 134,2
— 1‘ 1 Srl
101.4 104.4 89.9 33.0
Total Hardness | 103.2 114.3
(mg/1 Caco,) 7 AOB. os 115.7 s__115.5__110,1
a Aal
Total Dissolved 157.0 154.4 130.5 42.8
Solids 169.3 165.7
(mg/1 NaC1) ._, 148.8, 155.3 » 159.6 167.5
35°“ 10 5 0

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE
Figure 14, Average cross-channel patterns of water quality parameters

in the Snake and Clearwater Rivers during adult steelhead
migration - 1969, 1970, and 1971.

25


Clearwater
River

ZNorth shore

q— =Flow Direction

i 7 2 m 1 a
0 1,20 1.18
July 1-2 06 - - - 0
yp O14 : 9090
Snake River South shore
74— - 1.00
July 22-24 +22 - -  .70 -10
oy rn = 40
a Sol
80 1.11 .47
Aug. 11-13 - 77 49 .39 +04
my £ 8h 1. 10Q_.03
a , __ foo £
339 -78 .99
Aug. 26-28 - 39 -64 .85 75
Ly f AO 1 55.41
fay aoe 1 L Js VA
“59 -83 .80
Oct. 14-16 +22 -78 108 +23
ayes 1 30.20
Ly pt . \ Is vA
53 271 474
Nov. 11-16 51 «51 +99 .61 -20
ov i" 25, 1 136 20
a — Sol
oO G2 82 .59
Dec. 16-19 - - - 1.13 .20
1—y 4 6h 1 Al 422
35 10 5 0

KILOMETERS BELOW SNAKE~CLEARWATER CONFLUENCE
Figure A-8a. Cross-channel tannins and lignins patterns (mg/L Tannic

Acid) in the Snake and Clearwater Rivers during adult
steelhead migration, 1969.

84


Sept. 4-18

Oct. 15
Nov. 7

Nov. t-25

Figure A-6b,

Clearwater

River
Loe 4 — Flow Direction Vis A Shore
“93 95 85
96
Lip 95 97 L 105
ad Snake River South Shore
boy, 1 4 y 27 L
V—35 117 72
120

py p1201 __118 i 137

_ , {1

1L af f
a 86 63 37
120 130
Loz, 113 tl 138 l
35 °° to 5 °

Kilometers Below Snake-Clearwater Confluence

Cross-channel total hardness patterns (mg/L CaCO,)
in the Snake and Clearwater Rivers during adult steel-
head migration, 1970.

79


4er Legend

° A = 1969
° oA o a = 1970
990 goo oO = 1971
wl og
°
a aoa
° 000
‘ a
a
E er ooA
Fa Aa Qo
a oad
a ao
ooA
A
SF oo oAAA
A
oo 4
oa oa
° 4. 4. lh. i. A. 1 rt i. 4 L
7 214 1t4 i8 | 18 296 20 [3 I7 | 15 295 19 16 307 21 |4 18 2 16 30
4 26 Wo 25 WW 25] 8 22 (13 2% 10 24[8 22 2 24 9 23 1428 fl 25{ 9 23
Jon. | Feb. | Mor. Apr. Moy | Jun. Jul Aug. Sept. Oct. | Nov. Dec.

Figure 3. Snake River temperatures below the Snake-Clearwater confluence, 1969-71.


69

Table 2.

Ranking of independent variables according to their apparent relation to steelhead movement. Low
ranking indicates early selection in the regression equation, hence higher multiple correlation,

Year| Rank |Total Net Total Day Only Movements Night Only Movements
Movement Movement. Reversals _|Total Net Reversals |Total Net Reversals
1969] 1 |Day of Water Fish Water Water Day of Day of Total Fish
Year Temp. Length Temp. Temp. Year Year Flow Length
r=0.4959 r=0.3493 r=0.0905 r=0.4653 | r=0.4193 |r=0.1805_ | r=0.3683 |r=0,2310 | re0.1173
2 Fish Fish Moon Fish Fish Water Total Clw. R, | Snake R.
Length Length Phase Length Length Temp. Flow Flow Flow
r=0.5506 r=0.3755 r=0.1197 r=0.4866 | 4=0.4575 |r=0.4090 |r=0.4099 |r=0.2537 | r=0.1551
3 Snake R> Total Snake R. Total Snake R. |Moon Moon Day of Bar.
Flow Flow Flow Flow Flow Phase Phase Year Pressure
r=0.5738 r=0.3942 r=0.1353 r=0.4913 | r=0.4685 | r=0.4431_ |r=0.4158 |r=0.2617 | r=0.1639
1970/1 Water Day of Snake R. Water Dav of Snake R. : Day of Day of Water
Temp. Year Flow Temp. Year Flow Year Year Temp.
r=0,5683 r=0.4501 r=0.1596 r=0.5935 | r=0.4796 | r=0,1857 | r=0.6523 [r=0.5358 | r=0.1865
2 Clw. Re Clw. Re Water Fish Moon Total Clw. R. |Clw. R. | Day of
Flow Flow Temp. Length Phase Flow Flow Flow Year
r=0. 5859 r=0.4745 r=0.1900 r=0.5586 | r=0.4919 | r=0. 2092 r=0.6909 |r=0.5593 | r=0.2744
3 Snake R. Snake R. Day of Day of Clw. R. |Fish Bar. Bar. Snake R.
Flow Flow Year Year Flow Length Pressure | Pressure | Flow
£=0.5929 r=0.4797 r=0.2802 r=0.6008 }| r=0.4945 | r=0.2261 | r=0.7124 |r=0.6035 | r=0.3541
1971} 1 [Day of Water Total Day of Water Snake R- | Water Clw. R. | Moon
Year Temp. Flow Year Temp. Flow Temp. Flow Phase
x=0.6133 r20.2699 r=0.1556 r=0.6181 | r=0.2171 | r=0.2153_ | r=0.4845 | r=0.1562 | r=0.2766
2 Moon Moon Water Moon Moon Moon Fish Moon Clw. Re
Phase Phase Temp. Phase Phase Phase Length Phase Flow
r=0,6225, r=0.2852 r=0.1670 r=0,6252] r20.2470 | r=0. 2434 | r=0.5032_ | r=0.2026 | r=0.3073
3 Fish Clw. Re Snake R- Water Clw. R- Bar. Bar. Day of Water
Length Flow Flow Temp. Flow Pressure | Pressure | Year Temp.
20,6261 r=0.3011 r=0.2435 r=0.6262| r=g 9719 | r=0.2521 | r=0.5111 |r=0.2549 | r=0.3282



Clearwoter
iver

R
+— Flow Direction J few Shore
04

TOUS 705 -
Sept.4-i8| -02 .
ay | +06 L _ 1
eo Snake River South Shore
fo
L Sh 1 1 1
Oct. 15 “0 o 0
to Tr Tr
Nov. 7 toe O 1 (0) 1 9 1
Vig /
lL } fo 1 L 1
O23 .20 14
Nov. 1-25} Tr Tr
1 pgel0 4 209 F 202 i
35 i) 5 co)

Kilometers Below Snake- Clearwater Confluence

Figure A-10b. Cross-channel ammonia patterns (mg/L NH,) in the
Snake and Clearwater Rivers during adult” steelhead
migration, 1970.

*Tr = Trace

91


Sept. 4~i8

Oct. 15
to
Nov. 7

Nov. 1-25

Clearwater
iver

R
+— Flow Direction | Pfam Shore

1
80.3 82.4 80.3
81.0 92.7
1, 80.31 78.3.4 82.4 1
7 Snoke River South Shore
foo
Joys 1 L 1
"105.6 105.6 96.3
92.7 100.4
1,105.1 107.1 4 99.4 n
Aon. of
1 db L L 1 /
95.8 96.6 95.8
92.7 100.4
17, 95.3) 96.6 1 95.3 n
35°" 10 5 °

Kilometers Below Snake- Clearwater Confluence

Figure A-3b. Cross-channel oxygen saturation patterns (percent
saturation) in the Snake and Clearwater Rivers -

during adult steelhead migration, 1970,

70


Fish No, 69-8 Oct.8-Oct.25 ° 4— Flow Direction

z& Release Point
1 l 4

1s 10 5 © South Shore

North Shore

Fish No. 69-9 Oct9-Nov.2

Fish No. 69-11 Oct.14-Dec.2

ca

Fish No. 69-12 Oct.I7-Nov.24

Fish No. 69-13 Oct.I8-Dec.8

_ + a mo

Fish No. 69-14 Oct.28-Nov.26

Kilometers Below Snake-Clearwater Confluence

Figure 15 (Continued), Adult steelhead migration paths in the Snake
River, Lower Granite pool area, 1969.

31


€¥

15-16]
tats
13-14
rey
neta]
10-1]

9-10]

Above Confluence (km) Below Confluence (km) ———>
°

eet ee se

ra

ote! Beton!

Confluence
oto! Above]
Confluence

Total Above|

ong Batowl

Contivence

oa.
7

O = wn

Ih oncMnTeall

i lt Nin
ia

my calla?

Figure 18. Distribution of steelhead in the Snake River, 1969-71. Width

of bars expresses the percent of fish in each third of the
river width.


8y

10.6 km Below Confluence
Off Bottom Current Velocity m/sec.

o 50 1.00 100 . 50 °
or ft n n r 1
if
— 2br
€
=
=
a
oe
a
3e
ab
sl
L rT 1 1 j
co) 50 100 150 200
North Shore Meters South Shore

Fig. 20 (continued). Observed position of steelhead 0.2, 1.6 and

10.6 kilometers below the Snake-Clearwater
confluence in relation to current velocity
1 m off the bottom, 1969-71


spite of several days search as much as 25 km above and below the last
known position. No explanation (other than transmitter failure) was
found for these losses. Fish were never known to regurgitate tags
either in the live box or after release. One tag stopped transmitting
while the fish was still in the live box before release.

A total of 11 tags were recovered from sport fishermen. Five fish were
caught while still being tracked. We had 3 recoveries in 1969; 1.5 km
below confluence, 2 km below confluence, and directly across the river
from the release point where the particular fish had been stationary

for 3 weeks. In 1970 we had 4 recoveries; from the Salmon River near
Riggins, Idaho, 3.5 km below the Snake-Clearwater confluence, one 1970
tag was found on the bank of the Selway River (a tributary to the Clear-
water River) in April of 1971, and a tag was returned from a fish caught
in the Grand Ronde River near Troy, Oregon. Wehadfour 1971 tags recover-
ed; from 1.5 km below the confluence, 0.8 km up the Clearwater River,
and two 1971 tags recovered in the spring of 1972 . . . one was found
on the bank of the Salmon River and another lodged in bottom rocks 0.5
km up Alpowa Creek,

All fish caught by fishermen were in good condition, More fish were
probably caught but even though a publicized $10.00 reward was offered
for recovered tags the tag is not readily visible to a person cleaning
the fish. This high return of tags may indicate the tag and tagging
procedures had a minimal effect on the fish's behavior. The shortest
elapsed time between tagging and recovery of a fish by fishermen was
16 days.

Lateral Position in the Stream

Lateral distribution of steelhead across the Snake River igs detailed
in Figure.18. A well-defined preference for near-shore movement is
shown,

Fish passage observations from 1969 and 1970 in the river section 0.1-
0.4 km and 2.2-2.5 km below the Snake-Clearwater confluence were tested
by Chi Square to determine whether fish numbers passing on the Clear-
water or Snake side were significantly different than would be expected
by the ratio of Clearwater fish to Snake fish for each year. The low
number of fish following the Clearwater side through this section was
not significantly different from the number that would be expected to
pass upstream on that side based on Washington Water Power Dam counts
of total numbers of fish up the Clearwater River (P< .10). We con-
cluded that steelhead were not avoiding the Clearwater side, even though
effluent concentrations were higher there.

