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Assessing the Impacts of River Regulation on Native Bull Trout (Salvelinus Confluentus) and Westslope Cutthroat Trout (Oncorhynchus Clarkii Lewisi) Habitats in the Upper Flathead River, Montana, USA

September 2012
River Research and Applications 28(7)

DOI:10.1002/rra.1494

Authors:

Clint Muhlfeld

United States Geological Survey

Leslie Jones

State of Alaska

Daniel Kotter

Colorado State University

William Miller

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Hungry Horse Dam on the South Fork Flathead River, Montana, USA, has modified the natural flow regimen for power generation, flood risk management and flow augmentation for anadromous fish recovery in the Columbia River. Concern over the detrimental effects of dam operations on native resident fishes prompted research to quantify the impacts of alternative flow management strategies on threatened bull trout (Salvelinus confluentus) and westslope cutthroat trout (Oncorhynchus clarkii lewisi) habitats. Seasonal and life-stage specific habitat suitability criteria were combined with a two-dimensional hydrodynamic habitat model to assess discharge effects on usable habitats. Telemetry data used to construct seasonal habitat suitability curves revealed that subadult (fish that emigrated from natal streams to the river system) bull trout move to shallow, low-velocity shoreline areas at night, which are most sensitive to flow fluctuations. Habitat time series analyses comparing the natural flow regimen (predam, 1929–1952) with five postdam flow management strategies (1953–2008) show that the natural flow conditions optimize the critical bull trout habitats and that the current strategy best resembles the natural flow conditions of all postdam periods. Late summer flow augmentation for anadromous fish recovery, however, produces higher discharges than predam conditions, which reduces the availability of usable habitat during this critical growing season. Our results suggest that past flow management policies that created sporadic streamflow fluctuations were likely detrimental to resident salmonids and that natural flow management strategies will likely improve the chances of protecting key ecosystem processes and help to maintain and restore threatened bull trout and westslope cutthroat trout populations in the upper Columbia River Basin. Copyright © 2011 John Wiley & Sons, Ltd.

Study reaches in the upper Flathead River, Montana.

…

Weighted usable area versus discharge curves for each target species in reach 1 (a), reach 2 (b), and reaches 1 and 2 combined (c). The bottom right panel (d) summarizes the subadult bull trout night-time habitat by grouping the HSI values into three qualitative categories (low = 0.0 < HSI ≤ 0.3, medium = 0.3 < HSI ≤ 0.7, high = 0.7 < HSI ≤ 1.0).

…

Reach 1 aerial views of night-time subadult bull trout habitat simulated at flows equal to 105 m3 s−1, 339 m3 s−1, and 849 m3 s−1. Darker blue represents higher quality habitat, and white represents unsuitable habitat.

…

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Content uploaded by Clint Muhlfeld

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ASSESSING THE IMPACTS OF RIVER REGULATION ON NATIVE BULL TROUT

(SALVELINUS CONFLUENTUS) AND WESTSLOPE CUTTHROAT TROUT

(ONCORHYNCHUS CLARKII LEWISI ) HABITATS IN THE UPPER FLATHEAD RIVER,

MONTANA, USA

C. C. MUHLFELD,

*L. JONES,

D. KOTTER,

W. J. MILLER,

D. GEISE,

J. TOHTZ

and B. MAROTZ

US Geological Survey, Northern Rocky Mountain Science Center, Glacier National Park, West Glacier, Montana, USA

Miller Ecological Consultants, Inc., Fort Collins, Colorado, USA

Spatial Sciences & Imaging, Fort Collins, Colorado, USA

Montana Fish, Wildlife & Parks, Kalispell, Montana, USA

ABSTRACT

Hungry Horse Dam on the South Fork Flathead River, Montana, USA, has modiﬁed the natural ﬂow regimen for power generation, ﬂood

risk management and ﬂow augmentation for anadromous ﬁsh recovery in the Columbia River. Concern over the detrimental effects of dam

operations on native resident ﬁshes prompted research to quantify the impacts of alternative ﬂow management strategies on threatened bull

trout (Salvelinus conﬂuentus) and westslope cutthroat trout (Oncorhynchus clarkii lewisi) habitats. Seasonal and life‐stage speciﬁc habitat

suitability criteria were combined with a two‐dimensional hydrodynamic habitat model to assess discharge effects on usable habitats.

Telemetry data used to construct seasonal habitat suitability curves revealed that subadult (ﬁsh that emigrated from natal streams to the river

system) bull trout move to shallow, low‐velocity shoreline areas at night, which are most sensitive to ﬂow ﬂuctuations. Habitat time series

analyses comparing the natural ﬂow regimen (predam, 1929–1952) with ﬁve postdam ﬂow management strategies (1953–2008) show that

the natural ﬂow conditions optimize the critical bull trout habitats and that the current strategy best resembles the natural ﬂow conditions of

all postdam periods. Late summer ﬂow augmentation for anadromous ﬁsh recovery, however, produces higher discharges than predam

conditions, which reduces the availability of usable habitat during this critical growing season. Our results suggest that past ﬂow

management policies that created sporadic streamﬂow ﬂuctuations were likely detrimental to resident salmonids and that natural ﬂow

management strategies will likely improve the chances of protecting key ecosystem processes and help to maintain and restore threatened

key words: ﬂow regulation; dams; bull trout; westslope cutthroat trout; IFIM; ﬁsh habitat; two‐dimensional hydrodynamic habitat modelling

Received 22 October 2010; Revised 6 December 2010; Accepted 19 January 2011

INTRODUCTION

Dams are one of the greatest threats to river biodiversity

worldwide (Postel et al., 1996; Poff et al., 2007). Nearly

half of the world's large river systems have been modiﬁed

by dams and diversions for water, energy and transportation

(Nilsson et al., 2005). Dams fragment riverine systems and

modify the natural ﬂow regimen, thereby altering ﬂuvial

dynamics, streamﬂow processes, and biological diversity at

multiple spatial and temporal scales (Stanford et al., 1996;

Poff et al., 1997; Richter et al., 1997; Rosenberg et al.,

2000; Petts, 2009). The construction and operation of

hydroelectric dams modify both downstream and upstream

ﬁsh communities and habitats through inundation, ﬂow

modiﬁcation and fragmentation (Bain et al., 1988; Poff

et al., 1997; Murchie et al., 2008). Dams block ﬁsh

movements, causing genetic isolation (Heggenes and Roed,

2006) and loss of migratory populations (Gosset et al.,

2006; Northcote, 1997), and may produce large daily and

hourly streamﬂow ﬂuctuations that negatively impact ﬁsh

populations and lotic community structure (Cushman, 1985;

Poff and Ward, 1989), which have contributed to the

decline and extinction of many populations and species of

freshwater ﬁshes and native aquatic biota (Rahel, 2000;

Freeman et al., 2001). Consequently, conservation of

riverine ecosystems can be enhanced by understanding the

impacts of alternative dam operations on critical aquatic

habitats (Petts, 1984).

Dams in the Columbia River Basin of North America

have contributed to severe declines in anadromous ﬁsh

stocks during the latter part of the 20th century (Williams

et al., 1989). Most acknowledged are the declines of wild

*Correspondence to: C. C. Muhlfeld, US Geological Survey, Northern

Rocky Mountain Science Center, Glacier National Park, West Glacier,

Montana 59936, USA.

E‐mail: cmuhlfeld@usgs.gov

RIVER RESEARCH AND APPLICATIONS

River Res. Applic. 28: 940–959 (2012)

Published online 3 March 2011 in Wiley Online Library

(wileyonlinelibrary.com) DOI: 10.1002/rra.1494

salmon and steelhead runs, resulting from habitat alteration

and increased smolt and adult migration mortality associated

with hydroelectric dams along the Columbia and Snake

Rivers (Hatten et al., 2009; Kareiva et al., 2000).

Accordingly, recovery programmes have called for late

summer ﬂow augmentation in the Columbia River intended

to assist with the out‐migration of salmon and steelhead

smolts (ISAB, 1997; USFWS, 2000, 2006; NOAA‐Fisheries,

2000, 2008). Flow augmentation is provided, in part,

by releasing water from the Hungry Horse (South Fork

Flathead River) and Libby (Kootenai River) reservoirs in the

headwater reaches of the Columbia River in Montana. In

addition, these two headwater reservoirs provide approxi-

mately 40% of the usable water storage in the US portion of

the Columbia Basin power and ﬂood control operations

(B. Marotz, unpublished data). Despite these water‐use

demands from headwater storage areas, to our knowledge,

no studies have quantiﬁed the impacts of ﬂow management

strategies on native freshwater (resident) salmonids inhabit-

ing the headwaters of the Columbia River Basin.

The two native resident ﬁsh species affected by ﬂow

augmentation and dam operations in the Columbia River

Basin are the bull trout (Salvelinus conﬂuentus) and the

westslope cutthroat trout (Oncorhynchus clarkii lewisi).

Populations have declined throughout much of their native

ranges in western North America, including all portions of

the Columbia River Basin (Williams et al., 1989; Rieman

et al., 1997; Shepard et al., 2005), owing primarily to

habitat destruction, fragmentation and non‐native species.

As a result, bull trout are listed as a threatened species under

the US Endangered Species Act, and westslope cutthroat

trout are classiﬁed as a species of special concern throughout

their native range in the United States. Loss of habitat

connectivity and habitat modiﬁcation can be especially

detrimental to migratory populations because they require

large, relatively pristine and ecologically diverse connected

habitats for spawning, rearing and feeding (Schmetterling,

2001; Muhlfeld and Marotz, 2005; Muhlfeld et al., 2009b),

which is vital for metapopulation persistence (Rieman and

McIntyre, 1995; Rieman and Allendorf, 2001).

The upper Flathead River system in Montana, USA, and

British Columbia, Canada, is considered a range‐wide

stronghold for native bull trout and westslope cutthroat trout

populations (Fraley and Shepard, 1989; Muhlfeld et al.,

2009b). The ﬂow‐regulated portion of the Flathead River

upstream of Flathead Lake (Figure 1) provides critical

overwintering and rearing habitats for migratory populations

(Shepard et al., 1984; Fraley and Shepard, 1989; Muhlfeld

et al., 2003; Muhlfeld and Marotz, 2005; Muhlfeld et al.,

2009a). Since the construction of Hungry Horse Dam in

1952, the natural ﬂow regimen has been modiﬁed for power

generation, ﬂood risk management and ﬂow augmentation

for anadromous ﬁsh recovery in the Columbia River

downstream, by storing water derived from spring run‐off

and sporadically releasing it during the summer, fall and

winter months when ﬂows were historically low (Figure 2)

(Marotz et al., 1996). Concern over the detrimental effects of

ﬂow ﬂuctuations on native salmonid populations prompted

managers to restore and enhance critical river habitats

through ﬂow management strategies that balance human

water uses and the recovery and conservation of resident and

anadromous ﬁshes.

