U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2020–5068

Prepared in cooperation with the U.S. Army Corps of Engineers, Portland District

Temperature and Water-Quality Diversity and the Effects of 

Surface-Water Connection in Off-Channel Features of the 

Willamette River, Oregon, 2015–16
Cover. View looking southeast at off-channel feature on right bank of Willamette River, at river mile 

107.5, about 12 miles downstream from Albany, Oregon. Photograph by Joseph Mangano, 

U.S. Geological Survey, October 6, 2015.
Temperature and Water-Quality Diversity 

and the Effects of Surface-Water 

Connection in Off-Channel Features of the 

Willamette River, Oregon, 2015–16

By Cassandra D. Smith, Joseph F. Mangano, and Stewart A. Rounds

Prepared in cooperation with the U.S. Army Corps of Engineers, Portland District

Scientific Investigations Report 2020–5068

U.S. Department of the Interior

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

DAVID BERNHARDT, Secretary

U.S. Geological Survey

James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2020

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as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner.

Suggested citation:

Smith, C.D., Mangano, J.F., and Rounds, S.A., 2020, Temperature and water-quality diversity and the effects of 

surface-water connection in off-channel features of the Willamette River, Oregon, 2015–16: U.S. Geological Survey 

Scientific Investigations Report 2020–5068, 70 p., https://doi.org/10.3133/sir20205068.

ISSN 2328-0328 (online)
iii

Contents

Acknowledgments......................................................................................................................................viii

Executive Summary.......................................................................................................................................1

Introduction.....................................................................................................................................................2

Purpose and Scope ..............................................................................................................................6

Study Area..............................................................................................................................................7

Study Reaches.......................................................................................................................................8

Terminology............................................................................................................................................9

Water Quality................................................................................................................................9

Water-Quality Processes............................................................................................................9

Flow Type .......................................................................................................................................9

Relative Streamflow and Related River Stage ........................................................................9

Data-Collection Locales ...........................................................................................................10

Landforms....................................................................................................................................10

Site and Reach Names .............................................................................................................10

Methods.........................................................................................................................................................10

Field Data Collection...........................................................................................................................11

2015...............................................................................................................................................11

2016...............................................................................................................................................11

Data Processing .........................................................................................................................19

Published Datasets of Field Measurements ..................................................................................19

Field Observations and Geomorphic Characteristics of Off-Channel Features .......................21

Streamflow and Temperature Data at U.S. Geological Survey Streamgage Sites ..................21

Water-Quality Conditions of the Willamette River and Adjacent Off-Channel Features .................21

Main-Channel Water-Quality Conditions ........................................................................................21

Off-Channel Feature Water-Quality Conditions .............................................................................25

Heterogeneity Among Off-Channel Features ........................................................................25

Heterogeneity Within Alcoves .................................................................................................25

Factors Affecting Heterogeneity Within and Among Off-Channel Features ...................31

Comparing Off-Channel and Main-Channel Water Quality ..........................................................33

Effect of Upstream Morphology on Water Quality in Off-Channel Features ......................................34

Examples of the Relations Between Geomorphology, Surface-Water Connectivity, 

and Water Quality of Off-Channel Features ......................................................................37

Fairfield Alcove...........................................................................................................................39

Windsor Bar Alcove ..................................................................................................................39

Murphy Bar Alcove....................................................................................................................41

Blue Ruin Alcove ........................................................................................................................44

Harpers Bend Side Channel .....................................................................................................45

Importance of Upstream Connections on Water Quality of Off-Channel Features .................45

Linking Site Characteristics and Water-Quality Processes in Off-Channel Features ......................47

Site Classification Scheme ...............................................................................................................47

Theoretical Process Matrix ..............................................................................................................48

Conclusions and Implications for Research and Management ...........................................................50

References Cited..........................................................................................................................................52
iv

Appendix 1. Comparison of Off-Channel to Main-Channel Water Temperatures for 

Continuously Monitored Sites ......................................................................................................57

Appendix 2. Aerial Imagery from 1994 and 2016 for Select Off-Channel Features ........................67

Figures

1. Map showing the Willamette River Basin and large dams, northwestern Oregon ...........3

2. Maps showing study reaches and water-temperature monitoring sites along 

the Willamette River, Oregon, in 2015 (August–October) and 2016 (May–October) ..........4

3. Diagrams showing surface and subsurface flow paths of off-channel features 

of a river at various streamflows ...............................................................................................5

4. Graph showing measured streamflow conditions during the low-flow period of 

May–September in 2015 and 2016 compared to historical (2001–19) conditions 

in the Willamette River at Albany, Oregon, streamgage (U.S. Geological Survey 

station 14174000) ...........................................................................................................................7

5. Graphs showing hourly water-temperature measurements in the main channel 

Willamette River, Oregon, between river miles 67.1 and 164.2 ...........................................22

6. Graphs showing the 7-day moving average of the daily maximum water 

temperature measured at various sites in the Willamette River, Oregon .........................24

7. Graph showing hourly dissolved-oxygen measurements of the main channel 

Willamette River, Oregon, in the Independence monitoring reach in late 

summer 2015 and summer 2016 ................................................................................................25

8. Graphs showing hourly water-temperature measurements in monitored 

off-channel features of the Willamette River, Oregon, in late summer 2015 ....................26

9. Graphs showing hourly water-temperature measurements in monitored 

off-channel features of the Willamette River, Oregon, in summer 2016 ............................27

10. Image showing water-temperature measurements on July 20, 2016, at 6:30 p.m. 

Pacific standard time in the Willamette River and select off-channel features 

near Independence, Oregon .....................................................................................................29

11. Graphs showing water temperatures at the top, middle, and bottom of the 

water column in alcoves in the Willamette River, Oregon ...................................................29

12. Graphs showing dissolved-oxygen concentrations at the top, middle, and 

bottom of the water column in alcoves in the Willamette River, Oregon ..........................30

13. Graphs showing longitudinal profiles of synoptic point measurements recorded 

in the alcove at river mile 74.6 along the Willamette River near Salem, Oregon, 

and adjacent main-channel readings on August 27, 2015, at 2:00 p.m. Pacific 

daylight time ................................................................................................................................31

14. Graphs showing longitudinal profiles of water-temperature synoptic point 

measurements recorded in the alcove at river mile 97.7 along the Willamette 

River near Independence, Oregon, and adjacent main-channel readings .......................32

15. Schematic diagram showing 2008 lidar land-surface elevations and differences 

in size and height of upstream connection points for alcoves at river miles 97.7 

and 98.4 near Independence, Oregon .....................................................................................33

16. Map showing average water-temperature differences between alcoves 

and the main channel, and averaged dissolved-oxygen concentrations in 

alcoves, measured at the top and bottom of the alcove’s water column, in the 

Willamette River, Oregon ...........................................................................................................35
v

17. Graphs showing examples of three types of patterns resulting from a 

comparison of water temperatures in the main channel and in several 

off-channel features of the Willamette River, Oregon ..........................................................36

18. Graphs showing categories of features based on water-temperature 

comparisons to the main channel in the three monitoring reaches of the 

Willamette River, Oregon ...........................................................................................................37

19. Aerial photographs showing the location and important geomorphic features 

of five off-channel features and one main-channel location monitored with 

continuous water-quality monitors in summer 2016 along the Willamette 

River, Oregon ...............................................................................................................................38

20. Graphs showing hourly water-temperature and dissolved-oxygen 

measurements in the Fairfield alcove at river mile 67.1 along the 

Willamette River, Oregon, and streamflow at the Willamette River 

at Salem, Oregon, streamgage (U.S. Geological Survey station 

14191000) in September and October 2016 .............................................................................41

21. Graphs showing hourly water-temperature, dissolved-oxygen, and 

specific-conductance measurements in Windsor Bar alcove at river mile 74.6 

along the Willamette River, Oregon, and streamflow at the Willamette River at 

Salem, Oregon, streamgage (U.S. Geological Survey station 14191000) in June 

and July 2016 ...............................................................................................................................42

22. Graph showing hourly dissolved-oxygen concentrations in Murphy Bar alcove 

at river mile 97.7 (near Independence) along the Willamette River, Oregon, 

and streamflow at the Willamette River at Salem, Oregon, streamgage 

(U.S. Geological Survey station 14191000) in October 2016 .................................................42

23. Graphs showing hourly water-temperature measurements in the main-channel 

Willamette River, Oregon, at river mile 97.7, hourly water-temperature and 

dissolved-oxygen measurements in Murphy Bar alcove at river mile 97.7, 

and streamflow at the Willamette River at Salem, Oregon, streamgage (U.S. 

Geological Survey station 14191000) from May through October 2016 .............................43

24. Graphs showing hourly water-temperature and dissolved-oxygen 

measurements in Blue Ruin alcove at river mile 164.1, and streamflow at the 

Willamette River at Harrisburg, Oregon, streamgage (U.S. Geological Survey 

station 14166000) during 2016 ...................................................................................................44

25. Graphs showing hourly water-temperature and dissolved-oxygen 

measurements in Harpers Bend side channel at river mile (RM) 164.8 (near 

Harrisburg, Oregon), plotted with water-temperature data from the main 

channel at RM 164.2 and dissolved-oxygen data from the main channel at 

RM 97.7; and streamflow at the Willamette River at Harrisburg, Oregon, 

streamgage (U.S. Geological Survey station 14166000) .......................................................46

Tables

1. Sites and dates of data collection for continuous water-temperature sensors 

installed in off-channel features and the main-channel Willamette River, 

Oregon, in summers 2015 and 2016 ..........................................................................................12

2. Sites and dates of data collection for multiparameter water-quality monitors 

installed in off-channel features and the main-channel Willamette River, 

Oregon, in summers 2015 and 2016 ..........................................................................................17
vi

3. Sites and dates of data collection for pressure transducers and 

barometric-pressure sensors installed in off-channel features of the 

Willamette River, Oregon, from May to November 2016 ......................................................20

4. Sites and dates of data collection for temperature sensors (pendants) installed 

in a tree or on gravel bars upstream of off-channel features of the Willamette 

River, Oregon in summer 2016 ..................................................................................................20

5. Observational data collected at five off-channel features along the Willamette 

River, Oregon, where water-quality monitors were deployed in summer 2016 ................40

6. A site classification scheme linking broad patterns of measured water-quality 

conditions to site characteristics of off-channel features along the Willamette 

River, Oregon, in the low-flow summer periods of 2015 and 2016 ......................................48

7. Theoretical process matrix linking water-quality outcomes or conditions 

for water temperature and dissolved oxygen with processes and site 

characteristics that can combine to create the outcomes in off-channel 

features of the Willamette River, Oregon ...............................................................................49

Conversion Factors

International System of Units to U.S. customary units

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

meter (m) 1.094 yard (yd) 

Area

square meter (m2) 0.0002471 acre 

square kilometer (km2) 247.1 acre

square meter (m2) 10.76 square foot (ft2) 

square kilometer (km2) 0.3861 square mile (mi2)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F = (1.8 × °C) + 32.

Datums

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).
vii

Supplemental Information

Streamflow is measured, reported, and widely used in units of cubic feet per second (ft3/s) by 

resource managers and water agencies in the Willamette River Basin; therefore, cubic feet per 

second is used in this report. Reaches and sites in this report are referenced to river miles (RM) 

from U.S. Geological Survey topographic maps. All other units in this report and associated data 

releases are reported in the International System of Units (metric).

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm 

at 25 °C).

Concentrations of chemical constituents in water are given in milligrams per liter (mg/L).

Abbreviations

7dADM seven-day moving average of the daily maximum

CWR cold-water refuge

> greater than

≥ greater than or equal to

< less than

≤ less than or equal to

lidar light detection and ranging

NWIS National Water Information System

OAR Oregon Administrative Rule

PDT Pacific daylight time

PVC polyvinyl chloride

RM river mile

USACE U.S. Army Corps of Engineers

USGS U.S. Geological Survey

YSI Yellow Springs Instruments
viii

Acknowledgments

The authors thank the U.S. Army Corps of Engineers (USACE) for their support and assistance 

in this study. Norman Buccola, previously with the U.S. Geological Survey (USGS), was instrumental in the early phases of this project and both field seasons of data collection. Dave Piatt 

(USGS) was key in all field efforts as well as data processing for many of the continuous watertemperature sensors installed. Field assistance for synoptic data collection was also provided 

by David Weathers, Heather Bervid, Chauncey Anderson, Brandon Overstreet, Mackenzie Keith, 

Tess Harden, Alex Costello, Erin Poor, and James White (USGS), and Dan Turner (USACE). 

Krista Jones and Rose Wallick (USGS) assisted with this study through helpful discussions and 

feedback.
Temperature and Water-Quality Diversity and the Effects 

of Surface-Water Connection in Off-Channel Features of 

the Willamette River, Oregon, 2015–16

By Cassandra D. Smith, Joseph F. Mangano, and Stewart A. Rounds

Executive Summary

Water-quality conditions (including temperature) in 

the Willamette River and many of its adjacent off-channel 

features, such as alcoves and side channels, were monitored 

between river miles 67 (near Salem, Oregon) and 168 (near 

Eugene, Oregon) during the summers of 2015 and 2016. One 

or more parameters (water temperature, dissolved oxygen, pH, 

specific conductance, and [or] water depth) were continuously 

measured at sites in the main channel (9 sites in 2015; 5 sites 

in 2016) and select off-channel features (20 features in 2015; 

22 features in 2016). Multiple point measurements also were 

collected in the continuously monitored features and in a variety of other off-channel features to supplement the continuous 

datasets and provide longitudinal and depth-specific waterquality information.

This study was initiated in reaction to the unusually warm, dry weather and resulting low streamflows that 

occurred in the Pacific Northwest in 2015 and the need 

for flow managers to understand the effects of streamflow 

on water-quality conditions in off-channel features of the 

Willamette River. Field monitoring for this study was focused 

on documenting water-quality conditions during low summer 

streamflows and during fluctuations in streamflow, including when side channels (connected to the main channel at the 

upstream and downstream ends) became alcoves (connected 

to the main channel only at the downstream end) and reconnected to become side channels again. These field surveys 

provided extensive spatial and temporal datasets that were 

previously lacking for this river system.

Water in the main channel of the Willamette River 

upstream from river mile 50 near Newberg typically is well 

mixed during summer (June–August), with warm water temperatures (greater than 18 degrees Celsius) and high dissolvedoxygen concentrations (often greater than 7.7 milligrams per 

liter). In 2015 and 2016, water temperatures measured in the 

main channel near Salem, Independence, and Harrisburg (river 

miles 70.2, 97.7, and 161/164.2, respectively) did not meet the 

State of Oregon’s maximum water-temperature standard of 

18 degrees Celsius for the protection of fish rearing and migration. Continuous dissolved-oxygen concentrations measured in 

the main channel near Independence met the State of Oregon 

7-day minimum mean cold-water criterion of 6.5 milligrams 

per liter throughout the 2016 monitoring period, and instantaneous values during summer ranged from 8.0 to 10.5 milligrams per liter. Point measurements throughout the study 

reaches in 2016 also showed dissolved-oxygen concentrations 

in the main channel were consistently greater than 7.0 milligrams per liter. Other water-quality parameters (specific 

conductance and pH) also were measured in the main channel 

near Independence in 2016, but results are not extensively 

discussed in this report.

During low summer flows, a diverse suite of off-channel 

features such as side channels and alcoves exist adjacent to 

the main channel of the Willamette River; these features vary 

substantially in size, morphology, and connection to the main 

channel. Water quality in off-channel features was found 

to be heterogenous, and differences were measured vertically, longitudinally, seasonally, and among features. Despite 

temporal and spatial variability within individual features, 

comparison of continuous water-temperature data between 

the main channel and off-channel features revealed that some 

off-channel features were consistently cooler than the main 

channel, some were consistently warmer than the main channel, and others fluctuated between warmer or cooler than the 

main channel. The temperature of some off-channel features 

responded quickly to changes in the weather and to changes 

in main-channel temperatures, whereas other features reacted 

more slowly. Site-specific characteristics including upstream 

connection, depth, and presence or absence of aquatic or 

riparian vegetation were factors that seemed to affect the water 

quality of a feature.

Overlaying continuous water-quality data measured in 

an off-channel feature with main channel streamflow revealed 

that the surface-water connections between the main channel 

and off-channel feature exert important controls on waterquality conditions in off-channel features. Connections to the 

main channel at the upstream and downstream ends are controlled by the geomorphology of the off-channel feature and 

the streamflow of the river; during low summer flows, many 

off-channel features become disconnected at the upstream 

end from main-channel surface-water flow. Monitored offchannel features that were disconnected at the upstream end 
2 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

for multiple months tended to have large quantities of aquatic 

vegetation, vertical stratification of water-quality parameters, 

and cool water temperatures and low (hypoxic or anoxic) 

dissolved-oxygen concentrations in the deeper parts of the 

water column. Off-channel features that remained partially 

connected to upstream surface-water inflow were affected 

by the warm, oxygenated main-channel inputs; water-quality 

patterns differed per feature, which was likely related to the 

amount of main-channel water entering at the upstream connection. Partial or complete disconnection at the upstream end 

helped reveal other factors (biological processes, subsurface 

inputs [groundwater/hyporheic]) that affect a feature’s water 

quality, although quantifying the magnitude of these effects 

was beyond the scope of this study.

Results from this study showed a relation between 

the geomorphology, hydrology, ecology, and water quality 

(including temperature) of an off-channel feature. In offchannel features that became disconnected from upstream 

surface-water inputs from the main channel during summer, 

water quality was largely affected by local factors and different from the main channel. Downstream of Corvallis (river 

mile 131), extensive communities of invasive aquatic vegetation have become established in many off-channel features 

where frequent scouring is absent, and these plant communities affect water quality through physical and biological 

processes (for example, shading, respiration, and photosynthesis). Data from this study confirmed previous findings that 

many features that can be classified as cold-water refuges 

based on water temperature standards established by Oregon 

Department of Environmental Quality also contained low 

concentrations (less than 4 milligrams per liter, and in many 

cases less than 2 milligrams per liter) of dissolved oxygen, 

which are conditions that may not be suitable for sensitive 

fish species.

This study documents (1) key differences in water quality 

within and among off-channel features of the Willamette River 

during summer, and (2) the important effect of flow variations 

and main-channel connections on off-channel water quality. 

Based on data from this study, a simplified site classification 

scheme is proposed that links water-quality conditions in 

measured off-channel features with site-specific characteristics 

and summer streamflows. The Willamette River has a diverse 

array of off-channel features, however, and only a subset was 

measured during this study. Therefore, the site classification 

scheme was extended to create a theoretical process matrix 

that relates measured water-quality conditions (for example, 

cool water and low oxygen) to a list of the processes and 

site-specific characteristics that could create those conditions. 

This matrix allows researchers and resource managers to think 

critically about the processes (potentially competing) that may 

be occurring in off-channel features and to form hypotheses 

regarding how site-specific characteristics affect water-quality 

conditions. Future refinements to the proposed site classification scheme and theoretical process matrix could be made 

by collecting additional information on spatial and temporal 

water-quality heterogeneities within off-channel features under 

various flows by quantifying key processes that move water 

and heat through these systems and by studying the effects of 

biological processes on water quality.

Introduction

Riverine ecosystems with aquatic thermal diversity allow 

fish species with differing life histories and thermal requirements to coexist. The Willamette River within the Willamette 

River Basin in northwestern Oregon (fig. 1) is one such 

system that is home to native warm-water and cool-water 

fishes. Native species that tolerate warm water temperatures 

include the endemic Oregon chub (Oregonichthys crameri) 

and redside shiners (Richardsonius balteatus), among others, which are often found in off-channel features (Williams 

and others, 2014). Native fish species requiring cool water 

during one or more life stages include spring Chinook salmon 

(Oncorhynchus tshawytscha), cutthroat trout (O. clarkii), 

and winter steelhead (O. mykiss; Williams and others, 2014). 

The anadromous populations of these fishes rear in streams, 

migrate to the ocean, and then return to their natal stream to 

reproduce.

Anadromous fish in the Willamette River face a multitude 

of stressors such as habitat modification (Wallick and others, 

2013), migration barriers, disease, and altered water temperatures (National Marine Fisheries Service, 2008; Rounds, 

2010). Thermal requirements can be complex and depend on 

the species (Brett, 1952), population/race (Sauter and others, 2001), and gender of the fish (Jeffries and others, 2012). 

A wide range of published research has documented many 

effects of warming water temperatures on salmonids including 

smaller juveniles (Murray and McPhail, 1988), higher adult 

mortality during migration (Martins and others, 2011), shifts 

in migration timing (Quinn and Adams, 1996), and increased 

susceptibility to infectious diseases (Fryer and others, 

1976). Upper Willamette River Chinook salmon and Upper 

Willamette River steelhead are listed as threatened under the 

Federal Endangered Species Act of 1973 (Public Law 93–205, 

87 Stat. 884, as amended), which has led to water-quality 

regulations, flow and temperature management actions, 

and population monitoring to foster their survival (National 

Marine Fisheries Service, 2008).

The Willamette River has been designated as 

temperature-impaired and listed under Section 303(d) of the 

Clean Water Act (Public Law 92–500, 33 U.S.C. §1251 et seq. 

[1972]). The State of Oregon sets temperature standards for 

its major waterbodies to aid native fishes and protect aquatic 

life (Oregon Administrative Rule [OAR] 340–041–0028(4); 

Oregon Department of Environmental Quality, 2016a). For the 

Willamette River, the maximum allowed water temperature 

depends on the time of year and the location, corresponding to how and when sensitive fish species use particular 

river reaches (Oregon Department of Environmental Quality, 

2003, 2005). Reaches upstream from Newberg, Oregon (river 
Introduction 3

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

XX

0 10 20 MILES

0 10 20 KILOMETRS

Portland

Salem

Eugene

Area of figure 2

Columbia River

WILLAMETTE

RIVER

CASCADE RANGE

COAST RANGE

Base from 2012 U.S. Geological Survey 100-meter 

digital data. Coordinate system: UTM Zone 10 North,

North American Datum of 1983

123° 122°

45°

44°

EXPLANATION

X Large dam

OREGON

Willamette River

Basin

Middle Fork Willamette River

McKenzie River

North Santiam River

South Santiam River

Clackamas River

Figure 1. The Willamette River Basin and large dams, 

northwestern Oregon.

mile [RM] 50; fig. 2), have a summer (May 16–October 14) 

temperature requirement of 18 degrees Celsius (°C) or less, 

calculated as the 7-day moving average of the daily maximum 

(7dADM), to protect fish rearing and migration uses. During 

the salmon and steelhead spawning period (October 15–

May 15), the standard for Willamette River reaches upstream 

from Newberg requires the 7dADM to be 13 °C or less. The 

lowermost 50 RM of the Willamette River from Newberg to 

its confluence with the Columbia River are designated as a 

migration corridor, and the temperature standard requires a 

7dADM of 20 °C or less year-round. The Oregon Department 

of Environmental Quality wrote a narrative water-quality 

standard for cold-water refuges (CWRs) that recognizes the 

need to protect species habitat and to minimize additional 

anthropogenic warming when the 7dADM criterion is 

exceeded. This CWR narrative technically only applies to 

designated migration corridors such as the lower 50 RM of the 

Willamette River, but it is commonly referenced by researchers as a useful definition for CWRs in the Willamette River 

system. The definition is written as follows:

“Cold Water Refugia” means those portions of a 

water body where or times during the diel temperature cycle when the water temperature is at least 

2 degrees Celsius colder than the daily maximum 

temperature of the adjacent well-mixed flow of 

the water body (OAR 340–041–0002(10); Oregon 

Department of Environmental Quality, 2016b).

