Longitudinal Patterns of Fish Assemblages, 

Aquatic Habitat, and Water Temperature in the 

Lower Crooked River, Oregon

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2007–1125

Longitudinal Patterns of Fish Assemblages, 

Aquatic Habitat, and Water Temperature in the 

Lower Crooked River, Oregon

Christian E. Torgersen and David P. Hockman-Wert, U.S. Geological Survey; Douglas S. Bateman, University of 

Oregon; and Robert E. Gresswell, U.S. Geological Survey

Open-File Report 2007–1125

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2007

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Suggested citation:

Torgersen, C.E., Hockman-Wert, D.P., Bateman, D.S., and Gresswell, R.E., 2007, Longitudinal patterns of fish 

assemblages, aquatic habitat, and water temperature in the Lower Crooked River, Oregon: U.S. Geological Survey 

Open-File Report 2007-1125, 36 p.

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endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report.
iii

Contents

Introduction.................................................................................................................................................................... 1

Methods......................................................................................................................................................................... 3

Fish and Aquatic Habitat............................................................................................................................................ 3

Stream Temperature and Water Quality .................................................................................................................... 5

Data Analysis............................................................................................................................................................. 6

Results........................................................................................................................................................................... 7

Fish ............................................................................................................................................................................ 7

Aquatic Habitat..........................................................................................................................................................18

Temperature and Water Quality................................................................................................................................18

Fish–Habitat Relationships .......................................................................................................................................23

Discussion ....................................................................................................................................................................26

Acknowledgments ........................................................................................................................................................28

References ...................................................................................................................................................................28

Appendix A. Temporal variation in stream discharge during summer 2002 and 2004 .................................................30

Appendix B. Scatterplots depicting the relationships between daily maximum water temperature data at 

two reference sites (Hollywood and Pink; x-axis) and four other sites (Elliot, Grassland, Lone Pine, and 

Horney Hollow; y-axis), August 16–31, 2004................................................................................................................31

Appendix C. Regression results and coefficients for correction factors used to predict daily maximum water 

temperature at Elliot, Grassland, Lone Pine, and Horny Hollow sites...........................................................................33

Appendix D. Species matrix with proportional abundance of fishes sampled during electrofishing and 

angling surveys of the Lower Crooked River, July 20–August 3, 2004.........................................................................34

Appendix E. Habitat matrix evaluated for correlations with ordination axes in principal components 

analysis (PCA) of species in site space (see appendix C)............................................................................................35

Appendix F. Statistical output from principal components analysis (PCA) of electrofishing/angling sites 

in fish species space in PC-ORD..................................................................................................................................36
iv

Figures

Figure 1. Sampling locations for fishes and habitat in the Lower Crooked River, July 29–August 3, 2004 ................... 4

Figure 2. Spatial distribution of fishes observed during the snorkeling survey of the Lower Crooked River, 

July 29–August 3, 2004 ................................................................................................................................................. 9

Figure 3. Relative abundance of fishes observed during the snorkeling survey of the Lower Crooked River, 

July 29–August 3, 2004 ............................................................................................................................................... 10

Figure 4. Spatial distribution of rainbow trout and northern pikeminnow observed during electrofishing and 

angling surveys of the Lower Crooked River, July 29–August 3, 2004........................................................................ 11

Figure 5. Spatial distribution of sculpins and dace observed during electrofishing surveys of the Lower 

Crooked River, July 29 – August 3, 2004. ................................................................................................................... 14

Figure 6. Spatial variation in the average length and weight of rainbow trout and northern pikeminnow 

captured during electrofishing and angling surveys of the Lower Crooked River, July 29–August 3, 2004 ................. 15

Figure 7. Spatial variation in aquatic habitat types observed by snorkelers during a spatially continuous 

survey of aquatic habitat in the Lower Crooked River, July 29–August 3, 2004 .......................................................... 19

Figure 8. Spatial variation in substrate types observed by snorkelers during a spatially continuous survey 

of aquatic habitat in the Lower Crooked River, July 29–August 3, 2004...................................................................... 20

Figure 9. Spatial patterns of channel gradient, average and maximum depth, and wetted channel width in

the Lower Crooked River............................................................................................................................................ 21

Figure 10. Spatial variation in water temperature and water quality parameters measured during surveys 

of fishes and aquatic habitat in the Lower Crooked River, July 29–August 3, 2004..................................................... 22

Figure 11. Principal components analysis (PCA) of electrofishing/angling sites (blue circles) in fish 

species (black stars) space ......................................................................................................................................... 24

Tables

Table 1. Criteria for classifying channel unit type in surveys of aquatic habitat of the Lower Crooked River, 

July 29–August 3, 2004 ................................................................................................................................................. 5

Table 2. Percent abundance of fishes and stream length sampled during snorkeling, electrofishing, and angling 

surveys of fishes of the Lower Crooked River, July 29–August 3, 2004 ........................................................................ 8

Table 3. Counts of fishes and stream length sampled during an electrofishing survey of six sites in the 

Lower Crooked River, July 29–August 3, 2004............................................................................................................ 12

Table 4. Counts of fishes and total stream length sampled during an angling survey of six sites in the 

Lower Crooked River, July 29–August 3, 2004............................................................................................................ 13

Table 5. Summary of aquatic habitat and substrate for snorkeling and electrofishing/angling surveys of 

fishes and aquatic habitat in the Lower Crooked River, July 29–August 3, 2004......................................................... 16

Table 6. Summary of aquatic habitat and substrate for electrofishing/angling surveys of fishes and aquatic 

habitat at six sites in the Lower Crooked River, July 29–August 3, 2004..................................................................... 17

Table 7. Pearson correlations between primary and secondary axes and aquatic habitat variables for principal 

components analysis (PCA) of electrofishing/angling sites in fish species space........................................................ 25

Table 8. Pearson correlations between primary and secondary axes and the species matrix for principal 

components analysis (PCA) of electrofishing/angling sites in fish species space........................................................ 26
1

Longitudinal Patterns of Fish Assemblages, 

Aquatic Habitat, and Water Temperature in the 

Lower Crooked River, Oregon

By Christian E. Torgersen,1 David P. Hockman-Wert,2 Douglas S. Bateman,3 and Robert E. Gresswell4

Introduction

The Lower Crooked River is a remarkable groundwater-fed stream flowing through 

vertical basalt canyons in the Deschutes River Valley ecoregion in central Oregon (Pater and 

others, 1998). The 9-mile section of the river between the Crooked River National Grasslands 

boundary near Ogden Wayside and river mile (RM) 8 is protected under the National Wild and 

Scenic Rivers Act (16 U.S.C. 1271-1287) for its outstandingly remarkable scenic, recreational, 

geologic, hydrologic, wildlife, and botanical values (ORVs), and significant fishery and cultural 

values. Groundwater springs flow directly out of the canyon walls into the Lower Crooked River 

and create a unique hydrologic setting for native coldwater fish, such as inland Columbia Basin 

redband trout (Oncorhynchus mykiss gairdneri). To protect and enhance the ORVs that are the 

basis for the wild and scenic designation, the Bureau of Land Management (BLM) has identified 

the need to evaluate, among other conditions, fish presence and habitat use of the Lower 

Crooked River. The results of this and other studies will provide a scientific basis for

communication and cooperation between the BLM, Oregon Water Resources Department, 

Oregon Department of Fish and Wildlife, and all water users within the basin. These biological 

studies initiated by the BLM in the region reflect a growing national awareness of the impacts of 

agricultural and municipal water use on the integrity of freshwater ecosystems.