The purpose of this study was to quantify how ﬂow

management strategies have inﬂuenced the availability of

critical native salmonid habitats in the regulated portion of the

main‐stem Flathead River. Our objectives were as follows:

(i) develop site‐speciﬁc habitat suitability functions for

subadult bull trout, adult bull trout and westslope cutthroat

trout to characterize seasonal use of depth and velocity in the

Flathead River; (ii) use a two‐dimensional (2D) hydro-

dynamic model to simulate the microhabitat (depths and

velocities) conditions in the river as a function of streamﬂow;

(iii) combine the habitat suitability curves with the micro-

habitat conditions using a geographic information system

(GIS)‐based habitat model (Miller et al., 2003) to estimate

how the quantity and the quality of habitat vary spatially

over a range of discharges; and (iv) evaluate the impacts

of ﬁve postdam ﬂow management regimens (1953–2008) on

critical habitats and compare the results with predam natural

ﬂow conditions (1929–1952). Understanding discharge

effects on critical habitats is essential to developing

management programmes for recovery of resident ﬁshes

while simultaneously balancing management constraints

of power, ﬂood control and anadromous ﬁsh recovery.

STUDY AREA

The upper Flathead River drainage

The upper Flathead River drainage originates in the

Rocky Mountains of north‐western Montana, and British

Columbia, and includes the North Fork, Middle Fork, South

Fork, main‐stem Flathead River and Flathead Lake. The

drainage area is approximately 18 400 km

and is in the

headwaters of the upper Columbia River Basin. Our study

was conducted in the ﬂow‐regulated main stem of the

Flathead River between the South Fork Flathead River and

the Stillwater River (Figure 1). It was divided into two

reaches based on changes in geomorphology. Reach 1 is

mostly a single‐thread channel (average gradient = 0.23%)

that begins at the South Fork conﬂuence and extends

17.6 km downstream. Reach 2 is a 19.2‐km (average

gradient = 0.03%) anastomosing channel (multiple stable

channels that have a large area covered by mature

vegetation) that extends downriver to the conﬂuence with

the Stillwater River.

DAM IMPACTS ON NATIVE SALMONIDS 941

DOI: 10.1002/rra

A representative study section was selected in each reach

and was used to construct a 2D, spatially explicit habitat

model (Miller et al., 2003). The study section in reach 1

was 3.4 km (~500 000 m

), and the study section in reach 2

was 3.9 km (~820 000 m

). Native ﬁsh species found

in reaches 1 and 2 include bull trout, westslope cutthroat

trout, mountain whiteﬁsh (Prosopium williamsoni), long-

nose sucker (Catostomus catostomus), largescale sucker

(Catostomus macrocheilus) and sculpins (Cottus spp.).

Non‐native ﬁshes include rainbow trout (Oncorhynchus

mykiss), lake trout (Salvelinus namaycush) and lake

whiteﬁsh (Coregonus clupeaformis).

Hungry Horse Dam, South Fork Flathead River

The North, Middle and South Forks of the Flathead River

drain approximately 12 000 km

, with an average annual

discharge of 275 m

(measured at Columbia Falls). The

main stem of the Flathead River, beginning at the

conﬂuence of the South Fork, then ﬂows through

the Flathead Valley from Columbia Falls to Flathead Lake.

Hungry Horse Dam, located 8.5 km upstream of the South

Fork Flathead River conﬂuence with the main‐stem

Flathead River, was completed in 1952. The upstream

drainage area in the South Fork is 4248 km

, contributing

Figure 1. Study reaches in the upper Flathead River, Montana.

C. C. MUHLFELD ET AL.942

DOI: 10.1002/rra

approximately one‐third of the total discharge in the main‐

stem Flathead River. The dam regulates river discharge,

impedes upstream ﬁsh migration, isolates ﬁsh populations

upstream (Figure 1) and has modiﬁed the physical and

biological characteristics of the Flathead River downstream

(Appert and Graham, 1982; Fraley and Graham 1982;

Fraley and Decker‐Hess, 1987; Fraley et al., 1989; Hauer

et al., 1997). Hypolimnetic releases artiﬁcially cooled the

river from 1952 to 1996. In August of 1996, a selective

withdrawal system was installed on four penstocks of

the dam to control temperatures in the tailrace, which

restored the river temperatures to near predam conditions

(Christenson et al., 1996; Marotz et al., 1999). Power

production and ﬂood control operations, however, have

reversed the annual hydrograph, storing water derived from

spring run‐off and releasing it during summer, fall and

winter months when ﬂows were historically low (Marotz

et al., 1996). Consequently, ﬂow regulation has had a

relatively minimal effect on peak spring ﬂows and a greater

effect on base ﬂows and rates of change during base ﬂows

(Figure 2). Short‐term sporadic releases in the tailwater have

created an unproductive varial zone, increased substrate

embeddedness, and have decreased the diversity and the

productivity of macroinvertebrate communities (Ward and

Stanford, 1979; Hauer et al., 1994). Rapid ﬂow reductions

have also been shown to desiccate river margins and strand

insects, zooplankton, ﬁsh and ﬁsh eggs (Hauer and

Stanford, 1982; Perry et al., 1986; Hauer et al., 1994;

Hauer et al., 1997). Moreover, the dam has restricted the

movement and the establishment of non‐native species,

including lake trout and rainbow trout, from downstream

areas to areas upstream of the dam. Although the impacts of

ﬂow modiﬁcations on lower trophic levels are well

understood, before this study, the ﬂow impacts on native

salmonid habitats were unknown.

Native bull trout and westslope cutthroat trout

The upper Flathead River and Lake system is considered

one of the most biodiverse aquatic ecosystems in North

America (Hauer et al., 2007). Over the past century,

however, native ﬁsh populations have declined because of

major community changes in Flathead Lake (i.e. introduced

non‐native mysid shrimp and increase in the non‐native lake

trout population), habitat degradation and fragmentation,

introduction of non‐native invasive aquatic organisms and

the construction and operation of Hungry Horse Dam

(Liknes and Graham, 1988; Fraley and Shepard, 1989;

Spencer et al., 1991; Hitt et al., 2003; Boyer et al., 2008).

These species require the coldest water temperatures of any

native north‐west salmonid; clean substrates for spawning

and rearing; and complex habitat connections between river,

lake and headwater streams that support annual spawning

and feeding migrations (Liknes and Graham, 1988; Fraley

and Shepard, 1989).

The bull trout populations are migratory, whereas the

westslope cutthroat trout populations will either remain in

their home stream for life or migrate throughout the

Flathead system (Liknes and Graham 1988; Fraley and

Shepard 1989; Muhlfeld and Marotz 2005; Muhlfeld et al.,

2009b). Juvenile bull trout and cutthroat trout will rear in

natal streams for 1–4 years, and then as subadults, they will

move downstream during spring or fall to overwintering

areas in the dam‐inﬂuenced portions of the river and

Flathead Lake (Shepard et al., 1984; Muhlfeld and Marotz,

2005). Migratory bull and cutthroat trout grow to maturity

in the ﬂow‐regulated portion of the Flathead River or

Flathead Lake and then travel up to 250 km upriver to

spawn in natal streams that contain clean gravel, cold

groundwater recharge and protective cover. Bull trout begin

spawning migrations in the spring and summer and spawn

from late August through early October when water

temperatures fall below 9°C in low‐gradient reaches (Fraley

and Shepard, 1989). In contrast, westslope cutthroat trout

migrate upstream as ﬂows increase during spring run‐off

and spawn during peak spring ﬂows and as ﬂows decline

and temperatures rise to about 9°C (Muhlfeld et al., 2009b).

Understanding the seasonal habitat requirements of these

species and life stages in the dam‐inﬂuenced portion of the

Flathead River is critical for developing successful

conservation and recovery programmes.

METHODS

One of the most widely applied methodologies for

developing ﬂow recommendations is the instream ﬂow

incremental methodology (IFIM) (Bovee et al., 1998) and

its component hydraulic model, physical habitat simulation

(Milhous et al., 1989). 2D hydrodynamic simulation models

Figure 2. Typical hydrograph of the Flathead River for a ‘predam’

(1945) and ‘postdam’(1971) year.

DAM IMPACTS ON NATIVE SALMONIDS 943

DOI: 10.1002/rra

are now used in place of the original one‐dimensional

hydraulic simulation models (Leclerc et al., 1995; Stefﬂer

and Blackburn, 2002). In the approach used here, habitat

suitability functions are developed for key species to

characterize the microhabitat use of water depth and velocity

and are combined with the detailed depth and velocity

information derived from the hydrodynamic model to

estimate how habitat varies temporally and spatially over a

range of discharges in two river reaches (Kondolf et al., 2000).

Our approach addresses some of the criticisms of the IFIM

modelling approach (Poff et al., 1997), in terms of statistical

validity of physical habitat characterizations and biological

assumptions, by (i) developing seasonal and life‐stage

speciﬁc habitat suitability criteria over multiple temporal

scales (annual, seasonal, diurnal); (ii) statistically evaluating

a species and life stage that is most sensitive to changes in

ﬂow; (iii) analysing how a range of ﬂows (inter‐annual and

intra‐annual variation) inﬂuences critical habitats, as opposed

to establishing minimum ﬂows for target species; and (iv)

applying a 2D hydrodynamic habitat model, which integrates

hydraulic data simulations and habitat suitability data, in a

spatially explicit framework to estimate usable habitat at

various ﬂows.

Habitat use assessments

Radiotelemetry and snorkel surveys were used to inves-

tigate the habitat use by bull trout and westslope cutthroat

trout from 1999 to 2002 in the main‐stem Flathead River. The

habitat use data were collected to develop habitat suitability

functions for each species and life stage within the study

reaches (Rosenfeld, 2003). For each target species, ﬁsh were

classiﬁed into subadult (i.e. ﬁsh that emigrated from natal

streams to the river) or adult size classes based on length

frequency distributions. Bull trout <400 mm were classiﬁed

as subadult ﬁsh, whereas bull trout with lengths ≥400 mm

were classiﬁed as adults (Muhlfeld et al., 2003). For

westslope cutthroat trout, ﬁsh <300 mm were classiﬁed as

subadults, and ﬁsh ≥300 mm were classiﬁed as adults

(Muhlfeld et al., 2009a).