Water temperatures in the Willamette River commonly 

exceed the water-temperature standard’s rearing and migration 

criterion during parts of summer. At the Willamette River at 

Albany, Oregon, streamgage (U.S. Geological Survey [USGS] 

station 14174000, RM 119; fig. 2), temperatures reached 

greater than (>) 21 °C (7dADM) in June 2015. The unusually warm water temperatures followed an exceptionally low 

snowpack in 2015 (Mote and others, 2016) and low summer 

streamflow. High water temperatures may increase the importance of CWRs for the survival of sensitive cool-water fishes 

throughout the Willamette River.

Although water temperature is critical to fish health, fish 

also require other adequate water-quality conditions to survive 

and thrive. As with water temperature, dissolved-oxygen 

requirements for fish species are complex and not fully understood. However, salmonids are susceptible to low dissolvedoxygen concentrations (Carter, 2005), and high mortality was 

observed when salmonids were held in hypoxic (low oxygen) 

conditions for 24 hours (Doudoroff and Shumway, 1970). 

Dissolved-oxygen concentrations near or slightly above 2 milligrams per liter (mg/L) have been associated with behavioral 

changes and diminished swimming speeds (Davis, 1975), and 

effects of low dissolved oxygen may be exacerbated as the 

water temperature increases (Davison and others, 1959). The 

State of Oregon’s dissolved-oxygen criteria differ to protect 

various types of aquatic species. For example, the cold-water 

dissolved-oxygen criterion applies to waterbodies where salmonids and other cold-water species exist during most of year 

and specifies a 7-day minimum mean of 6.5 mg/L (Oregon 

Department of Environmental Quality, 2016c, table 21). The 

cool-water criterion protects native cool-water fishes (such 

as sculpin, smelt, and lamprey) with a 7-day minimum mean 

of 5.0 mg/L (Oregon Department of Environmental Quality, 

2016c, table 21). The main channel Willamette River is generally not dissolved-oxygen impaired (Pogue and Anderson, 

1995). However, past studies from the Willamette River and 

other riverine systems in Oregon have shown that areas classified as CWRs can have dissolved-oxygen gradients (vertical 

and longitudinal) and often have low dissolved-oxygen concentrations (less than [<] 3 mg/L; Ebersole and others, 2003; 

Gregory and Wildman, 2016).
4 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

Coast Fork

Willamette R

WILLAMET TE

RIVER

Yamhill R

Luckiamute R

Luckiamute R

Santiam R

Santiam R

N Santiam R

S

Santia m R

Marys R

Calapooia R

WILLAME

TTE

RIVER

WILLAME

TTE

RIVER

Willamette RiverWillamette River

Willamette R

Luckiamute R

Santiam R

Willamette R

Willamette RWillamette R

Long

Tom

R

McKenzie R

Middle Fk Willamette R

70

70

75 75

100

100

105 105

162 162

167 167

60

80

120

100

140

160

180

170

150

130

110

90

70

50 40

Newberg

Salem

Independence

Albany

Corvallis

Harrisburg

Eugene

Peoria

Willamette Mission

monitoring reach

Independence

monitoring

reach

Harrisburg

monitoring

reach

14197900

14192015

14174000

14166000

14166000

14158100

14191000

67.1

67.1

67.6

67.7

70.2 70.2

73.2

73.4

74.6

95.8

95.9

97.7

97.7 97.9

98.4

101

107.3

107.5

161

161.3

161.7

162.8

162.8

163.5

164.1

164.2

164.8

167.8

168.1

67.1

67.6

67.7

70.2 70.2

73.2

73.4

73.5 73.9

74.6

77.2

96.1

97.7

97.7

98.4

100.2 101

107.5

107.9 107.8

161.3

161.7

162.2 162.9

164.1

164.2

164.8

EXPLANATION

U.S. Geological Survey station 

2015 continuous temperature

sensors

2016 continuous temperature

sensors

Off-channel feature

Main channel

Off-channel feature

Main channel

70 River mile

73.4

77.2

70.2

73.2

14174000

123°15' 123°

45°

15'

45°

44°

45'

44°

30'

44°

15'

44°

2015 Willamette Mission

2015 Independence

2015

Harrisburg

2016

Harrisburg

2016 Independence

2016 Willamette Mission

Base from U.S. Geological Survey National

Elevation Dataset 30-meter digital elevation model.

Water features from National Hydrography Dataset.

Coordinate Reference System: UTM, Zone 10 North, 

horizontal datum is North American Datum of 1983.

0

0 10 MILES

10 KILOMETERS

0

0 10 MILES

10 KILOMETERS

Figure 2. Study reaches and water-temperature monitoring sites along the Willamette River, Oregon, in 2015 (August–October) 

and 2016 (May–October).
Introduction 5

CWRs can exist at a variety of locations within a river 

system, including alcoves, side channels, tributary junctions, 

deep pools, and seeps along a riverbank (Torgersen and others, 

2012). The Willamette River between Eugene and Newberg, 

Oregon, is a wide river with some dynamic reaches containing many side channels, alcoves, and gravel bars. However, 

historical practices of wood removal, bank stabilization, and 

flow management have disrupted natural processes that create 

and maintain off-channel features that may function as CWRs 

(Wallick and others, 2013). Additionally, the large sizes of 

Willamette River off-channel features affect how they function as CWRs; for example, thermal variability is common 

within a single feature. Gregory and others (2008) determined 

that most CWRs in the Willamette River system are in alcoves 

and tributary junctions; however, it is not clear how CWR 

temperatures vary during the summer. A network of CWRs 

along a river system may allow fish to migrate upstream or 

downstream from cold patch to cold patch during otherwise 

warm conditions, thereby enhancing their survival (Gregory 

and others, 2008).

Changes in main-channel streamflow, largely resulting 

from flow modifications at upstream dams, affect the main 

channel and off-channel features (fig. 3). Off-channel features 

typically remain connected to the river at the downstream 

end. A variety of subsurface flow paths may connect the main 

channel to the off-channel features, likely at all flows. During 

periods of high streamflow (often autumn through spring), 

off-channel features are connected to the main channel 

through surface flow at their upstream and downstream extent 

(fig. 3D), causing most off-channel features in the Willamette 

River to function as side channels during high streamflows. As 

streamflow increases from low to high, surface water typically 

will enter the feature at its downstream end before a connection forms with the main channel at its upstream end (fig. 3C). 

During low summer streamflows, off-channel features either 

disconnect at the upstream end (alcoves) or remain connected at the upstream end with various amounts of flow (side 

channels); the presence or absence of an upstream connection depends on the height of the landmass at the upstream 

connection point and stage in the main channel (figs. 3A–C). 

Minimum streamflows in the Willamette River from April to 

October are managed to meet or exceed flow objectives specified in the 2008 Biological Opinion (National Marine Fisheries 

Service, 2008). Flow objectives for the Willamette River are 

often exceeded in April and May due to unregulated inputs 

(snowmelt and runoff) from tributaries, but flow objectives 

were not met in the spring and early summer of 2015.

Side Alcove

channel

Main

channel

Side Alcove

channel

Main

channel

Side

channel

Side

channel

Main

channel

Alcove

Alcove

Main

channel

A. Unusually low streamflow B. Typical low streamflow C. Increasing streamflow D. High streamflow

Surface

flow

Subsurface

flow

Lower Streamflow Higher

EXPLANTION

Flow type and direction—Arrow size 

indicates relative magnitude of flow

Surface flow

Subsurface flow

Figure 3. Surface and subsurface flow paths of off-channel features of a river at various streamflows. A, unusually low streamflow. 

B, typical low streamflow (typical summer flows in the Willamette River, Oregon). C, increasing streamflow. D, high streamflow.
6 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

Off-channel features receive inputs of water from 

main-channel surface flow and through subsurface inputs; 

the quantity and physical properties of water inputs to an 

off-channel feature affect local temperature and dissolvedoxygen concentrations. Surface-water flow includes inputs 

from the upstream connection of features, tributary or other 

discrete inputs, or backwater from downstream connections. 

The temperature difference between surface-water inputs and 

an off-channel feature can vary greatly, contributing to either 

warming or cooling in an off-channel feature. Subsurface 

inputs occur when water traveling through river-bed gravels 

or near-river floodplain gravels exits the subsurface and enters 

the surface water (Fernald and others, 2001). Subsurface water 

gains and losses can affect stream temperatures and their diel 

patterns (Burkholder and others, 2008). Flow path length and 

residence time can affect subsurface water temperature, diel 

fluctuation magnitude, or daily peak timing (Arrigoni and 

others, 2008; Burkholder and others, 2008; Poole and others, 2008). Subsurface inputs with a long flow path tend to be 

cooler than main-channel water in summer and have minimal 

diel fluctuations (Poole and others, 2008). Similar to temperature, inputs of subsurface or main-channel water into an offchannel feature can also affect dissolved-oxygen concentrations and other water-quality parameters (Runkel and others, 

2003). Subsurface dissolved-oxygen concentrations are often 

low (Ebersole and others, 2003; Hinkle and others, 2014), 

potentially revealing areas of input. Upstream dam operations that control streamflow levels may affect water quality 

in off-channel features by affecting the quantity and timing of 

surface and subsurface inputs.

In addition to flow, localized site characteristics (including aquatic vegetation abundance and type, riparian vegetation cover, and feature morphology) and processes (such as 

primary production) directly or indirectly affect water temperature and dissolved-oxygen concentrations in off-channel 

features. Certain processes and inputs may become more 

evident during periods of low streamflow. Aquatic vegetation 

and dissolved-organic matter can decrease light penetration, 

thereby increasing stratification of water temperature and 

decreasing temperatures at depth (Takamura and others, 2003). 

Riparian vegetation can also decrease localized water temperature through shading of the water surface (Ebersole and others, 

2003). Off-channel features with shallow, stagnant water may 

warm more than moving water through accumulated absorption of solar insolation.

The types of aquatic vegetation plant communities (such 

as submerged and emergent) can affect the dissolved-oxygen 

concentrations in a waterbody. Submerged aquatic vegetation 

in Willamette River off-channel features (such as coontail 

[Ceratophyllum demersum] and Canadian waterweed [Elodea 

canadensis]) produce oxygen through photosynthesis and 

release that oxygen into the water column (Caraco and others, 

2006). However, invasive emergent macrophytes (Ludwigia

spp.) also are prevalent in many Willamette River off-channel 

features and tend to release oxygen to the air more so than to 

the water (Benton Soil and Water Conservation District, 2014). 

Ludwigia spp. have been associated with low dissolvedoxygen concentrations and high probabilities of water-column 

hypoxia (Caraco and others, 2006; Bunch and others, 2010). 

Plant and algal respiration and the decomposition of aquatic 

vegetation and other organic matter consumes oxygen and 

tends to decrease dissolved-oxygen concentrations.

The status, location, and susceptibility of CWRs along 

the Willamette River are not well known. A thorough documentation of water-quality conditions along the Willamette 

River and in its off-channel features is needed to understand 

where CWRs exist and how off-channel features might provide usable fish habitat for migration, spawning, and (or) rearing. This study provides spatially and temporally continuous 

datasets to address key knowledge gaps and to provide a foundation for understanding variations within and among sites. 

Organizing and discussing the connections between processes 

and water-quality conditions will provide information about 

how temperature, dissolved oxygen, and fish habitat might 

change as a result of varying flow conditions and other factors.

Purpose and Scope

This report documents water-quality conditions in select 

off-channel features of the Willamette River from Eugene 

to Newberg in northwestern Oregon (figs. 1, 2) during the 

summers of 2015 and 2016. Willamette River streamflow 

was particularly low in 2015 compared to 2000–19 (fig. 4), 

which was roughly when the current flow targets were adopted 

by U.S. Army Corps of Engineers (USACE) flow managers 

(National Marine Fisheries Service, 2008). Low streamflows 

and warm water temperatures in 2015 led to an increased need 

to understand the condition and location of potential CWRs 

and favorable fish habitat. Gregory and Wildman (2016)

completed annual surveys of water temperature and dissolvedoxygen conditions in off-channel features during summers 

2011–16. This study built on the Gregory and Wildman (2016)

surveys by deploying continuously recording temperature 

and dissolved-oxygen sensors each summer to collect more 

frequent field measurements over a large area and to include a 

temporal component. Additionally, researchers collected specific conductance and (or) pH data at select continuous sites 

and point-measurement locations as part of this study.

In addition to documenting water-quality conditions in 

the Willamette River’s main channel and off-channel features, 

this report describes how the geomorphology and hydrology of 

off-channel features affect their ecology and water quality. The 

report focuses on the processes and site characteristics that 

combine to create the measured water-quality conditions. This 

investigation provides insights regarding how main-channel 

flow connections and local factors (for example, vegetation 

and feature morphology) may affect water temperature and 

dissolved-oxygen conditions in off-channel features. To distill 

the complex conditions and processes affecting the sites that 

were monitored, a simplified site classification scheme is proposed, linking water-quality monitoring data with measured 
Introduction 7

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

18,000

20,000

22,000

24,000

Streamflow (discharge), in cubic feet per second

May June July

Date

August September

Willamette River at Albany, Oregon, streamgage (USGS station 14174000)

10th to 90th percentile (2001–19)

25th to 75th percentile (2001–19)

Median (2001–19)

2015

2016

EXPLANATION

Figure 4. Measured streamflow conditions during the low-flow period of May–September in 2015 and 2016 compared to historical 

(2001–19) conditions in the Willamette River at Albany, Oregon, streamgage (U.S. Geological Survey station 14174000).

and observed site characteristics. Considering that only a 

subset of off-channel features along the Willamette River were 

monitored, an accompanying theoretical process matrix is also 

proposed to describe the multitude of factors and processes 

that could interact to create a variety of water-quality conditions in off-channel features. The theoretical process matrix 

introduces and organizes the interacting processes that occur 

in aquatic environments and describes the water-quality conditions that may result. The proposed site classification scheme 

and theoretical process matrix are intended to assist resource 

managers and researchers in understanding the distribution, 

duration, and condition of CWRs in the system.

The overall goals of this report are to do the following:

1. Document continuous water-quality datasets (water temperature, dissolved oxygen, and other parameters) and 

water-quality point measurements in the main channel 

and off-channel features of the Willamette River during 

the summers of 2015 and 2016;

2. Describe the measured spatial and temporal variability in 

water-quality conditions within and among off-channel 

features and provide context for interpreting the waterquality data and its relevance for fish habitat;

3. Discuss the role of upstream surface-water connectivity 

on temperature, water quality, and ecology in offchannel features;

4. Develop a means of linking water quality in monitored 

off-channel features to the possible processes affecting 

the patterns and values in the data; and

5. Provide a basis for developing hypotheses regarding 

site-specific characteristics, processes, and the possible 

water-quality conditions that may exist in other offchannel features along the Willamette River.

Study Area

The Willamette River drains 28,800 square kilometers 

of forested, agricultural, and urban land between the Cascade 

Range and Coast Range of Oregon (fig. 1). The Willamette 

River begins at the confluence of the Middle Fork and Coast 

Fork Willamette Rivers near Eugene (figs. 1, 2) and flows 

north nearly 300 kilometers before joining the Columbia River 

near Portland, Oregon (fig. 1). During its route north, several 

tributaries add substantial flow to the river, especially the 

McKenzie, Santiam, and Clackamas Rivers (figs. 1, 2). Before 

the installation of USACE dams on some of the tributaries 

in the mid-1900s, much of the Willamette River between 

Eugene and Newberg (fig. 2) was a wandering gravel-bed river 

(Church, 1983) with a few short, geologically stable reaches; 

frequent channel migration created a mixture of single- and 

multi-threaded reaches containing a variety of wetted offchannel areas, large gravel bars of varying stability, and 

floodplain surfaces at a range of heights above the channel. 
8 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

The river meandered within its floodplain except where it 

flowed adjacent to tall, erosion-resistant Pleistocene floodplain 

surfaces or Tertiary bedrock of the Salem Hills (O’Connor and 

others, 2001).

Thirteen USACE dams and six other large dams have 

been built on tributaries of the Willamette River (fig. 1), 

affecting modern flow, sediment, and temperature regimes of 

the river. The primary purpose of many of the USACE dams 

is to support the USACE’s flood-risk management mission 

(U.S. Army Corps of Engineers, 2019); other benefits include 

power generation, recreation, and municipal and irrigation 

water supply. Although no large dams have been built on 

the main-channel Willamette River, flow management using 

storage in the tributary reservoirs has greatly altered the flow 

regime of the river. Peak flows have decreased and summer 

base flows have increased compared to pre-dam conditions 

(Rounds, 2010; Wallick and others, 2013). Measured at the 

Willamette River at Albany, Oregon, streamgage (USGS station 14174000; RM 119; fig. 2), the lowest summer streamflows have increased from an annual range of approximately 

1,900–3,300 cubic feet per second (ft3/s) to approximately 

3,700–5,300 ft3/s after the implementation of summer flow 

augmentation from reservoir releases beginning in the early 

1950s (U.S. Geological Survey, 2018). In combination with 

channel-stabilizing revetments, the dams also have decreased 

the supply of bed sediment by about 60 percent in Salem and 

Portland, Oregon (O’Connor and others, 2014).

Changes in streamflow and sediment supply as a result of 

the dams, in addition to the removal of instream large wood 

and other land-use changes, have altered the geomorphic 

regime of the Willamette River in the last century by reducing 

gravel-bar area, reducing instream wood supply to the river, 

and stabilizing the channel and its flanking landforms such as 

alcoves and side channels (Gregory and others, 2019; Sedell 

and Froggatt, 1984; Wallick and others, 2013). Willamette 

River morphology still changes on a nearly annual basis in 

reaches upstream from Peoria, Oregon (RM 142, about 10 RM 

upstream from Corvallis, Oregon; fig. 2), but the magnitude 

of channel change in those reaches is currently less than 

what occurred before the anthropogenic modifications to the 

system. Bank erosion, gravel bar growth, and the development 

of off-channel areas occur, which create and modify an array 

of off-channel features in the upper reach (Wallick and others, 

2013). The modern Willamette River channel downstream 

from Peoria is less dynamic, with only small, localized areas 

of geomorphological change. In these more stable reaches, 

relict off-channel features still exist and are connected to the 

main channel, but their morphologies rarely change on annual 

or decadal time scales (Wallick and others, 2013). Throughout 

the entire river system, side channels and alcoves vary in 

terms of their area, length, and the relative water-surface 

elevations at which they connect to the main channel.

Management of water temperature downstream from 

several USACE dams involves the use of multiple dam outlets 

to blend warm water from the reservoir surface with cooler, 

deeper reservoir water to meet a target downstream temperature. River reaches downstream from the large USACE dams 

quickly exchange heat with their surroundings, however, 

meaning that releases of cold water from upstream dams typically do not substantially cool the farther-downstream reaches 

of the Willamette River (Rounds, 2010). Modeling by Buccola 

and others (2016) and Rounds (2010) showed that the influence of the dams on main-channel temperature is minimal for 

reaches well downstream (many days or many dozens of river 

miles) of the large tributary dams. These results indicate the 

bounds that flow management has regarding cold-water habitats along the main channel and further emphasize the potential importance of CWRs along the Willamette River.

Study Reaches

Data collection for this study focused on the Willamette 

River’s main channel and its off-channel features in three 

intensively monitored reaches between Eugene and Newberg 

(fig. 2):

1. Willamette Mission monitoring reach (RMs 67 to 77, 

near Salem), within the laterally stable reach downstream from Salem.

2. Independence monitoring reach (RMs 96 to 108, near 

Independence, Oregon), within the laterally stable reach 

downstream from the confluence with the Santiam River.

3. Harrisburg monitoring reach (RMs 161 to 168, near 

Harrisburg, Oregon), within the laterally dynamic reach 

upstream from Harrisburg.

Reaches were chosen for monitoring on the basis of their 

relative ease of access as well as the need to sample river 

reaches with different characteristics along the Willamette 

River upstream from Newberg. These reaches included a 

variety of types of off-channel features that are representative of features found throughout the different river segments 

and geomorphic regimes of the Willamette River. Not all 

off-channel features were monitored within each reach, and 

the water-quality conditions measured in one off-channel 

feature do not represent all the off-channel features in that 

reach. Repeat water-quality point measurements were collected within the monitoring reaches, as well as at sites 

opportunistically measured outside of the three intensively 

monitoring reaches between RMs 57 and 175. A similar study 

to document water-temperature conditions in tributaries and 

off-channel features of the Willamette River downstream from 

Newberg occurred in 2016 and 2017 (Mangano and others, 2018c).
Introduction 9

Terminology

Certain terms relating to water quality, processes, landforms, streamflows, and data-collection sites are used consistently throughout this report. Some qualitative designations 

(like “high” and “low”) and basic terms are defined below.

Water Quality

In this report, the term “water quality” includes water 

temperature, dissolved oxygen, specific conductance, and pH. 

Temperature and dissolved-oxygen values were compared to 

State of Oregon water-quality standards or relevant biological 

thresholds.

• Water temperature—A physical property and a measure 

of the kinetic energy of atoms and molecules in aqueous solution, reported in degrees Celsius.

◦ Warm—Water temperatures >18 °C

◦ Cool—Water temperatures ≤18 °C

• Dissolved oxygen—Molecular oxygen dissolved in 

water, reported in milligrams per liter.

◦ High—Dissolved-oxygen concentrations ≥6.5 mg/L

◦ Moderate—Dissolved-oxygen concentrations ≥4 and 

<6.5 mg/L

◦ Low—Dissolved-oxygen concentrations ˂4 mg/L

◦ Anoxic—Dissolved-oxygen concentrations 

approaching zero mg/L

• Specific conductance—A measure of the waterbody’s 

capacity to conduct an electrical current; values are 

compensated to 25 °C and reported in microsiemens 

per centimeter.

• pH—A measure of the acidity or alkalinity of a solution based on a logarithmic scale of the concentration 

of hydrogen ions; values are reported in standard units.

Water-Quality Processes

• Photosynthesis—The process by which plants containing chlorophyll capture and use sunlight as an 

energy source to convert carbon dioxide and water into 

organic compounds, releasing oxygen as a byproduct.

• Primary production—The synthesis of organic compounds from dissolved or atmospheric carbon dioxide, 

typically as a result of photosynthesis, and associated with the release of oxygen to the atmosphere or 

water column.

• Reaeration—The process by which gases such as oxygen are transferred across the air/water interface of a 

waterbody. When the oxygen concentration in surface 

water is less than its solubility, oxygen can move from 

the atmosphere into the waterbody; when the concentration exceeds its solubility, excess oxygen is released 

to the atmosphere.

• Respiration—The consumption of dissolved oxygen by 

living organisms as a result of the routine production 

of energy from the oxidation of organic substances.

• Sediment oxygen demand—The rate at which dissolved 

oxygen in the water column is consumed as a result 

of the decomposition of organic matter in surficial 

sediments.

Flow Type

• Surface flow—Water that flows on and above the 

substrate.

• Subsurface flow—Water that flows through the substrate or riverbank material; this includes groundwater 

and hyporheic flow:

◦ Hyporheic flow—Water that moves through the subsurface adjacent to a stream and readily exchanges 

with surface flow and groundwater.

◦ Groundwater—Water in the saturated zone of a 

porous geological material, where all pore spaces are 

filled with fluid. The upper boundary of the saturated 

zone designates the water table.