44


Clearwater
iver

Ri
<+—Flow Direction | hes ren Shore
0

1
2.0 1.2 3.8

Sept.4-I8] 0.5
Loyzgll, 1.8 | 0.5 1
mas Snake River South Shore
7 1 t Ae VA
Oct. 15 0 0 7.1
to 2 0
Nov. 7 |, OI Oo A 0 !
Ly pd 1 1 Jol
"1S 1.7 6.0
Nov.1-25] 2 0
Lins O74 0 n 0 n
35 10 5 Qo

Kilometers Below Snake- Clearwater Confluence
Figure A-4b, Cross-channel carbon diexide patterns (mg/L free C02)

in the Snake and Clearwater Rivers during adult. steel-
head migration, 1970.

73


Sept, 2-8

Sept. 8-10

Sept. 21-24

Oct, 8-22

Nov. 4-11

Dec, 1-11

Figure A-7c.

Clearwater
ver

RB
4+— Flow Direction y
by pt n 1 22 {Nor
am) 99 70
. 123
wy p29 96 n 124 ni
‘ Snake River South
ay 1 1 Jn /
7! TSS 155 124
. 128
sy p12 121 1 97 1
raya : : Jn A
“* 186 143 149
202 143
ry p26 168 : 157 L
1 b i 1 1. / = /
“VTS 171 180
1 of peddle __166 1 125 1
ys S/L
“*" 188 182 173
7" 196, 190, 2 187 2
yp 7 . Js.
“166 172 186
200 205
1 __,, 168) 182 1 207 a
35° 10 5 0

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE

shore

shore

Cross-channel total dissolved solids patterns (mg/L NaCl)
in the Snake and Clearwater Rivers during adult steelhead

migration, 1971,

83


Fish No. 71-8 Aug.24-Aug.25 +— Fiow Direction North Shore
-——+

Release Point

1 L _
5

1
15 10 © South Shore

Fish No. 71-9 Aug.24-Aug.26

—) ts TaN

Fish No. 71-10 Aug.25-Aug.27

Fish No. 7I-ll Aug.25-Aug.29

Fish No. 7I-I2 Sept.l0-Sept.26

no

Fish No. 71-13 Sept.1O-Sept.13

Fish No. 71-14 Sept.il-Septi2

oe

Kilometers Below Snake-Clearwater Confluence

Figure 17 (Cont#n:ed), Adult steelhead migration paths in the Snake
River, Lower Granite pool area, 1971.

38


EPA-660/3~-73-017
February 1974

POLLUTION EFFECTS ON ADULT STEELHEAD MIGRATION

IN THE SNAKE RIVER

by

C. Michael Falter
Rudy R. Ringe
College of Forestry
University of Idaho
Moscow, Idaho 83843

Project 18050DMB
Program Element 181021

Project Officer
Dr. Gary Chapman
Western Fish Toxicology Station
1350 S. E. Goodnight Ave.
Corvallis, Oregon 97330

Prepared For
OFFICE OF RESEARCH AND: DEVELOPMENT
U.S. ENVIRONMENTAL PROTECTION AGENCY
WASHINGTON, D.C. 20460

For sale by the Superintendent of Documents, U.8. Government Printing Office, Washington, D.C. 20402 - Price $1.50


Sept. 2-8

Sept. 8-10

Sept. 21-24

Oct. 8-22

Nov. 4-11

Dec. I=11

Ri
<— Flow Direction | / -

Clearwater
iver

own Shore

hore

1 St fu 1
"238 211 182
1, 220 4 97 L159 A
oe Snake River South S!
rT f p- Ll L 1 S- /
“125 116 92
142 -
ay p55 102 F 131 bo
L SP fammarrde L L S wf
"163 107 173
90 247
p_, 274 9 196 ! 97 l
4}
Loy £ 1 1 1 S /
“80 90 118
p_,)59_ 1 192 n 132 n
1 tf lL L 1 / . /
“213 260 260
n 7 pil 1 102 1 289 L
fe [
1 J L L 1
TAIT 312 299
1, 329 254 i 420 i
35 °° to 5 °

Kilometers Below Snake-Clearwater Confluence

Figure A-13c. Cross-channel Total Volatile Matter patterns (mg/L
Total Volatile Matter) in the Snake and Clearwater
Rivers during adult steelhead migration, 1971.

101


No.

A-8b

A-8c

A-9a

A-9b

A-9c

A-10a

A-10b

A-10c

A-lla

A-11b

A-llc

APPENDIX - (Continued)

Cross-channel tannins and lignins patterns (mg/1
tannic acid) in the Snake and Clearwater Rivers
during adult steelhead migration, 1970

Cross-channel tannins and lignins patterns (mg/1
tannic acid) in the Snake and Clearwater Rivers
during adult steelhead migration, 1971

Cross-channel sulfate patterns (mg/1 80,4) in the
Snake and Clearwater Rivers during adult steelhead
migration, 1969

Cross-channel sulfate patterns (mg/l SO,) in the
Snake and Clearwater Rivers during adult steelhead
migration, 1970

Cross-channel sulfate patterns (mg/1 S0,) in the
Snake and Clearwater Rivers during adult steelhead
migration, 1971

Cross-channel ammonia patterns (mg/1 NH3) in the
Snake and Clearwater Rivers during adult steelhead
migration, 1969

Cross-channel ammonia patterns (mg/1 NH3) in the
Snake and Clearwater Rivers during adult steelhead
migration, 1970

Cross-channel ammonia patterns (mg/1 NH3) in the
Snake and Clearwater Rivers during adult steelhead
migration, 1971

Cross-channel transparency patterns (secchi disc feet)
in the Snake and Clearwater Rivers during adult
steelhead migration, 1969

Cross-channel transparency patterns (secchi disc feet)
in the Snake and Clearwater Rivers during adult
steelhead migration, 1970

Cross-channel transparency patterns (secchi disc feet)

in the Snake and Clearwater Rivers during adult
steelhead migration, 1971

61

86

87

88

89

90

91

92


0.2 km Below Confluence
Off Bottom Current Velocity m/sec.
° 50 1.00 180 100 50

Lo

or 1
it
27
<
é
3b Legend
021969
081970
«1971
ah
sk
1.6 km Below Confluence
Off Bottom Current Velocity m/sec.
9 80 100 100 50 °
a rl 1 ‘ ©
ib
e7
é
r-}
3k
ab
st
t rn Z 1 1 j
() $0 100 150 200
North Shore Meters ‘South Shore

Figure 20. Observed position of steelhead 0.2, 1.6 and 10.6
kilometers below the Snake-Clearwater confluence
in relation to current velocity 1 m off the bottom,
1969-71.

47


Clearwater
River

4— Flw Direction / - [worth shore

.
‘

July 1-2 - - - oe -
iy, 1 m=
Snake River South shore
1 Sf i 4 1 / - Z
- ~ €1.0
July 22-24 2.0 <1.0 - 2:8 3.0
iy pt 1 -_ 4:0,
pa _fpl
1.0 30.0 0
Aug. 11-13 - 7.0 2.0 <1,0 2.5
1 fp 2d L 0 4,0
yp hol
(0) QO 0.6
Aug. 26-28 yp bt ; <}:8 #:8 0.8
fy £ 1 1 1 /. /
721.0 2.0 -
Oct. 14-16 - - <1.0 <1.0 21.0
1 1h =1 n - -,
ponte fal 4 1 /- Z
Nov. 11-16 <1.0 - - + -
1 1} ine F 1 = — L
yt _ Sisal
2.0 42.0 1.0
Dec. 16-19 1.0 - - 3.0 0.5
p,, ld L 9.0 12.0
35° 10 5 0

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE

Figure A-12a. Cross-channel Pearl-Benson Index patterns (mg/L Standard
Calcium Spent Sulfite Liquor Solids) in the Snake and
Clearwater Rivers during adult steelhead migration, 1969,

96


South
shore
200 250

7 13 August 1970

DEPTH (m)

3 25 August 1970

DEPTH (m)

10 October 1970

Figure 11, Total dissolved solids (mg/1) profiles 6.1 km downstream
from the Snake-Clearwater confluence,

21


(as

DEPTH (m)

DEPTH (m)

N

w

>

North South
shore METERS shore

24 August 1970

8 August 1970
T1177

840) Zandog (\ £00 7 % TELSEBS a0
18 November 1970 13 January 1971
Figure 7. Total dissolved solids (mg/1) profiles 0.2 km downstream from the Snake-Clearwater

confluence.


Clearwater
iver

Ri
—Flow Direction | / 24 Jem Shore

Lf £ 1
"172 171 229
Sept. 4-18 | 159
L190 115 l 138 1
‘ Snake River South Shore
152
iy) 1 L L
Oct. 15 “YTB 93 1035
to 90 85
Nov. 7 tL 225 4 137 1 100 1
lL Sh 1 1 1
“US 78 80
Nov. 1-25] 95 183
pi, 14 = 1 158 L
35° 10 5 °

Kilometers Below Snake-Clearwater Confluence

Figure A-13b. Cross-channel Total Volatile Matter patterns (mg/L
Total Volatile Matter) in the Snake and Clearwater
Rivers during adult steelhead migration, 1970.

100


Table 1. Characteristics of the summer steelhead runs
in the lower Snake River, 1969-71.

and fish tracked

1969 1970 1971
Total steelhead over WWP Dam,
July-December 9,522 8,876 7,601
Total steelhead over Ice Harbor
Dam, July-December 65,187 50,817 67,125
Percent of Ice Harbor fish
passing over WWP Dam,
July-December 15% 18% 11%
Dates of fish tracking July 11- July 17- July 22-
Jan. 6 Nov. 18 Nov. 7
Number of fish tracked 24 28 37
Fish length: mean total length 73.6 73.9 68
range 61-93 64287 55-97
Water temperature Snake R, | 3.5-24.0 4.5-23.5 4.0-23.5
range during track
season (C) Clw. R. 1.0-24.0 0.5-24.0 1.0-25.5
River flow range Snake R. | 17.1-37.6 18.4-39.9 20.7-49.5
during track season
(cfs x 1000) Clw. R. 1.8-10.0 2.69.6 3.0-11,2

29


Po
a
T

Legend
o-~+-~= Reversals
+ +=Net
-—~-— = Total

Kilometers and/or Reversals Per Day
y
a e

4. 4

rf n lh
26.10-28.20 28.20-2830 2830-2840 2840-2850 2850-28.60

rn n n
2860-2870 2870-2880 2880-2890 2890-2900 2900——*

28.00-28.10
Barometric Pressure (inches Hg)
Figure 23. Steelhead migration rate (total and net kilometers per day) and/or reversals per
Averaged over 1969, 1970 and 1971.

day compared to barometric pressure.