Biological surveys are needed to better understand the aquatic ecosystem of the Lower 

Crooked River. This baseline information will be valuable to public land managers whose task is 

to balance resource use while protecting the unique attributes (e.g., ORVs) of the Lower Crooked 

River. The habitat requirements of coldwater fishes in this section of stream are of particular 

interest due to state and federal regulation of water temperature in order to protect and restore 

fish populations. Historical data on the distribution and abundance of stream fishes in the Lower 

Crooked River are limited to point observations by fishermen and local biologists because steep 

canyon walls have limited access to most of the river.

1

U.S. Geological Survey (USGS) Forest and Rangeland Science Center (FRESC), Cascadia Field Station, College of 

Forest Resources, Box 352100, Seattle, WA 98195

2 USGS FRESC Corvallis Research Group, 3200 SW Jefferson Way, Corvallis, OR 97331

3 Department of Forest Science, Oregon State University, Corvallis, OR 97331

4 USGS Northern Rocky Mountain Science Center, 1648 S. 7th Ave., Bozeman, MT 59717
2

Surveys of aquatic habitat (channel morphology and substrate composition) have been 

conducted for the BLM by the Oregon Department of Fish and Wildlife (ODFW) (ODFW,

1997), U.S. Forest Service (USFS, 2003), and the U.S. Fish and Wildlife Service (USFWS), but 

fish surveys using electrofishing gear have never been conducted in the isolated 11-mile section 

of the Crooked River Gorge, and visual observations with mask and snorkel have only been 

made at isolated point locations where hiking trails provide access to the river (K. Jones, Steve 

Marx, and Brett Hodgson, ODFW; P. Lickwar, USFWS; pers. comm.). Thus, there is a poor 

understanding of stream fish presence and distribution throughout Lower Crooked River.

Information on fish assemblages is available for the Deschutes River basin and applies 

generally to the Lower Crooked River because the two rivers were connected historically 

(Zimmerman and Ratliff, 2003). The construction of dams throughout the Deschutes River basin 

has eliminated historical runs of salmon and steelhead and prevented migration of bull trout and 

Pacific lamprey into the Crooked River system. Native fish species expected to occur in the 

Lower Crooked River include Columbia Basin redband trout (Oncorhynchus mykiss gairdneri), 

mountain whitefish (Prosopium williamsoni), sculpin (Cottus spp.), two species of dace 

(Rhinichthys spp.), two species of sucker (Catostomus spp.), northern pikeminnow 

(Ptychocheilus oregonensis), chiselmouth (Acrocheilus alutaceus), and redside shiner 

(Richardsonius balteatus). Threespine stickleback (Gasterosteus aculeatus), a species native to 

western Oregon, also occurs in the basin but is believed to be introduced (D. Markle, Department 

of Fisheries and Wildlife, Oregon State University, pers. comm.). Extensive stocking of rainbow 

trout has contributed to a large population of naturalized fish of hatchery origin in the Lower 

Crooked River. Due to the difficulty of differentiating between wild redband trout and 

naturalized rainbow trout of hatchery origin, the general classification of rainbow trout 

(Oncorhynchus mykiss) is used throughout this report to describe the fish that were observed in 

the Lower Crooked River. Exotic fish species expected to occur in the Lower Crooked River

include large- and smallmouth bass (Micropterus spp.), yellow perch (Perca flavescens), and 

brown bullhead (Ameiurus nebulosis) (Zimmerman and Ratliff, 2003).

The goal of this project was to examine longitudinal patterns in fish assemblages, aquatic

habitat, and water temperature in the Lower Crooked River during summer conditions. Specific 

objectives were to (1) characterize the spatial distribution of native and non-native fishes, (2) 

describe variation in channel morphology, substrate composition, and water temperature, and (3) 

evaluate the associations between fishes, aquatic habitat, and water temperature.
3

Methods

Fish and Aquatic Habitat

The survey of fishes and aquatic habitat in 11.8 miles of the Lower Crooked River was 

completed on July 29–August 3, 2004. Fish and aquatic habitat sampling was conducted from 

RM 7.8 to 19.6 (fig. 1). Visual assessments of fishes were conducted with mask and snorkel by a 

two-person crew between RM 7.8 and 19.6 (fig. 1). The snorkelers conducted the survey in a 

downstream direction but surveyed fishes in individual channel units (pools, glides, riffles, and 

rapids, sensu Bisson and others, 1982; table 1) in an upstream direction. Fish were identified and 

counted in either the entire channel unit, or in a portion of the channel unit, depending on the 

length of the unit. Units longer than 328 ft were sampled for fish only in the upper portion of the 

unit (~328 ft). Due to poor underwater visibility in the upper section of the Lower Crooked 

River, the snorkelers were not able to identify many cyprinids to the species level. Therefore, 

analyses on the relative abundance of cyprinid species were limited in scope.

Geographic coordinates were collected with a global positioning (GPS) unit at the 

downstream boundary of every channel unit and at the upper and lower boundaries of each 

electrofishing/angling site. Channel unit characteristics, including length, mean wetted width, 

mean depth, maximum depth, and percent substrate composition (i.e., bedrock, boulder, cobble, 

gravel, sand, and silt), were visually estimated in every channel unit between RM 7.8 and 19.6

and at each electrofishing/angling site. Estimates of distance (length and width) and depth were 

based on ocular calibrations in the field using a measuring tape for channel unit length and 

width, and the snorkeler’s body length for depth. Ocular calibrations were made daily for 

channel length and width, and hourly for depth estimates. Visual assessments of percent 

substrate composition in each channel unit were not validated with quantitative methods, such as 

pebble counts. Relative turbidity was measured underwater by the snorkelers in eight pools, three

riffles, and two glides with a modified Secchi disk (3.2 in. in diameter) attached to a calibrated

nylon cord. Secchi distance was recorded as the underwater distance at which snorkelers were 

able to resolve the pattern on the disk. Longer distances indicated better visibility and lower 

relative turbidity. Measurements of relative turbidity were collected throughout the Lower 

Crooked River.

Electrofishing and angling were used to collect fish in locations that were accessible by 

foot via roads and trails leading down into the Crooked River Gorge. Six sampling sites 1310–

3280 ft in length were distributed throughout the river section (fig. 1). Electrofishing with 

backpack gear in the wadeable portion of each site was used to capture fish that were 

subsequently identified to species, measured (length), and weighed. This method was particularly 

effective for collecting cryptic benthic and shallow-water species (dace and sculpins) that were 

not typically observed by snorkelers. Electrofishing crews consisted of two technicians using 

backpack electrofishing units (40–60 Hz, 200–500 volts DC, 6–8 millisecond fixed pulse width) 

and two additional technicians who assisted with capturing fish and processing data.
4

Figure 1. Sampling locations for fishes and habitat in the Lower Crooked River, July 29–August 3, 2004. Surveys of aquatic habitat included all channel units 

between the upper- and lowermost electrofishing/angling sampling sites.
5

Table 1. Criteria for classifying channel unit type in surveys of aquatic habitat of the Lower 

Crooked River, July 29–August 3, 2004.