Radiotelemetry was used to assess day and night habitat

use during fall and winter months. Seasons were delineated

based on historic temperature and ﬂow data in the Flathead

River and were classiﬁed as follows: winter (1 December–

31 March), spring (1 April–30 June), summer (1 July–15

September) and fall (16 September–30 November). Fall and

winter habitat use data were pooled because of some ﬁsh

being implanted in late October. Fish were captured in reaches

1 and 2 primarily by boat electroﬁshing and a few by angling

and passive traps (hoop nets). Each ﬁsh was surgically tagged

with a radio transmitter (Muhlfeld et al., 2003) that weighed

2.0–8.9 g (models MCFT‐3HM, MCFT‐3D, MCFT‐3EM;

Lotek Wireless Inc., Newmarket, ON, Canada), depending

on the size and weight of the ﬁsh, and was released near its

capture location. Transmitter life ranged from 40 to 399 days,

and each tag emitted a signal every 5 s at 148.730 MHz. Fish

were tracked from a jet boat equipped with a scanning

receiver (Lotek model W30), a whip antenna and a

directional yagi antenna. Tag location tests revealed that

location accuracy was within 2 m of the transmitter

(Muhlfeld et al., 2003), which was sufﬁciently accurate for

purposes of collecting habitat suitability data. At each ﬁsh

location, a brightly numbered rock (labelled for species and

size class) was placed at the focal point, and locations were

georeferenced (±1 m) using a global positioning system

(GPS) unit (TSC1 Asset Surveyor; Trimble Navigation Ltd,

Sunnyvale, CA, USA). The microhabitat and macrohabitat

use data were collected at each ﬁsh location, including

water depth (m) and mean water column velocity (m s

−1

Water depth and mean velocity were measured from the jet

boat using a US Geological Survey (USGS) A‐55 sounding

reel, a 13.6‐kg sounding weight, and a Price AA current

meter (Geo Scientiﬁc Ltd, Vancouver, BC, Canada). In a

GIS, point locations were overlaid onto a hydrography

map to assess the model results, which were highly

concordant with the ﬁsh location data (Miller et al., 2004).

Macrohabitat units were classiﬁed as rifﬂe, run or pool

(Bisson et al., 1982).

Snorkel surveys were used to collect the summer day

habitat use data in 1999 and 2000. Each study reach was

partitioned into 250‐m river sections using a GIS. The

length of each section was measured along the thalweg, and

the section boundaries were positioned perpendicular to the

stream bank. Divers snorkelled parallel to the stream bank

along a randomly chosen transect, beginning at the

upstream boundary and ﬂoating downstream noting ﬁsh

locations. The habitat use data were collected at each ﬁsh

location as described above.

Multivariate analysis of variance (MANOVA) was used

to simultaneously test for differences in habitat use of both

depth and velocity among target species and life stages.

Independent comparisons of depth and velocity were

conducted using analysis of variance (ANOVA) and

Bonferroni post hoc tests (Statistica, 1995).

Habitat suitability functions

An accurate characterization of microhabitat use by

native biota is crucial to developing reliable habitat

suitability functions, which is an integral step in assessing

ﬂow impacts on usable habitats (Jowett, 1992). Telemetry

and snorkel data were used to develop site‐speciﬁc habitat

suitability functions for select species and life stages in each

study reach. Paired depth and velocity data were used to

produce a three‐dimensional bivariate histogram of habitat

use. This three‐dimensional histogram was then ﬁt with an

C. C. MUHLFELD ET AL.944

DOI: 10.1002/rra

exponential polynomial equation by regressing depth and

velocity variables onto the frequency histogram surface

using a least‐squares regression smoothing procedure

(Bovee, 1986; Statistica, 1995; Miller Ecological Consultants,

Inc., 2001; Miller et al., 2003) with the following equation:

Z= exp(β

+β

D+β

V+β

DV +β

+β

where Z= number of ﬁsh observed; D= water column depth;

V= average water column velocity; andβ

,β

,...=equation

coefﬁcients. The best ﬁt to the three‐dimensional surface was

determined by selecting a ﬁnal model that produced the

largest coefﬁcient of determination with the fewest terms (e.g.

parsimonious model). All the exponential polynomial regres-

sion functions used third‐order terms for depth and velocity

and a ﬁrst‐order interaction term (Table I and Figure 2). The

ﬁnal regression equation was normalized to provide a

maximum habitat suitability index (HSI) of 1; HSI = ((1/N)

exp(β

+β

D+β

V+β

DV +β

+β

)),

where N= normalizing term; D= water column depth;

V= average water columnvelocity; and β

,β

,...=equation

coefﬁcients. These curves were combined with outputs from

the detailed hydrodynamic models to estimate how habitat

varies over a range of discharges (Miller et al., 2003).

Hydrodynamic model

A modiﬁed IFIM approach was used to quantify the

availability of water depths and velocities in each study

reach for various ﬂows of interest (Miller et al., 2003). This

methodology uses a combination of georeferenced ﬁeld data

(i.e. habitat use assessments), habitat suitability criteria (i.e.

habitat suitability functions) and a 2D river hydraulic

simulation model in a GIS. Model outputs provide a

quantitative characterization of habitat throughout the

reaches and illustrate the spatial variability of habitat at

various discharge rates. The Flathead River hydrodynamic

model was run and calibrated for 10 discharges (105, 127,

169, 226, 246, 283, 339, 424, 597 and 849 m

−1

) and ﬁeld

veriﬁed at multiple ﬂows.

Two‐dimensional hydraulic modelling

Hydraulic modelling was conducted to simulate the

changing hydraulic characteristics of the study segments at

various ﬂow rates (Miller et al., 2003). Variations in the

hydraulic character were then related to the species

hydraulic preferences and used to assess habitat availability.

RMA2 (U.S. Army Corps of Engineers (ACOE) Vicksburg,

MS, USA) (King, 1990) and Surface‐water Modeling

System's (SMS; U.S. Army Corps of Engineers (UCOE)

Vicksburg, MS, USA) preprocessing and postprocessing

software were used to model the river hydraulic character-

istics in the Flathead River. Detailed measurements of depth

and velocity were collected in each segment using a

forward‐scanning Doppler proﬁler, whereas survey‐grade

GPS (0.03 m accuracy) provided xand ylocations and

elevations for the digital terrain models. Other ﬁeld data

necessary for the hydraulic simulations included the

following: bathymetry data, water discharge(s) entering

the stream reach, water surface elevation throughout and at

the downstream end of the reach and channel roughness

estimates. With this data, RMA2 simulated the depth‐

averaged velocities in the xand ydirections at every node

within a ﬁnite element mesh.

Geographic information system model and weighted

usable area

The GIS model integrates hydraulic data simulations and

habitat suitability data in a spatial framework to estimate

usable habitat at various ﬂow rates (Miller Ecological

Consultants, Inc., Spatial Sciences and Imaging, 2003). The

habitat suitability equations (Table I) combined with the

georeferenced output from the hydraulic data sets produce

habitat use values, which are calculated based on the depth

and the velocity predicted at each point within the site. Each

spatially referenced 2‐m

cell has an associated HSI value,

which allows for a qualitative comparison of habitat

suitability within a GIS. HSI scores range from 0 to 1.0,

where values equal to 0 represent unsuitable habitat and

values equal to 1.0 represent the highest quality habitat. The

total usable habitat area (m

) in each reach was quantiﬁed

by the summation of the product of area and HSI value of

each cell at selected discharge rates. Each reach‐speciﬁc

total area was standardized by reach length (km) to produce

a weighted usable area (WUA) (m

−1

), which is deﬁned

as usable habitat available at the select discharge rate within

each reach. This process was repeated for all species and life

stages in each reach at the 10 ﬂows of interest. The

evaluation of available habitat at each discharge results in a

habitat–ﬂow relationship (i.e. WUA versus discharge curve)

for each species, which is then used as the data input for the

habitat time series analysis.

Identifying the most sensitive species and life stage

One of the most common methods for conducting this

type of instream ﬂow analysis is to base the assessment on a

single species and life stage that is most sensitive to changes

in ﬂow. We used this approach for the habitat time series

analysis while attempting to minimize potential adverse

impacts to other species and life stages. In many situations,

improvements in the primary target's habitat can be

achieved while retaining adequate habitat availability for

other species and life stages. This approach is called

‘keystone’or ‘cornerstone’species analysis (Bovee, 1986).

As part of the ‘keystone’approach, seasonal and diel

WUA versus discharge relationships for adult bull trout,

subadult bull trout and westslope cutthroat trout were

DAM IMPACTS ON NATIVE SALMONIDS 945

DOI: 10.1002/rra

Table I. Telemetry and snorkel data were used to develop seasonal site‐speciﬁc habitat suitability functions for each species and life stage in each study reach

Species Life stage Season(s) Reach Period Method Sample size r

Bull trout Subadult Fall and winter 1 and 2 Night Radiotelemetry 62 obs, 12 fish 0.99

HSI = (1/39.7878) exp(−((−2.944924) + (4.95138D)+(−17.72043V)+(−0.5488206DV)+(−3.746975D

) + (39.7878V

) + (1.056424D

) + (6.828736V

))

Bull trout Subadult Fall and winter 1 and 2 Day Radiotelemetry 300 obs, 33 fish 0.93

HSI = (1/30.81154) exp(−((0.689862) + (−1.87937D)+(−13.2634V) + (0.0801644DV) + (0.4020176D

) + (30.81154V

)+(−0.0220096D

)+(−15.90897V

))

Bull trout Adult Fall and winter 1 and 2 Day Radiotelemetry 373 obs, 23 fish 0.97

HSI = (1/10.2655) exp(−((1.141814) + (−4.833177D)+(−3.476033V) + (0.1908487DV) + (1.738853D

)+(−4.079766V

)+(−0.156164D

) + (10.2655V

))

Westslope cutthroat trout Juvenile and adult Fall and winter 1 Day Radiotelemetry 153 obs, 27 fish 0.9

HSI = (1/6.18764) exp(−((−1.5048) + (−1.08667D)+(−3.086353V)+(−1.248964DV) + (0.592707D

) + (1.636417V

)+(−0.0382413D

) + (6.18764V

))

Westslope cutthroat trout Juvenile and adult Fall and winter 2 Day Radiotelemetry 150 obs, 17 fish 0.88

HSI = (1/−60.0161) exp(−((3.13705) + (−2.297913D) + (20.58693V)+(−1.4665DV) + (1.00676D

)+(−60.0161V

)+(–0.0773899D

) + (55.1524V

))

Westslope cutthroat trout Juvenile and adult Summer 1 Day Snorkelling 143 obs 0.88

HSI = (1/−75.9382) exp(−((−5.0705) + (−2.152625D) + (34.20934V) + (2.34565DV) + (0.334153D

)+(−75.9382V

) + (0.0015202D

) + (48.8566V

))

Westslope cutthroat trout Juvenile and adult Summer 2 Day Snorkelling 63 obs 0.98

HSI = (1/14.84984) exp(−((4.484183) + (−5.51542D)+(−10.3783V)+(−1.85533DV) + (1.30197D

) + (14.84984V

) + (0.393951D

)+(−3.985407V

))

Habitat suitability equations were constructed by ﬁtting polynomial regression models to frequency distributions for paired depth and velocity observations (obs).