Sept.2-8

_ Sept. 8-10

Sept. 21-24

Oct. 8-22

Nov. 4=11

Dec. I-11

+— Flow Direction

Clea rwater
River

fos toon Shore

105.0 100.4 99.9
89.2 96.8
yy 100.4 100.4 | 105.1 n
Snake River South Shore
1 J fumed 1 hs L
7110.2 110.2 Tis: 2
89.2 6.8
r__, 108.3 109.2 4 110.7 te
1 F j Irs.of
136.5 109.2 108.2
106.0 106.1
1, 110.3 108.0 , 103.3,
1 L 1 1 1 / -[
"130.3 128.2 123.6
109.0 -
— 130.8 1 128.8 1
1_y p-—L 1 / _/
106.1 108.2 106.0
1 7206.4 107.6 4 108.7 n
yan | 1 fos.of,
“113.5 106.0 110.2
117.4 107.0
_y sLLL.@ 113.4 4 118.5 4
5 7 to 5 °

Kilometers Below Snake-Clearwater Confluence

Figure A~3c, Cross-channel oxygen saturation patterns (percent
saturation) in the Snake and Clearwater Rivers

during adult steelhead migration, 1971.

71


DEPTH (m)

DEPTH (m)

North South North South

shore METERS shore shore METERS shore
0 50 100 150 QU 50 100 150
T 3 1s tos | 15
a’ uo 0
ts
11 August 1970 25 August 1970

230 260
f is

zo | Il
490

t200|

y

17 November 1970 8 January 1971

Figure 13. Total dissolved solids (mg/1) profiles 10.6 km down-
stream from the Snake-Clearwater confluence.


Sept 2-8

Sept. 8-10

Sept. 21-24

Oct. 8-22

Nov 4-11

Dec. I-11

Figure A-9c.

Ri
+—Flow Direction WA
n l 1.0

Clearwater
ver

Jr Shore
31.5

lL Jk 1
717.5 17.0 13.5
31.0 .
1, 38-0, 18.0, 20.5 F
‘ Snake River South Shore
fr0
L f bk 1 1 1
731.0 35.0 32.0
31.0 .
Sy 34.04 31.0, 33.0 LL: 31.5
fs [
L D femmes 1 L
~7 “92.0 25.0 19.0
36.5 42.0
py 2391 22.0, 22.0 ,
toy, t tl JS VA
7/37.0 27.0 27.0
Ly 26.01 28,0 1 28.0 1
Ly, ! F / VA
"28,0 25.0 27.0
L of fal. Or 22.0 1 30.0 1
hs
1 SL L L L
7775.0 28.0 25.0
51.0 51.5
1, 25.0) 25.0 4 28.0 1
35 10 5 0

Kilometers Below Snake-Clearwater Confluence

Cross-channel sulfate patterns (mg/L SO) in the

Snake and Clearwater Rivers during adult
migration, 1971.

89

teelhead


Figure 1.

Lower
Granite
Dom (U.C.)

Hams
N ° 60
[ eer

| Kilometers

Lower Snake River, Idaho-Washington.

|
|
|

sony



Clearwater

River
_ <— Flow Direction /- Korth chore
, - 14.0 14.0
July 1-2 - - - + 14.0
oops j 16.0 16.0,
7 Snake River lin shore
ay 2 1 1 7
(aa 4.0 4.0
July 22-24 5.6 8.0 20.0 8.0
typ A 10.0 6.0,
toy 1 3.0 /
“4,2 5.0 0.8
Aug. 11-13 - 3.0 3.0 0 0
: 3.9 a 3.0 0 ,
7+
yt _Sosl
7" 2.0 4.0 6.5
Aug. 26-28 0 2.0 6.0 3.0 te)
r,, 1.9 1 0 oo
/
1 Lt 1 of
0 Oo 18.1
Oct, 14-16 0 0 0 0 0
Ly £ Oy A it) O 4
tt
1 1 1 1s/
() 0 5.0
Nov. 11-16 10) 0 0 0 10)
Ly O, 1 0 O41
typ 1 Jusl
"0 6.0
Dec. 16-19 - - - 0.5 0
L 0, 1 0 1
tt ots 5 7)

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE

Figure A-4a.

Cross-channel carbon dioxide patterns (mg/L free C05) in

the Snake and Clearwater Rivers during adult steelhead

migration, 1969.

72


Clearwater

River
q—Flow D:
By put 1 ow ee Lrorth shore
v3 °
July 1-2 49 - - - 58
typ 5h am 65 654
“ Snake River South shore
ESS * 7735
July 22-24 53 - 85 54 80
Ly pt 1 85 681
pa fo L
“75 70 27
Aug. 11-13 91 78 73 «90 -
sy p84 A 90 945
1 L i 1 rt hrs /
795 100 40
Aug. 26-28 90 97 105 105 105
ay) “1 1 120.1205
“U5 118 «54
Oct. 14-16 112 - 119 #125 138
Lyf 113, 1 137_ 131,
pt . _ fw [
“~ 120 13125
Nov. 11-16 126 119 105 «154 142
iy phd, ,___137_ 138,
. - 28
Dec. 16-19 - - - 131 -
Ly p——4 L - 1554
35° 10 5 0

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE
Figure A-6a. Cross-channel total hardness patterns (mg/L CaCO,) in the

Snake and Clearwater Rivers during adult steelhead
migration, 1969.

78


ACKNOWLEDGMENTS

The authors wish to thank Drs. Don Chapman and Ted Bjornn of the Idaho
Cooperative Fishery Unit for their counsel throughout this study.

Mr. Wes Ebel, National Marine Fisheries Service, and his supporting
staff permitted the use of their adult fish migrant trapping facilities
at Ice Harbor Dam.

We thank Dr. Richard Wallace, fishery scientist at the University of
Idaho, for his help and advice on steelhead behavior in 1969 and 1970.

The support of the Office of Research and Monitoring, Environmental

Protection Agency, especially the help provided by Project Officers
Drs. Gerry Bouck and Gary Chapman is sincerely appreciated.

vit


Clearwater

River
_ +— Flow Direction J from Shore
“89 84 78
Sept.4-18] 102 150
p,,91 4 88 Ll 96
iad Snake River South Shore
L J h L 1 1 /ol-
Oct. 15 7138 127 116
to 115
Nov. 7 | n 143 5 142 nl 162
a | 1 l / 20 L
“72 69 45
Nov. 1-25] 115 126
L_,,110 , 107 Al 128 t
35 °° lo 5 °

Kilometers Below Snake-Clearwater Confluence

Figure A-5b, Cross-channel bicarbonates patterns (mg/L CaCO 3)
in the Snake and Clearwater Rivers during adult?
steelhead migration, 1970.-

76


SELECTED WATER 1. Report No.] 2. , Teerunen Me
RESOURCES ABSTRACTS :

INPUT TRANSACTION FORM

4.

Title
Pollution Effects On Adult Steelhead Migration In
The Snake River

Authors}

Falter, C. M. and Ringe, R. R.

2.

University of Idaho

18050 DMB

Orcanizeion

7

U2 Type i Repore and *
” Pened eign

Environmental Protection Agency report number,
EPA-660/3-73-017, February 1974.

16

Abstens

We conducted a three-year field study in 1969-1971 to assess the rela-
tionship of Kraft mill effluent and pre-impoundment water quality to
adult steelhead trout (Salmo gairdneri Richardson) behavior in the Snake
River, Idaho-Washington. Steelhead were tagged with ultrasonic tags and
followed through a 25 km section of the proposed Lower Granite Reservoir.
We measured limmological parameters and compared with fish behavior. Mix-
ing patterns of the Clearwater River with the Snake River were also
assessed.

Mean water quality changes in the Snake River as a result of pollution
inputs in the study are very subtle. In terms of toxic effects from
chemical loading, Snake River water quality is not greatly altered ex-
cept in the immediate area of pollution input; we did not observe steel-
head avoidance of these localized problem areas.

No significant correlation could be made between any chemical water. qual-
ity parameter and steelhead behavior. However, as temperature dropped be-
low 15 C fish movement slowed, fish generally stopped moving at night, and
resting periods increased in length and number. Steelhead showed a pref-
erence to move in water with off-bottom current velocities of 0.2 to 0.5
m/sec and showed a definite pattern of crossover and resting points.

17b.

Ve.

17a,

Descriptors

/*Steelhead trout/*Kraft mill effluent/oxygen/water pollution effects
/*migration behavior/water temperature/water velocity/*ultrasonic
transmitters/pre-impoundment water quality

Identifiers
Snake River/Idaho-Washington/Lewiston, Idaho/anadromous fish/migration

COWRR Field & Grour

18,

Avadabpiiy Send To:

DEPARTMENT OF THE INTERIOR
WASHINGTON. D.C 20240

Justituen University of Idaho

WATER RESOURCES SCIENTIFIC INFORMATION CENTER



July 1-2

July 22~24

Aug. 11-13

Aug. 26-28

Oct. 14-16

Nov, 11-16

Dec. 16-19

Figure A-9a,.

Clearwater

; . River
_, Flow Direction . [North shore
9°" 10 12°12
- - - 4
15_,, 18, . 22,22
‘ Snake River South shore
yp Sl
- 21 9
21 - 27 16 19
{p—=1 nl 30 18
ps _f
a 26 18°63
31 24 21 22 25
py p24 2
ype fl
me 31 20 8
- 31 23 37
[2 3. _ BB,
ay pt A ‘ /\ A
43 40 9
39 43 39 48
ry p425 L 49 48
yp AL
ve— > 7
45 - - 43 46
ay pt 1 ~ 46
pw _/-L
- - - 8 -
sp 1 ~_ 37
35 7" 10 5

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE

Cross-channel sulfate patterns (mg/L S0,) in the Snake
and Clearwater Rivers during adult steelhead migration,

1969.

87


SECTION VII
DISCUSSION

Chemical parameters showed that no serious pre-impoundment water quality
problems exist in the Lower Granite pool area because of rapid mixing.
Bacteriological indicators, however, have shown that this portion of
the Snake River is below the bacterial standards for Class A waters in
the state of Washington (Falter and Funk 1973).

Existing reservoirs on the lower Snake River do not thermally stratify;
the water is in relatively constant exchange with the atmosphere (Falter
and Funk 1973). Lower Granite Reservoir is not expected to thermally
stratify. Therefore, after the proposed secondary treatment of incoming
domestic and Kraft wastes, we do not anticipate large masses of toxic
water in the reservoir.

Analysis of mixing patterns of the Snake and Clearwater River flows
below their confluence showed that dilution of the Kraft mill effluent
stream into the two flows occurs so rapidly that high concentrations of
the effluent are not detectable beyond 0.2 km below the confluence. At
20,000 cfs, mixing of the two flows was essentially complete 16 km below
the confluence, but when the total flow exceeded 40,000 cfs, the two
flows still were not completely mixed 35 km downstream.

Under present river conditions the high-temperature Kraft effluent
dilutes rapidly to a level where resulting Snake River temperatures and
water quality showed no apparent blockage or gross atypical migrational
behavior in sonic-tagged steelhead.

In ‘late August, 1970, maximum concentrations of approximately 2.6%
Kraft effluent occurred in midriver, 0.2 km below the confluence. In
November, 1970, concentrations of approximately 1.3% Kraft effluent
were found. Both of these values were well below the adverse concentra-
tion for juvenile sockeye salmon (Alderdice and Brett 1957). According
to Jones (1953) Bond showed that steelhead trout did not avoid paper
mill wastes in concentrations ranging from 1.5% to 4.5%. although coho
salmon avoided concentrations of 4.3% and chinook salmon avoided con-
centrations of 1.5%. These results indicate that effluent concentra-
tions even 0.2 km below the outfall are below threshold avoidance levels
for steelhead,

Impoundment of the study area could conceivably allow concentration of
Kraft effluent in low-velocity shoreline areas where the toxic effects
of Kraft effluent may adversely affect migrating adult steelhead.
Probability of poor mixing occurring is slight since PFI will be replac-
ing the single port discharge with a 120 m long submerged diffuser run-
ning the width of the river at the confluence,

55


TS

25

20-
>
Ss
a
=
é Legend
oe
g +--+ = Reversals 7
- + ~=Net
3 o—e— = Total J
5 /
.
: /
c
5 OF
ra
2
i

sh

en ne ee =
0-6 6-85 B5-1 113.5 135-16 16-185 185-21 a—
Temperature (C)

Figure 21. Three year average kilometers and/or reversals per day compared to temperature (C),

1959, 1970, 1971.