Relative Streamflow and Related River Stage

This study does not quantify specific streamflow 

ranges for the qualitative flow terms defined below because 

(a) streamflow increases downstream, causing different 

reaches to have different flow ranges, and (b) this study does 

not specifically address regulatory streamflow targets or 

minima. As used throughout this report, relative terms are 

defined below:

• High flows—Small flood or bank-full flows, such that 

the main channel is at or near capacity and nearly all 

off-channel features and active channel landforms are 

submerged. This type of flow was not observed during 

the monitoring timeframes of this study, but implications about how features function during this type of 

flow can be inferred from a feature’s morphology.

• Moderate flows—Streamflows that tend to occur in 

autumn or spring, when the main channel rises to inundate most active channel areas.
10 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

• Low flows—Typical low summer streamflows in the 

post-dam era (after 1950s).

• Unusually low flows—Lower than typical low summer 

streamflows in the post-dam era (after 1950s). These 

streamflows only occur in years when river streamflow 

is reduced by uncommon climatic effects (such as low 

precipitation or low snowpack) or anthropogenic factors (such as decreased reservoir releases or increased 

diversions for municipal or agricultural uses).

Data-Collection Locales

• Monitoring reach—A length of river where continuous 

monitors were deployed, and repeat point measurements were collected (fig. 2).

• Site—A place that was continuously monitored for 

water temperature or multiple water-quality parameters 

(see triangles and circles in fig. 2).

• Location—A place where water-quality point measurements were collected, often colocated with a site.

• Feature—An alcove or side channel (referred to as an 

off-channel feature). A feature may include a site (that 

is, a continuously monitored place) and one or more 

point-measurement locations.

Landforms

• Active bar—Channel-flanking gravel bars that 

are scoured and mobilized annually, resulting in 

sparse vegetation and potentially annual changes in 

their shape.

• Alcove—Off-channel feature that is connected to the 

main-channel surface-water flow at its downstream 

end but not connected by surface flow at its upstream 

end. An alcove may connect at its upstream end when 

streamflows increase, turning it into a side channel.

• Floodplain—Higher surfaces flanking the active channel built of sediment deposited during periodic flood 

events and, in some areas, eroded laterally by strong 

river flows.

• Main channel—Primary wetted channel where most 

river water flows during summer low-flow periods.

• Pleistocene floodplain/terrace—Generally the highest land surfaces adjacent to the Willamette River 

that are no longer inundated by flood waters. Along 

the Willamette River, these surfaces are underlain 

by a hard, coarse gravel layer that may limit channel 

migration.

• Revetments—Human-constructed bank stabilization 

assemblages (often large boulders), typically along the 

outer bends of the main river channel; historical revetments may be in off-channel features due to channel 

changes in the past.

• Side channel—Off-channel feature where surface water 

from the main channel is actively flowing through the 

feature from its upstream end to its downstream end. If 

main channel stage decreases, it is possible that surface 

flow may no longer enter the feature at its upstream 

end, turning it into an alcove.

• Stable bar—Channel-flanking and mid-channel bars 

that were once active gravel bars but are now stabilized 

by vegetation, with little change annually except by 

lateral erosion and vertical accretion of fine sediment.

Site and Reach Names

Reaches and sites along the main-channel Willamette 

River are referenced to river miles identified from local USGS 

topographic maps (fig. 2; Esri, 2014). Off-channel features 

in this study were identified based on the river mile of the 

feature’s downstream connection point to the main channel. Sites in the Harrisburg monitoring reach are referred to 

as “near” river mile values in their official USGS National 

Water Information System (NWIS; U.S. Geological Survey, 

2018) site name because of notable main-channel changes 

in that reach since topographic maps were published; in text 

and figures in this report, they are referred to as “at” a river 

mile. Feature names were only given to the five off-channel 

features in which multiparameter water-quality monitors were 

deployed in 2016; these names are based on nearby places or 

landforms on topographic maps. Location coordinates for all 

monitoring sites and synoptic point measurement locations are 

provided on tables within this report or as a field in the published datasets; using coordinates is the most definitive way of 

identifying a site or synoptic measurement location.

Methods

Three reaches between Eugene and Newberg were 

selected for intensive monitoring (fig. 2) during 2015 and 

2016. Continuous temperature sensors, multiparameter waterquality monitors, and pressure transducers were installed in 

each of the reaches, and synoptic measurements were periodically collected within these reaches to provide broader spatial 

detail than the continuous monitors could provide.

Within the three reaches, a variety of off-channel features with different characteristics (such as depth, size, 

presence/absence of aquatic vegetation, and connection to 

the main channel) were monitored. Water-temperature data 

were collected at all sites, whereas dissolved oxygen, specific 
Methods 11

conductance, pH, and (or) river stage data were collected at a 

subset of the continuous sites and point measurement locations. In a few areas, temperature sensors were deployed in 

pairs, with a sensor in the main channel near the off-channel 

feature, to assess temperature differences between the offchannel feature and the main channel. Water-temperature 

sensors and water-quality monitors were calibrated and operated in accordance with USGS standard protocols (Wagner 

and others, 2006). The methodology for synoptic measurements and pressure transducer data collection are described 

in detail in the metadata published with each dataset through 

USGS ScienceBase (Mangano and others, 2017, 2018a). 

Differentiating between groundwater and hyporheic inputs to 

off-channel features was beyond the scope of this study and 

was not attempted; this report refers to any groundwater or 

hyporheic flows as subsurface inputs.

Field Data Collection

The methods for the deployment of field sensors are 

described by year because of slight variations in the deployment methodology and sensors used each year. Most notably, 

the water-temperature sensors and water-quality monitors 

were deployed in the middle of the water column in 2016 

rather than on the bed of the river, as was done in 2015.

2015

Monitoring equipment was deployed in August 2015 and 

retrieved in October 2015. A total of 24 Onset Hobo model 

U22–001 Water Temp Pro v2 (Onset Computer Corporation, 

Bourne, Mass.) water-temperature sensors (hereafter referred 

to as “water-temperature sensors”) were deployed in offchannel features or the main-channel Willamette River 

(table 1; fig. 2). Many of the water-temperature sensors placed 

in off-channel features were paired with a main-channel 

water-temperature sensor, resulting in 16 sensors collecting 

data in off-channel features and 8 in the main channel for the 

2-month period. Water-temperature sensors were secured in 

30-centimeter segments of polyvinyl chloride (PVC) pipe, 

attached to short pieces of rebar for weight, cabled to vegetation on the bank, and placed on the bed of the river or offchannel feature. Sensors were programmed to record water 

temperature hourly.

Yellow Springs Instruments (YSI, Yellow Springs, Ohio) 

6-series multiparameter water-quality monitors (hereafter 

referred to as “water-quality monitors”) were deployed in 

four off-channel features and at one main-channel site in 2015 

(table 2). Water-quality monitors were secured in 1-meter 

(m) segments of PVC pipe (perforated to allow water to flow 

across the sensors), attached to a 20-cm cinder block, and 

secured to vegetation on the bank with a steel cable. The cinder block was positioned on the bed of the off-channel feature 

with the continuous water-quality monitor on top, but in some 

instances the top-heavy configuration likely tipped over and 

recorded data while the monitor was resting on the sediment. 

All monitors recorded hourly measurements for water temperature and dissolved oxygen, and four of the five monitors 

also measured pH and specific conductance.

Point measurements (spatially intensive measurements 

collected over a short period; hereafter referred to as “synoptic measurements or surveys”) were collected on 5 days in 

August and 5 days in October 2015. These synoptic surveys 

were conducted in a manner similar to measurements made by 

Gregory and Wildman (2016) in off-channel Willamette River 

locations between 2011 and 2016. Synoptic surveys were carried out to document longitudinal and vertical water-quality 

heterogeneity in the main channel and off-channel features, 

and for comparison with installed continuous temperature 

sensors. Synoptic measurements were typically collected 

between 9:00 a.m. and 6:00 p.m. Pacific daylight time (PDT). 

Multiple measurements at various depths and locations within 

individual off-channel features were collected as rapidly as 

possible (within about 30 minutes) to minimize the effects of 

diel warming. Equipment used to collect synoptic measurements included a YSI EXO2 water-quality monitor, a YSI 

6-series water-quality monitor, and a YSI EcoSense EC300A 

meter that measured temperature and specific conductance 

only. Monitors or meters were lowered into the water from a 

boat for individual synoptic point measurements, typically at 

multiple depths at the same location. Synoptic measurement 

locations were often colocated with deployed equipment or 

within off-channel features of the monitored reaches; additional measurements were collected during a 2-day trip from 

RM 72 to 122 (Salem to Albany; fig. 2). All measurements 

included location, date, time, depth below water surface, and 

water temperature, and most also included specific conductance, dissolved oxygen, and pH.

2016

The same equipment used in 2015, plus additional 

sensors, was deployed from about May to October 2016 at 

many of the same sites within the three intensively monitored 

reaches, but the methods of deployment differed from 2015. 

Eighteen water-temperature sensors were deployed in offchannel features, and an additional four were installed in the 

main channel (table 1; fig. 2). Water-temperature sensors were 

suspended in the water column above the sediment using foam 

and their own buoyancy, which floated them above cementblock anchors. Water-temperature sensors were positioned 

at about mid-depth in the water column, with depths ranging 

from 0.2 to 1.5 m above the bed. The cement blocks were 

attached to riparian vegetation with steel cables, and the sensors were configured to record measurements hourly.
12 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16 Table 1. Sites and dates of data collection for continuous water-temperature sensors installed in off-channel features and the main-channel Willamette River, Oregon, in summers 2015 and 2016. [Easting and northing coordinates are reference to the North American Datum of 1983, Universal Transverse Mercator Zone 10N. Feature monitored in 2015 and 2016: Sensors may have been placed in the same feature but in different locations within the feature in 2015 and 2016, resulting in different coordinates associated with the same NWIS site number. Abbreviations: NWIS, National Water Information System (U.S. Geological Survey, 2018); RM, river mile] Willamette River mile Feature monitored in 2015 and 2016 NWIS site name NWIS site number Easting (meters) Northing (meters) Site type Installation date Removal date Monitoring reach

(fig. 2)

Height

above

riverbed

(meters)

2015

67.1 Yes Willamette River alcove 

on right bank at RM 67.1

450808123004200 499076 4998007 Alcove 2015-08-18 2015-10-08 Willamette 

Mission

<0.1

67.1 No Willamette River on 

right bank at RM 67.1

450808123004500 499011 4998002 Main channel 2015-08-18 2015-10-08 Willamette 

Mission

<0.1

67.6 Yes Willamette River alcove 

on right bank at RM 67.6

450746123003100 499323 4997315 Alcove 2015-08-18 2015-10-08 Willamette 

Mission

<0.1

67.7 Yes Willamette River alcove 

on right bank at RM 67.7

450740123003600 499222 4997154 Alcove 2015-08-18 2015-10-08 Willamette 

Mission

<0.1

70.2 Yes Willamette River on 

right bank at RM 70.2

450601123010400 498605 4994090 Main channel 2015-08-18 2015-10-08 Willamette 

Mission

<0.1

73.2 Yes Willamette River on left 

bank at RM 73.2

450445123040500 494648 4991760 Main channel 2015-08-27 2015-10-08 Willamette 

Mission

<0.1

73.4 Yes Willamette River 

alcove on left bank at RM 73.4

450438123040900 494559 4991516 Alcove 2015-08-27 2015-10-08 Willamette 

Mission

<0.1

74.6 Yes Willamette River 

alcove on left bank at RM 74.6

450332123040800 494586 4989486 Alcove 2015-08-27 2015-10-08 Willamette 

Mission

<0.1

95.8 No Willamette River 

alcove on left bank at RM 95.8

445056123105600 485598 4966190 Alcove 2015-08-19 2015-10-07 Independence <0.1

97.7 Yes Willamette River 

alcove on left bank at RM 97.7

444938123094900 487060 4963775 Alcove 2015-08-19 2015-10-07 Independence <0.1

97.7 Yes Willamette River on 

right bank at RM 97.7

444945123095600 486906 4964001 Main channel 2015-08-19 2015-10-07 Independence <0.1

97.9 No Willamette River 

alcove on left bank at RM 97.9

444945123094200 487213 4963972 Alcove 2015-08-19 2015-10-07 Independence <0.1
Methods 13

Table 1. Sites and dates of data collection for continuous water-temperature sensors installed in off-channel features and the main-channel Willamette River, Oregon, in summers 2015 and 2016.—Continued[Easting and northing coordinates are reference to the North American Datum of 1983, Universal Transverse Mercator Zone 10N. Feature monitored in 2015 and 2016: Sensors may have been placed in the same feature but in different locations within the feature in 2015 and 2016, resulting in different coordinates associated with the same NWIS site number. Abbreviations: NWIS, National Water Information System (U.S. Geological Survey, 2018); RM, river mile]

Willamette

River mile

Feature

monitored

in 2015

and 2016

NWIS

site name

NWIS

site number

Easting

(meters)

Northing

(meters) Site type Installation date Removal date Monitoring reach (fig. 2) Height above riverbed (meters)

2015 —Continued

98.4 Yes Willamette River alcove 

on right bank at RM 98.4

444948123090100 488110 4964071 Alcove 2015-08-19 2015-10-07 Independence <0.1

107.3 No Willamette River 

on right bank at RM 107.3

444527123085100 488328 4956019 Main channel 2015-08-26 2015-10-06 Independence <0.1

107.5 Yes Willamette River alcove 

on right bank at RM 107.5

444517123084900 488367 4955713 Alcove 2015-08-26 2015-10-06 Independence <0.1

161 No Willamette River on 

right bank at RM 161

441613123102600 486120 4901907 Main channel 2015-08-20 2015-10-14 Harrisburg <0.1

161.7 Yes Willamette River alcove 

on right bank near RM 161.7

441540123101900 486269 4900885 Alcove 2015-08-20 2015-10-14 Harrisburg <0.1

162.8 No Willamette River side 

channel on left bank near RM 162.8

441446123103500 485925 4899223 Side channel 2015-08-20 2015-10-14 Harrisburg <0.1

162.8 No Willamette River alcove 

on left bank near RM 162.8

441447123103000 486021 4899240 Alcove 2015-08-20 2015-10-14 Harrisburg <0.1

163.5 No Willamette River alcove 

on right bank near RM 163.5

441428123095600 486772 4898677 Alcove 2015-08-20 2015-10-14 Harrisburg <0.1

164.2 No Willamette River on left 

bank near RM 164.2

441359123093800 487178 4897756 Main channel 2015-08-20 2015-10-14 Harrisburg <0.1

164.8 Yes Willamette River side 

channel on right bank at near RM 164.8

441351123090900 487826 4897515 Side channel 2015-08-20 2015-10-14 Harrisburg <0.1

167.8 No Willamette River on 

right bank near RM 167.8

441155123091900 487596 4893946 Main channel 2015-08-20 2015-10-14 Harrisburg <0.1
14 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16 Table 1. Sites and dates of data collection for continuous water-temperature sensors installed in off-channel features and the main-channel Willamette River, Oregon, in summers 2015 and 2016.—Continued [Easting and northing coordinates are reference to the North American Datum of 1983, Universal Transverse Mercator Zone 10N. Feature monitored in 2015 and 2016: Sensors may have been placed in the same feature but in different locations within the feature in 2015 and 2016, resulting in different coordinates associated with the same NWIS site number. Abbreviations: NWIS, National Water Information System (U.S. Geological Survey, 2018); RM, river mile] Willamette River mile Feature monitored in 2015 and 2016 NWIS site name NWIS site number Easting (meters) Northing (meters) Site type Installation date Removal date Monitoring reach

(fig. 2)

Height

above

riverbed

(meters)

2015 —Continued

168.1 No Willamette River side 

channel on right bank near RM 168.1

441152123085600 488105 4893836 Side channel 2015-08-20 2015-10-14 Harrisburg <0.1

2016

67.6 Yes Willamette River alcove 

on right bank at RM 67.6

450746123003100 499314 4997353 Alcove 2016-06-02 2016-10-25 Willamette 

Mission

0.6

67.7 Yes Willamette River 

alcove on left bank at RM 67.7

450740123003600 499211 4997141 Alcove 2016-06-02 2016-10-25 Willamette 

Mission

0.3

70.2 Yes Willamette River on 

right bank at RM 70.2

450601123010400 498631 4994089 Main channel 2016-06-02 2016-10-25 Willamette 

Mission

0.6

70.2 Yes Willamette River alcove 

on right bank at RM 70.2

450557123011100 498442 4993974 Alcove 2016-06-02 2016-10-25 Willamette 

Mission

0.6

73.2 Yes Willamette River on left 

bank at RM 73.2

450445123040500 494676 4991791 Main channel 2016-05-26 2016-11-10 Willamette 

Mission

0.6

73.4 Yes Willamette River 

alcove on left bank at RM 73.4

450332123040900 494560 4991528 Alcove 2016-05-26 2016-11-10 Willamette 

Mission

0.9

73.5 No Willamette River 

alcove on left bank at RM 73.5

450433123041300 494460 4991379 Alcove 2016-05-26 2016-11-10 Willamette 

Mission

0.3

73.9 No Willamette River alcove 

on right bank at RM 73.9

450408123034800 495014 4990619 Alcove 2016-05-26 2016-11-10 Willamette 

Mission

0.9

77.2 No Willamette River 

alcove on left bank at RM 77.2

450130123043800 493924 4985729 Alcove 2016-05-26 2016-11-10 Willamette 

Mission

0.6
Methods 15

Table 1. Sites and dates of data collection for continuous water-temperature sensors installed in off-channel features and the main-channel Willamette River, Oregon, in summers 2015 and 2016.—Continued[Easting and northing coordinates are reference to the North American Datum of 1983, Universal Transverse Mercator Zone 10N. Feature monitored in 2015 and 2016: Sensors may have been placed in the same feature but in different locations within the feature in 2015 and 2016, resulting in different coordinates associated with the same NWIS site number. Abbreviations: NWIS, National Water Information System (U.S. Geological Survey, 2018); RM, river mile]

Willamette

River mile

Feature

monitored

in 2015

and 2016

NWIS

site name

NWIS

site number

Easting

(meters)

Northing

(meters) Site type Installation date Removal date Monitoring reach (fig. 2) Height above riverbed (meters)

2016 —Continued

96.1 No Willamette River 

alcove on left bank at RM 96.1

445047123105500 485624 4965901 Alcove 2016-05-25 2016-10-24 Independence 0.6

98.4 Yes Willamette River alcove 

on right bank at RM 98.4

444948123090100 488239 4964005 Alcove 2016-05-25 2016-11-14 Independence 0.6

100.2 No Willamette River side 

channel on right bank at RM 100.2

444932123071200 490565 4963558 Main channel 2016-05-25 2016-11-14 Independence 0.6

101 Yes Willamette River alcove 

on right bank at RM 101

444927123064100 491236 4963434 Alcove 2016-05-25 2016-11-14 Independence 1.5

107.5 Yes Willamette River alcove 

on right bank at RM 107.5

444517123084900 488350 4955717 Alcove 2016-06-01 2016-11-14 Independence 0.2

107.5 Yes Willamette River alcove 

on right bank at RM 107.5

444517123084900 488350 4955717 Alcove 2016-06-01 2016-11-14 Independence 0.6

107.8 No Luckiamute River 

alcove on right bank at RM 0.1

444452123084700 488410 4954930 Alcove 2016-06-01 2016-11-14 Independence 0.6

107.9 No Luckiamute River on left 

bank at RM 0.1

444453123085300 488273 4954968 Tributary 2016-06-01 2016-11-14 Independence 0.6

161.3 Yes Willamette River side 

channel on left bank near RM 161.3

441558123103500 485965 4901496 Side channel 2016-05-24 2016-10-20 Harrisburg 0.6

161.7 Yes Willamette River alcove 

on right bank near RM 161.7

441540123101900 486290 4900907 Alcove 2016-05-24 2016-10-20 Harrisburg 0.6

162.2 No Willamette River alcove 

on right bank near RM 162.2

441515123104000 485797 4900128 Alcove 2016-05-24 2016-10-20 Harrisburg 0.3
16 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16 Table 1. Sites and dates of data collection for continuous water-temperature sensors installed in off-channel features and the main-channel Willamette River, Oregon, in summers 2015 and 2016.—Continued [Easting and northing coordinates are reference to the North American Datum of 1983, Universal Transverse Mercator Zone 10N. Feature monitored in 2015 and 2016: Sensors may have been placed in the same feature but in different locations within the feature in 2015 and 2016, resulting in different coordinates associated with the same NWIS site number. Abbreviations: NWIS, National Water Information System (U.S. Geological Survey, 2018); RM, river mile] Willamette River mile Feature monitored in 2015 and 2016 NWIS site name NWIS site number Easting (meters) Northing (meters) Site type Installation date Removal date Monitoring reach

(fig. 2)

Height

above

riverbed

(meters)

2016 —Continued

162.9 No Willamette River alcove 

on right bank near RM 162.9

441448123095800 486728 4899284 Alcove 2016-05-24 2016-10-20 Harrisburg 0.6

164.2 No Willamette River on 

right bank near RM 164.2

441401123093500 487240 4897818 Main channel 2016-05-24 2016-10-20 Harrisburg 0.6
Methods 17

Table 2. Sites and dates of data collection for multiparameter water-quality monitors installed in off-channel features and the main-channel Willamette River, Oregon, in summers 2015 and 2016.[Easting and northing coordinates are reference to the North American Datum of 1983, Universal Transverse Mercator Zone 10N. Due to the monitor’s proximity to the main channel, it measured main-channel conditions although the site’s name says it is in an alcove. Abbreviations: NWIS, National Water Information System (U.S. Geological Survey, 2018); RM, river mile; Temp, water temperature; DO, dissolved oxygen; SC, specific conductance]

Willamette 

River

mile

Feature

monitored

in 2015

and 2016

NWIS

site name

NWIS

site number

Easting

(meters)

Northing

(meters) Site type Installation date Removal date Monitoring reach (fig. 2) Height above riverbed (meters) Recorded parameters Temp DO SC pH

2015

70.2 Yes Willamette 

River alcove on right bank at RM 70.2

450557123011100 498443 4993981 Alcove 2015-08-18 2015-10-08 Willamette 

Mission

<0.3 X X X

95.9 No Willamette 

River alcove on left bank at RM 95.9

445053123105400 485635 4966094 Main 

channel

2015-08-19 2015-10-07 Independence <0.3 X X X X

101 Yes Willamette 

River alcove on right bank at RM 101

444927123064100 491195 4963429 Alcove 2015-08-19 2015-10-07 Independence <0.3 X X X

161.3 Yes Willamette 

River side channel on left bank near RM 161.3

441558123103500 485918 4901460 Side channel 2015-08-20 2015-10-14 Harrisburg <0.3 X X

164.1 Yes Willamette 

River alcove on left bank near RM 164.1

441355123094600 486998 4897643 Alcove 2015-08-20 2015-10-14 Harrisburg <0.3 X X X X
18 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16 Table 2. Sites and dates of data collection for multiparameter water-quality monitors installed in off-channel features and the main-channel Willamette River, Oregon, in summers 2015 and 2016.—Continued [Easting and northing coordinates are reference to the North American Datum of 1983, Universal Transverse Mercator Zone 10N. Due to the monitor’s proximity to the main channel, it measured main-channel conditions although the site’s name says it is in an alcove. Abbreviations: NWIS, National Water Information System (U.S. Geological Survey, 2018); RM, river mile; Temp, water temperature; DO, dissolved oxygen; SC, specific conductance] Willamette River mile Feature monitored in 2015 and 2016 NWIS site name NWIS site number Easting (meters) Northing (meters) Site type Installation date Removal date Monitoring reach

(fig. 2)

Height

above

riverbed

(meters)

Recorded parameters

Temp DO SC pH

2016

67.1 Yes Willamette 

River alcove on right bank at RM 67.1

450808123004200 499056 4998019 Alcove 2016-05-23 2016-10-26 Willamette 

Mission

0.6

X

X

X

74.6 Yes Willamette 

River alcove on left bank at RM 74.6

450332123040800 494553 4989432 Alcove 2016-05-23 2016-10-26 Willamette 

Mission

0.6

X

X

X

97.7 Yes Willamette 

River alcove on left bank at RM 97.7

444938123094900 486972 4963800 Alcove 2016-05-23 2016-10-25 Independence 0.6

X

X

97.7 Yes Willamette 

River on right bank at RM 97.7

444945123095600 486885 4964005 Main

channel

2016-05-23 2016-10-25 Independence 0.6

X

X

X

X

164.1 Yes Willamette 

River alcove on left bank near RM 164.1

441355123094600 486982 4897693 Alcove 2016-05-23 2016-10-26 Harrisburg 0.6

X

X

X

164.8 Yes Willamette 

River side channel on right bank near RM 164.8

441351123090900 487853 4897486 Side

channel

2016-05-23 2016-10-26 Harrisburg 0.6

X

X

X
Methods 19

As with the water-temperature sensors, the YSI continuous water-quality monitors also were elevated off the substrate 

during the 2016 field season. Two wire crates were stacked, 

fastened together, and weighted. YSI 6-series water-quality 

monitors were housed in perforated PVC pipe segments as in 

2015, and the housing was attached to the top of the stacked 

wire crates. The crates, secured to woody bank vegetation with 

a steel cable, allowed water to pass freely around and under 

the monitors while maintaining a constant height (0.6 m) 

above the substrate. Five continuous water-quality monitors were deployed in this manner in off-channel features. A 

sixth water-quality monitor was installed at mid-depth in the 

main-channel Willamette River (RM 97.7, near Independence; 

fig. 2) in a long, angled PVC pipe, perforated with holes, and 

secured to the bank. Water-quality monitors in the off-channel 

features recorded water temperature, dissolved oxygen, and 

specific conductance. The main-channel monitor recorded 

pH in addition to water temperature, dissolved oxygen, and 

specific conductance (table 2).