C. C. MUHLFELD ET AL.946

DOI: 10.1002/rra

evaluated for each reach at the 10 ﬂows of interest.

Exponential decay functions were ﬁt to these data to examine

the rate of change in habitat (slope), as ﬂow increases, and

strength (model ﬁtness) of the relationship between

discharge and habitat (PROC REG, SAS version 9.2; SAS

Institute Inc., Cary, NC, USA). This sensitivity analysis was

used in combination with site‐speciﬁc data and other

qualifying characteristics of ecological importance to select

the ‘keystone’species. After the selection was made, a

generalized linear model was used to determine the effect of

different reaches on habitat for the ‘keystone’species, and

time series model outputs for reaches 1 and 2 were aggregated

based on these results (PROC GLM, SAS version 9.2).

Habitat time series

Instream ﬂow assessments can be used to explore the

potential limiting conditions for speciﬁc species and life

stages through the application of habitat time series. The

habitat time series extension of the IFIM simulates the

temporal predictions of habitat availability, an important

step when examining the long‐term impacts on ﬁsh and

invertebrate populations. This process is the decision point

in IFIM because it allows for comparisons of ﬂow

management regimens, which can be used to inform future

management decisions. The premise of habitat time series

analysis is that habitat is a function of streamﬂow and that

streamﬂow varies over time. Therefore, to conduct the

habitat time series analysis, we obtained a baseline (predam)

time series and ﬁve alternative postdam time series of ﬂows

(1953–2008) in the main‐stem Flathead River. Mean daily

discharge rates from 1929 to 2008 were used to interpolate

daily usable habitat quantities from the habitat versus ﬂow

function (i.e. WUA versus discharge curves). We used these

model outputs to investigate the temporal and spatial

arrangement of available habitats under the ﬂow manage-

ment strategies used from 1929 to 2008.

Continuous mean daily discharge data from USGS

gauging station 12363000, on the Flathead River at

Columbia Falls, Montana, were grouped into six ﬂow

management periods, all of which varied in terms of time,

magnitude, frequency and duration of ﬂows resulting from

alternative management strategies. We assumed that

channel morphology and habitat suitability remained

constant over all periods. Management periods were

classiﬁed as follows:

Period 1 (Predam, 1929–1952)—Period 1 represents

natural ﬂow conditions in the Flathead River

before the installation of Hungry Horse Dam in

1952. The natural ﬂow regimen is characterized

by high spring ﬂows in late May or early June

associated with snowmelt, followed by stable

base ﬂow conditions in the late summer, fall

and winter. The number of days with ﬂows

exceeding 20% change from the previous day

ranged from 9 to 33 days per year.

Period 2 (1953–1968)—Period2istheﬁrst postdam

management period. The Hungry Horse Reservoir

reached full pool for the ﬁrst time in 1955, and

dam discharges were adjusted experimentally

during this time to ﬁne tune dam capabilities

and reservoir levels, producing erratic year‐to‐

year changes. The number of days with ﬂows

exceeding 20% change from the previous day

ranged from 40 to 113 days per year.

Period 3 (1969–1985)—Period 3 was a ﬂow management

period with sporadic and extreme hourly, daily and

weekday ﬂow peaking events for power generation

and ﬂood control. A minimum ﬂow requirement of

99 m

−1

was implemented in 1982 (15 December

through 15 April) to eliminate dewatering of

resident kokanee (Oncorhynchus nerka) spawning

areas. The number of days with ﬂows exceeding

20% change from the previous day ranged from

58 to 160 days per year.

Period 4 (1986–1994)—In 1986, radical peaking of ﬂow

rates became more intermittent, weekly pulses

became the norm and there were periods of

relatively high stable ﬂows in the fall and winter.

Reﬁll failures were common because of 4 years of

drought conditions. The number of days with

ﬂows exceeding 20% change from the previous

day ranged from 20 to 70 days per year.

Period 5 (1995–2000)—Late summer ﬂow augmentation

was initiated in 1995 to assist the out‐migration

of threatened Snake River fall Chinook salmon

(Oncorhynchus tshawytscha) in the Columbia

River Basin (ISAB, 1997). Beginning in 1995,

operational strategies attempted to ﬁll the Hungry

Horse Reservoir by 30 June and then draft 6.1 m

by the end of August. The August release

produced an unnatural second ﬂow peak follow-

ing the natural spring freshet. This differed

substantially from the natural hydrograph, which

historically had a gradual decline from peak ﬂows

in early June to basal low ﬂows in late July. The

number of days with ﬂows exceeding 20%

change from the previous day ranged from 20

to 75 days per year.

Period 6 (Mainstem Amendments, 2001–2008)—The

operational strategy for summer ﬂow augmenta-

tion changed in 2001 when the double peak was

smoothed out to restore river ﬂows closer to

natural conditions. The new variable ﬂow and

system ﬂood control strategy (Variable Flow;

VARQ) (ACOE, 1999) was called for by the

DAM IMPACTS ON NATIVE SALMONIDS 947

DOI: 10.1002/rra

2000 Biological Opinions (BiOp) on the oper-

ation of the Federal Columbia River Power

System by both the National Marine Fisheries

Service (NOAA‐Fisheries, 2000) and US Fish

and Wildlife Service (USFWS, 2000). VARQ

was intended to allow dam operators to store

more water before run‐off following a sliding

scale based on water supply from low to high‐

water years. This allowed for spring ﬂow aug-

mentation without compromising reservoir reﬁll

probability and was intended to create a naturalized

spring run‐off (within ﬂood constraints) while

simultaneously protecting resident ﬁsh in the

storage reservoir. In addition, a stable ﬂow release

requirement began in 2001 (15 September–15

December) to stabilize ﬂows for spawning habitats

of resident ﬁsh, requiring discharge rates to remain

between 99 and 127 m

−1

for this late fall and

early winter period. These operational changes

coupled with prescribed ﬂow ramping rates from

the dam (USFWS, 2006; NOAA‐Fisheries, 2008)

are herein referred to as the ‘Mainstem Amend-

ments’or management period 6. The number of

days with ﬂows exceeding 20% change from the

previous day ranged from 6 to 13 days per year.

Habitat magnitude and variability

The mean daily and mean monthly WUA values were

calculated from the time series model outputs to compare

predam and postdam ﬂow management regimens. ANOVA

was used to test for mean monthly differences in WUA

among management periods and to identify the months

with the largest variation in habitat availability due to

management strategies (PROC GLM, SAS version 9.2).

Welch's (1951) ANOVA was chosen for these tests because

the data did not meet the assumptions of equal variance and

group size across management periods required of standard

ANOVA techniques. A post hoc multiple comparison test

that assumes unequal variance (Games–Howell procedure)

was used to test for mean monthly differences in WUA

among postdam management periods. Period 1 was used as

a baseline condition in the post hoc analysis and was

contrasted to the ﬁve postdam ﬂow management periods

(PROC MIXED, SAS version 9.2). This allowed us to

identify management regimens that best replicate natural

ﬂow conditions in the river, thereby maximizing critical

habitat for the ‘keystone’species.

Habitat duration

Habitat duration curves are particularly useful for

assessing the impacts of alternative ﬂow regimens and for

examining habitat changes due to artiﬁcial inﬂuences. In the

IFIM analytical process, habitat duration curves are used to

represent the percentage of time a given habitat threshold is

equalled or exceeded. We developed monthly and seasonal

habitat duration curves for each management period by

sorting the time series data and expressing each data point

as a percentage of the total number of values. Cumulative

frequencies were then ordered from minimum to maximum

to create exceedance probabilities.

Habitat rate of change

The 2D hydrodynamic model allowed us to assess the

inﬂuence of river discharge on WUA, as well as rifﬂe

habitat. We examined simulated ﬂow scenarios between 100

and 850 m

−1

for WUA and rifﬂe habitat. Rifﬂe habitats are

important for the production of aquatic invertebrates and are

similarly affected by higher ﬂow regimens (Brooker and

Hemsworth, 1978; White et al., 1981; Poff and Ward, 1991).

Stable, low ﬂows maximize habitat for macroinvertebrates

and ﬁsh; therefore, maintaining the rifﬂe and nearshore

habitat through stable minimum ﬂows will ultimately have a

positive effect on ﬁsh community health and stream

biodiversity. Rifﬂe habitat was digitized using National

Agriculture Imagery Program 2005 digital orthoimagery and

veriﬁed by ﬁeld GPS observations. The daily discharge

value at the USGS Columbia Falls gauging station was

225 m

−1

during the aerial acquisition of orthoimagery,

which was used in combination with velocity and depth

ranges of >0.5 m s

−1

and <0.7 m, respectively, to deﬁne the

rifﬂe habitat. To further explore how increasing discharge

rates inﬂuence usable and rifﬂe habitat, we calculated the

percentage change in the area at 50 m

−1

increments. This

method was helpful to quantify the rate of habitat decline and

to identify optimum ﬂow scenarios, which maximize both

usable habitat and rifﬂe habitat, simultaneously.

RESULTS

Habitat use

Observed habitat use differed signiﬁcantly among species

and life stages of native salmonids inhabiting dam‐

inﬂuenced portions of the main‐stem Flathead River during

fall and winter (MANOVA, Wilks' lambda = 0.0221,

p< 0.0001). Bull trout adults and subadults occupied

daytime locations in deep, complex areas of the channel

(i.e. runs and pools with large woody debris), whereas

westslope cutthroat trout primarily used pools located along

the channel margins. At night, subadult bull trout moved to

shallow [mean depth = 1.0 m; standard deviation (SD), 0.7],

low‐velocity (mean = 0.22 m s

−1

; SD, 0.16) shoreline areas

of the river channel, presumably to feed (Muhlfeld et al.,

2003). ANOVA (F= 9.912, d.f. = 4,122; p< 0.0001) found

C. C. MUHLFELD ET AL.948

DOI: 10.1002/rra

that subadult bull trout used signiﬁcantly deeper areas of the

channel during the day and signiﬁcantly shallower areas

along the channel margins at night as compared with the

adult bull trout and westslope cutthroat trout. No statistically

signiﬁcant differences (p> 0.05) in habitat use among reaches

1 and 2 were detected for subadult and adult bull trout;

therefore, microhabitat data used in the habitat suitability

models were combined for both reaches. MANOVA results

also support no signiﬁcant differences for subadult and adult

westslope cutthroat habitat use in each reach; therefore, data

were combined for these life stages (Table I). The site‐speciﬁc

habitat suitability functions modelled from the observed

habitat use data and the associated metadata for each species

and life stage are reported in Table I.