Habitat type Gradient 

(percent)

Description

Pool 0 Cross-section is not uniform; water velocity is very slow. If stream 

channel were dewatered, pools would continue to hold water in a 

significant portion of their area, whereas other habitat types would not.

Glide 0.5 Uniform cross-section with no surface turbulence. In contrast to pools, 

glides have no significant scour and deposition.

Riffle 1–4 Typically shallow water depth with uniform cross-section; water 

velocity is relatively fast. Substrate is generally gravel or cobble, and 

surface turbulence is present but lacking hydraulic jumps.

Rapid 3–8 Pronounced surface turbulence, accompanied by high velocity flow 

and the formation of eddies and hydraulic jumps (standing waves) 

around the substrate.

Angling was employed to collect fish in portions of the sites that were too deep to sample 

with backpack electrofishing. The four-person angling crew, consisting of two anglers using 

artificial flies and two anglers using spinners and bait, systematically cast and retrieved their 

lures across the entire water surface in each site to sample all available habitats, including 

deepwater habitats adjacent to the area sampled during electrofishing. This method selected 

primarily for rainbow trout, northern pikeminnow, and chiselmouth, all of which responded 

readily to artificial flies, lures, and bait. The duration of the combined electrofishing and angling 

survey was approximately one day per site.

A variety of methods were used to assess fish distribution without accounting for 

variation in sampling efficiency among methods (electrofishing, snorkeling and angling) and

among sample sites. Although such differences in sampling efficiency can potentially complicate 

the interpretation of fish distribution patterns, the inaccessibility of the sampling locations, the 

large size of the river, and the rugged terrain in the Lower Crooked River canyon prevented us 

from using blocknets, multiple-pass removal methods, and mark-recapture studies to calculate 

sampling efficiencies. Given the logistical difficulties of sampling fishes in the Lower Crooked 

River, methods were selected to identify spatial patterns in fish distribution (Bateman and 

others, 2005) rather than obtain population estimates.

Stream Temperature and Water Quality

During the fish sampling period, stream discharge measured at 30-minute intervals by the 

USGS Oregon Water Science Center (OWSC) at the Osborne Canyon Station (RM 13) ranged

between 154 and 209 cubic feet per second (cfs) (appendix A). Spatial variation in stream 

temperature was assessed at six spatially dispersed locations in the Lower Crooked River (fig. 1).

Four Onset Optic StowAway water temperature data loggers were deployed by FRESC, and two 

additional data loggers were operated by the BLM Prineville District and the USGS OWSC. Due 

to a software malfunction, the FRESC data loggers did not collect data during the fish and 

aquatic habitat survey. However, these data loggers were redeployed immediately on August 15, 
6

2004, so that correction factors could be developed to reconstruct water temperatures at FRESC 

sites based on correlations with water temperatures measured by data loggers at Hollywood and 

Pink sites on August 16-31 (appendix B). R-squared values for the linear relationships that were 

used to develop temperature correction factors ranged from 0.96 to 0.98 (appendix C). Stream 

temperature data were summarized by calculating the 7-day average of daily maxima (7DADM)

for each site (July 29–August 4). Water quality parameters (pH, turbidity, conductivity) were 

measured at each electrofishing/angling site before and after electrofishing and angling with an

Orbeco-Hellige Pocket Comparator Model 605 (pH; Bromcresol Purple-D), a YSI Model 30 

conductivity meter, and a HACH Turbidimeter Model 2100P. Spatially continuous longitudinal 

patterns of stream temperature were evaluated using forward-looking infrared (FLIR) remote 

sensing of the Lower Crooked River conducted for the BLM by Watershed Sciences, Inc. 

(Watershed Sciences, 2004).

Data Analysis

Field data were mapped and analyzed in a geographical information system (GIS) (ESRI 

ArcGIS 9.0). River mile measurements were used to locate sampling sites in relation to the

distance upstream from the confluence of the Crooked River with the Deschutes River on 

Oregon and Washington Framework Hydrography data at a scale of 1:24,000 

(http://hydro.reo.gov). Longitudinal profiles of fish distribution and aquatic habitat data 

(collected during snorkeling and habitat surveys) were constructed by (1) summarizing data in 1-

mile bins based on stream length (fish abundance, habitat type, and substrate), (2) calculating the 

moving average of channel gradient in a 656 ft window based on 33-ft digital elevation models, 

and (3) applying locally weighted scatterplot smoothing (LOWESS) of maximum depth, mean 

depth, and wetted width (Trexler and Travis, 1993). Spatial binning of data on fish abundance, 

habitat type, and substrate was performed with 1-mile bins. The downstream terminus of each 

channel unit was used as the location of a channel unit. Each bin varied slightly in length. Bin 

values for fish abundance were standardized by the portion of the stream length that was sampled

to derive an estimate of number of fish per mile. Locally weighted scatterplot smoothing was 

calculated using SigmaPlot (Ver. 9.0) with a second-degree polynomial and sampling proportion 

of 0.3. 

Multivariate analysis of fish assemblage structure was performed using the electrofishing 

and angling data collected at six survey locations. Prior to multivariate analysis, rare species with 

fewer than 20 individuals (mountain whitefish, torrent sculpin, threespine stickleback) were 

removed, relative abundance was calculated, and the resulting species matrix (appendix D) was 

evaluated for normality. The coefficient of variation for species relative abundance was 

relatively high (91 percent), but the average skewness was low (0.50). As suggested by McCune 

and Grace (2002), the arc-sine square root transformation was used to reduce the overall 

variation in species relative abundance. After the transformation, the coefficient of variation for 

species relative abundance decreased to 55 percent. Principal components analysis (PCA) and 

biplots of correlations with ordination axes were used to evaluate spatial variation in fish 

assemblages in relation to aquatic habitat variables, water temperature, and water quality 

parameters (appendix E). The PCA ordination of sites in fish species space was calculated with 

correlations in the cross-products matrix, and scores for species in ordination space were 

calculated by weighted averaging (McCune and Grace, 2002).
7

Results

Fish

Cyprinids (dace, chiselmouth, and northern pikeminnow) comprised the majority of the 

fish assemblage observed in electrofishing and snorkeling surveys of the Lower Crooked River

(table 2). Less common fishes included salmonids (rainbow trout and mountain whitefish), 

catostomids (largescale sucker and bridgelip sucker), cottids (paiute sculpin, shorthead sculpin, 

and torrent sculpin), and one potentially introduced species of stickleback (D. Markle, 

Department of Fisheries and Wildlife, Oregon State University, pers. comm.).