Synoptic measurements were collected on 18 days 

between May 24 and November 14, 2016. Most measurements 

were recorded at the location of deployed equipment on days 

when that equipment was visited for maintenance, or during synoptic surveys within the three intensively monitored 

reaches. Additional synoptic measurements were collected 

when a crew surveying the bathymetry of the Willamette River 

also collected water-quality measurements in off-channel features between Independence and Eugene (RM 105–175; fig. 2) 

in late August 2016 (Mangano and others, 2017).

Pressure transducers were installed in seven off-channel 

features in 2016 (table 3; Mangano and others, 2018a) to 

record variations in stage within the off-channel features 

throughout the monitoring period. The transducers were 

encased in PVC pipes and attached to rebar that was driven 

into the bed of the off-channel feature, a method that ensured 

a constant deployment elevation. As the pressure transducers 

were not placed on the substrate, their readings do not indicate 

the absolute depth of water in the feature and rely on a local 

datum for each sensor. The water-surface elevations at five of 

the pressure transducers were surveyed using real-time kinematic global positioning system equipment, which allowed 

conversion of the sensor-depth measurements to water-surface 

elevations in the North American Vertical Datum of 1988. 

Three barometric pressure sensors—one in each reach—were 

deployed nearby so the sensor-depth measurements could be 

corrected for local variations in atmospheric pressure.

Onset Hobo Pendant temperature sensors (model 

UA–001–08; hereafter referred to as “pendant temperature 

sensors”) were deployed in May and June 2016 (table 4), when 

streamflow in the Willamette River was decreasing. Pendant 

temperature sensors were used in this study to evaluate when 

the upstream end of an off-channel feature was connected to 

the main channel. A pendant temperature sensor deployed on 

the substrate at the upstream end of an off-channel feature 

recorded its status (wet or dry) through a comparison of the 

pendant temperature, main-channel water temperature, and 

nearby air temperature data (method adapted from Arismendi 

and others, 2017). Four prominent off-channel features were 

chosen, and pendants were attached to the substrate (with steel 

cable and a Duckbill anchor) at the lowest point of the channel connecting the upstream end of the off-channel feature to 

the main-channel Willamette River. Two additional pendants 

were attached to nearby trees to measure local air temperature. 

Nearby AgriMet weather stations also were used as an airtemperature reference (Bureau of Reclamation, 2012).

Data Processing

Some continuous 2015 dissolved-oxygen datasets that 

consistently logged near-anoxic concentrations (close to 

zero mg/L and based on sensor performance) were deleted 

because of the high probability that the monitors were somewhat buried in the sediment and not accurately characterizing 

conditions in the water column. In 2016, multiple waterquality monitors recorded hypoxic and anoxic concentrations 

for extended periods, but the deployments on top of wire 

crates ensured that the monitors were measuring conditions in 

the water column, and those datasets were not deleted.

All water-temperature and dissolved-oxygen data referenced in this report and published online have been scrutinized following USGS protocols (Wagner and others, 2006). 

Data gaps are visible in some of the figures and were usually 

the result of equipment battery issues or the sensor having 

been temporarily removed from the waterbody. This report 

relies mostly on the continuous 2016 data while referencing 

the continuous 2015 data, where appropriate. Many synoptic 

measurements were collected in 2015 and are often used as 

examples.

Published Datasets of Field Measurements

Multiple datasets were collected and published from 

this 2-year study. These data are available online in NWIS 

(U.S. Geological Survey, 2018) or in ScienceBase (Mangano 

and others, 2017, 2018a, 2018b), as follows:

1. 2015 and 2016 continuous water-temperature data: 

NWIS, see table 1 for site numbers.

2. 2015 and 2016 continuous multiparameter monitor data 

(water temperature, dissolved oxygen, pH, and specific 

conductance): NWIS, see table 2 for site numbers.

3. 2015 and 2016 synoptic measurements: USGS data 

release in ScienceBase (Mangano and others, 2017).

4. 2016 pressure-transducer data: table 3, USGS data 

release in ScienceBase (Mangano and others, 2018a).

5. 2016 water-temperature pendant data: table 4, USGS 

data release in ScienceBase (Mangano and others, 2018b).
20 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16 Table 3. Sites and dates of data collection for pressure transducers and barometric-pressure sensors installed in off-channel features of the Willamette River, Oregon, from May to November 2016. [Easting and northing coordinates are referenced to the North American Datum of 1983, Universal Transverse Mercator Zone 10N. Abbreviation: RM, river mile] Willamette River mile Site name Easting (meters) Northing (meters) Site type Installation date Removal date Monitoring reach

(fig. 2)

Water

height

converted

to elevation

Pressure transducers

70.2 Pressure transducer at RM 70.2 498440 4993964 Alcove 2016-06-02 2016-11-10 Willamette Mission No97.7 Pressure transducer at RM 97.7 486981 4963786 Alcove 2016-05-25 2016-11-14 Independence Yes98.4 Pressure transducer at RM 98.4 488019 4964085 Alcove 2016-05-25 2016-11-14 Independence Yes

107.5 Pressure transducer at RM 107.5 488386 4955712 Alcove 2016-06-01 2016-11-14 Independence Yes161.4 Pressure transducer at RM 161.4 485887 4901427 Side channel 2016-05-24 2016-10-20 Harrisburg Yes162.8 Pressure transducer at RM 162.8 485910 4899213 Side channel 2016-05-24 2016-10-20 Harrisburg No164.8 Pressure transducer at RM 164.8 487870 4897446 Side channel 2016-05-24 2016-10-20 Harrisburg Yes

Barometric pressure transducers

67.1 Barometric pressure transducer at RM 67.1 499051 4998040 Air 2016-05-26 2016-10-25 Willamette Mission NA98.4 Barometric pressure transducer at RM 98.4 488019 4964085 Air 2016-05-25 2016-10-24 Independence NA

164 Barometric pressure transducer at RM 164 486972 4897700 Air 2016-05-24 2016-10-20 Harrisburg NA

Table 4. Sites and dates of data collection for temperature sensors (pendants) installed in a tree or on gravel bars upstream of off-channel features of the Willamette River, Oregon in summer 2016.[Easting and northing coordinates are referenced to the North American Datum of 1983, Universal Transverse Mercator Zone 10N. Abbreviation: RM, river mile]

Willamette

River mile Site name Easting (meters) Northing (meters) Sensor location Installation date Removal date Monitoring reach

(fig. 2)

68.2 Pendant sensor on ground at RM 68.2 499927 4996756 Ground 2016-06-02 2016-10-25 Willamette Mission68.2 Pendant sensor in air at RM 68.2 499923 4996759 Air 2016-06-02 2016-10-25 Willamette Mission96.3 Pendant sensor on ground at RM 96.3 485650 4965499 Ground 2016-05-25 2016-11-14 Independence96.3 Pendant sensor in air at RM 96.3 485647 4965494 Air 2016-05-25 2016-10-24 Independence98.9 Pendant sensor on ground at RM 98.9 488460 4963664 Ground 2016-05-25 2016-11-14 Independence

161.4 Pendant sensor on ground at RM 161.4 485838 4901421 Ground 2016-05-24 2016-10-20 Harrisburg
Water-Quality Conditions of the Willamette River and Adjacent Off-Channel Features 21

Field Observations and Geomorphic 

Characteristics of Off-Channel Features

During site visits in summer 2016, site characteristics were documented for the five off-channel features that 

contained water-quality monitors. Descriptions of substrate, 

aquatic vegetation, and general water color and transparency 

were based on qualitative observations. Substrate was identified either visually, as seen through clear water, or based on 

bed hardness when pressed with a metal rod or kayak paddle. 

Aquatic vegetation was noted as absent or present, with a relative abundance of emergent vegetation on the water surface or 

submerged vegetation seen through the water column or felt 

with a kayak paddle; the presence of vegetation attached to 

monitoring equipment when retrieved at the end of the field 

season was another indication of the presence of vegetation in 

or at the bottom of the water column. Water transparency (that 

is, relative turbidity) and color (for example, absent or darktannin colored) were visually categorized by looking through 

the water column to the deployed equipment on the bottom of 

the feature.

Geomorphic characteristics of the five features that 

contained water-quality monitors in summer 2016 were 

determined from field observations and remote-sensing 

applications. Depth of the off-channel features was measured 

by lowering a water-quality monitor with a depth sensor to 

the bed of the features during the various synoptic measurements; however, true bathymetric data were not collected in 

this study. Recent (2016) aerial photographs were used to 

measure surface area and to record planform morphology of 

the off-channel features. Lateral and longitudinal changes 

that occurred over the last two decades were evaluated by 

comparing Google Earth aerial photographs from 1994 and 

2016 (appendix 2). Width, length, and height above the water 

surface of the upstream connection points were visually 

inspected in the field and on aerial photographs and measured 

from existing 2008 light detection and ranging (lidar) datasets, where appropriate. Additionally, the presence and relative 

abundance of emergent aquatic vegetation was noted from 

aerial photographs.

Streamflow and Temperature Data at 

U.S. Geological Survey Streamgage Sites

USGS streamgages along the Willamette River were 

used as estimates of local river streamflow and additional water-temperature measurements for each reach. 

The Willamette River at Harrisburg, Oregon, streamgage 

(USGS station 14166000; RM 161.0; downstream end of the 

Harrisburg monitoring reach; fig. 2) measures stage, streamflow, and main-channel temperature. For the Independence 

and Willamette Mission monitoring reaches, the Willamette 

River at Salem, Oregon, streamgage (USGS station 14191000; 

RM 84.2) was used for stage and streamflow information, 

whereas the nearby Willamette River at Keizer, Oregon, 

streamgage (USGS station 14192015; RM 82.2) was used as 

an additional main-channel temperature reference. Although 

the Willamette River at Albany, Oregon, streamgage (USGS 

station 14174000; RM 119) is closer to some sites in the 

Independence monitoring reach, the Santiam and Luckiamute 

Rivers join the Willamette River between the Albany 

streamgage and the Independence monitoring reach, making 

it more appropriate to use the Salem streamgage as a streamflow reference for the two monitoring reaches (Independence 

and Willamette Mission) downstream from the Santiam River 

confluence.

Water-Quality Conditions of the 

Willamette River and Adjacent 

Off-Channel Features

This section presents the results of the 2015–16 waterquality monitoring of the main channel Willamette River and 

off-channel features and discusses patterns and implications of 

the data. The results are divided into three subsections focusing on (1) main-channel conditions, (2) off-channel feature 

conditions, and (3) comparisons between main-channel and 

adjacent off-channel conditions.

Main-Channel Water-Quality Conditions

Key result—Water in the main channel of the Willamette 

River upstream from Newberg (fig. 2) in summers 2015–16 

was typically well mixed, had warm water temperatures, and 

had high dissolved-oxygen concentrations.

Spatial and temporal variations in water quality were 

characterized in the main channel of the Willamette River 

using continuous water-quality monitors, water-temperature 

sensors, and synoptic measurements (tables 1 and 2). 

Main-channel temperatures in the Willamette River generally warmed in June and July and cooled in August and 

September (fig. 5). Diel temperature fluctuations in the main 

channel were often between 0.5 and 2.0 °C, with the largest fluctuations occurring in the more-downstream reaches. 

Longitudinal water-temperature patterns confirmed previous studies (Rounds, 2010) indicating that Willamette River 

water typically warms in summer as it flows downstream, 

although cooler inputs from the Santiam River caused localized decreases in temperatures in the main channel (fig. 5). 

Continuous water-temperature data from two sensors in the 

main-channel Willamette River about 24 RM apart (upstream: 

RM 97.7, near Independence; downstream: RM 73.2, near 

Salem; fig. 2), with no major inputs between, showed that 

the difference in daily maximum water temperature was less 

than 1.0 °C. Main-channel water temperatures within a reach 

(about 10 RM in length) were considered to be nearly identical 

for some analyses in this report.
22 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16 3028262422201816141210 May June July August September October EXPLANATION Main channel at RM 164.2 Side channel at RM 100.2 Main channel at RM 97.7 Main channel at RM 73.2 Main channel at RM 70.2 Date B. 2016 EXPLANATION Main channel at RM 167.8 Main channel at RM 164.2 Main channel at RM 161 Main channel at RM 107.3 Main channel at RM 97.7 Main channel at RM 95.9 Main channel at RM 73.2 Main channel at RM 70.2 Main channel at RM 67.1 Site type and river mile (RM; table 1) Site type and river mile (RM; table 1) 3028262422201816141210 A. 2015

Hourly water temperature, in degrees Celsius

Figure 5. Hourly water-temperature measurements in the main channel Willamette River, Oregon, between river miles 67.1 and 164.2. 

A, late summer 2015. 

B, summer 2016.
Water-Quality Conditions of the Willamette River and Adjacent Off-Channel Features 23

Vertical profiles of water-quality measurements showed 

the main channel to be homogeneous throughout the water 

column, even at substantial depths. Synoptic measurements at 

RM 91 (near Independence) on August 27, 2015, were taken 

at 0.5 and 4.4 m below the water surface, and the difference 

in water-quality parameters between the depths was minimal 

(differences: water temperature, <0.1 °C; dissolved oxygen, 

<0.1 mg/L; specific conductance, zero microsiemens per 

centimeter at 25 °C; pH, 0.1 standard units). This pattern of 

main-channel homogeneity was noted throughout all reaches 

and seasons during synoptic measurements. Relatively wellmixed conditions such as these are consistent with measurements by Gregory and Wildman (2016) and Mangano and 

others (2018c), which determined that even deep pools (>25 m 

deep) in the Willamette River tend to be isothermal in summer. 

The magnitude of main-channel water speed and the scale of 

turbulence caused by channel shape and morphology probably 

accounts for this mixing. The “Newberg Pool” and “Portland 

Harbor” reaches of the Willamette River downstream from 

RM 50 (not shown) do tend to vertically stratify at times in 

summer (Mangano and others, 2018c; Rounds, 2010), but this 

study focuses on reaches upstream from RM 50 where the 

river tends to be relatively well mixed.

Water temperature in the main channel did not meet the 

State of Oregon’s summer water-temperature standard for 

the study area upstream from RM 50 (rearing and migration 

use: 7dADM ≤18 °C between May 16 and October 14; OAR 

340–041–0028(4)(c); Oregon Department of Environmental 

Quality, 2016a) at times in 2015 and 2016 (fig. 6). For 

example, continuous water-temperature data from various 

sites upstream from RM 50 indicated that the river did not 

meet the rearing and migration criterion from late May (2015; 

fig. 6A) or late June (2016; fig. 6B) through mid-September. 

Water temperature generally increased at more-downstream 

sites, and 7dADM temperatures reached as high as 24 to 26 °C 

(fig. 6). Within the study reaches, RMs 70.2, 97.7, and 164.2 

reached maximum 7dADM values of 25.0, 23.3, and 21.5 °C, 

respectively, during 2016 (fig. 6B). Upstream reaches tended 

to warm later and cool earlier than the downstream reaches, 

except when an upstream site (such as the Willamette River at 

Owosso Bridge at Eugene, Oregon, USGS station 14158100, 

RM 178.7; fig. 2) was affected by warmer autumn releases 

from an upstream reservoir, showing that the upstream reaches 

of the Willamette River tend to meet the water-temperature 

standard more often.

Dissolved-oxygen concentrations in the main-channel 

Willamette River were measured continuously only in the 

Independence monitoring reach each year. Dissolved oxygen 

in the Independence monitoring reach typically decreased in 

late June and July and increased in August and September, 

largely in response to temperature-related changes in the water 

solubility of oxygen, which decreases with increasing temperature. Diel fluctuations of 1.5–2.0 mg/L were measured in both 

years (fig. 7). Continuous dissolved-oxygen concentrations 

from RM 97.7 (USGS station 444945123095600; fig. 2) met 

the State of Oregon cold and cool-water minimum dissolvedoxygen criteria (Oregon Department of Environmental 

Quality, 2016c, table 21) throughout the 2016 monitoring 

period and were never less than 7.7 mg/L (fig. 7). Longitudinal 

trends in dissolved oxygen were not determined in this study 

because only one dissolved-oxygen sensor was deployed in 

the river each year, and large diel fluctuations in dissolved 

oxygen make synoptic measurement comparisons (on multiple 

days and at various times) unreliable. Other studies previously have characterized dissolved-oxygen conditions in the 

Willamette River. For example, Pogue and Anderson (1995)

measured dissolved-oxygen conditions in the Willamette River 

upstream from Albany in late July and late August of 1994 and 

determined the river was well oxygenated (dissolved-oxygen 

concentrations were never less than 80 percent of its water 

solubility).

Water in the main channel likely remains welloxygenated for many reasons, such as (1) inputs of welloxygenated water from upstream, (2) flows that create 

sufficient turbulence and mixing that enhances reaeration 

from the atmosphere, (3) primary productivity of periphyton, 

and (4) only a moderate rate of sediment oxygen demand 

(Caldwell and Doyle, 1995). The measured diel variations in 

dissolved oxygen in the Independence monitoring reach are 

smaller than those that were measured farther upstream by 

Pogue and Anderson (1995), but many of the upstream reaches 

they sampled are shallower and known to be more affected 

by photosynthetic production and respiration by periphyton, 

which accounts for the difference in diel range. The general 

seasonal inverse relation between dissolved-oxygen concentration and water temperature measured in the Independence 

monitoring reach reflects the expected dependence of 

dissolved-oxygen solubility on water temperature. These 

dissolved-oxygen results, including the proposed controlling factors, are consistent with the findings of Pogue and 

Anderson (1995) for areas upstream from Albany.

Continuous data and synoptic measurements from the 

main-channel Willamette River revealed that the river in 

summer is well-mixed, warm, and contains high dissolvedoxygen concentrations. Vertical water-quality homogeneity 

was measured during both seasons and years of the study, and 

similar main-channel water temperatures persisted for many 

river miles. Cold-water fishes exposed to these warm water 

temperatures—warmer than the State of Oregon rearing and 

migration criterion—for a long period may be negatively 

affected by that thermal exposure. Additionally, fish confined 

to the main channel may need to travel substantial distances to 

find substantially cooler thermal conditions during the warm 

summer months. The potentially stressful thermal conditions 

in the main channel emphasize the potential importance of different, and perhaps more favorable, water-quality conditions 

in off-channel features.
24 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

16 24 9 17 25 3 11 19 27 4 12

May June July August

2015

September October

20 28 5 13 21 29 7 15 13

14

15

16

17

18

19

20

21

22

23

24

25

26

Willamette River main-channel water-temperature measurement 

location (at U.S. Geological Survey [USGS] station, if applicable)

RM 178.7 (USGS 14158100, at Owosso Bridge at Eugene, Oregon)

RM 161.0

RM 161.0 (USGS 14166000, at Harrisburg, Oreg.)

RM 119.3 (USGS 14174000, at Albany, Oreg.)

RM 97.7

RM 82.2 (USGS 14192015, at Keizer, Oreg.)

RM 70.2

Seven-day moving average of the daily maximum

water temperature, in degrees Celsius

16 24 9 17 25 3 11 19 27 4 12

May June July August

2016

September October

20 28 5 13 21 29 7 15 13

14

15

16

17

18

19

20

21

22

23

24

25

26

Seven-day moving average of the daily maximum

water temperature, in degrees Celsius

EXPLANATION

EXPLANATION

A. 2015

B. 2016

Willamette River main-channel water-temperature measurement 

location (at U.S. Geological Survey [USGS] station, if applicable)

RM 178.7 (USGS 14158100, at Owosso Bridge at Eugene, Oreg.)

RM 164.2

RM 161.0 (USGS 14166000, at Harrisburg, Oreg.)

RM 119.3 (USGS 14174000, at Albany, Oreg.)

RM 97.7

RM 82.2 (USGS 14192015, at Keizer, Oreg.)

RM 70.2

State of Oregon maximum 

water-temperature standard

State of Oregon maximum 

water-temperature standard

Figure 6. The 7-day moving average of the daily maximum water temperature measured at various sites in the Willamette River, 

Oregon. A, summer 2015. B, summer 2016.
Water-Quality Conditions of the Willamette River and Adjacent Off-Channel Features 25

7

8

9

10

11

12

May June July August September October

Date

Hourly dissolved oxygen, in milligrams per liter

EXPLANATION

2015 (at river mile 95.9)

2016 (at river mile 97.7)

Figure 7. Hourly dissolved-oxygen measurements of the main channel Willamette River, Oregon, in the Independence monitoring 

reach in late summer 2015 and summer 2016.

Off-Channel Feature Water-Quality Conditions

Key result—Water quality in off-channel features adjacent to the Willamette River typically is heterogenous, varying vertically, longitudinally, and seasonally within a single 

feature and among features.

Heterogeneity Among Off-Channel Features

Continuous water-temperature sensors deployed in 

20 off-channel features in 2015 and 22 features in 2016 

showed highly variable temperature patterns and ranges 

among features (figs. 8 and 9). Instantaneous water temperatures ranged from about 12 to 30 °C, with the highest daily 

maxima occurring in off-channel features in the Willamette 

Mission monitoring reach (fig. 2)—the most downstream of 

the sampled reaches (figs. 8 and 9). In both 2015 and 2016, 

diel water temperature fluctuations in off-channel features 

ranged from <1.0 °C to >8.0 °C. Sites that had minimal diel 

temperature changes tended to be either deep (and vertically 

stratified in the summer), shaded, or with a sensor position 

near the bottom of the water column on the substrate (2015 

only). Sites with large diel fluctuations tended to be shallow, 

not shaded, and affected by solar radiation.