Identiﬁcation of the most sensitive species and life stage

In both reaches, the available habitat is higher at lower

discharge rates and lower at higher discharges (Figure 3). In

addition, the WUA versus discharge relationship for

subadult bull trout night‐time habitat, grouping HSI values

into three qualitative categories (low = 0.0 < HSI ≤0.3,

medium = 0.3 < HSI ≤0.7 and high = 0.7 < HSI ≤1.0.),

shows a similar pattern of increased habitat availability at

low ﬂows (Figure 3). Exponential regression models ﬁtto

these data show that river discharge has a statistically

signiﬁcant (p< 0.05) negative effect on the availability of

WUA, demonstrating that increased river ﬂows rapidly

reduce critical habitat for all species, seasons and life stages

in both reaches (Table II). Speciﬁcally, the rate of habitat

decline was greatest for night‐time subadult bull trout habitat

(reach 1: slope = −0.0022; reach 2: slope = −0.0025), indi-

cating that the shoreline areas preferred by subadult bull trout

at night are most sensitive to changes in river discharge,

especially at lower ﬂows. Declining exponential regres-

sions for subadult bull trout night‐time habitat in reach 1

(y= 59 511.7 e

−0.0022x

) and reach 2 (y= 110 508.8 e

−0.0025x

)

suggest that the available habitat declines by approximately

11% with each 50 m

−1

increase in discharge.

Aerial plan views of reach 1 (Figure 4) show that the

spatial arrangement of night‐time subadult bull trout habitat

is more widely distributed through the channel at low ﬂows

as compared with high ﬂows. As river discharge increases,

subsequent increased velocities and depths reduce the total

availability of habitat for subadult bull trout, with most of

the usable night‐time habitat located along the lower

Figure 3. Weighted usable area versus discharge curves for each target species in reach 1 (a), reach 2 (b), and reaches 1 and 2 combined (c).

The bottom right panel (d) summarizes the subadult bull trout night‐time habitat by grouping the HSI values into three qualitative categories

(low = 0.0 < HSI ≤0.3, medium = 0.3 < HSI ≤0.7, high = 0.7 < HSI ≤1.0).

DAM IMPACTS ON NATIVE SALMONIDS 949

DOI: 10.1002/rra

velocity margins of the river channel and island complexes

rather than in the main channel.

Combined, results show that the reduction in suitable

nearshore habitat is especially detrimental to subadult bull

trout, suggesting that this species and life stage is most

sensitive to ﬂow variability. Based on this sensitivity

analysis, the site‐speciﬁc movement information, the

importance of night‐time feeding habitat to subadults and

the threatened status of the bull trout, we chose to base the

time series analysis on the availability of channel margin

habitat for subadult bull trout. Analysis of covariance, used

to examine the effect of different reaches on usable habitat

for subadult bull trout, shows that there is no signiﬁcant

difference in the slopes of the discharge/habitat relationship

among the reaches at night (F= 3.46, p= 0.0813). Because

the rate of habitat loss for subadult bull trout is equivalent

among reach types, the time series analyses results were

aggregated for reaches 1 and 2.

Habitat magnitude and variability

Time series results in Figure 5 show the mean daily

WUA (±SD) and the mean daily percentage change of

WUA for subadult bull trout habitat calculated for each ﬂow

regimen period. The daily change (variation) in WUA is

greatly reduced in periods 1 (predam) and 6 (Mainstem

Amendments), indicating that the most recent ﬂow regimen

(period 6) stabilized ﬂows and usable habitat on a daily,

monthly and seasonal basis, better than any other postdam

management regimen, and was most consistent with natural,

predam ﬂow conditions. Radical peaking of ﬂows and high

variability in usable habitat during period 3 (1969–1984) is

pronounced in this plot, as habitat variability is the highest

of all management periods. Because discharge and habitat

are highly negatively correlated (Table II) and small

increases in discharge result in signiﬁcant decreases in

available habitat (see Habitat rate of change), variation in

ﬂow dramatically reduces the amount of usable bull trout

habitat.

Mean monthly WUA values for subadult bull trout habitat

were calculated for each management regimen. Comparison

of management period means for each month supports the

conclusion that natural predam ﬂow conditions (period 1)

maximize the quantity of available habitat for all summer, fall

and winter months. The months of April, May, June and July

are subject to high spring ﬂows from snowmelt run‐off from

the Middle and North Forks, and ﬂows from Hungry Horse

Dam are released relatively constantly during these months.

ANOVA results indicate that monthly means are not equal

across management periods (p< 0.05) for any months

(Table III). Speciﬁcally, the months of January, February,

August and September had the greatest variation in habitat

availability because of ﬂow management, as evidenced by

the larger F‐values in Table III.

The Games–Howell post hoc comparison of means shows

that period 6 has the smallest mean difference in WUA of all

postdam management periods for the month of January,

February, March, October, November and December, as

compared with period 1 baseline conditions. This supports

the conclusion that the Mainstem Amendments (period 6)

simulate the natural ﬂow conditions and maximize the critical

subadult bull trout habitat better than all other postdam ﬂow

management regimens. Consistent with the ANOVA results,

comparison of mean monthly WUA values for periods 1 and

6 shows that the largest monthly mean differences are late

summer months and winter months. Speciﬁcally, late

summer discharge rates (period 1: mean = 88.62 m

−1

SD = 38.11; period 6: mean = 163.23 m

−1

, SD = 63.24)

and WUA values (period 1: mean = 198 695.18 m

−1

SD = 35 417.06; period 6: mean = 135 881.34 m

−1

SD = 44 579.72) are signiﬁcantly different for periods 1

and 6 (t=−24.62, p< 0.0001; t= 28.29, p< 0.0001). A

two‐sample t‐test shows that discharge rates for periods 1

and 6 (period 1: mean = 64.78 m

−1

, SD = 44.10; period 6:

Table II. Exponential regression model results including slope coefﬁcients (b), standard errors (SE) and coefﬁcients of determination (r

) are

estimated for all species and habitat types of interest in the main‐stem Flathead River, Montana

Reach Species bSE d.f. t‐value p‐value r

1WCT summer −0.0016 0.00027 1,8 −5.85 0.0040 0.8107

1WCT winter −0.0017 0.00041 1,8 −4.00 0.0040 0.6664

1Subadult BLT night −0.0022 0.00019 1,8 −11.77 <0.0001 0.9454

1Subadult BLT day −0.0013 0.00021 1,8 −6.07 0.0003 0.8216

1Adult BLT −0.0007 0.00016 1,8 −4.50 0.0020 0.7167

2WCT summer −0.0016 0.00015 1,8 −10.95 <0.0001 0.9375

2WCT winter −0.0017 0.00039 1,8 −4.39 0.0023 0.7068

2Subadult BLT night −0.0025 0.00037 1,8 −6.68 0.0002 0.8481

2Subadult BLT day −0.0012 0.00027 1,8 −4.36 0.0024 0.7042

2Adult BLT −0.0010 0.00017 1,8 −5.99 0.0003 0.8178

WCT, westslope cutthroat trout; BLT, bull trout.

C. C. MUHLFELD ET AL.

950

DOI: 10.1002/rra

mean = 119.87 m

−1

, SD = 38.08) and WUA values

(period 1: mean = 222 970.09 m

−1

, SD = 36 200.35;

period 6: mean = 169 813.18 m

−1

, SD = 28 710.35) are

signiﬁcantly different for the winter months as well

(t=−26.18, p< 0.0001; t= 32.59, p< 0.0001). Thus, late

summer discharge rates under the Mainstem Amendments

are signiﬁcantly higher than natural ﬂow conditions.

Winter ﬂows under the Mainstem Amendments are stable

with low variability; however, mean discharge values are

signiﬁcantly higher than natural ﬂow conditions resulting

from the 99 m

−1

minimum ﬂow requirement.

Habitat duration and rate of change

Seasonal and monthly habitat duration curves reveal that

predam conditions not only maximize the quantity of habitat

available but also sustain this quantity over the longest time

during the summer, fall and winter periods (Figure 6). The

winter habitat duration curves for each ﬂow management

regimen show that the Mainstem Amendments maintain the

most consistent quantity of habitat (~3 500 000 m

) over the

longest period (~80%) compared with any other postdam

management strategy. Periods 2 and 3 were able to supply

more habitat than period 6 but failed to sustain this quantity

over time. Winter and fall curves show that periods 1 and 6

maintain stable ﬂow regimens that maximize habitat

availability, whereas the curves for periods 2–5 demonstrate

high variability in habitat caused by high variability in

ﬂows. Spring duration curves are similar among all ﬂow

regimens, which is expected because spring run‐off is stored

by Hungry Horse Dam, whereas natural run‐off is occurring

on the Middle and North Forks, producing high spring ﬂows

in the main‐stem river. Summer duration curves indicate

that the Mainstem Amendments do not maximize or sustain

critical bull trout habitat during late summer as compared

with natural ﬂow conditions (Figure 6). Speciﬁcally, late

summer drafting associated with the Mainstem Amend-

ments produces higher discharges in the Flathead River,

which decreases the amount of usable bull trout habitat.

Subadult bull trout WUA exponentially declines between

50 and 250 m

−1

, with 46% of habitat loss occurring at

ﬂows from 100 to 200 m

−1

(Table IV). Rifﬂe habitat is

maximized at ﬂows between 150 and 250 m

−1

, and on

average, there is a 40% loss of rifﬂe habitat as ﬂows increase

Figure 4. Reach 1 aerial views of night‐time subadult bull trout habitat simulated at ﬂows equal to 105 m

−1

, 339 m

−1

, and 849 m

−1

Darker blue represents higher quality habitat, and white represents unsuitable habitat.

DAM IMPACTS ON NATIVE SALMONIDS 951

DOI: 10.1002/rra

Figure 5. Mean daily weighted usable area (WUA) (±SD) time series results and mean daily percentage change (absolute values) of WUA for

night‐time subadult bull trout habitat calculated for each ﬂow regimen period. The black line centred in grey is the mean daily WUA with

one standard deviation (grey shading), and the single solid black line represents the mean daily WUA percentage change. Alternative ﬂow

regimens are as follows: period 1, predam, 1929–1951 (a); period 2, 1953–1968 (b); period 3, 1969–1984 (c); period 4, 1985–1994 (d);

period 5, 1995–2000 (e); and period 6, Mainstem Amendments, 2001–2008 (f).