The distribution of fishes in the Lower Crooked River was marked by an upstream–

downstream gradient dominated by salmonids in downstream reaches and cyprinids in upstream 

reaches (figs. 2 and 3). Patterns of total fish abundance indicated that cyprinids (including 

northern pikeminnow and unidentified cyprinids) were the most commonly observed fish, 

particularly in the upper sections of the Lower Crooked River (fig. 2). Total abundance of 

rainbow trout was also high in the downstream-most section of the river (fig. 2). Patterns of 

relative abundance were similar to patterns of total abundance but exhibited more abrupt changes 

with distance upstream (fig. 3). This was particularly apparent in the distributions of rainbow 

trout and unidentified cyprinids, which transitioned dramatically in dominance from one to the 

other over a relatively short distance (RM 11 and 13) (fig. 3). Longitudinal patterns of northern 

pikeminnow were more variable at small scales (1–2 miles) than those of rainbow trout and 

mountain whitefish (fig. 2). Spatial patterns of mid-water fishes (e.g., rainbow trout and northern 

pikeminnow) derived from snorkeling, electrofishing, and angling were similar among the three 

methods (fig. 4; tables 3 and 4). Mid-water fishes are species that occupy positions midway 

between the water surface and the stream bottom and, therefore, are easier to observe during 

snorkeling. Benthic fishes (e.g., sculpins and dace) are species associated with the stream bottom 

and typically take refuge in crevices between cobbles and boulders; this makes them particularly 

difficult to detect by snorkelers. Thus, electrofishing provided a more detailed assessment of the 

distribution of benthic fishes. Two species of cottids (Paiute sculpin and shorthead sculpin) 

exhibited an inversely correlated pattern, with shorthead sculpin more abundant in downstream 

sites and Paiute sculpin more abundant in upstream sites (fig. 5, table 3). Longnose dace and 

speckled dace also exhibited opposing distributions (fig. 5, table 3).

Analysis of spatial trends in the average length and weight of rainbow trout and northern 

pikeminnow captured during electrofishing and angling surveys indicated that the average size of 

these two species was inversely correlated (fig. 6). Northern pikeminnow were larger in 

downstream reaches, whereas rainbow trout tended to be larger in upstream reaches.
8

Table 2. Percent abundance of fishes and stream length sampled during snorkeling, electrofishing, and 

angling surveys of fishes of the Lower Crooked River, July 29–August 3, 2004.

[A dash (–) indicates that a species was observed but represented less than 1 percent of the total abundance]

Sampling method

Snorkeling Electrofishing Angling

Family and species (percent)

Salmonidae

Rainbow trout (Oncorhynchus mykiss) 23 21 59

Mountain whitefish (Prosopium williamsoni) 1 – 1

Cyprinidae

Chiselmouth (Acrocheilus alutaceus) 19 10

Northern pikeminnow (Ptychocheilus oregonensis) 11 7 28

Longnose dace (Rhinichthys cataractae) 12

Speckled dace (Rhinichthys osculus) – 24

Unidentified cyprinids 64 1

Catostomidae

Bridgelip sucker (Catostomus columbianus) –

Largescale sucker (Catostomus macrocheilus) – –

Unidentified catostomids – 6

Cottidae

Paiute sculpin (Cottus beldingi) 2

Shorthead sculpin (Cottus confusus) 6

Torrent sculpin (Cottus rhotheus) 1

Unidentified cottids – 1

Gasterosteidae

Threespine stickleback (Gasterosteus aculeatus) –

Total fish observed (number)

12,735

2,035 574

Stream length sampled (ft)

27,920

12,126 12,001
9

Figure 2. Spatial distribution of fishes observed during the snorkeling survey of the Lower Crooked River, 

July 29–August 3, 2004. Abundance estimates are summarized in 1-mile bins standardized by the length of 

stream surveyed. Asterisk (*) symbols indicate that fish were present, but there were fewer than 10 

individuals observed.
10

Figure 3. Relative abundance of fishes observed during the snorkeling survey of the Lower Crooked River, 

July 29–August 3, 2004. Relative abundances are summarized in 1-mile bins. Asterisk (*) symbols indicate 

that fish were present, but relative abundance was less than 1 percent.
11

Figure 4. Spatial distribution of rainbow trout and northern pikeminnow observed during electrofishing and 

angling surveys of the Lower Crooked River, July 29–August 3, 2004. Asterisk (*) symbols indicate that 

rainbow trout were present, but their abundance was less than 0.1 fish/ft.
12

Table 3. Counts of fishes and stream length sampled during an electrofishing survey of six sites in the 

Lower Crooked River, July 29–August 3, 2004.

[Sites are listed in order of occurrence from downstream (left) to upstream (right) (see figure 1 for site locations)]

Sampling site

Pink Horny 

Hollow

Lone Pine HollywoodGrasslandElliot

Family and species (abundance)

Salmonidae

Rainbow trout 97 132 137 53 2 1

Mountain whitefish 1 4 1

Cyprinidae

Chiselmouth 2 1 66 140 174

Northern pikeminnow 1 2 1 30 68 37

Longnose dace 2 81 44 70 35 3

Speckled dace 1 4 5 122 271 92

Unidentified cyprinids 1 2 3 1 1

Catostomidae

Bridgelip sucker 4

Largescale sucker 1 1 1

Unidentified catostomids 8 25 11 32 49 2

Cottidae

Paiute sculpin 1 29 20

Shorthead sculpin 27 64 27 2

Torrent sculpin 12 6

Unidentified cottids 15 4 2

Gasterosteidae

Threespine stickleback 1 3

Total fish collected (number) 152 320 242 412 593 316

Stream length sampled (ft) 1,765 2,231 1,470 3,248 2,116 1,296

Species richness 10 10 9 11 11 10
13

Table 4. Counts of fishes and total stream length sampled during an angling survey of six sites in the 

Lower Crooked River, July 29–August 3, 2004.

[Sites are listed in order of occurrence from downstream (left) to upstream (right) (see figure 1 for site locations)]

Sampling site

Pink Horny 

Hollow

Lone Pine HollywoodGrasslandElliot

Family and species (abundance)

Salmonidae

Rainbow trout 68 86 84 44 46 12

Mountain whitefish 3 3

Cyprinidae

Chiselmouth 4 11 41

Northern pikeminnow 12 7 11 35 42 56

Unidentified cyprinids 2 1 4

Catostomidae

Largescale sucker 1 1

Total fish collected (number) 80 95 95 88 107 109

Stream length sampled (ft) 1,640 2,231 1,470 3,248 2,116 1,296

Species richness 2 3 2 6 6 3
14

Figure 5. Spatial distribution of sculpins and dace observed during electrofishing surveys of the Lower 

Crooked River, July 29–August 3, 2004. The asterisk (*) symbol indicates that speckled dace were present, 

but their abundance was less than 0.1 fish/ft.
15

Figure 6. Spatial variation in the average length and weight of rainbow trout and northern pikeminnow 

captured during electrofishing and angling surveys of the Lower Crooked River, July 29–August 3, 2004.

Error bars indicate the standard error of the mean.
16

Table 5. Summary of aquatic habitat and substrate for snorkeling and 

electrofishing/angling surveys of fishes and aquatic habitat in the Lower Crooked 

River, July 29–August 3, 2004.