Many of the off-channel features followed broadly 

similar multiday patterns in water temperature, but some offchannel features were consistently cool with patterns that bore 

no resemblance to main-channel temperatures or weatherrelated influences. The temperature ranges of off-channel features were highly variable within a study reach, such that no 

single site’s temperature pattern is necessarily representative 

of a reach (figs. 8 and 9). Reaches contained warm features 

with large diel fluctuations and cool features with small diel 

fluctuations. Water-temperature diversity among features was 

substantial; for example, a comparison of measurements from 

the Independence monitoring reach (RM 96–101) on July 20, 

2016, at 6:30 p.m. Pacific standard time shows that the mainchannel water temperature was 20.6 °C, whereas off-channel 

features within the reach at that time ranged from 13.8 to 

26.0 °C (fig. 10). Other reaches displayed similar patterns during the 2015 and 2016 monitoring periods.

Heterogeneity Within Alcoves

Synoptic surveys conducted within alcoves revealed 

substantial water-quality heterogeneity, often vertically and 

longitudinally. Water temperatures measured at the top of 

alcoves were warmer than water temperatures at the bottom of 

the alcove (fig. 11); temperatures at the top and bottom of the 

water column varied as much as 7 °C within some features. 

Dissolved-oxygen concentrations also showed variations 

between the top and bottom of the water column in alcoves; 

values varied as much as 11.4 mg/L within one feature 

(fig. 12). In most alcoves, dissolved-oxygen concentrations at 

the surface were higher than those at the bottom of the water 

column. Alcoves with higher dissolved oxygen at the bottom 

of the water column likely had submerged aquatic vegetation 

that was producing oxygen through photosynthesis at the time 

of the measurement. For water temperature and dissolved oxygen, the values and the magnitude of the difference between 

the top and bottom measurements were dependent on the 

alcove’s morphology, the stage of the river, and the presence 

or absence of vegetation.
26 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

Site type and river mile (RM; table 1)

Main channel at RM 97.7

Alcove at RM 107.5

Alcove at RM 101

Alcove at RM 98.4

Alcove at RM 97.9

Alcove at RM 97.7

Alcove at RM 95.8

EXPLANATION

10

12

14

16

18

20

22

24

26

28

B. 2015 Independence monitoring reach

10

12

14

16

18

20

22

24

26

28

30

Site type and river mile (RM; table 1)

Main channel at RM 70.2

Alcove at RM 74.6

Alcove at RM 73.4

Alcove at RM 70.2

Alcove at RM 67.7

Alcove at RM 67.6

Alcove at RM 67.1

EXPLANATION

A. 2015 Willamette Mission monitoring reach

10

12

14

16

18

20

22

24

August September October

2015

Site type and river mile (RM; table 1)

Main channel at RM 161

Side channel at RM 168.1

Side channel at RM 164.8

Alcove at RM 164.1

Alcove at RM 163.5

Side channel at RM 162.8

Alcove at RM 162.8

Alcove at RM 161.7

Side channel at RM 161.3

C. 2015 Harrisburg monitoring reach EXPLANATION

Hourly water temperature, in degrees Celsius

Figure 8. Hourly water-temperature measurements in monitored off-channel features of the Willamette River, 

Oregon, in late summer 2015. A, Willamette Mission monitoring reach. B, Independence monitoring reach. 

C, Harrisburg monitoring reach. Note that some temperature records were deleted if data were suspect.
Water-Quality Conditions of the Willamette River and Adjacent Off-Channel Features 27 3028262422201816141210 May June July August September October EXPLANATION Site type and river mile (RM; table 1) Main channel at RM 97.7 Tributary at RM 107.9 Tributary alcove at RM 107.8 Alcove at RM 107.5 (0.2 meter above bed) Alcove at RM 107.5 (0.6 meter above bed) Alcove at RM 101 Alcove at RM 98.4 Alcove at RM 97.7 Alcove at RM 96.1 2016 B. 2016 Independence monitoring reach

Site type and river mile 

(RM; table 1)

Main channel at RM 73.2Alcove at RM 77.2Alcove at RM 74.6Alcove at RM 73.9Alcove at RM 73.5Alcove at RM 73.4Alcove at RM 70.2Alcove at RM 67.7Alcove at RM 67.6Alcove at RM 67.1

EXPLANATION

302826

24

22201816

14

1210

A. 2016 Willamette Mission monitoring reach

Hourly water temperature, in degrees Celsius

Figure 9. Hourly water-temperature measurements in monitored off-channel features of the Willamette River, Oregon, in summer 2016. 

A, Willamette Mission monitoring reach. 

B, Independence monitoring reach. 

C, Harrisburg monitoring reach. Note that some temperature records were deleted if data were suspect.
28 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16 3028262422201816141210 May June July August September October 2016 Site type and river mile (RM; table 1) Main channel at RM 164.2 Side channel at RM 164.8 Alcove at RM 164.1 Alcove at RM 162.9 Alcove at RM 162.2 Alcove at RM 161.7 Side channel at RM 161.3 EXPLANATION C. 2016 Harrisburg monitoring reach

Water temperature, in degrees Celsius

Figure 9. —Continued
Water-Quality Conditions of the Willamette River and Adjacent Off-Channel Features 29

EXPLANATION

Water temperature, in degress 

Celsius, on July 20, 2016 

at 6:30 p.m.

≤16.9

17.0 to 19.9

20.0 to 22.9

23.0 to 25.9

≥26.0

River mile

N

Alcove

13.8° C

Alcove

17.8° C

Alcove

26.0° C

Alcove

19.9° C

Flow direction

Main channel

20.6° C

Willamette River

Independence, Oregon

0 500 METERS

0 1,500 FEET

100 99

98

97

96

98

Figure 10. Water-temperature measurements on July 20, 2016, at 6:30 p.m. Pacific standard time in the Willamette 

River and select off-channel features near Independence, Oregon.

Willamette Mission

monitoring reach

Independence

monitoring reach

Harrisburg

monitoring reach EXPLANATION

Synoptic measurement—

A veritcal line connects 

those in the same alcove

Top of water column

Middle of water column

Bottom of water column

10

15

20

25

30

10

15

20

25

30

Water temperature, in degrees Celsius Water temperature, in degrees Celsius

River mile

A. August 18–26, 2015

B. July 25–August 26, 2016

55 65 75 85 95 105 115 125 135 145 155 165 175

Figure 11. Water temperatures at the top, middle, and bottom of the water column in alcoves in the Willamette River, Oregon. 

A, August 18–26, 2015. B, July 15–August 26, 2016. Synoptic data shown are only from alcoves, which were disconnected from 

the main channel at the upstream end. Shallow alcoves were only measured with one top (near surface) measurement. Often, 

multiple top and bottom measurements were collected at different locations within a large alcove.
30 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

Willamette Mission

monitoring reach

Independence

monitoring reach

Harrisburg

monitoring reach EXPLANATION

Synoptic measurement— A veritcal line connects 

those in the same alcove

Top of water column

Middle of water column

Bottom of water column

0

4

8

12

16

Dissolved oxygen, in milligrams per liter

0

4

8

12

16

Dissolved oxygen, in milligrams per liter

A. Synoptic measurements from August 18–26, 2015

B. Synoptic measurements from July 25–August 26, 2016

River mile

55 65 75 85 95 105 115 125 135 145 155 165 175

Figure 12. Dissolved-oxygen concentrations at the top, middle, and bottom of the water column in alcoves in the Willamette 

River, Oregon. A, August 18–26, 2015. B, July 25–August 26, 2016. Synoptic data shown are only from alcoves, which were 

disconnected from the main channel at the upstream end. Shallow alcoves were only measured with one top (near surface) 

measurement. Often, multiple top and bottom measurements were collected at different locations within a large alcove.

A longitudinal profile of water-quality synoptic measurements was collected to examine spatial heterogeneities in 

the alcove at RM 74.6 on August 27, 2015, at 2:00 p.m. PDT 

during low river-stage conditions (fig. 13). As shown by measurements collected from the main channel and progressing 

towards the upstream end of the alcove, water temperatures 

and specific conductance near the surface generally increased, 

whereas dissolved-oxygen concentrations near the surface 

generally decreased. In addition, the vertical heterogeneity 

(differences between surface and bottom measurements) of 

water temperature, dissolved oxygen, and specific conductance 

generally increased from the main channel to the upstream end 

of the alcove, with dissolved-oxygen concentrations becoming low near the bottom. In 2016, two continuous temperature 

sensors were installed in an alcove at RM 107.5 at different 

depths (0.2 m and 0.6 m above the bed). Comparing the readings from these sensors show that vertical heterogeneity can 

persist for many months in one alcove (fig. 9B).

Repeat longitudinal and vertical profiles of water-quality 

synoptic measurements were collected in the alcove at 

RM 97.7 on August 19, 2015, and October 7, 2015 (fig. 14). 

These profiles show overall cooler temperatures in the main 

channel and the alcove in autumn, yet vertical stratification still exists in both seasons. The difference between top 

and bottom measurements was less pronounced in October. 

For both example alcoves (figs. 13 and 14), the downstream 

portion of off-channel water (nearest the main channel) was 

likely mixing with water from the main channel, but differences became more pronounced at the upstream end because 

(1) water was isolated and less affected by water from the 

main channel and more affected by other factors such as 

weather conditions; (2) the depth of the feature decreased 

towards the upstream end, making the water more susceptible 

to environmental heat inputs and sediment oxygen demands; 

and (3) subsurface inputs may have been proportionately 

greater towards the upstream end of the alcove.
Water-Quality Conditions of the Willamette River and Adjacent Off-Channel Features 31

87 8082

94

85 85

91

83

88

84

89

82

82

76

76

0

0.5

1.0

1.5

2.0

0 100 200 300

Distance from entrance of alcove, in meters

80

85

85

90

95

Specific conductance,

in microsiemens 

per centimeter at 25 

degrees Celsius

EXPLANATION

Main

channel

Alcove

5.39.54.4

2.5

7.0 7.4

4.5

7.6

4.8

8.0

4.4

11.1

9.8

10.0

9.9

0

0.5

1.0

1.5

2.0

Depth below water surface, in meters

2

4

6

8

10

12

Dissolved oxygen, in

milligrams per liter

Approximate bed of alcove

A. Water temperature

B. Dissolved oxygen

C. Specific conductance

21.725.422.7

21.0

23.7 23.3

21.8

23.7

21.1

23.5

18.9

23.8

20.7

21.6

21.6

0

0.5

1.0

1.5

2.0

18

20

22

24

26

Water temperature, in

degrees Celsius

Figure 13. Longitudinal profiles of synoptic point measurements recorded in the alcove at river mile 74.6 along the 

Willamette River near Salem, Oregon, and adjacent main-channel readings on August 27, 2015, at 2:00 p.m. Pacific daylight 

time. A, water temperature. B, dissolved oxygen. C, specific conductance.

Factors Affecting Heterogeneity Within and 

Among Off-Channel Features

Water-quality heterogeneity occurred in off-channel features with various site characteristics. In off-channel features 

with abundant aquatic vegetation, biological processes greatly 

affected the water quality. Aquatic vegetation produces oxygen 

through photosynthesis, and the type of vegetation (submerged or emergent) affects how much dissolved oxygen from 

photosynthesis is released to the water column as opposed to 

directly to the atmosphere (Caraco and others, 2006). Large 

coverages of floating aquatic vegetation may inhibit reaeration of oxygen across the air/water interface. Emergent aquatic 

vegetation may shade the water underneath and decrease the 

incoming energy flux from sunlight, resulting in cooler water 

temperatures at depth. Additionally, an increased sediment 

oxygen demand due to an accumulation of large amounts of 

plant-derived organic matter would tend to decrease dissolvedoxygen concentrations near the substrate (Rounds and Doyle, 

1997). Although determining the independent effects of plant 

assemblages (such as submerged, emergent, biofilms) on water 

quality were beyond the scope of this study, the combined 

effects often were observed.

Data collected in off-channel features with large quantities of emergent aquatic invasive plants (including Ludwigia

spp.) revealed a steep vertical stratification in water temperature and dissolved-oxygen concentrations. The highest water 

temperature measured during a synoptic survey occurred on 

August 19, 2015, at 5 p.m. PDT in an off-channel feature 

at RM 97.7 that had abundant emergent aquatic vegetation 

(fig. 14). The water temperature and dissolved-oxygen concentration at the surface (0.2 m) were 28.2 °C and 6.9 mg/L, 

respectively (Mangano and others, 2017). At 0.8 m deep 

(near the bottom), the water temperature was 18.4 °C and the 

dissolved-oxygen concentration was 0.7 mg/L. In this offchannel feature, the water temperature decreased by about 

10 °C and dissolved oxygen by 6 mg/L in 0.6 m of depth; the 

vertical gradient was similar when measured again in 2016. 

The cooler water temperatures and lower dissolved-oxygen 

concentrations may be attributed to decreased solar energy 

infiltration as the result of shading by aquatic macrophytes 

and the accumulated effect of respiration and sediment oxygen 

demand. In contrast, measurements collected in a nearby 

off-channel feature (RM 98.4; near Independence; fig. 15) 

on the same date and at a similar time (August 19, 2015, at 

3:23 p.m. PDT) showed that water-temperature readings at 
32 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

24.0

24.0

28.2

20.5

18.4

18.1

21.0

17.5

23.4

23.4

15.3

13.0

15.4

13.3

14.6

12.5

16.8

16.6

16.7

16.6

A. August 19, 2015

B. October 7, 2015

−100 0 100 200 300 400

0.0

0.5

1.0

1.5

2.0

0.0

0.5

1.0

1.5

2.0

Distance from entrance of alcove, in meters

Depth below water surface, in meters

10

15

20

25

30

Water temperature, in

degrees Celsius

EXPLANATION

Main

channel

Alcove

Approximate bed of alcove

Approximate bed of alcove

Figure 14. Longitudinal profiles of water-temperature synoptic point measurements recorded in the alcove at river 

mile 97.7 along the Willamette River near Independence, Oregon, and adjacent main-channel readings. A, August 19, 2015. 

B, October 7, 2015.

0.2 and 1.8 m depth differed by about 3 °C. Aerial photographs (taken in 2016) showed that the off-channel feature at 

RM 98.4 did not contain abundant aquatic vegetation on the 

surface, which may have contributed to the smaller vertical water-temperature gradient. The morphology of the two 

alcoves (including the feature’s elevation at its upstream 

seasonal river-connection point) may be critical in determining the amount of aquatic vegetation that establishes in each, 

with more-frequent flushing flows passing through the alcove 

at RM 98.4 due to its lower and broader upstream connection 

point. Surface water passes less frequently through the relatively higher upstream end of the alcove at RM 97.7, which 

likely allows (or does not disrupt) the establishment of aquatic 

vegetation and the accumulation of sedimentary organic matter (fig. 15).

Vertical stratification and water-quality heterogeneity 

also are affected by factors other than aquatic vegetation. 

Measurements collected in the alcove at RM 164.1 near 

Harrisburg (on August 20, 2015) showed a 5.5 °C (water temperature) and 2.5 mg/L (dissolved oxygen) decrease between 

the top (0.1 m) and bottom (3.1 m). This feature did not 

contain large amounts of aquatic vegetation, and the vertical 

heterogeneity may have been caused by substantial depth or 

from subsurface inputs (cooler, with lower dissolved-oxygen 

levels) that might enter the feature at the bottom. Depth also 

can affect temperature and dissolved-oxygen concentrations 

due to decreased sunlight infiltration and a greater separation 

of bottom waters from the air/water interface. A large fraction 

of the solar energy flux is absorbed at the surface of the water 

column, which tends to heat the surface preferentially.

In some off-channel features, continuous temperature 

measurements clearly documented the presence and persistence of cool water that was largely unaffected by changing 

weather conditions (figs. 8 and 9). Whereas the water temperature in many off-channel features varied with consistent 

patterns that seemed to be in response to changes in weather 

conditions, measurements in alcoves at RMs 67.1, 70.2, 74.6, 

96.1, 97.7, 101, 107.5, and 164.1 all showed a substantial 

disconnection from such weather patterns. Several of these 

alcoves were distinctly cooler than the main channel and had 

almost invariant or slowly varying temperatures, which may 

be indicative of a source of cool water entering the alcove, 

likely from subsurface inputs. Quantifying subsurface inputs 

was outside the scope of this study, but no other process can 

account for such cool water that persists for extended periods 

during summer.

The off-channel measurements from this study indicate 

that site-specific characteristics such as subsurface inputs, 

presence and abundance of aquatic and riparian vegetation, 

depth, and mixing at the air/water interface may all affect 

water temperature and dissolved-oxygen conditions in offchannel features of the Willamette River. Biological processes 

affected by those characteristics, such as photosynthesis and 

respiration, contribute to the measured heterogeneity. The 
Water-Quality Conditions of the Willamette River and Adjacent Off-Channel Features 33

!

!

!

!

Height above water surface,

in meters

9

6

3

0 (water surface)

Monitoring equipment

Water-quality monitor

Water-temperature sensor

Pressure transducer

Pendant temperature sensor

River mile (RM)

EXPLANATION

Flow

direction

Outer alcove; 

not investigated

Base modified from 2008 Oregon Department of Geology and Mineral Industries 

digital elevation data, 1-meter resolution. 

Inset photo: 2016 U.S. Department of Agriculture digital data, 1-meter resolution.

UTM Zone 10 North, NAD 1983.

!

!

!

!!

!

RM 97.7 alcove

RM 98.4 alcove

Gravel pit

High, narrow, and 

indistinct upstream 

connection point for 

alcove at RM 97.7

Low and broad 

upstream connection 

point for alcove at 

RM 98.4

Willamette River main channel

Independence, Oregon

3 kilometers

!

! !

!!

!

Abundant aquatic

vegetation

Lack of aquatic

vegetation

RM 97.7

alcove

RM 98.4 alcove

0 0.1 0.2 0.3 MILES

0 0.1 0.2 0.3 KILOMETERS

N

99

98

98

Figure 15. Schematic diagram showing 2008 lidar land-surface elevations and differences in size and height of upstream connection 

points for alcoves at river miles 97.7 and 98.4 near Independence, Oregon. Mean daily streamflow (discharge) of the Willamette River 

at Salem, Oregon (USGS gage 14191000) was 9,690 cubic feet per second during lidar acquisition.

relative effects of those characteristics and processes resulted 

in a wide variety of water-quality conditions found in offchannel features; the water-quality heterogeneity indicates that 

suitable regions, or microhabitats, within these features likely 

exist for fishes with various life-history requirements. Each 

off-channel feature is somewhat unique, but observations of 

site-specific characteristics, such as the presence or absence 

of shading, presence and abundance of aquatic plants, and the 

feature’s morphology can help to explain the water-quality 

conditions occurring in each off-channel feature and categorize them in useful ways.

Comparing Off-Channel and Main-Channel 

Water Quality

Key result—Water temperatures in off-channel features 

can be warmer than, can be cooler than, or can fluctuate 

between warmer or cooler than main-channel temperatures in 

response to river stage and various site characteristics.

Water-quality conditions in off-channel features can 

differ from main-channel conditions at all temporal scales 

measured in this study. Water-quality parameters measured 

in the main-channel Willamette River serve as a reference for 

water quality measured in off-channel features. Representing 

the main-channel water temperature with a single measurement location for a reach is usually acceptable because of the 

relative homogeneity of temperature conditions in the main 

channel within each monitoring reach. However, conditions 

in off-channel features are heterogeneous, and reporting a 

water temperature from a single off-channel location is not 

an adequate characterization of off-channel conditions in 

the reach and may not even be an adequate representation of 

conditions within that single feature, which complicates data 

interpretation and the generalization of conclusions.

Synoptic measurements of water temperature and dissolved oxygen revealed substantial thermal diversity at various 

depths within alcoves and relative to the main channel. When 

multiple top (near surface) measurements were collected 

within one feature, the measured values were averaged so that 

a single “representative” top value could be compared to the 
34 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

closest main-channel synoptic measurement; multiple bottom measurements within one feature were also averaged for 

comparison (fig. 16). During the summers of 2015 and 2016 

(July and August), water temperatures near the bottom of 

sampled alcoves were on average 1.7 °C cooler than the main 

channel. Water temperatures at the top of the water column 

of sampled alcoves were an average of 0.3 °C warmer than 

the main channel. The bottom water-column temperature was 

cooler in 77 percent of the features, and the top water-column 

temperature was cooler in 41 percent of the features compared 

to the main channel (fig. 16). 

Dissolved-oxygen concentrations in the alcoves were 

often lower than or similar to those measured in the main 

channel near the feature. Dissolved-oxygen concentrations 

in the main channel generally fluctuated between 8 and 

10 mg/L each day. Of the 60 alcoves with top dissolvedoxygen measurements, 38 percent were less than the main 

channel (<8 mg/L), 45 percent were similar to the main 

channel (8–10 mg/L), and 17 percent were greater than the 

main-channel dissolved-oxygen concentration (>10 mg/L). 

Of the 53 alcoves with bottom dissolved-oxygen measurements, 60 percent were less than, 27 percent were similar to, 

and 13 percent were greater than the main-channel dissolvedoxygen concentrations. Of the features with dissolved-oxygen 

concentrations lower than those in the main channel, many had 

concentrations less than 4 mg/L, a threshold used by Gregory 

and Wildman (2016) to indicate dissolved-oxygen levels in 

which native fish may survive but are still likely to be stressed 

(fig. 16).

Generally, main-channel water temperatures increased 

through July or August and then decreased, yet the many 

continuous temperature sensors deployed in off-channel 

features show a variety of temperatures compared to the main 

channel. Although limited to one location all season (on the 

bed of the feature in 2015 and mid-water column in 2016), 

the continuous monitors provide temporal patterns that cannot be discerned from the infrequent synoptic measurements. 

Comparisons between hourly off-channel and main-channel 

water temperatures revealed three broad categories in summer 

months: (1) off-channel features that were consistently cooler 

than the main channel, (2) off-channel features that were consistently warmer than the main channel, and (3) off-channel 

features with temperatures that fluctuated between warmer 

and cooler than the main channel, sometimes daily (figs. 17

and 18). Of the three types of off-channel features shown in 

figure 17, only the alcove at RM 107.5 had temperatures that 

were at least 2 °C cooler than the main channel at some point 

during the summer; cool features may act as CWRs for certain 

species of fish when stressful thermal conditions occur in the 

main channel.

Off-channel features ranged from about 10 °C warmer 

than the main channel to 10 °C cooler than the main channel, 

and patterns of temperature comparisons were diverse (appendix 1). Water-temperature patterns tended to change in autumn 

when river flows increased and air temperatures decreased. 

The Willamette Mission monitoring reach had the highest 

proportion of monitored off-channel features that were cooler 

than the main channel (fig. 18). Field observations of sampled 

off-channel features noted the highest occurrence of aquatic 

invasive Ludwigia spp. in that reach. Dense aquatic invasive 

vegetation was also present in some off-channel features in 

the Independence monitoring reach (for example, alcove at 

RM 97.7), and water temperatures in those features were also 

cooler than the main channel.

A total of 10 off-channel features monitored in this 

study were cooler than the main channel during July and 

August 2016 (fig. 18; appendix 1). Five of the 10 features 

(alcoves at RMs 67.1, 70.2, 73.5, 97.7, and 107.5) contained 

abundant emergent aquatic vegetation. Three of the 10 cool 

features (alcoves at RMs 74.6 and 96.1, and side channel at 

RM 161.3) were bordered by gravel bars that may have been 

supplying potentially cooler inputs from subsurface flow. 