C. C. MUHLFELD ET AL.952

DOI: 10.1002/rra

from 200 to 400 m

−1

. Thus, both rifﬂe habitat and WUA

are signiﬁcantly higher at lower ﬂows (<250 m

−1

DISCUSSION

Conservation of river biodiversity and native biota requires

understanding the impacts of ﬂow regulation on critical

habitats and populations. Several studies have shown that

dam operations have profound effects on anadromous

ﬁshes, yet before this study, few studies have examined the

impacts of ﬂow management strategies on native salmonid

habitats in the upper Columbia River Basin. Habitat time

series analyses comparing the natural ﬂow regimen to ﬁve

postdam ﬂow management strategies indicate that sporadic

ﬂow ﬂuctuations were likely detrimental to native salmonid

populations. Time series results show that the current

management strategy simulates natural ﬂow conditions and

maximizes critical subadult bull trout habitat better than all

other postdam periods. Late summer ﬂow augmentation for

anadromous ﬁsh recovery, however, produces higher

discharges in the river, which reduces the amount of suitable

bull trout habitat. Combined, these data indicate that

unnatural ﬂow modiﬁcations negatively impact resident ﬁsh

habitats and suggest that natural ﬂow management strategies

that stabilize and maximize the availability of channel margin

habitats are beneﬁcial to the resident ﬁshes in the upper

Columbia River Basin.

Populations of bull trout and westslope cutthroat trout in

the headwaters of the Columbia River Basin are of na-

tional and international conservation concern. Recovery

programmes have focused on maintaining natural habitat

connections, providing a diversity of complex habitats over a

large spatial scale, to conserve the full expression of life

history traits and metapopulation persistence. Our habitat use

results from this study and companion studies (e.g. Muhlfeld

et al., 2000; Muhlfeld et al., 2003; Muhlfeld and Marotz,

2005) illustrate the importance of the dam‐inﬂuenced portion

of the Flathead River to migratory bull trout and westslope

cutthroat trout populations. Furthermore, our study provides

a better understanding of the impacts of dam operations on

critical riverine habitats, which may be used to inform

recovery and management programmes and predict how

water resource management decisions inﬂuence populations

in the upper Columbia River Basin and other similar

freshwater systems.

Habitat time series analyses comparing the natural ﬂow

regimen to ﬁve postdam ﬂow management strategies

indicate that stable ﬂow releases during the low‐ﬂow periods

provide more habitat than variable ﬂow management

regimens. These results are consistent with many studies

that have shown that dam operations that produce

ﬂuctuating or abnormally high discharges disrupt ﬂuvial

processes and modify biological characteristics (Ward and

Stanford, 1979; Cushman, 1985; Poff et al., 1997). Our

study complements other studies in the Flathead River that

have shown that ﬂow regulation has dramatically altered

the physical characteristics of the riverine environment and

lower trophic levels of the aquatic ecosystem (Stanford,

1975; Stanford and Hauer, 1978; Hauer and Stanford, 1982;

Fraley and Graham, 1982; Fraley and Decker‐Hess, 1987;

Beattie et al., 1988; Hauer et al., 1994; Christenson et al.,

1996; Hauer et al., 1997; Marotz et al., 1999) by quantifying

ﬁsh habitat changes in the river.

This study provides evidence that sporadic ﬂow ﬂuctua-

tions negatively impact lateral areas of the channel and are

likely detrimental to bull trout populations. In a companion

study, we evaluated the diel habitat use and movements of

subadult bull trout in the regulated reaches of the Flathead

River (e.g. reaches 1 and 2 in this study) and found that

radio‐tagged ﬁsh commonly moved from deep, mid‐channel

areas during the day to shallow, low‐velocity areas along the

channel margins without overhead cover at night (Muhlfeld

et al., 2003). Diel shifts in habitat use have been reported for

other populations of bull trout (Baxter and McPhail, 1997;

Goetz, 1997; Banish et al., 2008) and are common for other

stream‐dwelling salmonid species, including juvenile

westslope cutthroat trout and mountain whiteﬁsh

(C. Muhlfeld, unpublished data). Furthermore, exponential

regressions ﬁt to the discharge/habitat relationship showed

that subadult bull trout habitat is the most sensitive species

and life stage to changes in ﬂow. Similarly, using life stage

population modelling, Staples (2006) found that the

population growth rate of the bull trout population in the

upper Flathead River was most sensitive to changes in

subadult survival rates. Thus, the habitat changes observed

in this study may lead to potential changes in survival of

Table III. Analysis of variance tests for differences in the mean

quantity of night‐time bull trout habitat available from each ﬂow

regimen management period

Month d.f. F‐value p‐value

April 5,868 3.06 0.0095

June 5,840 42.74 <0.0001

July 5,954 59.35 <0.0001

November 5,878 73.43 <0.0001

May 5,828 88.48 <0.0001

October 5,934 154.91 <0.0001

December 5,905 227.84 <0.0001

March 5,870 246.58 <0.0001

August 5,864 314.65 <0.0001

February 5,776 358.21 <0.0001

January 5,874 383.2 <0.0001

September 5,775 516.46 <0.0001

Mean differences in management periods were tested for each month of

the year.

DAM IMPACTS ON NATIVE SALMONIDS 953

DOI: 10.1002/rra

native ﬁshes. Future work is needed to more closely link

changes in habitat conditions with population demography.

Our results suggest that dams should be operated to

achieve more natural ﬂow conditions for the recovery of

native resident ﬁshes in the headwaters of the Columbia

River and may have broader implications for other bull trout

and westslope cutthroat trout populations that inhabit large

rivers below hydroelectric projects. For example, bull

trout occupy several tailraces of the upper Clark Fork,

Kootenai, Snake and Columbia Rivers (Rieman et al., 1997;

Swanberg, 1997; Homel and Budy, 2008; Monnot et al.,

2008), which are likely affected by ﬂow ﬂuctuations for

hydropower generation and summer ﬂow augmentation in a

similar fashion to that of the Flathead River bull trout

population. Our IFIM approach provides a useful tool for

managers interested in balancing the needs of native resident

ﬁshes with hydropower production, ﬂood risk management

and summer ﬂow augmentation for anadromous ﬁsh

Figure 6. Seasonal habitat duration curves, winter (a), spring (b), summer (c), fall (d) and monthly duration curves, August (e) and

September (f), are shown for subadult bull trout night habitat in the upper Flathead River, Montana. Alternative ﬂow regimens are as

follows: period 1, predam, 1929–1951; period 2, 1953–1968; period 3, 1969–1984; period 4, 1985–1994; period 5, 1995–2000; and

period 6, Mainstem Amendments, 2001–2008.

C. C. MUHLFELD ET AL.954

DOI: 10.1002/rra

recovery. Other studies have used similar approaches to

assess the impacts of ﬂow modiﬁcations on salmon

spawning, rearing and migration corridors in the lower

Columbia River (Tiffan et al., 2002; Dauble et al., 2003;

Hatten et al., 2009) and in other freshwater systems

throughout the world (Freeman et al., 2001).

Flow ramping rates

Our IFIM approach provides empirical data for managing

seasonal river ﬂows and ramping rates because it quantiﬁes

the total availability of suitable ﬁsh and rifﬂe habitat at

various ﬂows of interest. Ramping rates prescribed for the

Flathead River (USFWS, 2006; NOAA‐Fisheries, 2008)

are designed to restore ﬂood plain function and reduce the

deleterious effects on biological production by minimizing

the impacts of ﬂow changes on aquatic organisms that use

the varial zone (Jamieson and Braatne, 2001). Spring dam

discharges are gradually ramped down following the spring

freshet and stabilized, and daily and hourly maximum

ramp‐down rates are more gradual than ramp‐up rates and

are more gradual (~17 m

−1

)atlowerﬂows

(<227 m

−1

). We found that small increases in river

discharge markedly reduce the availability of usable bull

trout habitat, and these changes are more pronounced at

lower ﬂows. For example, a discharge increase from 100 to

150 m

−1

results in 1 870 102 m

of habitat loss (in reaches 1

and 2) and suggests that ﬂow increases below 250 m

−1

affect greater proportions of available habitat for bull trout

and macroinvertebrate production. Thus, these data support

the current 250 m

−1

threshold and sensitivity to ramp‐

down rates.

Summer ﬂow augmentation

Recovery programmes for salmon and steelhead stocks

have called for late summer ﬂow augmentation intended to

assist with the out‐migration of smolts in the lower

Columbia River (ISAB, 1997; USFWS, 2000, 2006;

NOAA‐Fisheries, 2000, 2008). In an attempt to reduce

adverse impacts to resident ﬁsh, the most current objective

of the summer operation strategy is to mimic the natural

spring run‐off event, within ﬂood constraints, gradually

reducing dam discharge toward stable ﬂows for the

biologically productive summer and fall periods. Our

data indicate that smoothing the discharge is beneﬁcial to

river biota because the width of the unproductive varial

zone is reduced, which provides suitable habitat for

native ﬁsh and invertebrate communities. However,

summer ﬂow augmentation produces higher ﬂows during

late August and early September in the Flathead River,

which signiﬁcantly reduces the quantity and availability

of bull trout and westslope cutthroat trout habitat. Food

web dynamics of the river environment are also severely

affected by higher variable ﬂows, causing signiﬁcant

impacts to the aquatic ecosystem (Perry et al., 1986;

Stanford and Hauer, 1992).

The scientiﬁc rationale for late summer ﬂow augmentation

in the main‐stem Columbia River has been controversial. The

BiOp (USFWS, 2000, 2006; NOAA‐Fisheries, 2000, 2008)

concluded that ﬂow augmentation was necessary because

slow water movement and high water temperatures at that

time of year negatively impact the endangered salmon and

steelhead. Biologists in the headwater areas found that the

impacts of reservoir drawdowns on resident ﬁsheries are

Table IV. Simultaneous evaluation of rifﬂe habitat and WUA available to bull trout in the main‐stem Flathead River, Montana

Discharge (m

−1

)WUA (m

−1

)Riffle habitat (m

−1

)WUA % change Riffle habitat % change

100 186 937.59 9 452.24 ——

150 136 120.05 12 005.21 −27.18 27.01

200 97 465.67 12 178.03 −28.40 1.44

250 78 310.36 12 179.13 −19.65 0.01

300 74 202.20 11 323.39 −5.25 −7.03

350 67 257.72 9 647.25 −9.36 −14.80

400 60 223.51 7 334.28 −10.46 −23.98

450 54 874.12 6 455.97 −8.88 −11.98

500 51 176.21 6 410.98 −6.74 −0.70

550 47 478.29 6 482.01 −7.23 1.11

600 43 787.03 6 257.81 −7.77 −3.46

650 40 230.64 5 598.96 −8.12 −10.53

700 36 674.25 4 952.65 −8.84 −11.54

750 33 117.86 4 141.10 −9.70 −16.39

800 29 561.48 3 352.27 −10.74 −19.05

850 26 034.04 2 665.97 −11.93 −20.47

Rifﬂe habitat and WUA are compared at 50 m

−1

intervals for discharge rates ranging from 100 to 850 m

−1

WUA, weighted usable area.