[Percentages of aquatic habitat and substrate type are based on stream length]

Habitat survey type

Snorkeling Electrofishing/angling

Channel unit type (percent)

Pools 30 48

Riffles 47 21

Rapids 7 8

Glides 16 23

Channel unit dimensions (ft)1

Maximum depth (ft) 8.2 (3.3-16.4) 6.6 (2.3-13.1)

Depth (ft) 4.9 (1.6-13.1) 3.3 (1.6-8.2)

Wetted width (ft) 56 (33-82) 69 (49-98)

Unit length (ft) 328 (16-3,281) 246 (79-1,476)

Substrate type (percent)

Bedrock 1 0

Boulder (>10 in) 31 35

Cobble (2.5-10 in) 32 22

Gravel (0.1-2.5 in) 19 4

Sand (gritty - 0.1 in) 15 23

Silt (fine not gritty) 2 15

1 Expressed as median and range.
17

Table 6. Summary of aquatic habitat and substrate for electrofishing/angling surveys of fishes and aquatic habitat at six sites in the Lower 

Crooked River, July 29–August 3, 2004.

[Percentages of aquatic habitat and substrate type are based on stream length]

Sampling site

Pink Horny Hollow Lone Pine Hollywood Grassland Elliot

Channel unit type (percent)

Pools 84 32 27 76 15 35

Riffles 0 15 16 19 52 21

Rapids 7 0 7 5 9 25

Glides 9 53 50 0 24 18

Channel unit dimensions (ft)1

Maximum depth 10.8

(8.2-11.5)

8.2

(4.9-13.1)

7.5

(4.9-11.5)

5.9

(3.3-9.8)

5.2

(3.3-8.2)

3.9

(2.3-9.2)

Depth 5.9

(4.9-8.2)

4.9

(2.6-6.6)

3.9

(2.3-5.6)

3.3

(2.0-4.9)

3.0

(1.6-5.2)

2.3

(1.6-4.3)

Wetted width 82

(72-92)

72

(69-75)

72

(66-98)

66

(59-85)

66

(52-66)

52

(49-79)

Unit length 295

(125-1,050)

525

(98-1,083)

223

(108-525)

312

(164-1,476)

223

(115-1,099)

197

(79-328)

Substrate type (percent)

Bedrock 0 0 0 0 0 0

Boulder (>10 in.) 38 34 45 19 50 36

Cobble (2.5-10 in.) 11 5 39 13 37 50

Gravel (0.1-2.5 in.) 1 1 7 4 10 2

Sand (gritty - 0.1 in.) 24 36 9 44 2 0

Silt (fine not gritty) 27 23 0 20 0 12

1 Expressed as median and range.
18

Aquatic Habitat

Spatial patterns in the distribution of pools, glides, riffles, and rapids were highly variable 

among the electrofishing/angling sites (tables 5 and 6) and throughout the Lower Crooked River, 

as revealed by the spatially continuous survey of aquatic habitat conducted by snorkelers (fig. 7). 

Riffles were the most common habitat type as a percentage of total stream length (47 percent), 

but pools and glides also constituted relatively large proportions of the total stream length (30 

and 16 percent, respectively) (table 5). Pools were distributed throughout the entire river section 

but were most pronounced in presence at RM 8, between RM 12 and RM 14, and at RM 19; 

riffles occurred primarily in the upstream portion of the river with varying degrees of presence 

downstream (fig. 7). Glides and rapids exhibited patchy distributions compared to pools and 

riffles (fig. 7). 

Spatial patterns of gravel, cobble, and boulder substrates were remarkably consistent 

throughout the entire river section (fig. 8). Cobbles and boulders were the most common 

substrate types (table 5). Sand and silt were patchier in distribution than other substrates and 

were most common in downstream reaches (fig. 8). Channel gradient ranged between 0.5 and 1.5 

percent and was punctuated by several high- and low-gradient reaches at RM 11–12, 14, and 18–

19 (fig. 9). Water depth increased gradually in a downstream direction, whereas wetted width 

was highly variable throughout the Lower Crooked River (fig. 9).

Temperature and Water Quality

Stream temperature and water quality parameters changed dramatically in a downstream 

direction in the Lower Crooked River (fig. 10). Water temperature, conductivity, and turbidity 

decreased, and pH increased in a downstream direction. Secchi distance provided a method to 

assess longitudinal changes in underwater visibility during the snorkeling survey of fishes. The 

underwater visibility encountered by the snorkelers increased approximately 6 fold (from 3 to 18 

ft) from the upper to the lower sections of the snorkeling survey of fishes (fig. 10). Longitudinal 

patterns in 7DADM and remotely sensed water temperature indicated substantial cooling from 

groundwater inputs downstream of RM 13.7 (fig. 10). 
19

Figure 7. Spatial variation in aquatic habitat types observed by snorkelers during a spatially continuous 

survey of aquatic habitat in the Lower Crooked River, July 29–August 3, 2004. Percentages based on 

stream length are summarized in 1-mile bins.
20

Figure 8. Spatial variation in substrate types observed by snorkelers during a spatially continuous survey of 

aquatic habitat in the Lower Crooked River, July 29–August 3, 2004. Percentages based on stream length 

are summarized in 1-mile bins.
21

Figure 9. Spatial patterns of channel gradient, average and maximum depth, and wetted channel width in 

the Lower Crooked River. Depth and wetted width measurements were collected by snorkelers during a 

spatially continuous survey of aquatic habitat conducted in July 29–August 3, 2004.
22

Distance upstream (mi)

8 10 12 14 16 18 20

Secchi distance (ft)

0

5

10

15

20

25

Turbidity (NTU)

1

2

3

4

5

6

7

8

Secchi Distance

Turbidity

Temperature (F)

60

65

70

75 7DADM

FLIR

Conductivity (mhos/in)

300

400

500

600

700

800

900

Pink

Horny Hollow Lone Pine

Hollywood

Grassland

Elliot

pH

6.8

6.9

7.0

7.1

7.2

7.3

7.4

7.5

Conductivity

pH

Figure 10. Spatial variation in water temperature and water quality parameters measured during surveys of 

fishes and aquatic habitat in the Lower Crooked River, July 29–August 3, 2004. Seven-day average of daily 

maximum water temperature (7DADM) and thermal IR remote sensing data were collected in July 29–

August 4, 2004 and August 27, 2002, respectively.
23

Fish–Habitat Relationships

Changes in water temperature and turbidity corresponded with distinct spatial structuring 

of fish assemblages in the Lower Crooked River. In only 11 miles, the river transformed from a 

warm, turbid cyprinid stream to a clear, cold trout river. Longitudinal patterns in fish 

distribution, aquatic habitat, and water temperature suggested that temperature and, potentially, 

turbidity were the primary physical drivers of fish assemblage structure in the Lower Crooked 

River. 