We determined vertical profiles of current velocities with a cable-
suspended Ott current meter, Model C-31 (Epic, Inc.) operated from a
double-anchored boat. Velocities were calculated over the range of
river flows encountered from July-December.

WATER QUALITY

Chemical aspects of the Snake and Clearwater Rivers were analysed ac-
cording to APHA (1965) and EPA (1969). Total hardness, ammonia, and
tannins were analysed by the Hach technique (Hach Chemical Company) and
the Pearl-Benson Index as standardized in the pulp and paper industry
(Barnes et al, 1963). The Pearl-Benson or nitroso technique was devel-
oped for detection of sulfite waste liquors, but it also indicates the
presence of lignin sulfonate compounds in Kraft liquors. Total volatile
solids of the water were determined gravimetrically by ashing three to
six replicated samples.

We conducted water sampling intermittently from July through December
of 1969, September through November of 1970, and July through November
of 1971. Sampling was restricted to peak months of adult summer steel-
head migration in the study area. A grass fire on July 27, 1970, at
our field tracking facility destroyed much of our water sampling and
analysis equipment, thus setting back water analysis until September of
that year. We established stations on the two rivers in order to physi-
cally and chemically measure incoming river flows into the study area,
mixing patterns of water quality parameters at various distances below
the Snake-Clearwater confluence, and in the total Snake flow leaving
the study area after complete mixing.

FISH TRACKING

Test steelhead were picked up in all three track years from the National
Marine Fishery Service trapping facilities at Ice Harbor Dam (RK 16).

We netted fish from the top of the fish ladder, anesthetized them with
MS-222 (Tricaine methanesulfonate), and carried them in canvas bags to

a waiting tank truck on top of the dam. They were then trucked upstream
to the Snake River release point 15 km downstream from the Snake-Clear-
water confluence. Ice, recirculation, and compressed oxygen were used
to maintain the fish during the three to four hour transport. A maximum
of six fish were hauled per trip in the 750 liter tank.

On arrival at the release point, we again anesthetized the fish prior
to removal from the tank, measured total length, and inserted an ultra-
sonic transmitter into the fish stomachs via a tube and plunger assembly.

These sonic ‘tags were the standard sonic transmitters SR69 and SR69A

manufactured by Smith-Root, Inc., Seattle. The two types of tags used
were cylindrical, 6.4 cm and 8.9 cm long, 1.4 and 1.9 cm in diameter,

13


Fish No. 71-36 Oct.27-Nov.7 4— Flow Direction North Shore
— FS elease Point

n 1 n n
15 10 5 OQ South Shore

Fish No. 71-37 Oct.27-Nov.7

i | | |

Kilometers Below Snake-Clearwater Confluence

Figure 17 (Continued), Adult steelhead migration paths in the Snake
River, Lower Granite pool area, 1971.

42


Legend

Clearwater
<> : Cross_over area River

Wms = Resting area Flow_/ / /
North

Wirt Leir-

15 5 shore

KILOMETERS FROM SNAKE-CLEARWATER CONFLUENCE

Figure 19, Principal cross-over and resting areas preferred by sonic-
tagged steelhead migrating through the Lower Granite pool
area, 1969-71.

Complete cross-sectional profiles of current velocity were taken 0.2,
1.6, and 10.6 km below the confluence, but we have presented current
velocities from bottom to 1.5 m off the bottom since this is a depth
representative of adult passage (Figure 20). A plot of steelhead loca-
tions through the velocity stations indicates that off-bottom current
velocity is a more important determinant of lateral location than is
either depth or distance from shore. At each station most fish passed
through off-bottom current velocities of 0.2-0.5 m/sec over a wide
range of depths and distances from shore,

Steelhead Travel Rates and Reversals

Steelhead travel rates and reversals (changes of direction) as related
to 8 independent variables (fish length, day of year, water temperature,
Clearwater River discharge, Snake River discharge, total combined dis-
charge, barometric pressure, and moon phase) were analysed by computer-
ized stepwise multiple regression on an IBM 360/40 computer. Dependent
variables were total movement (up and downstream), net movement up-
stream, and reversals (noted as direction change up or downstream of
greater than 100 m). Day and night behavior was compared separately
and in combination.

The total variation attributable to the independent variables was
usually quite low, ranging from 1 to 50% over the 27 sets of analyses
(9 dependent variables x 3 years). Day of year showed the highest
correlation in 9 of the 27 tests (Table 2) and was always one of the 3
most important independent variables, Water temperature showed the
highest correlation in 8 out of the remaining 18 regressions and failed
to appear in the top 3 rankings only once. Since day of year and water
temperature vary inversely together and are closely related, we do not
feel that these two variables can be realistically separated. This day
of year or water temperature relationship showed highest correlation
with steelhead behavior in 17 out of 27 tests. Barometric pressure was
consistently poorly correlated, ranking in the top three variables only

46


Clearwater

River
4— Flow Direction
1 1 - Korth

Ly pt shore
July 1-2 - - - + -
L of b i | 1 = = 1 ,
Snake River South shore
yp _/. L
= 75 40
July 22-24 71 - 85 72 83
Ly, 1 105 80 ,

hs 1

Aug. 11-13 116

>
'

1
5
ol

Aug. 26-28 - - - 100 -
by p= L -120 4
TOV" 110 47
Oct. 14-16 101 - 113 128 133
Lp 123 n 123 135 4
_ _fs Ll
tts 95 23
Nov. 11-16 109 112 104 111 134
1, 114 1 125 131 4

7! T37 114 24
Dec, 16-19 - - - 112 144
1_,,_126 A 142 139 4
35° «10 5 ()

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE
Figure A-5a. Cross-channel bicarbonates patterns (mg/L CaCO3) in the

Snake and Clearwater Rivers during adult steelhead
migration, 1969.

75


Lower Granite Dam

z

Washington | Idaho

Pollution Sources

D> urban Sewage

@—> Food Processing Wastes
O—> Kraft Pulping Wostes
WWW Cattle Feed Lots

= Rapids

' Washington
Water Power

UZ)

: Clarkston

Kilometers

‘Figure 4, Lower Snake River study area with pollution sources and
major river rapids.


5 times. Moon phase never ranked below 3rd but was the lst selected
variable only once, Ranking of river discharge showed little pattern
and fluctuated widely.

During the July through December steelhead migration period, dissolved
constituents of the Snake River varied from lowest to highest natural
annual levels (Figures A-7a, b, and c). Therefore, a meaningful
analysis had to subdivide a year's migration data into groups according
to the naturally occurring water quality variation. Rapid week to week
variation in the Snake River water chemistry limited comparable fish
groups to a month's duration. The resulting breakdown of steelhead
data into groups relating to natural seasonal changes in water quality
left too few degrees of freedom for strong positive correlation.

We averaged total movement, net movement, and reversals over all 3 study
years and compared them to water temperature, river flow, and barometric
pressure (Figures 21, 22, and 23). The apparent relationship cf total
and net movement to temperature is readily seen as rates change from a
mean rate of 0.5 km/day at 3 C to 15.3 km/day at 23.5 C (Figure 21).
Reversals show no relationship with temperature.

The rate-flow relationship (Figure 22) probably is a further expression
of the already described rate-temperature relationship. Total and net
movement are high at low flows (high temperatures), low at intermediate
flows (typical of fall and early winter cold flows), then high again at
high flows (early summer when river temperatures are rising rapidly).
Reversals show no relationship with flow.

Total and net movement show an optimal relationship with barometric
pressure (Figure 23). Maximum total and net rates are 5.0 and 3.0 kn/
day at 28.45 in. Hg. Migration rates drop at higher and lower barometr-
ic pressures. Reversals show no obvious relationship with barometric
pressure.

Above vs Below Confluence Migration Rates

Comparison of the combined Snake and Clearwater movements above versus
below confluence net upstream movement shows that 1970 fish moved 43%
faster above the confluence than below it. In 1971 fish above the con-
fluence moved 38% slower than they moved below the confluence (Table 3).
Dworshak Dam, a high storage project on the North Fork of the Clearwater
River closed its gates on September 27, 1971, thereby reducing the
Clearwater flow by one-half. Fish tracked after that date had a higher
occurrence of milling and reversals in the lowest 2 km of the Clearwater
River. Such behavior would reduce the net upstream rate.

50


vor
lo

10

11

12

13

14

FIGURES

Lower Snake River, Idaho-Washington

Snake River flow volume below the Snake-Clearwater
River confluence, 1969-71

Snake River temperatures below the Snake-Clearwater
River confluence, 1969-71

Lower Snake River study area with pollution sources
and major river rapids

Schematic breakdown of free-flowing vs post-impoundment
steelhead and water quality comparisons in the Lower
Granite pool area

Temperature (C) profiles 0.2 km downstream from the
Snake-Clearwater confluence

Total dissolved solids (mg/1) profiles 0.2 km downstream
from the Snake-Clearwater confluence

Temperature (C) profiles 2.4 km downstream from the
Snake-Clearwater confluence

Total dissolved solids (mg/1) profiles 2.4 km downstream
from the Snake-Clearwater confluence

Temperature (C) profiles 6.1 km downstream from the
Snake-Clearwater confluence

Total dissolved solids (mg/1) profiles 6.1 km dowstream
from the Snake-Clearwater confluence

Temperature (C) profiles 10,6 km downstream from the
Snake-Clearwater confluence

Total dissolved solids (mg/1) profiles 10.6 km down-
stream from the Snake-Clearwater confluence

Average cross-channel patterns of water quality

parameters in the Snake and Clearwater Rivers during
adult steelhead migration, 1969, 1970, and 1971

iv

11

16

17

18

19

20

21

22

23

25


Sept. 4-8

Oct. 15
Nov. 7

Nov.1-25

joy 1

Clearwater
iver

R
<—Flow Direction p: Kom Shore

yi
At

7.16 7.30 7.09
7.44 8.64
te 2d 6.96 4 1.2241
“ Snake River South Shore
ho.1f,
1 + / L L i=
10.27 10.71 10.82 10.10 1097
ty, Lh09 10.84 4 10.46 4
_ Se
L 1 1 1
“11.93 12.23 12.50
10.27 10.97
i 7, 11.37 11.51 4 11.06 4
35 7" 10 5 ; °

Kilometers Below Snake-Clearwater Confluence

Figure A-2b. Cross-channel oxygen patterns (mg/L) in the Snake and
Clearwater Rivers during adult steelhead migration,

1970.

67


North South North South
shore METERS shore shore METERS shore
0 50 100 150
+ eal
ae7s ah

DEPTH (m)

11 August 1970

25 August 1970

TIF

DEPTH (m)
w Nn

LS

17 November 1970

8 January 1971

Figure 12, Temperature (C) profiles 10.6 km downstream from the

Snake-Clearwater confluence.