DAM IMPACTS ON NATIVE SALMONIDS 955

DOI: 10.1002/rra

substantial (Marotz et al., 1996; Marotz et al., 1999).

Although ﬂow augmentation is assumed to have a positive

survival and migratory beneﬁt for summer migrants, such

as Snake River fall Chinook salmon, this has not been

empirically shown. Any potential beneﬁts of ﬂow augmen-

tation on anadromous salmon should be weighed against

the deleterious effects of augmentation on resident trout

habitat in the upper basin.

CONCLUSIONS

Our data demonstrate that unnatural ﬂow management

regimens (for power production, ﬂood risk management

and ﬂow augmentation) negatively impact bull trout and

westslope cutthroat trout habitats in the headwater reaches

of the Columbia River Basin. Our data provide empirical

support for the BiOp, which recommend that Hungry

Horse Dam operate conservatively, releasing stored water

gradually over the summer, fall and winter months to avoid

unnatural ﬂow ﬂuctuations. However, summer ﬂow

augmentation for anadromous ﬁsh recovery unnaturally

increases ﬂows during August and September, thereby

reducing the amount of usable ﬁsh habitat in the Flathead

River. Our results suggest that the river ecosystem would

beneﬁt by stabilizing ﬂows and restoring the natural ﬂow

regimen during late summer months.

The natural ﬂow paradigm provides an ecological view on

water management that recognizes the complex relationships

between the ﬂow regimen and ecosystem function (Poff

et al., 1997; Richter et al., 1997; Petts, 2009). We used an

instream ﬂow model coupled with site‐speciﬁcﬁsh habitat

use data to evaluate how the critical components of the

natural ﬂow regimen (e.g. magnitude, frequency, duration,

timing and rate of change of hydrologic conditions) affect

the availability of usable habitat among several ﬂow

management strategies. Our results suggest that past ﬂow

management policies that created sporadic ﬂow ﬂuctuations

were likely detrimental to native salmonid habitats. Our

analyses demonstrate that natural ﬂow regimens stabilize

and maximize the availability of channel margin habitats and

are likely beneﬁcial to the recovery and conservation of rare

and threatened salmonids in the upper Columbia River

Basin. Modiﬁcation of the Hungry Horse Dam operating

regimen to approach the natural ﬂow regimen as much as

possible under the current management constraints will

improve the chances of protecting key ecosystem processes

and help to maintain and restore the threatened bull trout and

westslope cutthroat trout populations.

ACKNOWLEDGEMENTS

The authors thank Bonneville Power Administration, Montana

Fish, Wildlife & Parks and the US Geological Survey for

funding and administration of the project. They thank

S. Glutting, R. Hunt, D. Belcer and M. Boyer for assistance

in the ﬁeld; G. Pess, A. Wilcox, K. Tiffan, C. Kendall, P.

Van Eimeren, J. Giersch, S. Carrithers, S. Reller, J.

Kershner and one anonymous reviewer for reviews of the

previous drafts. Any use of trade, product or ﬁrm names is

for descriptive purposes only and does not imply

endorsement by the US Government. This research was

conducted in accordance with the Animal Welfare Act and

its subsequent amendments.

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DAM IMPACTS ON NATIVE SALMONIDS 959

DOI: 10.1002/rra

Dam operations may improve aquatic habitat and offset negative effects of climate change

Article

Feb 2018
J ENVIRON MANAGE

Dam operation impacts on stream hydraulics and ecological processes are well documented, but their effect depends on geographical regions and varies spatially and temporally. Many studies have quantified their effects on aquatic ecosystem based mostly on flow hydraulics overlooking stream water temperature and climatic conditions. Here, we used an integrated modeling framework, an ecohydraulics virtual watershed, that links catchment hydrology, hydraulics, stream water temperature and aquatic habitat models to test the hypothesis that reservoir management may help to mitigate some impacts caused by climate change on downstream flows and temperature. To address this hypothesis we applied the model to analyze the impact of reservoir operation (regulated flows) on Bull Trout, a cold water obligate salmonid, habitat, against unregulated flows for dry, average, and wet climatic conditions in the South Fork Boise River (SFBR), Idaho, USA.

Flow and spawning habitat relationships for Dolly Varden: Understanding habitat-population dynamics in the Canadian Western Arctic

Article

Full-text available

Dec 2019

Northern form Dolly Varden (Salvelinus malma malma) have been designated as a species of Special Concern in Canada due to declines in population abundance and potential threats. Concern over detrimental effects of low flows on population abundance prompted research on how variability in discharge regimes influence habitat availability. Habitat suitability indices for prespawning and spawning adult anadromous Dolly Varden from two streams were integrated into a two‐dimensional hydrodynamic habitat model to assess the effect of flow variability on usable habitat. Regional hydrographs were used to identify an ecologically relevant range of flows that provided optimal spawning habitat for these populations and examine the relationship between abundance and discharge. Adults spawned in the tail end of pools at moderate water depths and water velocities, and used pebble‐ to cobble‐sized substrate for building redds; whereas, prespawning adults occupied deeper pools with moderate velocities and used cobble for cover. Model outputs showed that spawning habitat availability was optimized at flow rates between 1.6 and 3.0 m3/s and between 1.0 and 6.0 m3/s in Fish Hole Creek (FHC) and Little Fish Creek, respectively. A positive relationship between flows during the fall spawning period and abundance of the FHC population suggests that higher flows coinciding with optimal habitat availability may have contributed to positive recruitment. To strengthen and refine this habitat–population relationship for Dolly Varden in this area requires investigation of a broader suite of variables associated with environmental regimes and physical habitat in reaches used for spawning.

Review of aquatic species habitat simulation method and modelling

Article

Apr 2019

An ecohydraulics virtual watershed: Integrating physical and biological variables to quantify aquatic habitat quality

Article

Full-text available

Nov 2018

Advances in remote sensing coupled with numerical modeling allow us to build a “virtual ecohydraulics watershed” at the micro‐habitat scale. This approach is an integrated modeling framework with a cascade of models including physical (hydrologic, hydraulic and stream water temperature) and biological (fish habitat) modeling at a resolution and extent important for aquatic and terrestrial organisms. We applied this approach to quantify the impacts of discharges and water temperature on habitat quality and spatial/temporal habitat use patterns of Bull Trout, a federally listed species along the South Fork Boise River (SFBR). We coupled process‐based snow melt and hydrologic models to predict water availability within the watershed. The model fed one‐ and two‐dimensional hydrodynamic models to predict stream hydraulics and water temperature using high‐resolution (meter scale) river bathymetric data. This information was then used in an aquatic habitat modeling to characterize habitat quality distribution as a function of discharges. Our results showed that the summer thermal regime of river system would alter available habitat. The high spatial resolution analysis allows modeling to predict the importance of lateral‐habitats, which serve as vital refugia during high flow events for many fish species. The advances in remote sensing, numerical modeling and understanding of physical‐biological processes provide us an opportunity to conceptualize new process‐based integrated modeling tools to analyze human impacts at a catchment scale, for example dam operation and climatic variability on aquatic habitat and status, and further to develop restoration protocols in a virtual domain before field studies are developed and/or structures built.

Long-Term Trends in Abundance and Size of Sport Fishes in the Flathead River, Montana, Following Changes in Hydroelectric Dam Operations

Article

Full-text available

May 2018
NORTHWEST SCI

We studied long-term trends in catches per unit effort (CPUE; fish h-1) of four sport fish taxa in the Flathead River, Montana, following changes in hydroelectric operations at the Sliš Ksanka Qisp Project (SKQP; formerly Kerr Dam). Prior to 1997 SKQP operations caused frequent, unnatural flow fluctuations. In 1997 the dam was changed from a power-peaking and load-following facility to a base-load facility. The new operations included seasonal minimum flows and ramping rates that greatly reduced flow fluctuations. Autumn trends in CPUEs of two size classes (substock and stock) of northern pike (Esox lucius), Oncorhynchus spp., brown trout (Salmo trutta), and smallmouth bass (Micropterus dolomieu) were monitored using nighttime electrofishing during 1984–86 before operational changes and again at the onset of operational changes in 1998 and continuing through 2008. We observed little difference in CPUEs between 1984–86 and 1998, the first year after changes, but we documented strong increasing trends in CPUEs of both sizes of all taxa, except stock northern pike, over the long term following operational changes. We also examined long-term patterns in the size structure (total length; TL mm) of fishes following operational changes. All taxa had either initial downward shifts in median TL, decreases in minimum sizes of fish captured, or both, a pattern consistent with enhanced recruitment and survival of smaller fishes. We conclude that modifications in dam operations were associated with increases of four sport fish taxa in the Flathead River and that similar normative flow applications might benefit riverine fish populations elsewhere.

A social-ecological perspective for riverscape management in the Columbia River Basin

Article

Full-text available

Jan 2018

Riverscapes are complex, landscape-scale mosaics of connected river and stream habitats embedded in diverse ecological and socioeconomic settings. Social–ecological interactions among stakeholders often complicate natural-resource conservation and management of riverscapes. The management challenges posed by the conservation and restoration of wild salmonid populations in the Columbia River Basin (CRB) of western North America are one such example. Because of their ecological, cultural, and socioeconomic importance, salmonids present a complex management landscape due to interacting environmental factors (eg climate change, invasive species) as well as socioeconomic and political factors (eg dams, hatcheries, land-use change, transboundary agreements). Many of the problems in the CRB can be linked to social–ecological interactions occurring within integrated ecological, human–social, and regional–climatic spheres. Future management and conservation of salmonid populations therefore depends on how well the issues are understood and whether they can be resolved through effective communication and collaboration among ecologists, social scientists, stakeholders, and policy makers.

Influencia del hábitat físico sobre la ictiofauna - cuenca baja río Dagua: caso de la quebrada Jesús

Thesis

Full-text available

Dec 2013

Olga Lucía Pulido Méndez

Aquatic Habitat Response to Climate-Driven Hydrologic Regimes and Water Operations in a Montane Reservoir in the Pacific Northwest, USA

Article

Full-text available

May 2017

Freshwater systems are progressively becoming more stressed with increased human demands combined with expected trends in climate, which can threaten native biota and potentially destabilize the ecosystem. Numerical models allow water managers to evaluate the combined effects of climate and water management on the biogeochemical processes thereby identifying opportunities to optimize water management to protect ecosystem function, biodiversity and associated services. We used a 3D hydrodynamic model (ELCOM) coupled with an aquatic ecosystem dynamic model (CAEDYM) to compare two scenarios across three climatic and hydrologic conditions (extreme wet, extreme dry and average) for Deadwood Reservoir (USA). Additionally, we collected water temperature, water chemistry and biological data from the reservoir and inflowing tributaries to validate the model, as well as migration and growth data from Bull Trout (Salvelinus confluentus) the top predator of the food web. Modeled scenarios identified that reducing minimum outflows from 1.4 to 0.06 m³ s⁻¹ during the fall and winter months resulted in higher reservoir elevations and cooler water temperatures the following year, which extended reservoir rearing during the summer and fall seasons. The scenarios with reduced stream flow during the fall and winter seasons indicate benefits to the reservoir ecosystem, particularly during dry years, and could reduce the effects of climatic warming.