Two of the features (alcove at RM 164.1 and side channel at 

RM 164.8) were bounded by gravel bars and revetments. Sitespecific characteristics of these cool features (such as potential 

subsurface inputs, presence of revetments, and the presence 

of emergent aquatic vegetation) were not mutually exclusive, 

and multiple combinations likely could produce cool water in 

off-channel features.

Three out of the 21 off-channel features monitored in 

2016 were warmer than the main channel in July and August 

(fig. 18; appendix 1). Water-temperature sensors deployed at 

RM 107.9 and 107.8 were placed in a small, slow-moving 

tributary and adjacent alcove, respectively. The off-channel 

feature at RM 161.7 was relatively shallow (2.1 m) and may 

(or may not) have been affected by runoff from gravel mining 

operations that bordered the site.
Effect of Upstream Morphology on Water Quality in Off-Channel Features 35

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A. August 18–26, 2015 B. July 25–August 26, 2016

Eugene

Corvallis

Harrisburg

Albany

Independence

Salem

Eugene

Corvallis

Harrisburg

Albany

Independence

Salem

Willamette River

Santiam River

Lukiamute River

N McKenzie Riv er

Calapooia River

Willamette River Willamette River

Santiam River

Lukiamute River

McKenzie Riv er

Calapooia River

Willamette River

TopBottom

# #

Water-temperature difference between the 

main channel and the average alcove 

water temperature on day of sampling, in 

degrees Celsius—By location in water 

column

<−2

−2 to −0.5

−0.5 to 0.5

0.5 to 2

>2

# #

# #

# #

# #

Average dissolved-oxygen concentration 

within each alcove on day of sampling, 

in milligrams per liter—By location in 

water column

< 4

≥ 4

River mile

* *

* *

EXPLANATION

Negative values 

indicate an alcove 

was cooler than the 

main channel.

80

120

100

140

160

170

150

130

110

90

70

80

120

100

140

160

170

150

130

110

90

70

80

Figure 16. Average water-temperature differences between alcoves and the main channel, and averaged 

dissolved-oxygen concentrations in alcoves, measured at the top and bottom of the alcove’s water column, in the 

Willamette River, Oregon. A, August 18–26, 2015. B, July 25–August 26, 2016.
36 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

−10

−8

−6

−4

−2

0

2

4

6

8

10

A. Alcove at river mile (RM) 107.5 minus main channel at RM 107.3

−10

−8

−6

−4

−2

0

2

4

6

8

10

B. Alcove at RM 95.8 minus main channel at RM 97.7

−10

−8

−6

−4

−2

0

2

4

6

8

10

Aug 19 Aug 31 Sept 11 Sept 23 Oct. 5

C. Alcove at RM 98.4 minus main channel at RM 97.7

Alcove warmer than main channel

Alcove cooler than main channel

EXPLANATION

Water-temperature difference between main channel and off-channel feature, in degrees Celsius

2015

Figure 17. Examples of three types of patterns resulting from a 

comparison of water temperatures in the main channel and in several 

off-channel features of the Willamette River, Oregon. These data were 

collected in the Independence monitoring reach in 2015, and sensors 

were located at the bottom of the feature. A, alcove cooler than the 

main channel. B, alcove warmer than the main channel. C, alcove 

fluctuated between warmer and cooler than the main channel.

Many of the off-channel features that fluctuated 

between warmer and cooler than the main channel in July 

and August alternated daily, whereas others fluctuated at 

different intervals with no obvious pattern (appendix 1; 

figs. 8 and 9). Daily fluctuations in temperature differences 

may simply have been due to a larger diel temperature 

range in the off-channel feature relative to the main channel. The main channel typically is deeper and contains 

more water than the off-channel features per unit surface 

area. As a result, the heat content in the main channel relative to the heat flux across the air/water interface is larger 

than in off-channel areas, and main-channel temperatures 

will change less over the course of a day when exposed 

to the same environmental heat fluxes across the air/water 

interface. Alternatively, the fluctuations in temperature 

differences may be partly due to a lag in peak water temperature caused by subsurface flows moving through surrounding gravel bars on different time scales (Arrigoni and 

others, 2008). Water-temperature sensors were deployed 

on the bottom of off-channel features in 2015, potentially 

making them more susceptible to the effect of subsurface 

inputs through the substrate as compared to measurements 

collected in 2016. In 2015, more off-channel features with 

water-temperature differences that fluctuated daily between 

warmer and cooler than the main channel were found in the 

Independence and Harrisburg monitoring reaches compared to the Willamette Mission monitoring reach, which 

may be related to the importance of subsurface flows moving though the larger and more numerous active gravel bars 

found in the upper reaches of the Willamette River than are 

typically found in more-downstream reaches. Half of the 

fluctuating off-channel features measured water temperatures that were 2 °C cooler than the main channel for at 

least 1 hour in July or August (appendix 1); however, the 

length of time that the water temperature in the feature was 

2 °C cooler than the main channel varied, and any potential 

value as a cold-water refuge to sensitive fish is unknown.

Effect of Upstream Morphology 

on Water Quality in Off-Channel 

Features

Off-channel water quality can change abruptly when 

upstream surface-water connection and disconnection 

occurs (effectively turning an alcove into a side channel, 

and back again), or when quick rises in river stage cause 

main-channel water to flow into an alcove from the downstream connection point (see fig. 3). The upstream end of 

an off-channel feature becomes connected by surface water 

to the main-channel flow when river stage reaches a critical height and overtops the landmass separating an alcove 

from the main channel. River stage and the geomorphology 

of the off-channel feature are key factors that dictate when 
Effect of Upstream Morphology on Water Quality in Off-Channel Features 37

Cooler

Fluctuated

Warmer

Cooler

Fluctuated

Warmer

66 68 70 72 74 76 78 80 96 98 100 102 104 106 108 110 160 162 164 166 168 170

A. July–August 2015

B. July–August 2016

River mile

Off-channel feature water temperature 

compared to main channel

2

6

12

Total

per year

3

8

10

Willamette Mission 

monitoring reach

Independence 

monitoring reach

Harrisburg 

monitoring reach

EXPLANATION

Feature measured at least 2 degrees Celsius cooler than the 

main channel at some point during July or August—

Shown as a black circle around colored point 

Figure 18. Categories of features based on water-temperature comparisons to the main channel in the three monitoring reaches of the 

Willamette River, Oregon. A, July–August 2015. B, July–August 2016. Water-temperature sensors were deployed on the bottom of the 

main channel and off-channel features in 2015 and in the middle of the water column in 2016. An off-channel feature was considered 

“cooler than the main channel” if it was cooler during the warmest months of the summer monitoring period (July–August; when 

Willamette River streamflow is at its lowest).

upstream connection/disconnection occurs, how much streamflow enters the off-channel feature, and how long that connection persists. Willamette River streamflow in the summer of 

2015 and the late summer of 2016 was unusually low for the 

modern flow-management era (since 2000; fig. 4), so the timing and duration of any connection or disconnection in other 

years may be different from what was observed in this study.

In addition to the morphology and elevation of a feature’s 

upstream connection point, other geomorphic characteristics, such as the composition of the substrate and landforms 

bounding a feature, are critical in determining the potential 

magnitude and flow paths of any subsurface inputs. Water 

can more easily travel through coarse gravel substrate than 

fine floodplain material or bedrock; thus, an alcove adjacent 

to landforms primarily composed of gravel (such as active 

bars and stable bars) may be more likely to receive substantial 

inputs of subsurface flows than features adjacent to landforms 

composed of less-permeable material (such as Pleistocene terraces, bedrock outcrops, or floodplains; Burkholder and others, 

2008). Water color may indicate the potential paths of water 

inputs or the presence of organic matter present in off-channel 

features; for example, natural subsurface inputs are likely to 

be colorless (Chapelle and others, 2016) and may be visible in 

an alcove with highly colored water that has an accumulation 

of organic matter from aquatic or terrestrial plants. Colored 

subsurface inputs may indicate a dynamic exchange between 

surface and subsurface water (Regan and others, 2017).

Examples of the Relations Between 

Geomorphology, Surface-Water Connectivity, 

and Water Quality of Off-Channel Features

Key result—Upstream surface-water connection and 

disconnection, and related site characteristics, are important 

factors affecting water quality in off-channel features.

The patterns in the off-channel water temperatures collected in this study were the combined result of multiple processes and site characteristics, such as connections to the main 

channel, shading or lack of shading, stratification, presence 

or absence of submerged or emergent aquatic plants, and the 

magnitude and nature of any subsurface inputs. Using known 

site characteristics, some patterns in the data can be tied to 

certain processes, and strong hypotheses can be constructed 

to explain other patterns. Relying on water-temperature data 

alone, however, is insufficient to conclusively determine the 

processes that produce all patterns in the data. To better understand which processes are important, such as the timing and 

strength of upstream surface-water connection and disconnection, other datasets were needed. Data from dissolved-oxygen 

sensors, pendant temperature sensors, pressure transducers, 

and nearby streamgages were helpful in determining when 

upstream connection or disconnection may have occurred. 

Because multiple lines of evidence were needed, this analysis and discussion of upstream connections focuses on the 

five off-channel features where multiple types of equipment 

(specifically multiparameter water-quality monitors and, in 

some features, pendant temperature sensors and pressure transducers) were deployed in 2016 among the three monitoring 

reaches (fig. 19).
38 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

Stable bar

Stable bar

Stable bar

Stable bar

Active

bar

Active

bar

Floodplain

Floodplain

Floodplain

Floodplain gravel pit

Pleistocene terrace

Active bar

Fairfield alcove

Blue Ruin

alcove

Harpers Bend

side channel

Murphy Bar alcove

Main channel

Floodplain

Winsor Bar

alcove

Willamette River

Willamette River

Willamette River

Willamette River

Pendent buried

(never recovered)

Monitoring equipement

not shown for this alcove

Monitoring equipement

not shown for these alcoves

EXPLANATION

Alcove outline

Upstream connection path outline

Edge of Pleistocene terrace surface

Flow direction of Willamette River

River mile (RM)

Monitoring equipment

Water-quality monitor

Water-temperature sensor

Pressure transducer

Pendant temperature sensor 98

Base from 2016 U.S. Department of Agriculture digital data, 

1-meter resolution. UTM Zone 10 North, NAD 1983

Pleistocene

terrace

Approximate path of

Spring Valley Creek

250 meters

A. Fairfield alcove (RM 67.1) B. Blue Ruin alcove (RM 164.1) and 

 Harpers Bend side channel (RM 164.8)

C. Murphy Bar alcove (RM 97.7) and main channel (RM 97.7) D. Windsor Bar alcove (RM 74.6)

98

68

67

75

164

165

Figure 19. Location and important geomorphic features of five off-channel features and one main-channel location monitored 

with continuous water-quality monitors in summer 2016 along the Willamette River, Oregon. A, Fairfield alcove (river mile [RM] 67.1). 

B, Blue Ruin alcove (RM 164.1) and Harpers Bend side channel (RM 164.8). C, Murphy Bar alcove (RM 97.7) and main channel 

(RM 97.7). D, Windsor Bar alcove (RM 74.6).
Effect of Upstream Morphology on Water Quality in Off-Channel Features 39

Fairfield Alcove

The Fairfield alcove at RM 67.1 (fig. 19A) near Salem 

is a large off-channel feature between a stable bar and a tall 

Pleistocene terrace surface (O’Connor and others, 2001; 

fig. 19A; table 5). It functioned as an alcove during typical 

summer low flows in 2015–16 and connected to the main 

channel at the upstream end during moderate flows. To connect the upstream point of this feature with the main channel 

required an increase in stage of about 1 m compared to summer low-flow conditions, as estimated from field observations 

and from 2008 lidar data. This feature had narrow connection 

points at the upstream and downstream ends. Water in Fairfield 

alcove was highly colored (likely from tannins) compared 

to the main channel, and aquatic vegetation (Ludwigia spp., 

among others) was abundant. Maximum depth measured during low-flow synoptic visits was 1.3 m, and more than 0.5 m 

of soft, unconsolidated organic matter had accumulated at the 

bottom in many areas. Historical aerial photographs showed 

that this feature has remained stable since 1994 (appendix 2).

A water-quality monitor was deployed in this alcove 

in May 2016, and the upstream end of this off-channel 

feature was already disconnected from the main channel as observed in the field during equipment installation. 

Negligible dissolved-oxygen concentrations were measured 

during the study period until mid-October, when streamflow 

in the Willamette River (measured at the Salem streamgage; 

USGS station 14191000) increased from 10,000 to more than 

40,000 ft3/s in 6 days. Pendant temperature data collected 

at the upstream end of this off-channel feature revealed that 

the upstream end reconnected when streamflow at the Salem 

streamgage was around 25,000 ft3/s. During this increase in 

flow, the river began flowing into the off-channel feature, first 

at the downstream end and then at the upstream end, flushing the feature with river water and increasing the dissolvedoxygen concentration from zero mg/L to about 9 mg/L and 

the water temperature from 12.5 °C to about 14.0 °C (similar 

to the main-channel dissolved-oxygen and water-temperature 

conditions at the time; fig. 20).

Increases in main-channel streamflow may affect offchannel water quality through an influx of water into the 

off-channel feature at its downstream end, even if the feature remains disconnected at its upstream end. Dissolved 

oxygen and water temperature in the Fairfield alcove 

responded to two short-duration flow increases in early 

October 2016. Streamflow at Salem increased twice from 

7,000 to 13,000 ft3/s between October 6 and October 8, 

2016, which corresponded to a 0.6-m increase in stage at the 

Salem streamgage; pendant data revealed the stage increase 

was not enough to connect the upstream end of the alcove to 

the river. Main-channel water likely flowed into the feature 

at the downstream connection point due to a difference in 

stage between the main channel and alcove, indicated by the 

temporary increase in water temperature and dissolved-oxygen 

concentration in the alcove (fig. 20). Such water inputs at 

the downstream entrance of the alcove could also explain 

why the increase in dissolved-oxygen concentration started 

on October 14, 2 days before the pendant temperature data 

showed the upstream connection of the off-channel feature.

Windsor Bar Alcove

The Windsor Bar alcove is a relatively small off-channel 

feature at RM 74.6 that is between an active gravel bar and a 

tall Pleistocene terrace surface in a reach of the river that is 

straight and lacks channel complexity (O’Connor and others, 

2001; fig. 19D; table 5). Spring Valley Creek is 150 m away, 

behind the Pleistocene terrace wall to the west of this feature 

and is 3 m higher in elevation than the side-channel water surface during the summer. The upstream end of the off-channel 

feature is connected to the main channel at all but unusually 

low flows; such unusual low flows did occur during this study, 

allowing data to be collected when this feature was an alcove. 

At moderate and high flows, surface water from the main 

channel overtops the bounding gravel bar and the feature is no 

longer separated from the main channel. Water in the feature is 

typically clear but has distinct areas of opaque, whitish water, 

possibly due to the erosion of sediment out of the silty, lightcolored Pleistocene terrace wall. Aquatic vegetation in 2016 

was minimal, perhaps because this off-channel feature often 

receives high river flows, and the bed is composed of hard, 

coarse-grained material. Maximum depths measured during 

low-flow synoptics were 1.8 m (fig. 13). Historical aerial photographs show that the gravel bar separating this feature from 

the main channel has transitioned from a stable bar with dense 

vegetation to an active bar with little vegetation between 1994 

and 2016 (appendix 2).

Data from this site illustrate that rapid, distinct changes 

in water-quality parameters occurred within the alcove when 

the upstream end of the feature became disconnected from 

main-channel surface flow. When the monitoring equipment 

was installed in late May 2016, the upstream end of this 

feature was connected to the main channel. It is likely that the 

upstream end of the feature became disconnected on June 30 

when streamflow at the Salem streamgage was approximately 

8,200 ft3/s; the disconnection was visually confirmed during 

a site visit in late July. Over the course of only 1 hour, water 

temperature in this feature decreased by 5 °C, dissolved oxygen decreased by 5 mg/L, and specific conductance increased 

by 10 microsiemens per centimeter at 25 °C (fig. 21). 

Subsurface inputs with long flow paths (about >100 m) are 

often cool in summer and tend to have a steady temperature 

(Poole and others, 2008), with low dissolved-oxygen concentrations and elevated specific conductance (Ebersole and others, 2003; Hinkle and others, 2014). Subsurface inputs were 

likely a contributing source to this off-channel feature, which 

became apparent when it transitioned from a side channel to 

an alcove. Although the subsurface inputs were likely contributing when the feature was both a side channel and an alcove, 

these water-quality changes suggest that subsurface flows have 

a more dominant effect on this feature’s water quality when it 

is an alcove.
40 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16 Table 5. Observational data collected at five off-channel features along the Willamette River, Oregon, where water-quality monitors were deployed in summer 2016.

[Maximum depth: Maximum depth during summer low flow synoptic point measurements. Feature type at different flow conditions: See section, “Terminology” for definitions of relative flow terms. Abbreviation: RM, river mile]

Site name and

river mile

(fig. 19)

Wetted area

during

summer low

flows

(square

meters)

Maximum

depth

(meters)

Open water

aquatic

vegetation

Dominant bed

texture and

substrate

Water clarity Upstream connection Feature type at different flow conditions

Fairfield alcove

RM 67.1

32,000 1.3 Abundant Soft; unconsolidated fine 

sediments and organic matter

Highly colored (tannins) and low transparency Relatively narrow connec- tion point; distinct chan- nel over stable floodplain Unusually low: alcove Low: alcove Moderate: side channel

High: side channel

Windsor Bar 

alcoveRM 74.6

9,000 1.8 Sparse Hard; sand and gravel Clear with localized 

light-colored opaque (silty) areas

Flow over an active gravel 

bar

Unusually low: alcoveLow: side channelModerate: main channelHigh: main channel

Murphy Bar 

alcoveRM 97.7

23,000 1.2 Abundant Soft; unconsolidated fine 

sediments and organic matter

Highly colored (tannins) and low transparency Narrow connection points; flow over densely veg- etated stable bar Unusually low: alcove Low: alcove Moderate: unknown

High: side channel

Blue Ruin alcove

RM 164.1

35,000 3.1 Sparse Hard; sand and gravel Clear, high transparency Wide and low connection points; flows over stable 

and active gravel bar

Unusually low: alcoveLow: likely alcoveModerate: side channelHigh: side channel

Harpers Bend 

side channelRM 164.8

6,000 2.4 Moderate Hard; sand and gravel Clear, moderate transparency Flow behind active gravel bar (continuously connected through this study) Unusually low: side channel Low: side channel Moderate: main channel

High: main channel
Effect of Upstream Morphology on Water Quality in Off-Channel Features 41

Alcove Side channel

Timing of upstream connection indicated by 

submerged pendent temperature sensor

0

2

4

6

8

10

12

14

Hourly dissolved oxygen, in milligrams per liter

26 29 2 5 8 11 14 17 20 23 26

11.0

11.5

12.0

12.5

13.0

13.5

14.0

14.5

Houlry water temperature, in degrees Celsius

October

2016

September

0

10,000

20,000

30,000

40,000

50,000

Streamflow, in 

cubic feet per second

Willamette River at Salem, Oregon, streamgage (U.S. Geological Survey station 14191000)

Fairfield alcove at river mile 67.1

Water temperature

Dissolved oxygen

EXPLANATION

Figure 20. Hourly water-temperature and dissolved-oxygen measurements in the Fairfield alcove at river mile 67.1 

along the Willamette River, Oregon, and streamflow at the Willamette River at Salem, Oregon, streamgage (U.S. 

Geological Survey station 14191000) in September and October 2016.

Murphy Bar Alcove

The Murphy Bar alcove at RM 97.7 sits between a stable 

bar with mature trees and a floodplain berm with a gravel 

pit behind it (fig. 19C; table 5). This alcove has a narrow 

upstream connection that is overtopped at high flows; however, even then, main-channel flow into the alcove likely 

would be minimal and have reduced velocity because of the 

constricted connection (fig. 15). Water in the alcove is highly 

colored, and abundant aquatic vegetation (Ludwigia spp., 

among others) is present, especially along the north end of the 

feature. Mature trees surround the alcove, and the substrate 

is composed of a thick (about 1-m) layer of unconsolidated 

organic matter. Maximum depths measured during low-flow 

synoptics were 1.2 m. Historical aerial photographs show that 

this feature has remained stable since 1994 (appendix 2).

This off-channel feature functioned similarly to Fairfield 

alcove during the 2016 monitoring period and showed 

that water quality can change because of main-channel 

surface-water inputs from the upstream and downstream ends 

of the feature. Murphy Bar alcove had been recently connected to the main channel when the water-quality monitor 

was installed, but dissolved-oxygen concentrations (measured 

0.6 m above the substrate) decreased after installation and 

began approaching zero mg/L. The patterns observed in the 

dissolved-oxygen data suggested that oxygen consumption 

occurred; given the observed conditions in the alcove discussed above, consumption is probably the result of respiration and organic-matter decomposition and a lack of oxygenated upstream surface-water input. The dissolved-oxygen 

concentrations remained low (generally around zero mg/L) 

all summer until river flows increased in October (fig. 22). 

The months of anoxic conditions measured at this site were 

likely due to a high sediment oxygen demand derived from the 

large accumulation of sedimentary organic matter observed in 

the alcove.
42 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

Side channel Alcove

Timing of upstream disconnection indicated 

by changes in water-quality parameters

Water temperature

Dissolved oxygen

Specific conductance

EXPLANATION

65

68

71

74

77

80

83

86

89

92

95

Hourly specific conductance, in microsiemans per centimeter

0

2

4

6

8

10

12

14

16

18

20

Hourly dissolved oxygen, in milliagrams per liter

15 18 21 24 27 30 3 6 9 12 15

12

13

14

15

16

17

18

19

20

21

22

Hourly water temperature, in degrees Celsius

Streamflow, in 

cubic feet per second

June July

2016

0

3,000

6,000

9,000

12,000

15,000 Willamette River at Salem, Oregon, streamgage (U.S. Geological Survey station 14191000)

Windsor Bar alcove at river mile 74.6

Figure 21. Hourly water-temperature, dissolved-oxygen, and specific-conductance measurements in Windsor Bar alcove at river 

mile 74.6 along the Willamette River, Oregon, and streamflow at the Willamette River at Salem, Oregon, streamgage (U.S. Geological 

Survey station 14191000) in June and July 2016.

Alcove Side channel

Estimated timing of upstream 

connection indicated by 

pressure transducer elevation

October 2016

Dissolved-oxygen concentration in 

Murphy Bar alcove at river mile 97.7

Streamflow at the Willamette River at 

Salem, Oregon, streamgage (U.S. 

Geological Survey station 14191000)

EXPLANATION

0

5,000

10,000

15,000

20,000

25,000

30,000

35,000

40,000

45,000

50,000

Streamflow, in cubic feet per second

4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

0

1

2

3

4

5

6

7

8

9

10

Hourly dissolved oxygen, in milligrams per liter

Figure 22. Hourly dissolved-oxygen concentrations in Murphy Bar alcove at river mile 97.7 (near Independence) along the 

Willamette River, Oregon, and streamflow at the Willamette River at Salem, Oregon, streamgage (U.S. Geological Survey 

station 14191000) in October 2016.
Effect of Upstream Morphology on Water Quality in Off-Channel Features 43

The high elevation of the upstream connection point 

of this feature and the quick rise in stage in October 2016 

prevented an exact determination of when this alcove became 

reconnected. Comparing pressure-transducer data to the site’s 

lidar topography suggests that river stage must rise about 

3 m from 2016’s summer low-flow stage (about 6,000 ft3/s 

at Salem) before the upstream connection point would be 

overtopped (fig. 15). By comparing sensor-depth data from 

a pressure transducer deployed in this alcove to streamflow 

changes at the Salem streamgage, it is estimated that an 

upstream connection might occur in this alcove when streamflow at the Salem streamgage is about 35,000 ft3/s; increases 

in dissolved-oxygen concentration at streamflows less than 

35,000 ft3/s probably were the result of river water entering at 

the downstream end of the feature (fig. 22). The slow decline 

in dissolved-oxygen concentrations in the alcove after the 

stage increased in October 2016 suggests that oxygen demands 

in the alcove are greater than the rate at which the alcove was 

being supplied with well-oxygenated water. This pattern is 

likely due to the high and narrow upstream connection point; 

additional inputs of water with lower oxygen concentrations 

(subsurface input) also may have contributed to the decline.