22


Sept.2-8

Sept. 8-10

Sept. 21-24

Oct. 8-22

Nov. 4-11

Dec. <li

Ri
+— Flow Direction /-

Clearwater

ver

ron Shore

7.85 7.77 7.85
7.95 7.88
p, ,-2,771 7.88 i 7.93 Ll
oan Snake River South Shore
Lp = n S- [
8.20 8.13 8.09 8.08 7.88
__, 8-48; 8.13 i 8.28 Lt
hrosf
1 J b 1 1. L
8.11 8.24 8,22
8.42 7.72
1, 805, 8.29, 8.19
prof
dey fomnend 1 1
7.70 7.99 7.95
1 8.051 1.95 1 8.124 :
1 tf 1 1 i /- /
8.24 7.78 8.35
8.33 -
1 7 pon254 8.32 1 8.34 1
yo _ ful
7.93 7.90 7.98
8.33 7.33
pe 292) 2.88 1 7.85 n
35 °° 10 5 0

Kilometers Below Snake-Clearwater Confluence

Figure A-lc. Cross-channel pH patterns in the Snake and Clearwater
Rivers during adult steelhead migration, 1971.

45


U.S. Army Corps of Engineers. 1970. Annual fish passage report,
Columbia River Projects, 1970. U.S. Army Corps of Engineers,
North Pacific Division.

U.S. Geological Survey. 1969, 1970, 1971. River flow and temperature
records. U.S.G.S., Portland, Oregon.

Webb, William Edward. 1958. Preliminary studies to determine the
nature of the principal toxic constituents of Kraft pulp mill
waste. M.S. thesis, Oregon State College.

Whitney, Arthur N., and John C, Spindler. 1959. Effects of Kraft
paper wastes on a Montana stream. Trans. Am. Fish. Soc. 88(2):153.

Williams, H.D, 1969. Effect of Kraft mill effluent on structure and
function of periphyton. Ph.D. dissertation, Oregon State Univer-

sity.

58


SECTION VI
RESULTS

Temperature patterns of the two streams were similar from year to year
throughout the study. Midsummer Clearwater River temperatures exceeded
Snake River temperatures before temperature equalization in late August.
Maximal annual Snake River temperatures (25 C) coincided with minimal
annual Snake River flows (A18,000 cfs) in late August. The Clearwater
River cooled more rapidly in September than the Snake and remained at
lower temperatures through winter.

Snake and Clearwater River flows decreased to annual lows in late August
then increased moderately through December (Figure 2). The Clearwater
River contributed its greatest percentage to the combined flow in late
November.

Total dissolved solids (TDS) in the Snake River were substantially
higher than TDS in the Clearwater River throughout the study (Figures
A-7a to A-7c). TDS in both streams attained an annual high in November,
probably due to surface flushing of accumulated debris after extended
periods of little rainfall.

MIXING PATTERNS
0.2 Km Below the Snake-Clearwater Confluence

At 0.2 km below the confluence, mixing took place at a swirling inter-
face of the Snake and Clearwater flows (Figures 6 and 7), The location
of the interface in the stream width depended on the magnitude and
proportion of the Snake and Clearwater River flows. An increase in the
proportion of Snake River water to the total flow forced the interface
toward the north or Clearwater side.

The mixing interface, as indicated by temperature, occupied a 55m
portion of the stream cross-section in early August. but narrowed to a
width of 40 m and moved closer to the north shore in November and
January (Figure 6). Kraft effluent was always contained between the
two river flows at this station. In early August, Kraft effluent was

a vertical column of warmer water at 55 m and in November it was a warm
surface flow between 55 m and 75 m. Kraft effluent appeared as a ver-
tical column of water of high TDS at 110 m across the channel in the
late August profile (Figure 7) but was undetectable at any other time
or at any of the downstream profiles.

a5


Fish No. 69-15 Nov.2 4— Flow Direction North Shore
iy Release Point

1 rt 1 1
15 10 5 © South Shore

Fish No. 69-16 Nov.7-Dec.I5

Fish No. 69-17 Nov.20-Jan.6

ea | , |

Fish No. 69-18 Nov.20-Dec.l2__

Fish No. 69-19 Nov. 20-Nov.26

hi

Kilometers Below Snake-Clearwater Confluence

Figure 15 (Contiriued), Adult steelhead migration paths in the Snake
River, Lower Granite pool area, 1969.

32


es

N
a a
T T

n
a
T

Kilometers and/or Reversals Per Day

Legend
o-+-+= Reversals /
+--+ = Net /

-—+—+ = Total

Figure 22.

1 1 1 n 4
0-23 23-25.5 255-28 28-30.5 30.5733 33-355 355-38 38—
River Flow (CFS -1000)

Three year average kilometers per day and/or path reversals per day compared to
Snake River flow volume, 1969, 1970, and 1971.


8T

DEPTH (m)

DEPTH (m)

North South North South
shore METERS shore shore METERS shore
i?) 50 100 150 200 0 50 100 200

13 August 1970

150
23.22 2gas 1 r

24 August 1970

lan ae

10 October 1970

Figure 8.

Temperature (C) profiles 2.4 km downstream from the Snake-Clearwater

confluence,

343 | 455

v - T
3530 £44495) ryples} 241 2.22

14 January 1971


Sept. 4-18

Oct. 15
to
Nov. 7

Nov. 1-25

Figure A-8b.

+—Flow Direction |

Clearwater
iver

Ri
/ - rom Shore

1 / 1
7238 0 =
Ly t +60 Ll : 1
ue Snake River South Shore
1 ff L 1 n / /
“ ,20 39 45
by ph 35 0 ae
tL SL lL 1 1 /- /
“439 99 -61
1,61 4 59 il 02 t
35 °° to 5 °

Kilometers Below Snake- Clearwater Confluence

Cross-channel tannins and lignins patterns (mg/L
Tannic Acid) in the Snake and Clearwater Rivers

during adult steelhead migration, 1970.

85


Fish No. 71-15 Sept.ll 4— Flow Direction North Shore

Y/ Release Point

1 n n 1
15 10 5 © South Shore

Fish No. 7I-I6 Sept.24-Oct.4

_\ ay, Vn

Fish No. 7I-17 Sept.24-Sept.27

Tos M_A TN

Fish No. 71-18 Sept.26-Oct.3

Vit \ ~.

Fish No. 71-19 Sept.26-Sept.30

Fish No. 7!-20 Oct.8

7 NY

Fish No. 7l-2t Oct.8
T

Kilometers Below Snake-Clearwater Confluence

7 (Continued). Adult steelhead migration paths in the

Figure 1
Snake River, Lower Granite pool area, 1971.

39


Sept.2-8

Sept. 8-10

Sept. 21-24

Oct. 8-22

Nov, 4-1!

Dec. I-11

Figure A-6c.

Clearwater
River

Lod +— Flow Preeti Ss Los Shore

hore

770 70

1276, 73 t 82
ae Snake River South S|

SL

1 7h 1 1
799 95

ry ,-1004 105 l 103 1

Jol

L J 1 i 1

7 TO 105 94
102

' 112, 108 fi 103
Le

a) 1 1 1 S- VA
‘ATS 122 Tis

1,228 4 133 Il 127 L

i tk 1 l 1 / /
71E6 138 T4I

1 53 148 A 153 A

4. / b L L L / x /
7139 135 125

164

y Pah n 146 n 150 1

5 ce)
Kilometers Below Snake-Clearwater Confluence

Cross-channel total hardness patterns (mg/L CaC03)
in the Snake and Clearwater Rivers during adult
steelhead migration, 1971.

80


SECTION VIII
LITERATURE CITED

Alderdice, D.F., and J.R. Brett. 1957. Some effects of Kraft mill

effluent on young Pacific salmon. J. Fish. Res. Bd. Can. 14(5):
783-795.

American Public Health Association. 1965. Standard methods for the
examination of water and waste water. 12th edition, A.P.H.A.,
A.W.W.A., and W.P.C.F.

Barnes, C.A., et al. 1963. A standardized Pearl-Benson, or Nitroso,
method recommended for estimation of spent sulfite liquor or sulfite
waste liquor concentration in waters. Technical Association of the
Pulp and Paper Industry 46(6) :347-351.

Environmental Protection Agency. 1969. Methods for chemical analysis
of water and wastes. EPA, Cincinnati, 312 p.

Falter, C.M., and W.H. Funk. 1973. Joint water quality study by Wash-
ington State University and the University of Idaho on the Lower
Granite damsite area, Final Report submitted to: U.S. Army Corps
of Engineers, Walla Walla.

Jones, Benjamin Franklin. 1955. The avoidance reactions of chinook
salmon, Oncorhynchus tshawytscha (Walbaum), and coho salmon,
Oncorhynchus kisutch (Walbaum), to paper mill effluents. M.S.
thesis, Oregon State College. 32 p.

Miller, E. 1972. Study of pollutional loads in the area of the Snake-
Clearwater River confluence. M.S. thesis, Washington State Univer-
sity.

Nikolsky, G.V. 1963. The ecology of fishes. Academic Press, New York.
352 p.

Oregon Fish Commission. 1967. The 1966 status report on Columbia
River fisheries. Oregon Fish Commission, Portland. 97 p.

Stammer, H.A. 1958, Toxicity towards fish shown by various slime-

controlling agents used in the paper and pulp industry. Papier
Darmstadt 12:41-44; Water Poll. Abs. 31(11) Abs. No. 2243; Sport
Fish. Abs. 4(1) Abs, No. 2157.

Strickland, Roy. 1967, Sonic tracking of steelhead in the Ice Harbor ;
Reservoir, 1967, Washington Game Department.

57


Clearwater

iver
4— Flow Direction Aoxth shore

——a>—y¥p-—1. 1 1
July 1-2 - - - + -
vh— Spake River * South shore
oe _/L
July 22-24 - - - - -
L d $- = rt = = 1
ms L 1 n /. L
7 ~—S
Aug. 11-13 - - - -
1 ] on | 1 iad = 1.
st _ /vL
re TRS ; 141 37
Aug. 26-28 - 142 142 142 148
ay, 14a 1 145 145
po F . fs L
7157 153° 92
Oct. 14-16 134 - 155 156 170
a 154 1 167 171,
ye _AL
152 141° 23
Nov. 11-16 171 158 145 165 175
1 15) 1 165.172 4
ey gt =a m Is VA
- - 19
Dec. 16-19 - - - 148 149
(7 1 - 182 4
35 10 5 0

KILOMETERS BELOW SNARE-CLEARWATER CONFLUENCE
Figure A-7a. Cross-channel total dissolved solids patterns (mg/L NaCl)

in the Snake and Clearwater Rivers during adult steelhead
migration, 1969,

81


Clearwater

River
: ra +—Flow Direction .55Morth shore
Tannins and 70.53 0.75 0.89 0.82
Lignins (mg] 0.25 0.25
/1 Tannic oy 057 0.76 . 0.52 0.34
Acid) ‘ Snake River South shore
a Aol
"26.7 27.1 22.8 9.6
Sulfates (mg/| 30.9 32.5
1) py £21. 25.6 1 29.4 36.3,
ty p—t 1 Aol,
0.19 0.19 0. 21 0.32
Ammonia (mg/ | 0.12 0.74
1 Ly 0223 0.18, 0.14 0.22
poy, 1 hs 7 /
6.8 6.1 G. 0
Transparency |7.4 9.7
(feet) 1, 8% 6.3 1 8.3 10.7%)
yp Sol
Pearl Benson 4.3 5.3 15.0 0.4
Index 1,2 .
(mg/1 CaSSL) py p Saks 7.2 \ 5,6 8.3)
pe _ fs L
147 160 210 42
Total Volatilp 108
Solids Ly £ 150 156 1 145__ 67
(mg/1) 35 “" 10 5 0

Figure 14 (Continued).

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE

Average cross-channel patterns of water quality

parameters in the Snake and Clearwater Rivers
during adult steelhead migration - 1969, 1970,

1971.