Principal components analysis (PCA) of fish assemblage and aquatic habitat associations 

indicated that differences in fish species composition in the six sites were related primarily to 

environmental gradients in 7DADM (water temperature), turbidity, depth, percent rapid habitat, 

and wetted width (fig. 11 and table 7; see appendix F for statistical output from PC-ORD). The 

primary ordination axis explained 64 percent of the variance in species distance matrix, and the 

correlations between the primary ordination axis scores and aquatic habitat variables suggested 

that there were strong positive and negative influences (r > 0.7 and r < -0.7) of habitat factors on 

fish assemblage structure (table 7). Strong correlations (r > 0.9 and r < -0.9) between the primary 

axis and the species matrix indicate that the three sites positioned on the left side of the primary 

axis (Elliot, Grassland, and Hollywood) were cyprinid-dominated sites (i.e., chiselmouth, 

speckled dace, and northern pikeminnow) associated with higher water temperatures and 

turbidity (table 8 and fig. 11). In contrast, sites positioned on the right side of the primary axis 

were dominated by rainbow trout and shorthead sculpin; these sites were associated with lower 

water temperature and turbidity, and greater water depth and wetted width (table 8 and fig. 11). 

The secondary axis in the ordination explained 28 percent of the variation in fish assemblage 

structure and was correlated primarily with percent rapid habitat (r = 0.7) (table 7, fig. 11). Thus, 

the position of a site with respect to the secondary axis indicated whether the site could be 

characterized as a “rapid habitat” fish assemblage (fig. 11). Species that were negatively 

associated (r < -0.7) with the secondary axis included longnose dace, Paiute sculpin, and 

catostomids (table 8). It is important to note, however, that “rapid habitat” was also negatively 

correlated with the primary axis (r = -0.7) (table 7); thus, the relative influences of “rapid 

habitat” on fish assemblage structure were difficult to interpret in this analysis. 
24

Figure 11. Principal components analysis (PCA) of electrofishing/angling sites (blue circles) in fish species 

(black stars) space. Data were collected during a survey of fishes and aquatic habitat in the Lower Crooked 

River, July 29–August 3, 2004. Biplot overlays (red lines) indicate the relative magnitude and direction 

(positive or negative) of correlations of environmental variables (percent “rapid” channel unit type, 7-day 

average of daily maximum water temperature, turbidity, wetted width, and depth) with ordination axes. The 

centroid of the ordination is indicated with a “+” symbol. The positions of sites with respect to the ordination 

axes indicate their relative similarity in fish assemblage structure, whereas the positions of species illustrate 

their relative association with the ordination axes. Species analyzed include chiselmouth (CM), northern 

pikeminnow (NP), speckled dace (SD), Paiute sculpin (PS), catostomids (SU), longnose dace (LD), rainbow

trout (RT), and shorthead sculpin (SS). See tables 7 and 8 for correlations between axis scores and 

species and aquatic habitat matrices.

Elliot

Pink

Grassland

Hollywood

Horny

Hollow

Lone

Axis 2 (28%)

Pine

Axis 1 (64%)

Rapid (%)

7DADM

Depth

Wetted

width

CM

SD

NP

SU

PS

LD

RT

SS

Turbidity +
25

Table 7. Pearson correlations between primary and secondary 

axes and aquatic habitat variables for principal components 

analysis (PCA) of electrofishing/angling sites in fish species 

space.

Habitat variable Axis 1 Axis 2

Pool (percent) 0.17 0.06

Riffle (percent) -0.63 -0.45

Rapid (percent) -0.71 0.67

Glide (percent) 0.57 0.00

Max. depth 0.86 0.11

Mean depth 0.86 0.10

Wetted width 0.83 -0.13

Unit length 0.60 -0.28

Boulder (percent) 0.05 0.23

Cobble (percent) -0.60 0.38

Gravel (percent) -0.33 -0.51

Sand (percent) 0.43 -0.49

Silt (percent) 0.34 0.16

7DADM 1 -0.97 -0.08

Turbidity -0.78 0.02

1 Seven-day average of daily maximum water temperature.
26

Table 8. Pearson correlations between primary and secondary axes and 

the species matrix for principal components analysis (PCA) of 

electrofishing/angling sites in fish species space.

Species Axis 1 Axis 2

Rainbow trout 0.95 0.09

Chiselmouth -0.96 0.22

Northern pikeminnow -0.99 0.13

Longnose dace 0.46 -0.72

Speckled dace -0.93 -0.35

Catostomids 0.29 -0.89

Paiute sculpin -0.45 -0.83

Shorthead sculpin 0.98 0.13

Discussion

The unique groundwater-influenced thermal environment of the Lower Crooked River 

created an environment in which coldwater fish (salmonids and cottids) were distributed among 

species that typically characterize a coolwater fish assemblage (cyprinids and catostomids). 

Fishes in the Lower Crooked River exhibited thermal preferences that were generally similar to 

those described in the literature for Pacific Northwest fish assemblages (Zaroban and others, 

1999). However, some species exhibited anomalous distribution patterns with respect to their 

thermal preferences described in the literature. For example, the classification of longnose dace 

as a coolwater fish according to Zaroban and others (1999) was unusual in the Crooked River 

because this species was more closely associated with rainbow trout, a coldwater species, than it 

was with coolwater cyprinids, such as chiselmouth and northern pikeminnow. Moreover, the 

presence of large rainbow trout in the warmest water encountered during the survey (fig. 6) 

suggested that large trout may use warmer, potentially more productive habitats to capitalize on 

abundant food resources, such as macroinvertebrate grazers feeding on algae. More information 

on salmonid diet and growth in the upper section of the Lower Crooked River is needed to 

understand how large trout are able to cope with high water temperature and turbidity in this 

section of the river.
27

The high turbidity and generally poor visibility in the upper section of the Lower 

Crooked River could potentially affect the ability of rainbow trout to locate and successfully 

consume prey. However, turbidity levels in the Lower Crooked River were much lower (< 8 

NTU) than those known to cause avoidance behavior (> 20 NTU) in salmonids (Waters, 1995).

Effects of turbidity on salmonids have been evaluated extensively in laboratory experiments, and 

although adult mortality due to moderate turbidity levels (<100 NTU) is rare, the impacts of 

sedimentation on reproductive success and the early life stages of salmonids can be significant 

(Chapman, 1988). The smaller average size of rainbow trout in the downstream section of the 

Lower Crooked River is likely related to increased survival of eggs, fry, and juveniles in the 

relatively cool downstream reaches of the Lower Crooked River. These early life history stages 

of rainbow trout are particularly sensitive to environmental extremes, such as elevated water 

temperature, and therefore may have limited survival in the relatively warm upstream reaches of 

the Lower Crooked River. Further investigation of the effects of turbidity on rainbow trout in the 

upper section of the Lower Crooked River is necessary to determine potential impacts on 

salmonid feeding behavior and growth.

High water temperature has a significant influence on salmonid behavior and growth in 

high desert streams (Li and others, 1994). Several species of coldwater fishes have been shown 

to behaviorally thermoregulate by locating thermal refugia several degrees cooler than ambient 

water temperatures (Torgersen and others, 1999; Ebersole and others, 2003). Spatial 

heterogeneity in water temperature is particularly pronounced in the Lower Crooked River due to 

groundwater inputs and may provide thermal refugia important for the existence of coldwater 

fishes such as rainbow trout, mountain whitefish, and sculpins. Recent studies by Gamperl and 

others (2002) and Rodnick and others (2004) provide experimental evidence that the 

physiological tolerance of redband trout (O. mykiss ssp.) in warm water (>68°F) exceeds that of 

rainbow trout. Thus, redband trout and naturalized rainbow trout of hatchery origin may have 

different distributions in the Lower Crooked River, with redband trout occupying sections of the 

river that are higher in temperature. Additional studies on genetic variability of rainbow trout in 

the Lower Crooked River are needed in order to describe spatial variation in redband versus 

rainbow trout population structure and behavior.