Water temperature in this feature remained below 20 °C, 

and its temperature patterns tracked somewhat with those in 

the main channel in 2016, but with cooler temperatures and 

more muted variations (fig. 23). The similarity in summertime 

temperature patterns between the alcove and main channel, 

with alcove temperature patterns that lagged and were muted 

relative to main-channel temperatures, suggests that inputs of 

radiative heat and cool subsurface flows existed in this alcove. 

The lagged and muted patterns could be partly indicative of 

the time scales of subsurface flow through the upstream gravels. As with Fairfield alcove, water temperature in Murphy 

Bar alcove was likely buffered by riparian shading and the 

emergent aquatic vegetation on the surface and in the water 

column. Diel temperature fluctuations were about 0.3 °C in the 

off-channel feature versus 2.0 °C in the main channel. Alcove Side channel

Estimated timing of upstream 

connection indicated by 

pressure transducer elevation

Murphy Bar alcove water temperature

Main channel water temperature

Murphy Bar alcove dissolved oxygen

EXPLANATION

0

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

Hourly dissolved oxygen, in milligrams per liter

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

Hourly water temperature, in degrees Celsius

May June July August

2016

September October

 25 3 12 21 30 9 18 27 5 14 23 10 19 28 7 16 25

Streamflow, in

cubic feet per second

0

10,000

20,000

30,000

40,000

50,000 Willamette River at Salem, Oregon, streamgage (U.S. Geological Survey station 14191000)

Murphy Bar alcove and main channel at river mile 97.7

Figure 23. Hourly water-temperature measurements in the main-channel Willamette River, Oregon, at river mile 97.7, 

hourly water-temperature and dissolved-oxygen measurements in Murphy Bar alcove at river mile 97.7, and streamflow 

at the Willamette River at Salem, Oregon, streamgage (U.S. Geological Survey station 14191000) from May through 

October 2016.
44 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

Blue Ruin Alcove

The Blue Ruin alcove at RM 164.1 is a large and deep 

off-channel feature that was part of the main channel as 

recently as 1994 (fig. 19B; table 5; appendix 2). The feature 

is between a stable bar and a low floodplain surface, and the 

western bank is stabilized by revetments. The upstream connection point for this feature is complex, with multiple long, 

low channels cutting into an old gravel bar. A stage increase of 

about 1 m above summer low-flow stage (based on 2008 lidar) 

is required to connect the upstream end of this alcove to the 

river. The downstream connection point with the main channel 

is wide, and the off-channel feature is likely scoured during 

high-flow conditions. The alcove has minimal aquatic vegetation (mostly submerged), and the water is clear in summer, 

making it possible to see the gravel and sand bottom of the 

alcove; the maximum depth during low-flow synoptic measurements was 3.1 m.

Patterns and magnitudes of water temperature and 

dissolved-oxygen concentration in Blue Ruin alcove were 

markedly different from main-channel water-quality conditions from May through October 2016 (alcove at RM 164.1 in 

fig. 9). The Blue Ruin alcove was disconnected at its upstream 

end when water-quality monitoring equipment was installed 

0.6 m above the substrate on May 24, 2016. Dissolved-oxygen 

concentrations and fluctuations in this feature were characteristic of photosynthesis and respiration by algae and the few 

benthic aquatic plants, with limited sediment oxygen demands 

due to a lack of any substantial accumulation of organic matter 

in the sediments. Anoxic conditions were not observed, but 

dissolved-oxygen concentrations were below 4 mg/L for a 

large part of the monitoring period (fig. 24). Blue Ruin alcove 

is deep with sand and gravel substrate and may have had subsurface inputs, which could supply cool water with minimal 

diel water-temperature fluctuation. Water temperature at 0.6 m 

above the bed was often at least 5 °C cooler than the mainchannel water temperature and remained below 14.3 °C all 

summer (fig. 24). The increase in Willamette River streamflow 

Water temperature

Dissolved oxygen

EXPLANATION

0

2

4

6

8

10

12

14

16

Hourly dissolved oxygen, in milligrams per liter

24 3 13 23 3 13 23 2 12 22 11 21 11 21

0

2

4

6

8

10

12

14

16

Hourly water temperature, in degrees Celsius

Streamflow, in

cubic feet per second

May June July

2016

August September October

0

5,000

10,000

15,000

20,000 Willamette River at Harrisburg Oregon, streamgage (U.S. Geological Survey station 14166000)

Murphy Bar alcove and main channel at river mile 97.7

Figure 24. Hourly water-temperature and dissolved-oxygen measurements in Blue Ruin alcove at river mile 164.1, and 

streamflow at the Willamette River at Harrisburg, Oregon, streamgage (U.S. Geological Survey station 14166000) during 

2016.
Effect of Upstream Morphology on Water Quality in Off-Channel Features 45

that occurred in October 2016 caused an increase in the feature’s dissolved-oxygen concentration and a decrease in water 

temperature, indicating an influx of water from the main channel at either the upstream or downstream end; this feature did 

not contain a pressure transducer or a pendent, so determining 

when the upstream connection occurred was not possible. 

The water-quality characteristics of this off-channel feature 

are likely affected by minimal aquatic vegetation, frequent 

scouring during winter high flows (and the associated absence 

of an accumulation of sedimentary organic matter), depth, and 

potential subsurface inputs.

Harpers Bend Side Channel

The active gravel bar bordering the Harpers Bend side 

channel at RM 164.8 near Harrisburg is completely inundated 

by main-channel flow during moderate- and high-flow conditions. During low-flow summer conditions, this feature is a 

side channel with a small input of main-channel surface-water 

flow all summer (fig. 19B; table 5). This feature is between 

a low floodplain surface stabilized with revetments and an 

active gravel bar that has been growing annually due to erosion of the riverbank on the opposite side of the main channel 

(appendix 2). The downstream connection point is wide during 

high flows but becomes narrower as flow decreases through 

the summer; the upstream connection point is a distinct, narrow channel. Terrestrial vegetation was sparse on both sides of 

the off-channel feature, and moderate amounts of submerged 

aquatic vegetation were found near the downstream end. The 

water was clear, providing a view of the cobble substrate about 

2.4 m below the water surface during summer.

Based on the dissolved-oxygen dataset and observations 

during several field visits, this off-channel feature did not 

completely disconnect from the main channel at the upstream 

end during the 2016 data-collection period. Dissolved-oxygen 

concentrations in the side channel (measured 0.6 m above 

the substrate) were characteristic of main-channel solubilitydriven concentrations and patterns until the diel fluctuations increased in late June and July (fig. 25); main-channel 

dissolved-oxygen conditions were not monitored in this reach, 

but the data from RM 97.7 provide a useful comparison from 

a main-channel site where dissolved-oxygen concentrations 

were mostly a function of oxygen solubility. The increased 

dissolved-oxygen diel fluctuations in Harpers Bend side channel relative to main-channel conditions, along with changes 

in the specific conductance (not shown), corresponded to a 

decrease in stage in the feature recorded from a pressure transducer. The decreased stage and increased dissolved-oxygen 

fluctuations indicated that biological activity (photosynthesis 

and respiration) was having more of an effect on dissolved 

oxygen than the limited upstream surface-water inputs during periods of lower water level in the main channel. The 

dissolved-oxygen pattern from July through September likely 

was indicative of an increased residence time and an associated increase in primary production. Anoxic dissolved-oxygen 

concentrations were not measured during the summer of 2016, 

which could indicate that main-channel water inputs probably 

continued to affect the site throughout the season, and that 

the site had small oxygen demands that were insufficient to 

overcome other oxygen inputs.

The water-temperature pattern in this feature also supports the interpretation that a small amount of water from the 

main channel was flowing into the feature throughout the 2016 

study period, and some cooler subsurface inputs were also 

present. The main-channel and side-channel water-temperature 

patterns and diel fluctuations were nearly identical through 

early July, but the side-channel water temperature was cooler 

than main-channel temperatures from July through September, 

indicating that the small main-channel inputs were not dictating the temperature in the off-channel feature (fig. 25). Given 

the presence of the gravel substrate and the adjacent active 

gravel bar, cooler subsurface inputs likely were important 

in affecting the feature’s water temperature. The absence of 

emergent aquatic vegetation may be due to periodic and wintertime high-flow velocities that probably are strong enough 

to flush out weakly rooted vegetation and prevent a heavy 

accumulation of organic material in the sediments.

Importance of Upstream Connections on Water 

Quality of Off-Channel Features

Data from this study revealed a strong relation between 

site geomorphology and the water quality of the river’s 

off-channel features. An analysis of multiple datasets (water 

temperature, dissolved oxygen, pressure transducer, pendant, 

and stage) collected in the main channel and in the off-channel 

features revealed how water quality in an off-channel feature 

is affected by several factors, especially the nature of surfacewater connections at the upstream (and downstream) end of 

the feature. The five off-channel features that were intensively 

monitored in 2016 differed substantially in their geomorphological characteristics such as their size, adjacent landforms, 

and height of their upstream connection location, which 

together with other factors contributed to different waterquality patterns and conditions.

The surface-water connection between the main channel and the upstream part of these five off-channel features 

varied with streamflow, resulting in a range of connection/

disconnection dates and duration of connectivity during the 

2016 monitoring period. Murphy Bar, Blue Ruin, and Fairfield 

alcoves became disconnected from the main channel at their 

upstream ends at typical summer low flows, Windsor Bar 

alcove became disconnected at unusually low summer flows, 

and the upstream end of Harpers Bend side channel never 

completely disconnected during the flow conditions in 2016. 

The occurrence and duration of disconnection was highly variable among the studied features and depended on the height of 

their upstream connection point relative to local main-channel 

stage. Reconnection to the river at the upstream end was rapid 

and somewhat coincident for most of these features because 

the river stage increased quickly in 2016 in response to rains 

in October.
46 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

Harpers Bend side channel

Main channel

EXPLANATION

Harpers Bend side channel

Main channel

EXPLANATION

Streamflow, in

cubic feet per second

May June July

2016

August September October

0

1

2

3

4

5

6

7

8

9

10

11

12

13

Hourly dissolved oxygen, in milligrams per liter

25 3 12 21 30 09 18 27 5 14 23 10 19 28 7 16 25

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

Hourly water temperature, in degrees Celsius

0

5,000

10,000

15,000

20,000 Willamette River at Harrisburg Oregon, streamgage (U.S. Geological Survey station 14166000)

Harpers Bend side channel at river mile 164.8 and main channel at river mile 164.2

Harpers Bend side channel at river mile 164.8 and main channel at river mile 97.7

Missing data

in alcove

Missing data

in alcove

Figure 25. Hourly water-temperature and dissolved-oxygen measurements in Harpers Bend side channel at river 

mile (RM) 164.8 (near Harrisburg, Oregon), plotted with water-temperature data from the main channel at RM 164.2 

and dissolved-oxygen data from the main channel at RM 97.7; and streamflow at the Willamette River at Harrisburg, 

Oregon, streamgage (U.S. Geological Survey station 14166000).
Linking Site Characteristics and Water-Quality Processes in Off-Channel Features 47

When these off-channel features were disconnected from 

the river at their upstream end, their water-quality conditions 

began to diverge from and in some cases became extremely 

different from main-channel conditions. Similarly, reconnection quickly changed the water quality of these features, 

making it more like main-channel conditions. The morphology 

of an off-channel feature may also be correlated to other sitespecific characteristics that can affect water-quality conditions. 

For example, off-channel features that were connected at the 

upstream end during low flows did not contain large amounts 

of emergent aquatic vegetation. Infrequent high, scouring 

streamflows and frequent moderate streamflows may affect 

the feature’s depth, any accumulation of fine sediment, and the 

establishment of emergent aquatic vegetation.

Linking Site Characteristics 

and Water-Quality Processes in 

Off-Channel Features

Data collection for this study encompassed two summers and dozens of sites, included quantitative and qualitative 

measurements, and focused on off-channel and main-channel 

water-quality conditions of a major river system. Analysis of 

the various datasets revealed many commonalities and provided insights into the many factors that affect water quality in 

off-channel features. Using those insights, a site classification 

scheme and a theoretical process matrix were created to help 

distill and organize the key findings. The site classification 

scheme is an organizational aid that summarizes common 

or contrasting outcomes among the intensively measured 

off-channel sites, using measured water-quality patterns and 

ranges and site-specific characteristics to create four broad 

categories of water-quality conditions measured in this study. 

The theoretical process matrix extends the site classification 

scheme to more generally list the processes and site-specific 

characteristics that are likely to combine to create the various 

water-quality conditions that occur in off-channel features.

Site Classification Scheme

Despite the fact that each off-channel feature along the 

Willamette River is unique in its shape, size, connection to 

the river, or in its water-quality patterns over the course of 

the summer, the various data collected in this study revealed 

enough similar and contrasting patterns to allow the creation 

of a site classification scheme organized around general site 

characteristics and categories of water-quality outcomes. The 

scheme relies on all the continuous water-temperature datasets, dissolved-oxygen datasets, and synoptic measurements 

collected in off-channel features of the Willamette River in 

summers 2015–16, but draws particularly from the datasets 

collected at the intensively monitored sites in 2016. The site 

classification scheme categorizes sites first as alcoves or side 

channels and then further categorizes expected water-quality 

conditions based on a set of site characteristics (table 6). The 

scheme is applicable during typical summer low flows, when 

many off-channel features adjacent to the Willamette River 

function as alcoves.

Potentially the most important characteristic of an offchannel feature that affected water-quality conditions was the 

presence or absence of an upstream connection to the main 

channel during summer low flows (represented in the first column of the site classification scheme; table 6). These features 

have upstream connection points with different bed elevations, 

which dictate the timing and duration of connection with the 

main channel. When connected at the upstream end, the alcove 

becomes a side channel and its water quality is more likely to 

reflect conditions in the main channel. Other site-specific characteristics that were important in determining water-quality 

conditions in the off-channel features included the presence 

of aquatic invasive plants, any accumulation of sedimentary 

organic matter, water transparency (turbidity), shading, and 

depth. Sites could be categorized according to their resulting 

water-quality conditions, as follows:

1. Features with cool water temperatures and depleted 

dissolved oxygen—Such features tended to contain 

abundant emergent aquatic vegetation, highly colored 

water with low transparency, some accumulation of sedimentary organic material, some shading from aquatic or 

riparian vegetation, a relatively high-elevation upstream 

connection point, and typically were disconnected at the 

upstream end during summer low flows (table 6).

2. Features with cool water temperatures and oxygenated 

water—This type of feature lacked emergent aquatic 

vegetation or much sedimentary organic matter, had high 

transparency and a moderately high-elevation upstream 

connection point, and typically was disconnected at the 

upstream end during summer low flows. The features 

were deep and not shaded by vegetation (table 6), possibly due to nearby active gravel bars and (or) high-energy 

flushing flows during winter.

3. Features with cool, fluctuating water temperatures 

and variable, but oxygenated, water—Such features 

contained submerged aquatic vegetation, transparent 

water, a low-elevation upstream connection point, and 

remained connected at the upstream end during summer. 

The features were moderately deep and not shaded by 

vegetation (table 6).

4. Features with warm water temperatures and unknown 

dissolved-oxygen concentrations—These features 

typically were shallow, with a high or moderately high 

upstream connection point, and were not shaded by vegetation (table 6).
48 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

Table 6. A site classification scheme linking broad patterns of measured water-quality conditions to site characteristics of off-channel 

features along the Willamette River, Oregon, in the low-flow summer periods of 2015 and 2016.

Upstream connection to the

main channel during typical

summer low flows

Relevant site-specific

characteristics observed Typical water-quality conditions

Disconnected from main-channel 

surface flow at the upstream end 

(an alcove)

Large quantities of emergent aquatic plants Consistently cool water temperatures below 

surface 

Depleted oxygen concentrations in the middle and 

lower water column

Low transparency

An accumulation of organic-rich sediments

Shaded by vegetation

Small quantities of emergent aquatic plants, or 

none

Consistently cool water temperatures below 

surface 

Oxygenated water below surface Little to no accumulation of organic matter in 

sediments

Not shaded by vegetation

High transparency

Deep

Not shaded by vegetation Consistently warm water temperatures below 

surface 

Unknown oxygen conditions

Shallow

Connected to main-channel

surface flow at the upstream end 

(a side channel)

Presence of submerged aquatic vegetation Cool and variable water temperatures below 

surface 

Oxygenated water below surface with potential for 

large diel variations

Not shaded by vegetation

High transparency

Moderately deep

This site classification scheme, and the water-quality categories created during typical summer low flows, likely apply 

to other off-channel features along the Willamette River that 

were not measured. This scheme is a first attempt at identifying the dominant mechanisms and processes affecting waterquality conditions in off-channel features and is only intended 

to broadly characterize the features monitored in this study by 

linking monitoring data to site characteristics. It is possible 

that additional factors, not measured or identified in this study, 

also are important in determining water-quality conditions in 

off-channel features. Additional data collection would be helpful in identifying any other relevant site-specific characteristics that could be used to refine the site classification scheme.

Theoretical Process Matrix

The site classification scheme is limited by sample size 

and the methods used in this study and may not fully represent 

the complexity of the Willamette River system or the diversity of water-quality conditions that occur in its off-channel 

features. Another useful approach to organizing the results and 

insights from this study is embodied in a proposed “theoretical process matrix,” which lists the water-quality conditions 

commonly observed in off-channel features and links them 

to a suite of processes and site-specific characteristics that 

are likely to combine to create such conditions (table 7). This 

matrix draws insights not just from this study, but also from 

a general knowledge of the principles of physics, chemistry, 

limnology, geology, and stream ecology.

The theoretical process matrix can be applied when 

researching the conditions occurring in any off-channel 

feature. For example, Blue Ruin alcove at RM 164.1 had cool 

water that was likely a function of depth (affecting vertical 

stratification) and the presence of sand and gravel substrate 

(affecting subsurface inputs). The Fairfield alcove at RM 67.1 

was anoxic while it was disconnected at the upstream end. 

The anoxic conditions probably resulted from a combination 

of shading (by riparian and emergent vegetation) and a high 

accumulation of organic matter decomposing in the sediments. 

Such site characteristics reduce the light available for photosynthesis in the water column and cause sediment oxygen 

demands that exceed photosynthetic production.
Linking Site Characteristics and Water-Quality Processes in Off-Channel Features 49

Table 7. Theoretical process matrix linking water-quality outcomes or conditions for water temperature and dissolved oxygen with 

processes and site characteristics that can combine to create the outcomes in off-channel features of the Willamette River, Oregon.

Water-quality condition Process affecting

the condition Site characteristic affecting the process

Water temperature

Cool water Reduced solar insolation Shaded (by riparian vegetation, emergent aquatic vegetation, or topography)

Vertical stratification Sufficient depth for stratification to occur

Insufficient mixing (by wind and [or] turbulence) to disrupt stratification

Low transparency (high turbidity or color)

Cool water input (often groundwater or hyporheic input)Location in the floodplain and active channel

Presence and abundance of gravel

Warm water High solar insolation Not shaded (by riparian vegetation, emergent aquatic vegetation, or 

topography)

Absence of vertical stratification Shallow (insufficient depth for stratification to occur)

Mixing by wind or flow does not allow for vertical stratification

Warm water input Upstream connection with the main channel during summer low flows

Strong inflow at downstream connection point due to river stage increase

Presence of point source or warm tributary input

Daily fluctuations in water 

temperature

Ambient air-temperature fluctuations and solar insolationHigh surface area to volume ratio plus exposure to sunlight plus moderate to long residence time

Fluctuating water input Presence of point source or tributary input with fluctuating temperature

Small upstream connection with the main channel during summer low 

flows plus high surface area to volume ratio plus exposure to sunlight 

plus moderate to long residence time

Dissolved oxygen

Oxygenated Photosynthetic production 

exceeds oxygen demands

Not shaded plus presence of submerged aquatic plants and (or) algae

Low oxygen demands (lack of organic matter in sediments)

Oxygenated water input (often 

main-channel input or point 

source)

Upstream connection with the main channel during summer low flows

Strong inflow at downstream connection point due to river stage increase

Presence of oxygenated point sources or tributary inputs

Aeration Sufficient mixing by wind or flow

Low dissolved oxygen Reduced solar insolation causing reduced photosynthetic 

oxygen production

Shaded (by riparian vegetation, emergent aquatic vegetation, or topography)

Vertical stratification causing a 

greater chance for hypolimnetic oxygen depletion

Sufficient depth for stratification to occur

Insufficient mixing (by wind and [or] turbulence) to disrupt stratification

Low transparency (high turbidity or color)

Oxygen demands exceed photosynthetic productionHigh accumulation of organic matter being broken down by microbial 

respiration

A lack (or recent senescence) of algae or plants that photosynthesize

Low-oxygen water input (often 

groundwater or hyporheic 

input)

Location in the floodplain and active channel

Presence and abundance of gravel

Length (time scale) of flow path for the groundwater or hyporheic input

Daily fluctuations in 

dissolved-oxygen concentrations

Photosynthesis and respiration 

and solar insolation

Not shaded plus presence of aquatic plants and (or) algae plus moderate 

to long residence time
50 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

Certain water-quality outcomes in off-channel features 

could be caused by one or more combinations of processes and 

site characteristics. Therefore, this theoretical process matrix 

lists multiple factors that could affect water-quality conditions. For example, cool water temperatures at a location could 

reflect reduced solar insolation, vertical stratification, a cool 

water input, or a combination of these factors. A site-specific 

characteristic that could contribute to vertical stratification 

includes sufficient depth for stratification to occur, insufficient wind- or flow-induced mixing, low transparency (high 

turbidity or color), or a combination of these characteristics. 

The matrix can be used to better understand the various combinations of water temperature and dissolved-oxygen conditions that may exist (for example, warm water temperatures 

and daily fluctuations in dissolved-oxygen concentrations). 

Alternatively, the site-specific characteristics and processes 

identified in the matrix can be used by researchers and flow 

managers to gain a general understanding of the causes of 

certain water-quality conditions and to infer potential conditions in an off-channel feature without having to monitor that 

feature intensively.

Competing processes in the theoretical process matrix 

also introduces several questions:

1. Would the water temperature in an off-channel feature be 

cool or warm if it had a warm water input and reduced 

solar insolation?

2. How would the addition of subsurface inputs affect the 

dissolved oxygen in a feature with high photosynthetic 

production?

3. Would increasing summer flows in the Willamette River 

result in warm temperatures in off-channel features 

(by connecting them to the main channel and flushing 

them with warm surface water, and potentially pushing out emergent aquatic vegetation), or would the 

increased surface flows lead to increased cool subsurface 

inputs, or both?

4. How would infrequent moderate or high summer 

streamflows affect water temperature in a feature with an 

established emergent aquatic vegetation community?