Characterizing the movements and habitat use of two fish species of concern in a regulated ecosystem

Article

Full-text available

Oct 2021
HYDROBIOLOGIA

In freshwater ecosystems in the northwest United States, the distribution and movements of fish between their essential habitats are particularly impacted by the presence of hydroelectric dams. Bull Trout Salvelinus confluentus and Westslope Cutthroat Trout Oncorhynchus clarkii var. lewisi are two fish species of concern inhabiting the Pend Oreille River between Idaho and Washington states. The purpose of this study was to identify the behavior and habitat use of Bull Trout and Westslope Cutthroat Trout in the restricted area of the Pend Oreille River, downstream of Albeni Falls Dam (AFD), using a long-term radio-telemetry dataset. Between 2015 and 2018, 24 Bull Trout and 24 Westslope Cutthroat Trout were captured, tagged, and released downstream AFD. Among the fish tagged, 79% (n = 19 of 24) of Bull Trout and 67% (n = 16 of 24) of Westslope Cutthroat Trout were detected during the study period. Our results revealed movements of fish towards tributary confluences mostly in May, June, and July for both species with Bull Trout traveling longer distances than Westslope Cutthroat Trout. Although the sample size was limited, Bull Trout individual movements towards the dam suggested attempts to re-ascend the river, indicating the importance of restoring upstream connectivity.

Threats to at‐risk salmonids of the Canadian Rocky Mountain region

Article

Dec 2019

Trout and charr, members of the salmonid family, have high conservation value but are also susceptible to anthropogenic threats in part due to the specificity of their habitat requirements. Understanding historical and future threats facing these species is necessary to promote their recovery. Of freshwater trout and charr in the Canadian Rocky Mountain region, westslope cutthroat trout (Oncorhynchus clarkii lewisi), bull trout (Salvelinus confluentus; a charr species) and Athabasca rainbow trout (Oncorhynchus mykiss) are of conservation concern. And indeed, range contractions and declining populations are evident throughout much of their ranges. Range contraction was most evident in the southern Alberta designatable unit (DU) of westslope cutthroat trout. Diminished populations were also evident in the downstream watersheds of the Alberta bull trout range, and throughout the Athabasca rainbow trout range. We assessed historical and future threats to evaluate the relative importance of individual threats to each DU and compare their impact among species. Individual threats fall into the broad categories of angling, non‐native species and genes, habitat loss and alteration, and climate change. Severity of each threat varies by DU and reflects the interaction between species’ biology and the location of the DU. Severity of threats facing each DU has changed over time, reflecting extirpation of native populations, changes in management and industry best practices, expansion of non‐native species and progressing climate change. The overall threat impact for each DU indicates a high probability of substantial and continuing declines and calls for immediate action.

Diel Behavior of Juvenile Bull Trout and its Influence on Selection of Appropriate Sampling Techniques

Conference Paper

Full-text available

Jan 1997

Fred Goetz

Diel activity patterns of juvenile bull trout ( <200 mm) were described in Jack Creek, Metolius River, Oregon, to improve sampling efficiency. I show that fry (age 0) counts were significantly higher (P<0.001) during the day, while counts of juvenile fish (age I and 2) were significantly higher (P<0.001) at night. The highest counts of juveniles occurred during a "quiet period" immediately after dusk, when fish were inactive, out of cover, and easily counted with underwater flashlights. In a comparison of four sampling methods during 1989 and 1990, electrofishing estimates were significantly correlated with day (r=0.81) and night (r=0.89) snorkeling counts, but not with streambank counts. In a comparison of day and night snorkeling in ten Cascade Mountain streams from 1989-1991, total density estimates were significantly greater (P<0.01) for night snorkeling than day. These studies suggest that surveys of abundance, distribution, and habitat use of bull trout should include night surveys as well as day.

Downstream migration of the European eel (Anguilla anguilla) in the Elbe River, Germany: movement patterns and the potential impact of environmental factors

Article

Full-text available

Feb 2015
RIVER RES APPL

Recruitment of European eels (Anguilla anguilla) has declined to the extent that they have been added to the IUCN Red List of Threatened Species. Therefore, it is critical to ensure that eels complete their outward river migration in order to contribute to the available spawning stock. We conducted a four-year (2007-2011) telemetry study to understand the migratory behaviour and potential impact of environmental factors on the eel during this critical life stage. Out of 399 female eels tagged with acoustic transmitters, only 28 % demonstrated clear downstream migratory behaviour. Fifty-five percent were detected exhibiting no downstream migration behaviour and 17 % were not detected at any monitoring station. Movement patterns of downstream-migrating (silver) eels were characterised by nocturnal activity and seasonal migration, with distinct peaks in autumn and spring. Migration was often discontinuous and exhibited phases of active locomotion and expanded stopovers. The most important determinants of movement activity were water temperature, cumulative precipitation, and moonlight, although the significance varied by season and location in the river basin. Our results evidence a discontinuous, stepwise migration over an extended period. Furthermore, our findings indicate that migration success depends on holding duration prior to tagging, and environmental predictors with varying importance depending on the season, as well as the locations of capture, tagging and release. DOI: 10.1002/rra.2881

The impact of Hungry Horse Dam on the fishery of the Flathead River : final report

Book

Jan 1982

Effects of reduced stream discharge on fish and aquatic macroinvertebrate populations ( rainbow trout Salmo gairdneri).

Article

A study was made of the responses of aquatic insects and juvenile rainbow-steelhead trout Salmo gairdneri to flow related changes in habitat, and of the predictive capability of 3 hydraulic simulation models that are currently used to make instream flow recommendations.-from US Govt Reports Announcements, 22, 1982

Movements of and Habitat Use by Fluvial Bull Trout in the Blackfoot River, Montana

Article

Sep 1997

Tim R. Swanberg

The seasonal movements and habitat use by fluvial bull trout Salvelinus confluentus in the Blackfoot River drainage, western Montana, were investigated by using radiotelemetry and snorkel surveys from May 1994 to October 1995. Twenty-four bull trout made upriver migrations (mean distance, 63 ± 21 km), 33% of which were related to spawning. In June of both years fish began migrations, which appeared to be cued by an increase in maximum daily water temperature (to 17.7°C in 1995) and a decrease in discharge from peak runoff. Larger fish began moving at cooler temperatures and earlier dates than smaller fish. Migrations occurred nocturnally and were generally rapid (grand mean, 4.4 ± 2.2 km/d). Daily rates of migration were correlated with maximum daily temperatures. Spawning bull trout ascended tributaries in late June to early July, 67 ± 10 d before spawning. Nonspawning fish entered the lower portions of these tributaries after spawning fish and remained in them 28 ± 18 d before returning downriver in late August. While in Monture Creek, a major spawning tributary for the Blackfoot River, adult bull trout used deep pools and were positively associated with habitat units containing mountain whitefish Prosopitan williamsoni. Eighty-six percent of migrants returned downriver to within 20 m of sites occupied in the spring. In 1994, two nonmigrating fish in the Blackfoot River used the confluence of a cold tributary, but no such behavior was observed in 1995. Results suggested that water temperature influenced the movement of fluvial bull trout and that tributary habitat was important for both spawning and nonspawning fish. Results also demonstrated the large spatial scale and diversity of habitats required to sustain fluvial bull trout populations.

Review of Ecological Effects of Rapidly Varying Flows Downstream from Hydroelectric Facilities

Article

Jul 1985

R. M. Cushman

Rapid changes in flow below hydroelectric facilities result from peaking operations, where water is typically stored in a reservoir at night and released through turbines to satisfy increased electrical demand during the day. Potential impacts of these short-term, recurring disturbances of aquatic systems below dams are important considerations in hydropower development. Reduced biotic productivity in tailwaters may be due directly to flow variations or indirectly to a variety of factors related to flow variations, such as changes in water depth or temperature, or scouring of sediments. Many riverine fish and invertebrate species have a limited range of conditions to which they are adapted. The relatively recent pattern of daily fluctuations in flow is not one to which most species are adapted; thus, such conditions can reduce the abundance, diversity, and productivity of these riverine organisms. Information needs for site-specific evaluations of potential impacts at hydroelectric peaking projects are outlined, along with management and mitigation options to reduce anticipated adverse effects.

Occurrence of Bull Trout in Naturally Fragmented Habitat Patches of Varied Size

Article

May 1995

Bull trout Salvelinus confluentus and other salmonids in the Pacific Northwest are believed at risk of local and regional extinctions because of ongoing habitat loss and fragmentation. Biologists have focused on defining and protecting critical stream channel characteristics, but there is little information regarding the scale or spatial geometry of habitat that may be necessary for the species' long-term persistence. We investigated the influence of habitat patch size on the occurrence of bull trout by determining the presence or absence of fish in naturally fragmented watersheds of the Boise River basin in Idaho. We defined patches of potential habitat for bull trout as watersheds above 1,600 m elevation, a criterion based on the presumed restriction of local populations by stream temperature. We used logistic regression to investigate the possible influence of patch size as well as stream width and gradient on the occurrence of bull trout at reach, stream, and patch scales of analysis. Both stream width and patch size were significant in the models, but individual effects could not be clearly resolved because of collinearity. The predicted probability of occurrence based on patch size alone was less than 0.10 for patches smaller than about 1,000 ha and more than 0.50 for patches larger than about 2,500 ha. Our results support the hypothesis that area of available habitat influences the distribution of disjunct populations of bull trout. An area effect is consistent with the predictions of island biogeography and metapopulation theory, and our work suggests that larger-scale spatial processes may be important to the persistence of species like bull trout.

Impounded Rivers

Article

Apr 1987

The importance of morphodynamic processes at riffles used as spawning grounds during the incubation time of nase (Chondrostoma nasus)

Article

Jan 2007
HYDROBIOLOGIA

Stefan Schmutz

Integrated Operational Rule Curves for Montana Reservoirs and Application for Other Columbia River Storage Projects

Conference Paper

Jun 1999

Assessing the Impacts of River Regulation on Native Bull Trout (Salvelinus Confluentus) and Westslope Cutthroat Trout (Oncorhynchus Clarkii Lewisi) Habitats in the Upper Flathead River, Montana, USA

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