26


SECTION IL
RECOMMENDATIONS

Water quality parameters should be measured after Lower Granite Dam is
closed to show effects of localized pollution problem areas which might
result from poor dispersion of wastes in the reservoir.

Adult steelhead migration behavior through the reservoir after its com-
pletion in 1975 should be studied for comparison to the altered post-
impoundment limnology of the "run-of-river" reservoir.

Lay-over and over-wintering areas for steelhead should be described to
determine whether Dworshak release temperature and flow can affect steel-
head behavior in the upper areas of Lower Granite pool.


Fish No. 71-29 Oct.16-Oct.25 4— Flow Direction North Shore

4 ——- =
Release Point aN -"
n a =

15 10 5 © South Shore

Fish No. 71-30 Oct.t7-Oct.26

er CT

Fish No. 71-3! Oct.17-Oct.29

Fish No. 71-33 _Oct.27-Oct.28

Vv | , ,

Fish No. 7I-34 Oct.27-Oct.29

Fish No. 71-35 Oct.27-Nov.7

Kilometers Below Snake-Clearwater Confluence

Figure 17 (Continued), Adult steelhead migration paths in the
Snake River, Lower Granite pool area, 1971.

41


1.

SECTION I
CONCLUSIONS

The Snake River shows only slight deterioration of water quality
from the pollution load it receives in the Lewiston area.

Mixing of the Snake and Clearwater River flows is inversely related
to flow volume,

We were unable to relate steelhead behavior to pollution inputs in
the Lewiston area under free-flowing conditions.

River temperature is positively correlated with steelhead travel
rates.

Wide variations in steelhead behavior were noted from fish to fish
and from year to year.

Above confluence steelhead behavior is not significantly different
than below confluence behavior.


Fish No. 70-16 Sept.26-Sept.29 —\ Flow Direction

North Shore

=
‘Release 7a
Point 7 j
oe = :

15 10 5

Fish No. 70-7 Sept.26-Sept.29

°

South Shore

Fish No. 70-18 Sept.27-Oct.6

\

z n L

Fish No. 70-19 Oct.3-Oct. 21

“v. | |

Fish No. 70-20 Oct.!7-Nov.5

Fish No. 70-21 Oct.I7-Nov.8

Te

Fish No. 70-22 Oct.I7-Nov.5

[MO ke" V ,

Kilometers Below Snake-Clearwater Confluence

Figure 16 (Continued}, Adult steelhead migration paths in the Snake

River, Lower Granite pool area, 1970.

35


and 9 and 42 g respectively, Transmission life was approximately 20
days for the smaller tag and approximately 45 days for the larger tag
at 70 KHz (t 1.5 KHz). The smaller tags were used early in the season
when we could expect fish to pass through the study area within 15 days;
the large tags were used later in the season when the fish were tracked
up to six weeks. Different pulse rates were used so that more than one
fish could be tracked at a time, Ultrasonic signals were picked up in
the water by a hand-held directional hydrophone (Smith-Root, Inc.). The
hydrophone supplied input to a battery-powered TA-60 Sonic Receiver
(Smith-Root, Inc.) for conversion to an audible pulse.

We held tagged fish in Im x lm x 2m nylon mesh live boxes in water 1-1.5
m deep 12 to 48 hours before release into the Snake River. No discern-
ible differences in fish behavior or movement were observed between
different holding times. Fish were released as men and equipment became
available to track fish. Early in the tracking program, two boats each
with two men tracked a single fish; with increased tracking proficiency
one man in a single boat could take a lateral bearing on a fish, then
rapidly move behind the fish and take another bearing for an effective
triangulation of position. Since most fish were 15-25 m from shore,
estimated distances from shore were checked by throwing a weighted,
marked line to shore. We logged a fish's position in relation to per-
manent shoreline markers (power poles, trees, houses, rock points, and
artificial markers erected in the absence of other permanent natural
markers).

In the first track year, we attempted to triangulate fish positions at
chemical stations by pairs of portable hydrophones situated on shore a
known distance apart, and zeroed on a compass bearing. This proved too
time-consuming for use on fast moving fish and no more accurate than
position fixes by boat. In subsequent years, all position fixing was
done from boats.

Early in the track seasons (or at any other times if a fish moved con-
tinuously) we tracked the fish day and night. During times of little
movement of fish, we checked fish locations only periodically through-
out the day. We followed fish paths with particular care near our
water quality stations and near the Snake-Clearwater confluence.

Night tracking was conducted just as day tracking but with the use of
hand-held airplane landing lights to locate shoreline markers. Care
was taken to keep the light from flashing over a fish's position.

During tracks, we maintained continuous records of wind velocity, baro-

metric pressure, cloud cover, and maximum-minimum air temperature.
River flow volumes were obtained from USGS records.

14


Kraft pulping effluent adversely affects fish and other aquatic life
(Stammer 1958; Whitney and Spindler 1959; Webb 1958; and Williams
1969). The reduced velocities and turbulence in the reservoir area
can compound these detrimental effects by allowing concentrations
of effluent to remain undispersed, thus concentrating waste assimi-
lation into a smaller area (U.S. Public Health Service 1964).

3. Runoff from cattle feedlots and winter cattle feeding operations
above Lewiston near the Snake River contributes significant amounts
of nitrogen loading (Miller 1972).

Steelhead trout (Salmo gairdneri Richardson) in the Snake River are a
major fish resource with 60,000 to 100,000 adult steelhead annually
migrating through the Lower Granite pool area to upstream spawning
areas in Idaho and Oregon. The run peaks in September-early October at
a time of minimal water quality (Oregon Fish Commission 1967). Upstream
migrating fish are confronted with lowest flows, highest concentrations
of pollutants, lowest oxygen concentrations, and highest temperatures
of the year,. Chinook salmon runs through the area have averaged 77,000
- « » 36,000 spring chinook, 24,000 summer chinook, and 17,000 fall
chinook (U.S. Corps of Engineers 1970). Summer steelhead runs stand to
be affected most from a deterioration of water quality because of their
timing.


15

16

17

18

19

20

21

22

23

FIGURES - (Continued)

Adult steelhead migration paths in the Snake River,
Lower Granite pool area, 1969

Adult steelhead migration paths in the Snake River,
Lower Granite pool area, 1970

Adult steelhead migration paths in the Snake River,
Lower Granite pool area, 1971

Distribution of steelhead in the Snake River, 1969-71.
Width of bars expresses the percent of fish in each
third of the river width

Principal cross-over and resting areas preferred by
sonic-tagged steelhead migrating through the Lower
Granite pool area, 1969-71

Observed position of steelhead 0.2, 1.6, and 10.6 km
below the Snake-Clearwater confluence in relation to
current velocity 1 m off the bottom, 1969-71

Steelhead migration rate (total and net km/day) and/or
reversals per day compared to river temperature (C).
Averaged over 1969, 1970, and 1971

Steelhead migration rate (total and net km/day) and/or
reversals per day compared to Snake River flow.
Averaged over 1969, 1970, and 1971

Steelhead migration rate (total and net km/day) and/or
reversals per day compared to barometric pressure.
Averaged over 1969, 1970, and 1971

37

43

46

47

51

52

53


Clearwater
iver

R
+ Flow Direction j fp 55 Koon Shore

i ah
7.90 7.90 8.10
Sept. 4-18 7.90 8.3
ty, 1.99 8.05 4 8.10 L
« Snake River South Shore
fe
a7 L i.
Oct. 15 7 B42 8.40 8.41
to | 7.96 8.29
Nov. 7 1, p87 8.42 4 8.61 n
prof
iy 1 at i .
“7,89 7.79 7.58
Nov.!-25] 7.96 8.2;
8.96 8.11 tl 8.17 1
Lu,
35 °° 10 5 °

Kilometers Below Snake-Clearwater Confluence

Figure A-lb. Cross-channel pH patterns in the Snake and Clearwater
Rivers during adult steelhead migration, 1970.

64


6T

North South North South
shore METERS shore shore METERS shore
9 50 100 150 200 Q 50 100 150 290
0
1
=
m 2
&
wy
a3
4
13 August 1970 24 August 1970
0.
T

230

PRY,

10 October 1970 14 January 1971

Figure 9.

Total dissolved solids (mg/l) profiles 2.4 km downstream from the Snake-Clearwater
confluence.


The Lower Granite pool will extend from Lower Granite Dam upstream 59 km
on the Snake and 8 km on the Clearwater River. Elevation of the study
section ranges from 206 meters to 216 meters above mean sea level with
a gradient of 0.60 m/km.

Downstream from the Clearwater River, the Snake River will by 1975, be
a contiguous series of low-head impoundments formed by Ice Harbor Dam
(RK 16), Lower Monumental Dam (RK 68), Little Goose Dam (RK 113), and
the incomplete Lower Granite Dam (RK 174). Asotin Dam is currently an
authorized but unfunded low-head project at RK 235,

The Snake River flows into the Lower Granite pool area a turbulent,
geologically youthful stream. . Chemically, however, it shows the inten-
sive changes it has sustained in south Idaho from irrigation, food pro-
cessing, urban, and cattle feedlot discharges. The three upstream im-
poundments at RK 397, RK 439, and RK 459 (Hell's Canyon, Oxbow, and
Brownlee) slightly improve the chemical quality of the Snake River
flowing out of south Idaho before reaching the Lewiston area. Snake
River flows and temperatures for the three pre-impoundment study years
(1969, 1970, and 1971) show control by these existing upstream storage
projects (Figures 2 and 3). The Clearwater River was unregulated for
the study years, except for the small Washington Water Power Dam at
Clearwater RK 11 and Dworshak Dam on the North Fork of the Clearwater
River. Gates at Dworshak Dam were closed on September 27, 1971, causing
abrupt flow decreases in the Clearwater.

Several significant waste water flows enter this area (Figure 4):

1. The cities of Lewiston-Clarkgton with a combined population of
33,000 contribute 10 x 103 m 3/day of primary treated sewage, and
2. 5 x 103 m3/day of secondary treated sewage (Miller 1972). All
sewage will be receiving secondary treatment by Lower Granite pool
filling in 1975. Asotin, south of Lewiston-Clarkston, contributes
an additional small amount of primary treated sewage.

2. Potlatch Forests, Incorporated, of Lewiston operates a Kraft process
pulping operation which discharges 121.1 x 103 m3/day of primary
treated wastes into the Snake River immediately above the Clearwater
River confluence. These wastes contain 40.9 x 10° kg/day 5-day BOD,
142.4 x 103 kg/day COD, 25.4 x 103 kg/day 80,4, and 45.4 kg/day Na.
Potlatch Forests plans to initiate secondary treatment with an
aerated lagoon by 1975. Because it will still contain high COD and
dissolved materials, the effluent will contribute to the physical
and chemical changes when Lower Granite Dam impounds the free-flow-
ing stream. Increased algal and bacterial growth, as well as
slightly increased temperatures and reduced dissolved oxygen in the
backwater areas, are expected after the river slows (U.S. Public
Health Service 1964; Falter and Funk 1973).


2.4 Km Below the Snake-Clearwater Confluence

The mixing interface occupied a 130 m section in midstream in early
August (Figures 8 and 9). In early August, significant temperature
change (P < .01) occurred across the entire stream width except for a
70 m section in midstream. The interface widened to a 130 m broken
pattern at midstream in October but in January the interface narrowed
to 90 m and approached the north shore.

6.1 Km Below the Snake-Clearwater Confluence

The portion of the cross-section from 165 m to the south shore was ex-
cluded from analysis since this is a slough area which is separated from
the main stream flow.