The presence of rainbow trout in locations that exceeded the proposed Oregon water 

temperature standard of 68°F 7DADM for Great Basin redband trout (O. mykiss newberrii) and 

salmonid migration corridors (ODEQ, 2005) raised questions about how the upper section of the 

Lower Crooked River should be classified in terms of thermal habitat. Only three of the 

lowermost electrofishing/angling sites in this survey were classified as coldwater fish 

assemblages due to the relative abundance of rainbow trout. These three sites had 7DADM water 

temperatures that did not exceed the Oregon water temperature standard of 64.4°F for salmonid 

rearing. Based on the high relative abundance of rainbow trout detected during snorkeling 

surveys downstream of RM 12 (>50 percent of the total number of fish observed in a one-mile 

bin), the entire section of the Lower Crooked River downstream of RM 12 may be classified as 

coldwater fish habitat. The trout population in this lower section of the Lower Crooked River is

dependent on groundwater that enters the river downstream of RM 13.7 and maintains water 

temperatures close to or below the proposed Oregon water temperature standard for salmonid 

rearing habitat.
28

Acknowledgments

The authors thank the following individuals and agencies for their assistance and support 

in conducting the fish survey of the Lower Crooked River: Michelle McSwain (BLM Prineville

District Office), Steve Swanson (BLM National Science Technology Center, Denver, Colorado), 

Rosy Mazaika (BLM Oregon State Office), Peter Lickwar (U.S. Fish and Wildlife Service), Don 

Ratliff (Portland General Electric), Gary Lytle (Deschutes Valley Water District), and Tom, 

Vicky, and Pat Holecheck. The field crew that collected these data in the rugged and remote 

Lower Crooked River included David Leer, Aaron Berger, Hannah Paden, Jeremy Romer, Matt 

Strickland, Steven Clark, Hank Keogh, Miles Johnson, Daniel Jones, and Joe Naughton.

References

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tool for identifying spatial pattern in fish distribution. Journal of Freshwater Ecology 20: 335-

345.

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types in small streams, with examples of habitat utilization by salmonids during low 

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habitat inventory information. American Fisheries Society, Western Division, Bethesda, 

Maryland, USA.

Chapman, D.W. 1988. Critical review of variables used to define effects of fines in redds of large 

salmonids. Transactions of the American Fisheries Society 117: 1-21.

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morphology, and salmonid abundance in northeastern Oregon streams. Canadian Journal of 

Fisheries and Aquatic Sciences 60: 1266-1280.

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Keeley, M. S. Powell, and H. W. Li. 2002. Metabolism, swimming performance, and tissue 

biochemistry of high desert redband trout (Oncorhynchus mykiss ssp.): Evidence for 

phenotypic differences in physiological function. Physiological and Biochemical Zoology 75: 

413-431.

Li, H. W., G. A. Lamberti, T. N. Pearsons, C. K. Tait, and J. C. Buckhouse. 1994. Cumulative 

effects of riparian disturbances along high desert trout streams of the John Day Basin, Oregon. 

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McCune, B., and J. B. Grace. 2002. Analysis of ecological communities. MjM Software Design, 

Gleneden Beach, OR.

ODFW. 1997. Oregon Department of Fisheries and Wildlife Aquatic Inventory Project Stream 

Report. Survey of the Crooked River conducted by K. Jones, J. Rogers, K. Kenaston, M. 

Buchanan, and J. Burke.

ODEQ. 2005. Oregon Department of Environmental Quality. Draft Proposed Rule Revisions to 

OAR Chapter 340, Division 041: Water Quality Standards. 

[http://www.deq.state.or.us/wq/standards/WQStdsTurbidity.htm]

Pater, D. E., S. A. Bryce, T. D. Thorson, J. Kagan, C. Chappell, J. M. Omernik, S. H. Azevedo, 

and A. J. Woods. 1998. Ecoregions of western Washington and Oregon. U.S. Geological 

Survey, Reston, Virginia.
29

Rodnick, K. J., A. K. Gamperl, K. R. Lizars, M. T. Bennett, R. N. Rausch, and E. R. Keeley. 

2004. Thermal tolerance and metabolic physiology among redband trout populations in southeastern Oregon. Journal of Fish Biology 64: 310-335.

Torgersen, C. E., D. M. Price, H. W. Li, and B. A. McIntosh. 1999. Multiscale thermal refugia 

and stream habitat associations of chinook salmon in northeastern Oregon. Ecological 

Applications 9: 301-319.

Trexler, J. C., and J. Travis. 1993. Nontraditional regression analysis. Ecology 74: 1629-1637.

USDA Forest Service. 2003. Crooked River within the Cooked River National Grassland. 2003 

Level II Stream Survey Report. Lookout Mountain Ranger District, Ochoco National Forest.

Prineville, OR

Waters, T. F. 1995. Sediment in streams: Sources, biological effects, and control. American 

Fisheries Society Monograph 7.

Watershed Sciences. 2004. Aerial survey of the Crooked River: Thermal infrared and color 

videography. Remote sensing survey conducted by R. Faux. Watershed Sciences, Inc., 

Corvallis, Oregon.

Zaroban, D., M. Mulvey, T. Maret, R. Hughes, and G. Merritt. 1999. Classification of species 

attributes for Pacific Northwest freshwater fishes. Northwest Science 73: 81-93.

Zimmerman, C. E., and D. E. Ratliff. 2003. Controls on the distribution and life history of fish 

populations in the Deschutes River: Geology, hydrology, and dams. Pages 51-70 in J. E. 

O'Connor, and G. E. Grant, editors. A peculiar river: Geology, geomorphology, and hydrology 

of the Deschutes River, Oregon. American Geophysical Union, Washington, DC.
30

Appendix A. Temporal variation in stream discharge during summer 2002 

and 2004.
31

Appendix B. Scatterplots depicting the relationships between daily 

maximum water temperature data at two reference sites (Hollywood and 

Pink; x-axis) and four other sites (Elliot, Grassland, Lone Pine, and Horney 

Hollow; y-axis), August 16–31, 2004.

Temperature (C)

16 17 18 19 20 21 22

Temperature (C)

16

17

18

19

20

21

22

23

24

Hollywood / Elliot 

Temperature (C)

16 17 18 19 20 21 22

Temperature (C)

16

17

18

19

20

21

22

23

Hollywood / Grassland 
32

Appendix B. (continued)

Temperature (C)

13.8 14.0 14.2 14.4 14.6 14.8 15.0 15.2 15.4 15.6

Temperature (C)

15.0

15.5

16.0

16.5

17.0

17.5

18.0

Pink / Lone Pine 

Temperature (C)

13.8 14.0 14.2 14.4 14.6 14.8 15.0 15.2 15.4 15.6

Temperature (C)

12.5

13.0

13.5

14.0

14.5

15.0

15.5

16.0

Pink / Horny Hollow 
33

Appendix C. Regression results and coefficients for correction factors 

used to predict daily maximum water temperature at Elliot, Grassland, 

Lone Pine, and Horny Hollow sites. 