The mixing interface, as indicated by temperature, occupied most of the
stream width in early August and October but occurred only in a 40m
section near the south shore in late August when temperatures of the
two rivers equalized (Figure 10). Temperature variation across the
stream width was greatest in early August, decreased to the seasonal
low in late August, and increased slightly in October.

No significant variation in TDS across the stream width occurred at this
station during the study (Figure 11).

10.6 Km Below the Snake-Clearwater Confluence

The mixing interface, as indicated by significant temperature gradients,
occupied the entire stream cross-section in early August but steadily
narrowed through the fall and winter as flows increased (Figure 12).

The mixing interface, as indicated by TDS, occupied midstream sections
in August. In November through January, the interface widened and
moved toward the south shore as the Clearwater River flow made its
largest contribution of the season to the total flow.

WATER QUALITY

Because temperature and TDS profiles as well as top and bottom chemical
samples showed near complete surface to bottom mixing in 1969, a near
surface water sample was assumed to be representative of all depths.

There is a high range in temporal and spatial variation as shown in the
cross-channel distribution of the measured water quality parameters and
longitudinal mixing patterns (Figures A-la to A-13c). Although all
chemical data are presented in Figures A-la to A-13c, a more meaningful
pre-impoundment description of the pool area is shown by three-year
mean cross-channel patterns (Figure 14).

24


Clearwater
River

+—_ Flow’ Direction
—_ / North shore
27
*July 1-2 27 - 0
sy pls 1 22,4
Snake River South shore
*July 22-24 ot 3
‘u - 31 - 35 - -
¥ bp _ Bo
ys . F / x L
- 17 -
*Aug. 11-13 18 16 - 20
sy p19 1 13-4
pp _S/-L
Aug. 26-28 - - -- -
Sp “1 rt = =. 1
-_ _/.L
“* 10.0 7.0 7.0
7.5 5.8 11.5

Oct. 14-16 10.0 -
Ly eB ST,

7433 12.5 6.0
Nov. 11-16 8.0 9.0 9.5 8.0 -
py pe Doh 10.0 10.5)
a _hsl
te 33
Dec. 16-19 - - - 9.0
1 L ~ 4. = 1
35° 10 5

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE
Figure A-lla. Cross-channel transparency patterns (Secchi Disc feet)

in the Snake and Clearwater Rivers during adult steel-
head migration, 1969.

*indicates turbidity readings in JTU's.

93


Sept 2-8

Sept. 8-10

Sept. 21-24

Oct. 8-22

Nov. 4-H!

Dec. I-1I

Figure A-8c.

Clearwater

River
Fj +— Flow Direction /. fren Shore
rT St
705 7-20 20
ry 20h 234 1 OL L
oe Snake River South Shore
71.60 1.70 1.85
"158, 1.68 4 1.43 4, +
ayer ; _/L
1.61 1.60 1.90
2.624 1.69 3 1.70 1
—7 1 1 /- [.
10 0 0
1,208 1 213 n 205. l
L of fe 1 1 L /. /
“02 O01 +02
i _,,01 4 02 1 02 '
t}
i J L L 1 /- /
7410 T.50 2.00
172280 5 1.40 L 1.40 1
35 10 5 ro)

Kilometers Below Snake -Clearwater Confluence

Cross-channel tannins and lignins patterns (mg/L
Tannic Acid) in the Snake and Clearwater Rivers
during adult steelhead migration, 1971.

86


240r

210 F

180 F

I5SOrF

Flow (CFS 1000)

120 F

8

cof \

30F

Legend
o2-=1969
= 1970
= 1971

wrereees

Figure 2.

j 1 1 L 1 r l j i
7 24/4 «#8 5 i@ 1 IS 296 20 5 17 1 15 295 19 16 307 21 la ie j2 6 30
14 28 Wl 25 25/8 22] 13 2% 10 24/8 22] 12 26 9 23] 14 26 tl 25 9 23
Jan. | Feb. | Mar. | Apr. May | Jun. Jul. Aug. | Sept. Oct. | Nov. Dec.

Snake River flow volume below the Snake - Clearwater confluence, 1969-71.


Clearwater
ver

Ri
+— Flow Direction /, ron Shore
Tr

n 7 |
713 v19 714
Sept. 2-8 | 0
Lgl, -10 ' .07 1
ae Snake River South Shore
LL, / WA
b 1 L a i
“51 49 53
Sept. 8-10 0 Tr
1 7 pao L 49 L 39 1:
ee _ Sf af
aT +22 25
Sept. 21-24 | .058 54
L226 4 +30 A +19 tL
7 /
a f \ /. VA
725 72k 726
Oct. 8-22 | - -
Ly 2261 +24 ! 22 1
1 ff 1 L L / /
th
Nov. 4-11] | , : . .
1 —. 1 = i = L
4/
VA ° [
L 7 L 1 L
“14 15 +20
Dec. t=} 74, N 09
poy pl5 +14 n 14 n
35 7 lo 5 °

Kilometers Below Snake-Clearwater Confluence

Figure A-10c, Cross-channel ammonia patterns (mg/L NH,) in the
Snake and Clearwater Rivers during adult’ steelhead
migration, 1971.

*Tr = Trace

92


Clearwater
ver

Ri
+— Flow Direction /- fren Shore

3.0 3.0 12.0
Sept. 4-te] -
27.0 4 5.0 tl 4.0 1
ad Snake River South Shore
yp _/L
Oct. 15 ar 0 3.0
to [= -
Now? | 510 8.0 \ 4.0 4
| 7 a 1 L /. /
“"7.0 4.0 50
Nov. 1-25] - -
L325 4 5.0 L 1.5 I
35 °° 10 5 °

Kilometers Below Snake-Clearwater Confluence

Figure A-12b. Cross-channel Pearl-Benson Index patterns (mg/L Standard
Calcium Spent Sulfite Liquor Solids) in the Snake and
Clearwater Rivers during aduit steelhead migration, 1970.

97


No,

A-4c

A-5a

A-5b

A-Sc

A-6a

A-6b

A-6c

A-7a

A-7b

A-7c

A-8a

APPENDIX - (Continued)

Cross-channel carbon dioxide patterns (mg/l free C02)

in the Snake and Clearwater Rivers during adult
steelhead migration, 1971

Cross-channel bicarbonates patterns (mg/l CaC03)
in the Snake and Clearwater Rivers during adult
steelhead migration, 1969

Cross~channel bicarbonates patterns (mg/l CaC03)
in the Snake and Clearwater Rivers during adult
steelhead migration, 1970

Cross-channel bicarbonates patterns (mg/1 CaC03)
in the Snake and Clearwater Rivers during adult
steelhead migration, 1971

Cross-channel total hardness patterns (mg/l CaCO3)
in the Snake and Clearwater Rivers during adult
steelhead migration, 1969

Cross~channel total hardness patterns (mg/1 CaCO)
in the Snake and Clearwater Rivers during adult
steelhead migration, 1970

Cross-channel total hardness patterns (mg/1 CaCO,)
in the Snake and Clearwater Rivers during adult
steelhead migration, 1971

Cross-channel total dissolved solids patterns
(mg/1 NaCl) in the Snake and Clearwater Rivers
during adult steelhead migration, 1969

Cross-channel total dissolved solids patterns
(mg/1 NaCl) in the Snake and Clearwater Rivers
during adult steelhead migration, 1970

Cross-channel total dissolved solids patterns
(mg/1 NaCl) in the Snake and Clearwater Rivers
during adult steelhead migration, 1971

Cross-channel tannins and lignins patterns (mg/l

tannic acid) in the Snake and Clearwater Rivers
during adult steelhead migration, 1969

60

75

76

77

78

79

80

81

82

83

84


Clearwater
River

¢— Flow Direction /. f
1 1 - shore

= 10.50 10.50
July 1-2 _ - - - 9.85
-. 110.40 10.40
“ Snake River South shore
7A * 7.55 8.93
July 22- . - 7.69 9.76 10.36
uly 22-24 in — = 1 3:82 18:08
wy! 1 4 -48/
77.97 759 8.24
Aug. 11-13 8.72 8.14 7.98 9.29 9.80
1 ,8.28 : 8.16 9,30
pa 1 Awl,
tas 7758.03
Aug. 26-28 8.97 8,13 7.70 9.07 9.54
Loi, 8.15 1 8.37 9,42
a a nN 1 prof
"9,22 10.90 11.31
Oct. 14-16 8.93 10.41 10.09 10.29
1 yp 988 1 10,13 9,22
bepg 1 1 Aart
"10.75 10.68 12.26
Nov. 11-16 10.76 10.73 10.84 10.95 10,72
sy p-10,87 1 10,73 10,79
bp i \ \aA
"10.56 10.97 13.16
Dec, 16-19 - - 11.82 11.60
ny pe 9247 1 10.92 11.55
35... ~«210 5 0

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE

Figure A-2a. Cross-channel oxygen patterns (mg/1) in the Snake and
Clearwater Rivers during adult steelhead migration, 1969.

66


TT

Free_flowing Conditions

10 km op

5 ke

Clearwater river

Skmoe

SNAKE
RIVER

Wkms

15 ind

Flow

Figure 5.

Above pollution

+ Below pollution

Post_impoundment
10km T —
5 kd Impounded

Clearwater river

10km

1Skmd

comparisons in the Lower Granite pool area.

SNAKE
RIVER

Flow

above pollution

Impounded
r below pollution

Schematic breakdown of free-flowing vs post-impoundment steelhead and water quality


Clearwater
iver

Ri
; <+— Flow Direction / - fern Shore

1 df
6.5 6.0 6.2
Sept.4-I8] 9,0 -
bt 46.5 1 6.0 1 6.5 1
oe Snake River South Shore
(7 a} 1 1 /. /
Oct. 15 TT 7.1 6.7
to - -
Nov. 7 17.8.0 4 1.8 n 8.9 1
yp SL
“1.9 1.2 1.
Nov. 1-25} = -
L220 4 1.9 4 7.0 F
35°" 10 5 : C)

Kilometers Below Snake-Clearwater Confluence

Figure A-11b. Cross-channel transparency patterns (Secchi Disc feet)
in the Snake and Clearwater Rivers during adult steelhead
migration, 1970.

94


oT

North South North South
shore METERS shore shore METERS shore

DEPTH (m)
w nN

&

24 August 1970

8 August 1970 TT
Oe iN, 2
.\ : es a
Soy
18 November 1970 13 January 1971

Figure 6. Temperature (C) profiles 0.2 km downstream from the Snake-Clearwater confluence.


Rest Areas

Resting areas did increase in frequency as fish approached the con-
fluence (Figure 19). As with cross-over points, the frequency of
individual fish use of rest areas increased markedly later in the track
season. Stopping points became more frequent and longer until November
when resting or stopping times exceeded the six week tag life.

A favored rest area was 2.7-3.5 km below the confluence on both shores,
even though highest mean Pearl-Benson Indexes and total volatile solids
were on the north shore 2.5 km below the confluence (Figure 14). After
mid-September, fish commonly sat for extended periods 100-200 m below
the Clearwater River mouth.

At a rest stop, fish did not remain completely motionless. Normal
resting behavior involved some milling around in an area 20-50 m in
diameter, occasionally moving toward mid-channel, but not to the other
side of the river. Resumption of upstream travel did not always follow
milling activity, but greatly increased milling activity or "restless-
ness" usually preceded resumption of upstream travel.

We attempted to disturb several resting fish by shining a spotlight
directly down on a known fish position at night. The fish did not |
avoid the light in less than 2.5 m water depth. Likewise, efforts to
disturb a fish day or night by boat activity (propeller or jet boat)
directly over the fish were successful only in water shallower than
2.5m

Attempts to observe tagged steelhead in deep water with SCUBA failed.
A diver would position himself on the bottom in a predicted location
to intercept an upstream moving fish, but the divers were consistently
avoided. In one instance when a fish had been sitting in a slough for
two weeks at 4.5 C, divers attempted unsuccessfully to observe the
fish while guided by sonic trackers on the surface. The fish never
left a 40 m diameter area and we were unable to force it from the
slough into faster water. The fish settled down in the same area after
the divers left. :

Depth of Migration and Preferred Current Velocity

Several times each year, we visually sighted tagged steelhead passing
upstream over shoal areas.. These observed steelhead were always within
10-20 cm of the bottom. Low velocity water was preferred to high
velocity water. If a swift, turbulent stretch was ahead of a fish, the
fish would often cross over below the rapids seeking out a lower velo-
city vector, whether the new path was shallow or deep water. Thus, in
some areas fish often travelled several hundred meters through water
only 1-2 m deep.

45


Clearwater
ver

Ri
1 ¢ Flow Direction /. [north shore

July 1-2 - - - - -
rT of = 4. =, =
Snake River South shore
aa _/-l
- 05 .12
July 22-24 - - 104 413 13
bay pat 1 _ 303 1
—lby A+ t 1 [23 VA
16 .08 .13
Aug. 11-13 - 17 04 .05 -20
Ly p16 1 Tr .07 4
bay pt n 1 /35 L
a" 429 59 63
Aug. 26-28 - 31 37 659 49
“8 by 232 : 13h 138 |
Lay fot 1 L /.ss
Oct. 14-16 - - 130=- -O1
Lyf 52 A .03 .21,
yp _ SorL
ad 0 215.29
Nov. 11-16 14 07 130.18 0
bey 05 1 0 131
7}
yp _frarL
tO 2G - 645
Dec. 16-19 - - - 38 26
Ly p28 4 24 124 4
35 10 . 5 0

KILOMETERS BELOW SNAKE-CLEARWATER CONFLUENCE
Figure A-10a. Cross-channel ammonia patterns (mg/L NH,) in the Snake
and Clearwater Rivers during adult steethead migration,
1969.

*Tr = Trace

90


the Snake River from July to September; while Group B (principally
Clearwater River stocks) enters the Snake River from September to
November.

In 1969 and 1970, as opposed to 1971, steelhead studied were larger
individuals and a larger proportion of each year's fish were tracked
later into the fall and winter (Table 1). Clearwater River fish com-
prised 15 and 18% of the total Snake River run in 1969 and 1970, but
only 11% in 1971.

Since our major concern in this tracking program was to detail individ-
ual fish behavior in the Lower Granite area, individual fish paths are
described for each fish tracked in 1969, 1970, and 1971 (Figures 15, 16,
and 17).

In July, August, and part of September in all three tracking years, fish
moved 24 hours a day. We could discern no rate or behavior differences
between night movement and day movement at these times. After early
October, however, fish rested with greater frequency and for longer
periods; movements became very sporadic later in the season.

Fish in 1969 or 1970 were not tracked more than 2 km downstream from
the release point. In 1971, however, one fish moved 50 km below the
release point and was still moving actively downstream through Little
Goose Reservoir at last sighting.

All fish showed a preference for traveling 20-30 m out from either
shore in the Snake River (Figures 15, 16, 17, and 18). Tagged fish
migrated in mid-channel only when crossing over to the opposite shore.
No fish showed sustained upstream movement in mid-channel. The fish
tracked through the shallow first kilometer of the Clearwater River
(0.5-1.0 m deep) did, however, travel in mid-channel. As water temper-
ature and fish movement dropped, some fish did remain stationary near
the middle of the river.

Depending on water conditions, the sonic transmitter could be detected
from 10 to 1000 m away but had an average range of 300-400 m in quies-
cent water of average late summer and fall transparency. The transmit-
ter signal was masked by noises emitted from rocks rolling along the
river bottom and by entrained air from rapids, therefore it was usually
impossible to follow fish in rapids. When a fish entered a rapids area
we went to the head of the rapids and waited for the fish to come
through. The Kraft mill effluent also attenuated or reflected the
transmitter signal in the first kilometer downstream from the Snake-
Clearwater confluence. Occasionally we would locate a tagged fish in
the effluent plume only to lose the signal immediately. The fish would
often appear in the same general area again after several hours of
search, Some fish that entered rapids were never located again in

28


SECTION V
METHODS
MIXING PATTERNS

Pre-impoundment mixing patterns of the Snake and Clearwater Rivers down-
stream from their confluence were established to compare with migration
patterns of adult steelhead. Samples at three points across the river
could not adequately describe mixing patterns of these two large river
flows in sufficient detail for comparison with steelhead movements. We
selected the parameters of temperature and total dissolved solids to
define mixing patterns of the Snake and Clearwater Rivers below their
confluence for two reasons: (1) The two streams' temperature regimens
are usually out of phase, hence degree of mixing should be apparent,
and (2) Total dissolved solids levels of the two streams are always
dissimilar, with no overlap throughout the year.

Cross-sectional profiles of temperature and total dissolved solids were
constructed from vertical profiles taken at intervals across the Snake
River at four points . . . 0.2 km, 2.4 km, 6.1 km, and 10.6 km below
the Snake-Clearwater confluence in 1970 and early 1971, We used a
digital thermistor (Digetec, United Systems, Inc.) with an instrument
accuracy of t 0.15 C. Total dissolved solids were measured with a
conductivity meter (Hach Chemical Company) and remote 12 m lead. Verti-
cal temperature and total dissolved solids profiles were taken at 18 m
intervals across the stream. At each point, the boat was held steady
in the river current by two 30 kg anchors.

We plotted the temperature and TDS series as cross-sectional profile
maps from which we assessed general longitudinal and seasonal trends in
mixing of the Snake River, Clearwater River, and Kraft effluent.

To obtain indices of mixing for seasonal comparison at sampling stations,
computerized least-squares analyses of variance were run on selected
temperature and TDS profiles which represented seasonal changes in mix-
ing at each station, The least-squares analysis of variance separated
variation in temperature and TDS within the profile into: (1) a compo-
nent which resulted from changes in temperature and TDS with depth; and
(2) a component caused by changes in temperature and IDS across the
width of the stream. The F-values and mean squares for each station

and seasonal pattern served as indices of mixing for seasonal comparison.

Duncan's Muitiple Range Test was used to test for significant differences
between mean temperatures and between mean TDS of adjacent width loca-
tions in cross-sectional profiles, These tests disclosed the locations
and widths of mixing interfaces for each station and season.

12


Temperatures of the Snake River leaving the study area ranged from 3.0
C to 23.5 C with the fluctuations resulting primarily from seasonal
climatic changes. Temperature increases from Kraft effluent entering
the river at temperatures above 30 C and volumes of approximately
113,500 to 121,000 m3/day were usually undectable. The great dilution
effect of the river water accounted for the difficulty in identifying
Kraft effluent by temperature as little as 200 m below the outfall.

Differences in river temperature or other aspects of water quality
across the stream width was not shown to significantly affect the
lateral position in the stream of migrating adult summer steelhead.

Multiple correlation showed steelhead travel rates to be most highly
correlated with time of year and water temperature. Extreme variation
between individual fish kept correlation coefficients very low.

Net and total upstream movement was less than 1 km/day in the 0-11 C
temperature range, then increased to 5 km/day at 18.5 C, and increased
very rapidly to 16 km/day at 21 C. This correlation does not prove a
cause and effect relationship between temperature and rate of movement.
However, other evidence implies that a cause and effect relationship
may exist for temperature. Body temperatures of most fish do not
differ more than 0.5 C-1.0 C from that of the surrounding water. There-
fore, changes in the metabolic rate, hence rate of migration, relate
closely to changes in temperature of the surrounding water. Changes in
temperature can trigger the start of processes such as migration and
spawning (Nikolsky 1963).

56


TABLES

Page
Characteristics of the summer steelhead runs and 29
fish tracked in the lower Snake River, 1969-71
Ranking of independent variables according to their 49
apparent relation to steelhead movement. Low ranking
indicates early selection in the regression equation,
hence higher mltiple correlation
Comparison of mean net upstream movement (km/day) 54

above and below the Snake-Clearwater confluence.
Only fish with net upstream movement and tracks of
less than six days duration are represented

vi


Sept. 4-18

Oct. 15
Nov. 7

Nov. 1-25

Figure A-9b.

Clecrwoter
ver

Ri
+— Flow Direction ; jp.

° ro Shore
34

34.5 0
begs - I - A
o Snake River South Shore
sa /
db 1 1 1
“33.0 33.0 28.0
19,1 20.8
n of pat. Or 33,0 n 32.0 1
1 tb 1 iN 1 fol
ue - 13.0
19.1 20.8
7a 1 = 1 = 1
35 °° to 5 °

Kilometers Below Snake- Clearwater Confluence

Cross-channel sulfate patterns (mg/L S0,) in the
Snake and Clearwater Rivers during adult steelhead
migration, 1970.

88


Fish No. 70-i+2 May5

— Flow Direction

North Shore

“Release Point

15

Fish No. 70-3 Julyl6-Julyl7

1
© South Shore

Fish No. 70-5 Aug.3-Aug.4

_\ _ ,

Fish No. 70-6 Aug.5-Aug.6

Fish No. 70-7 Aug.|7-Aug.21

HY NT

Fish No, 70-8 Aug.20-Aug. 21

L

—

Figure 16.

L
Kilometers Below Snake-Ciearwater Confluence
Adult steelhead migration paths in the Snake River,

Lower Granite pool area, 1970.

33


Clearwater
iver

R
+— Flow Direction fo. ror Shore

Ll J fn
5.0 4.5 4.3
Sept. 2-8}. -
Le» p22 5.0 L 5.0 1
1 P= Snake River South Shore
Ly, —t n l fo.0
“U5 6.0 6.0
Sept. 8-10 | . 10.0
8-5 8.0 L 10.5 Li
7 F
1 ob 1 i” 1 SJ /
7.5 9.0 8.0
Sept. 21-24 | 7.5 11.0
pf:5 4 9.0 L 10.0 L
fof
ayaa n L
“7.0 7.2 7.0
Oct. 6-22 | 74
L wy p20 1 7.0 n - l
1 7 fot 1 : 1 /- VA
"6.8 6.8 5.3
Nov. 4=1l} -
Ly p> L 2.0 n 5.9 L
n yuma 1 n hha /
"SAS 7.0 4.5
Dec. I-11] 2,2 7.0
1 6.0 4 6.0 1 8,0 1
35 7h 10 5 0

Kilometers Below Snake -Clearwater Confluence

Figure A-llc. Cross-channel transparency patterns (Secchi Disc feet)
in the Snake and Clearwater Rivers during adult steelhead

migration, 1971.

95


Fish No. 70-23 Octl7-Nov.14 4— Flow Direction North Shore
Release Point

ae — = = oat

15 10 5 9 South Shore

Fish No. 70-24 Oct.I7-Nov.7

Fish No. 70-25 Nov.!2-Nov.14

A, | |

Fish No. 70-26 Nov.12-Nov.I5

Fish No. 70-27 Nov.|2-Nov.|8

1 tL.

Kilometers Below Snake- Clearwater Confluence

Figure 16 (Continued), Adult steelhead migration paths in the Snake
River, Lower Granite pool area, 1970.

36