[Data collected at all sites on August 16-31, 2004 were used to estimate water temperatures at selected sites (Elliot, 

Grassland, Lone Pine, and Horny Hollow) during the period July 29 – August 4, 2004]

Site R 2 Y-intercept Slope

Hollywood / Elliot 0.98 -2.576 1.210

Hollywood / Grassland 0.96 1.956 0.931

Pink / Lone Pine 0.97 -5.628 1.491

Pink / Horny Hollow 0.98 -10.874 1.704
34

Appendix D. Species matrix with proportional abundance of fishes 

sampled during electrofishing and angling surveys of the Lower Crooked 

River, July 20–August 3, 2004. 

[Ordination of the species matrix was calculated with principal components analysis (PCA). See figure 11 for 

definitions of species codes]

Species

Site RT CM NP LD SD SU PS SS

Pink 0.76 0.01 0.06 0.01 0.00 0.04 0.00 0.12 

Horny H. 0.54 0.00 0.02 0.20 0.01 0.06 0.00 0.16 

Lone Pine 0.69 0.00 0.04 0.14 0.02 0.03 0.00 0.08 

Hollywood 0.20 0.14 0.13 0.14 0.25 0.07 0.06 0.00 

Grassland 0.07 0.22 0.16 0.05 0.40 0.07 0.03 0.00 

Elliot 0.03 0.51 0.22 0.01 0.22 0.00 0.00 0.00 
35

Appendix E. Habitat matrix evaluated for correlations with ordination axes in principal components 

analysis (PCA) of species in site space (see appendix C).

Habitat variable

Site

Percent

pool 

Percent

riffle

Percent

rapid

Percent

glide

Max.

depth 

(m)

Mean 

depth 

(m)

Wetted 

width 

(m)

Unit

length

Percent

boulder

Percent

cobble

Percent

gravel

Percent

sand

Percent

silt 7DADM

Turbidity

Pink 84 0 7 9 3.3 1.8 25 90 38 11 1 24 27 15.1 1.8

Horny H. 32 15 0 53 2.5 1.5 22 160 34 5 1 36 23 15.1 2.1

Lone Pine 27 16 7 50 2.3 1.2 22 68 45 39 7 9 0 17.2 1.9

Hollywood 76 19 5 0 1.8 1 20 95 19 13 4 44 20 21.2 2.0

Grassland 15 52 9 24 1.6 0.9 20 68 50 37 10 2 0 21.7 6.5

Elliot 35 21 25 18 1.2 0.7 16 60 36 50 2 0 12 23.0 4.8
36

Appendix F. Statistical output from principal components analysis (PCA) 

of electrofishing/angling sites in fish species space in PC-ORD.

********* PRINCIPAL COMPONENTS ANALYSIS -- sites in species space **********

PC-ORD, Version 4.36 

7 Jul 2006, 13:46

 

Cross-products matrix contains CORRELATION COEFFICIENTS among species 

CROSS-PRODUCTS MATRIX

---------------------

rbt 0.1000D+01

cm -0.9385D+00 0.1000D+01

np -0.9058D+00 0.9680D+00 0.1000D+01

lnd 0.2698D+00 -0.5396D+00 -0.5812D+00 0.1000D+01

sd -0.9255D+00 0.8121D+00 0.8675D+00 -0.1997D+00 0.1000D+01

suc 0.1840D+00 -0.4602D+00 -0.3736D+00 0.6253D+00 0.8441D-01 0.1000D+01

pai -0.4186D+00 0.2167D+00 0.3690D+00 0.3093D+00 0.6882D+00 0.5922D+00

 0.1000D+01

shor 0.9299D+00 -0.8974D+00 -0.9508D+00 0.3505D+00 -0.9578D+00 0.1804D+00

 -0.5735D+00 0.1000D+01

--------------------------------------------------------------------------------

 VARIANCE EXTRACTED, FIRST 8 AXES

 ---------------------------------------------------------------

 Broken-stick

 AXIS Eigenvalue % of Variance Cum.% of Var. Eigenvalue

 ---------------------------------------------------------------

 1 5.125 64.056 64.056 2.718

 2 2.210 27.624 91.681 1.718

 3 0.430 5.381 97.062 1.218

 4 0.202 2.531 99.593 0.885

 5 0.033 0.407 100.000 0.635

 6 0.000 0.000 100.000 0.435

 7 0.000 0.000 100.000 0.268

 8 0.000 0.000 100.000 0.125

 ---------------------------------------------------------------

 FIRST 6 EIGENVECTORS

--------------------------------------------------------------------------------

 Eigenvector

species 1 2 3 4 5 6

--------------------------------------------------------------------------------

rbt 0.4212 0.0590 -0.3507 -0.3864 -0.0429 0.3049

cm -0.4239 0.1474 0.1931 0.1656 0.5451 0.1875

np -0.4358 0.0866 -0.1068 -0.1009 0.3027 0.2047

lnd 0.2041 -0.4837 0.7854 -0.1409 0.0373 0.1433

sd -0.4113 -0.2322 -0.0363 0.1756 -0.4738 -0.4703

suc 0.1182 -0.6003 -0.3632 0.6080 0.1143 0.3318

pai -0.2006 -0.5582 -0.2795 -0.5813 0.3096 -0.2706

shor 0.4336 0.0867 -0.0123 0.2340 0.5240 -0.6363

--------------------------------------------------------------------------------

 COORDINATES (SCORES) OF sites 

---------------------------------------------------------------------------------------------

 Axis (Component)

 sites 1 2 3 4 5 6

---------------------------------------------------------------------------------------------

 1 Pink 1.8437 1.4074 -1.1470 0.0309 0.1112 0.0000

 2 Horny 2.6624 -0.4576 0.7851 0.6031 0.0978 0.0000

 3 Lone 2.0790 0.0250 0.2894 -0.6080 -0.2639 0.0000

 4 Holly -1.2901 -2.0068 -0.0052 -0.4838 0.2352 0.0000

 5 Grass -2.2915 -1.2880 -0.4921 0.4949 -0.2176 0.0000

 6 Eliot -3.0037 2.3200 0.5699 -0.0370 0.0373 0.0000

---------------------------------------------------------------------------------------------

Writing weighted average scores on 6 axes for 8 species into file for graphing.

********************************** End of PCA **********************************
Publishing support provided by the U.S. Geological Survey

 Publishing Network, Tacoma Publishing Service Center

For more information concerning the research in this report, contact the

 Director, Forest and Rangeland Ecosystem Science Center

 U.S. Geological Survey

 777 NW 9th Street, Suite 400

 Corvallis, Oregon, 97330

 http://fresc.usgs.gov/
Torgersen and others—Longitudinal Patterns of Fish Assemblages, Aquatic Habitat, and Water Temperature in the Lower Crooked River, Oregon—Open-File Report 2007–1125