In such situations, actual water-quality conditions would 

depend on the strength of the individual and competing 

processes. In other situations, processes may reinforce each 

other to strengthen a result. For example, the presence of 

large amounts of decomposing organic matter could lead to 

low oxygen conditions through an enhanced sediment oxygen 

demand, whereas the concomitant input of subsurface water 

(typically with low dissolved oxygen) would reinforce the 

resulting low-oxygen condition. With additional data collection and modeling, it may be possible to determine the relative 

importance of each of the site-specific characteristics and 

processes. More information is needed to begin to quantify 

the effects of these site-specific characteristics and processes 

controlling water-quality conditions in off-channel features of 

the Willamette River system.

Conclusions and Implications for 

Research and Management

Summer water temperatures in the main channel of the 

Willamette River are warm (>18 °C) and may cause stress to 

cold-water fishes. Warm main-channel conditions emphasize 

the importance of understanding water-quality conditions in 

off-channel features and their relation to streamflow, which 

was the objective of this study. The number of off-channel 

features that function as CWRs for fishes depends on the local 

geomorphology, hydrology, and ecology of a river reach or 

feature. This study identified geomorphic characteristics, such 

as the relative height of an upstream connection necessary for 

main-channel water to enter an off-channel feature, as important effects on the hydrology and water quality of off-channel 

features. The timing, duration, and quantity of surface-water 

inputs to off-channel features affect the local ecology (the 

presence or absence of aquatic vegetation) and the substrate 

(the presence or absence of accumulations of organic matter), both of which in turn affect the water temperature and 

dissolved-oxygen concentration in off-channel features.

Certain site-specific characteristics of an off-channel 

feature may be important indicators of the water-quality 

conditions and the potential relation between water quality and 

the site’s geomorphology. Water-quality heterogeneity exists 

within and among off-channel features, but the predominant 

water-quality conditions measured in this study were used to 

make useful generalizations. Four categories of water-quality 

conditions were measured and classified in this study, although 

others likely exist:

1. Features with cool-water temperatures and depleted dissolved oxygen.

2. Features with cool-water temperatures and oxygenated water.

3. Features with cool, fluctuating water temperatures and 

variable, but oxygenated, water.

4. Features with warm-water temperatures and unknown 

dissolved-oxygen concentrations.

Based on observational and measured data from this 

study, off-channel features in category 1 tended to have large 

quantities of emergent aquatic vegetation, thick accumulations of decomposing organic matter, a steep vertical gradient 

of water temperature and dissolved oxygen, and a relatively 

high-elevation upstream connection point that kept the 

feature disconnected at the upstream end and prevented the 

throughput of river water during the low-flow summer period. 

Off-channel features in category 2 typically were controlled 

by a moderately high-elevation upstream connection point and 

lacked abundant emergent aquatic vegetation. Off-channel 

features in category 3 remained connected at the upstream end 

throughout the summer, and biological activity likely contributed to any pronounced diel fluctuations of dissolved oxygen. 

Dissolved-oxygen concentrations and patterns are unknown 
Conclusions and Implications for Research and Management 51

for off-channel features in category 4 because only water 

temperature was measured in this type of feature. Both water 

temperature and dissolved-oxygen concentration are critical 

factors for supporting healthy and diverse aquatic ecosystems; 

therefore, it is important to measure and study both to better 

understand the role and ecological function of these offchannel features.

Because of the various elevations of upstream connection points and other factors affecting water-quality conditions in off-channel features, not all features will respond the 

same way or at the same time in response to flow changes. 

Flow management using upstream storage reservoirs in the 

Willamette River Basin may be able to affect the conditions in 

off-channel features and the quality of habitat in those features 

for target aquatic species. For example, managed releases of 

water from upstream reservoirs during summer could temporarily connect the upstream ends of certain off-channel features, thereby flushing well-oxygenated, but potentially warm, 

main-channel water through those features. These managed 

flow releases might also disrupt the establishment of invasive 

aquatic vegetation and the buildup of organic matter, which in 

turn might minimize the oxygen demand from organic-matter 

decomposition. Increasing streamflows so that water enters 

an off-channel feature at its downstream end (but not the 

upstream end), may affect water-quality within an off-channel 

feature without requiring substantial flow increases. Using 

summer flow operations to disconnect features at the upstream 

end may result in localized cool-water temperatures in some 

features; however, a negative effect on dissolved-oxygen concentrations could also occur.

In addition to flow management, restoration practices can 

affect water quality in off-channel features. For example, excavating channels or reducing the elevation of the upstream ends 

of targeted off-channel features could allow main-channel surface water to flow freely through those off-channel features at 

lower streamflows. It is possible that increasing the frequency 

and amount of surface flows through off-channel features that 

are often disconnected at the upstream end might reduce the 

establishment of aquatic invasive plant communities, which 

in turn could reduce the abundance of decomposing organic 

matter and prolonged anoxic conditions. Current practices of 

manually removing emergent aquatic plant communities may 

also lead to a lower oxygen demand from decomposition but 

could result in a greater influx of heat by removing floating 

plants that block solar insolation; however, chemically treating 

emergent aquatic plant communities may increase the available organic matter for decomposition. Allowing or enhancing 

the channel migration process that creates and maintains active 

gravel bars in certain river reaches may promote cool subsurface inputs to wetted off-channel features. Many factors affect 

temperature (shading, depth, subsurface flows, and mainchannel throughput) and dissolved oxygen (photosynthesis, 

respiration, decomposition of sedimentary organic matter, and 

inputs from various water sources) in the off-channel features 

of the Willamette River. Reconciling how flow management 

and restoration activities affect water temperature and dissolved oxygen (and therefore, fish habitat) in off-channel 

features is complex, and the site classification scheme and 

theoretical process matrix introduced in this report can assist 

with better understanding the interaction of potentially confounding variables influencing water-quality processes.

Quantifying the effects of site-specific characteristics 

and the relative inputs of subsurface flow into off-channel 

features is a logical next step to strengthen the site classification scheme and theoretical process matrix outlined here. 

Currently, it is unclear how increasing or decreasing summer flows will affect the quantity of subsurface flows into 

off-channel features. To fill current data gaps and provide 

more information and insights for research and management, water quality in specific off-channel features could be 

monitored over a wide range of conditions, such as during 

gradual decreases in river stage, gradual increases in river 

stage, and during intermittent high flows in the Willamette 

River. Comprehensive studies of water-quality conditions in 

off-channel features with various types (emergent and submerged) and abundance of vegetation would strengthen the 

site classification scheme. Future monitoring could target 

the collection of continuous vertical and longitudinal (threedimensional) water-quality data, which may reveal regions 

within off-channel features that function as CWRs during climatic extremes. In addition, supplementary data could be used 

to develop models to better understand and predict water quality in off-channel features in response to numerous scenarios. 

The off-channel features of the Willamette River are diverse 

and dynamic and respond to a wide variety of processes and 

factors. A better understanding of those factors and processes 

should lead to a better means of predicting and managing the 

water-quality conditions that occur there.
52 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

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Appendix 1. Comparison of Off-Channel to Main-Channel Water Temperatures for Continuously Monitored Sites 57

Appendix 1. Comparison of Off-Channel to Main-Channel Water Temperatures 

for Continuously Monitored Sites

Patterns resulting from a comparison of off-channel water temperatures to temperatures in the main channel are presented 

in this appendix for all continuously monitored sites. For each graph, the hourly main-channel water temperature was subtracted 

from the hourly off-channel temperature. Values greater than zero show that the off-channel feature was warmer than the main 

channel, whereas values less than zero show that the off-channel feature was cooler than the main channel. Graphs with a blue 

box in the top right corner indicate that the off-channel water temperature generally was cooler than the main-channel water 

temperature during July and August. Red boxes indicate that the off-channel water temperature generally was warmer than the 

main-channel water temperature during July and August. Red/blue boxes indicate that the off-channel water temperature fluctuated between warmer and cooler than the main-channel water temperature during July and August. Off-channel features and 

main-channel sites are referred to by their river mile location (tables 1 and 2).
58 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

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−10

−8

−6

−4

−2

0

2

4

6

8

10

08/27/1508/29/1508/30/1509/01/1509/02/1509/04/1509/05/15

09/07/1509/08/1509/10/1509/11/1509/13/15

09/14/15

09/16/15

09/17/1509/19/1509/20/1509/22/1509/23/1509/25/15

09/26/1509/28/1509/29/1510/01/1510/02/15

10/04/1510/05/15

Alcove at RM 74.6 minus main channel at RM 73.2

Date

Difference in temperature between main channel and off-channel feature, in degrees Celsius

2015—Willamette Mission monitoring reach

Off-channel feature cooler than the main channel during August

Off-channel feature that fluctuates between warmer and cooler than the 

main channel during August

EXPLANATION
Appendix 1. Comparison of Off-Channel to Main-Channel Water Temperatures for Continuously Monitored Sites 59

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/19/1508/21/1508/23/1508/25/1508/26/1508/28/1508/30/1509/01/1509/02/1509/04/1509/06/1509/08/1509/09/1509/11/1509/13/1509/15/1509/16/1509/18/1509/20/1509/22/1509/23/1509/25/1509/27/1509/29/1509/30/1510/02/1510/04/15

Alcove at river mile (RM) 95.8 minus main channel at RM 97.7

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/19/1508/21/1508/23/1508/25/1508/26/1508/28/1508/30/1509/01/1509/02/1509/04/1509/06/1509/08/1509/09/1509/11/1509/13/1509/15/1509/16/1509/18/1509/20/1509/22/1509/23/1509/25/1509/27/1509/29/1509/30/1510/02/1510/04/15

Alcove at RM 97.7 minus main channel at RM 97.7

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/19/1508/21/1508/23/1508/25/1508/26/1508/28/1508/30/1509/01/1509/02/1509/04/1509/06/1509/08/1509/09/1509/11/1509/13/1509/15/1509/16/1509/18/1509/20/1509/22/1509/23/1509/25/1509/27/1509/29/1509/30/1510/02/1510/04/15

Alcove at RM 97.9 minus main channel at RM 97.7

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/19/1508/21/1508/23/15

08/25/1508/26/1508/28/15

08/30/1509/01/1509/02/1509/04/15

09/06/1509/08/1509/09/15

09/11/1509/13/1509/15/15

09/16/1509/18/1509/20/1509/22/15

09/23/1509/25/1509/27/15

09/29/1509/30/1510/02/1510/04/15

Acove at RM 98.4 minus main channel at RM 97.7

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/19/1508/21/1508/23/1508/25/1508/27/1508/28/1508/30/1509/01/1509/03/1509/05/1509/06/1509/08/1509/10/1509/12/1509/14/1509/15/1509/17/1509/19/1509/21/1509/23/1509/24/1509/26/1509/28/1509/30/1510/01/1510/03/1510/05/15

Alcove at RM 101 minus main channel at RM 95.9

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/26/15

08/28/1508/29/1508/31/1509/01/1509/03/1509/04/1509/06/1509/07/15

09/09/1509/10/1509/12/1509/13/15

09/14/1509/16/1509/17/1509/19/1509/20/1509/22/1509/23/1509/25/1509/26/1509/28/1509/29/1509/30/1510/02/1510/03/15

Alcove at RM 107.5 minus main channel at RM 107.3

Date

Difference in temperature between main channel and off-channel feature, in degrees Celsius

2015—Independence monitoring reach

Off-channel feature warmer than the main channel during August

Off-channel feature cooler than the main channel during August

Off-channel feature that fluctuates between warmer and cooler than the 

main channel during August

EXPLANATION
60 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/20/1508/22/1508/24/1508/26/1508/28/1508/30/1509/01/1509/03/1509/05/1509/07/1509/09/1509/11/1509/13/1509/15/1509/17/1509/19/1509/21/1509/23/1509/25/1509/27/1509/29/1510/01/1510/03/1510/05/1510/07/1510/09/1510/11/15

Side channel at river mile (RM) 161.3 minus main channel at RM 161

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/20/1508/22/1508/24/1508/26/1508/28/1508/30/1509/01/1509/03/1509/05/1509/07/1509/09/1509/11/1509/13/1509/15/1509/17/1509/19/1509/21/1509/23/1509/25/1509/27/1509/29/1510/01/1510/03/1510/05/1510/07/1510/09/1510/11/15

Alcove at RM 161.7 minus main channel at RM 161

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/20/1508/22/1508/24/1508/26/1508/28/1508/30/1509/01/1509/03/1509/05/1509/07/1509/09/1509/11/1509/13/1509/15/1509/17/1509/19/1509/21/1509/23/1509/25/1509/27/1509/29/1510/01/1510/03/1510/05/1510/07/1510/09/1510/11/15

Side channel at RM 162.8 minus main channel at RM 161

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/20/1508/22/1508/24/1508/26/1508/28/1508/30/1509/01/1509/03/1509/05/1509/07/1509/09/1509/11/1509/13/1509/15/1509/17/1509/19/1509/21/1509/23/1509/25/1509/27/1509/29/1510/01/1510/03/1510/05/1510/07/1510/09/1510/11/15

Alcove at RM 162.8 minus main channel at RM 161

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/20/1508/22/1508/24/1508/26/1508/28/1508/30/15

09/01/1509/03/1509/05/1509/07/1509/09/1509/11/1509/13/1509/15/1509/17/1509/19/1509/21/1509/23/1509/25/15

09/27/1509/29/1510/01/1510/03/1510/05/15

10/07/1510/09/1510/11/15

Alcove at RM 163.5 minus main channel at RM 161

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/20/1508/22/1508/24/1508/26/1508/28/1508/30/1509/01/1509/03/1509/05/1509/07/1509/09/1509/11/1509/13/1509/15/1509/17/1509/19/1509/21/1509/23/1509/25/1509/27/1509/29/1510/01/1510/03/1510/05/1510/07/1510/09/1510/11/15

Alcove at RM 164.1 minus main channel at RM 161

Date

Difference in temperature between main channel and off-channel feature, in degrees Celsius

2015—Harrisburg monitoring reach

Off-channel feature warmer than the main channel during August

Off-channel feature cooler than the main channel during August

Off-channel feature that fluctuates between warmer and cooler than the 

main channel during August

EXPLANATION
Appendix 1. Comparison of Off-Channel to Main-Channel Water Temperatures for Continuously Monitored Sites 61

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/20/1508/22/1508/24/1508/26/1508/28/1508/30/1509/01/1509/03/1509/05/1509/07/1509/09/1509/11/1509/13/1509/15/1509/17/1509/19/1509/21/1509/23/1509/25/1509/27/1509/29/1510/01/1510/03/1510/05/1510/07/1510/09/1510/11/15

Side channel at river mile (RM) 164.8 minus main channel at RM 167.8

−10

−8

−6

−4

−2

0

2

4

6

8

10

08/20/1508/22/1508/24/1508/26/1508/28/1508/30/1509/01/1509/03/1509/05/1509/07/1509/09/1509/11/1509/13/1509/15/1509/17/1509/19/1509/21/1509/23/1509/25/1509/27/1509/29/1510/01/1510/03/1510/05/1510/07/1510/09/1510/11/15

Side channel at RM 168.1 minus main channel at RM 167.8

Date

Difference in temperature between main channel

and off-channel feature, in degrees Celsius

2015 – Harrisburg monitoring reach (continued)

Off-channel feature cooler than the main channel during August

Off-channel feature that fluctuates between warmer and cooler than the 

main channel during August

EXPLANATION
62 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/27/1606/01/16

06/07/1606/13/16

06/18/1606/24/1606/30/1607/05/16

07/11/1607/16/1607/22/16

07/28/1608/02/1608/08/16

08/14/1608/19/1608/25/1608/30/16

09/05/1609/11/1609/16/16

09/22/1609/28/1610/03/1610/09/16

10/14/1610/20/16

Alcove at river mile (RM) 67.1 minus main channel at RM 73.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

06/03/1606/08/1606/14/1606/19/1606/24/1606/30/1607/05/1607/10/1607/16/1607/21/1607/27/1608/01/1608/06/1608/12/1608/17/1608/22/1608/28/1609/02/1609/08/1609/13/1609/18/1609/24/1609/29/1610/04/1610/10/1610/15/1610/21/1610/26/16

Alcove at RM 67.6 minus main channel at RM 73.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

Alcove at RM 67.7 minus main channel at RM 73.2 06/03/16 06/08/16 06/14/16 06/19/16 06/24/16 06/30/16 07/05/16 07/10/16 07/16/16 07/21/16 07/27/16 08/01/16 08/06/16 08/12/16 08/17/16 08/22/16 08/28/16 09/02/16 09/08/16 09/13/16

09/18/1609/24/1609/29/1610/04/1610/10/1610/15/1610/21/1610/26/16

−10

−8

−6

−4

−2

0

2

4

6

8

10

06/03/1606/08/1606/14/1606/19/1606/24/1606/30/1607/05/1607/10/1607/16/1607/21/1607/27/1608/01/1608/06/1608/12/1608/17/1608/22/1608/28/1609/02/1609/08/1609/13/1609/18/1609/24/1609/29/1610/04/1610/10/1610/15/1610/21/1610/26/16

Alcove at RM 70.2 minus main channel at RM 73.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/27/1606/01/1606/07/1606/13/1606/18/1606/24/1606/30/1607/05/1607/11/1607/16/1607/22/1607/28/1608/02/1608/08/1608/14/1608/19/1608/25/1608/30/1609/05/1609/11/1609/16/1609/22/1609/28/1610/03/1610/09/1610/14/1610/20/16

Alcove at RM 74.6 minus main channel at RM 73.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/27/1606/02/1606/08/1606/14/1606/21/1606/27/1607/03/1607/09/1607/15/1607/22/1607/28/1608/03/1608/09/1608/15/1608/22/1608/28/1609/03/1609/09/1609/16/1609/22/1609/28/1610/04/1610/10/1610/17/1610/23/1610/29/1611/04/16

Alcove at RM 73.4 minus main channel at RM 73.2

Date

Difference in temperature between main channel and off-channel feature, in degrees Celsius

2016—Willamette Mission monitoring reach

Off-channel feature cooler than the main channel during July and August

Off-channel feature that fluctuates between warmer and cooler than the 

main channel during July and August

Site data are not included in analyses because of missing data or another 

(primary) sensor in the feature

EXPLANATION
Appendix 1. Comparison of Off-Channel to Main-Channel Water Temperatures for Continuously Monitored Sites 63

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/26/1606/02/1606/08/1606/14/1606/20/1606/27/1607/03/1607/09/1607/15/1607/21/1607/28/1608/03/1608/09/1608/15/1608/21/1608/28/1609/03/1609/09/1609/15/1609/21/1609/28/1610/04/1610/10/1610/16/1610/22/1610/29/1611/04/16

Alcove at RM 73.9 minus main channel at RM 73.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/26/1606/02/1606/08/1606/14/1606/20/16

06/27/1607/03/1607/09/16

07/15/1607/21/1607/28/1608/03/1608/09/1608/15/1608/21/1608/28/1609/03/1609/09/1609/15/1609/21/1609/28/1610/04/1610/10/1610/16/1610/22/1610/29/1611/04/16

Alcove at RM 77.2 minus main channel at RM 73.2

Date

Date

2016—Willamette Mission monitoring reach (continued)

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/26/1605/30/1606/03/1606/07/1606/10/1606/14/1606/18/1606/21/1606/25/1607/02/1607/12/1609/10/1609/15/1609/19/1609/22/1609/26/1609/30/1610/04/1610/07/1610/11/1610/15/1610/18/1610/22/1610/26/1610/29/1611/02/1611/06/16

Alcove at river mile (RM) 73.5 minus main channel at RM 73.2

Difference in temperature between main channel and off-channel feature, in degrees Celsius

Off-channel feature cooler than the main channel during July 

and August

Off-channel feature that fluctuates between warmer and cooler 

than the main channel during July and August

EXPLANATION
64 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

−10

−8

−6

−4

−2

0

2

4

6

8

10

Alcove at RM 107.5 (0.6 meters above riverbed) minus 

main channel at RM 100.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/26/1605/31/1606/06/1606/12/1606/17/1606/23/1606/29/1607/04/1607/10/1607/15/1607/21/1607/27/1608/01/1608/07/1608/13/1608/18/1608/24/1608/29/1609/04/1609/10/1609/15/1609/21/1609/27/1610/02/1610/08/1610/13/1610/19/16

Alcove at river mile (RM) 96.1 minus main channel at RM 100.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/25/16

05/31/1606/05/16

06/11/1606/17/16

06/22/1606/28/16

07/04/1607/09/16

07/15/1607/20/1607/26/16

08/01/1608/06/1608/12/1608/18/16

08/23/1608/29/16

09/03/1609/09/16

09/15/1609/20/1609/26/1610/02/1610/07/1610/13/1610/18/16

Alcove at RM 97.7 minus main channel at RM 97.7

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/26/1606/01/1606/08/1606/14/1606/20/1606/27/1607/03/1607/09/1607/16/1607/22/1607/29/1608/04/1608/10/1608/17/1608/23/1608/29/1609/05/1609/11/1609/18/1609/24/1609/30/1610/07/1610/13/1610/19/1610/26/1611/01/1611/08/16

Alcove at RM 98.4 minus main channel at RM 100.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/26/1606/01/1606/08/1606/14/1606/20/1606/27/1607/03/1607/09/1607/16/1607/22/1607/29/1608/04/1608/10/1608/17/1608/23/1608/29/1609/05/1609/11/1609/18/1609/24/1609/30/1610/07/1610/13/1610/19/1610/26/1611/01/1611/08/16

Alcove at RM 101 minus main channel at RM 100.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

06/02/1606/08/1606/14/1606/20/1606/26/1607/02/1607/09/16

07/15/1607/21/1607/27/16

08/02/1608/08/1608/14/16

08/20/1608/27/1609/02/1609/08/1609/14/1609/20/1609/26/16

10/02/1610/08/1610/15/16

10/21/1610/27/16

11/02/1611/08/1606/02/1606/08/1606/14/1606/20/1606/26/1607/02/1607/09/16

07/15/1607/21/1607/27/16

08/02/1608/08/1608/14/16

08/20/1608/27/1609/02/1609/08/1609/14/1609/20/1609/26/16

10/02/1610/08/1610/15/16

10/21/1610/27/16

11/02/1611/08/16

Alcove at RM 107.5 (0.2 meters above riverbed) minus

main channel at RM 100.2

Date

Difference in temperature between main channel and off-channel feature, in degrees Celsius

2016—Independence monitoring reach

Off-channel feature cooler than the main channel during July and August

Off-channel feature that fluctuates between warmer and cooler than the 

main channel during July and August

Site data are not included in analyses because of missing data or another 

(primary) sensor in the feature

EXPLANATION
Appendix 1. Comparison of Off-Channel to Main-Channel Water Temperatures for Continuously Monitored Sites 65

−10

−8

−6

−4

−2

0

2

4

6

8

10

06/02/1606/08/1606/14/1606/20/1606/26/1607/02/1607/09/1607/15/1607/21/1607/27/1608/02/1608/08/1608/14/1608/20/1608/27/1609/02/1609/08/1609/14/1609/20/1609/26/1610/02/1610/08/1610/15/1610/21/1610/27/1611/02/1611/08/16

Tributary at RM 107.9 minus main channel at RM 100.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

06/02/1606/08/1606/14/1606/20/1606/26/1607/02/1607/09/1607/15/1607/21/1607/27/1608/02/1608/08/1608/14/1608/20/1608/27/1609/02/1609/08/1609/14/1609/20/1609/26/1610/02/1610/08/1610/15/1610/21/1610/27/1611/02/1611/08/16

Alcove at river mile (RM) 107.8 minus main channel at RM 100.2

Date

Difference in temperature between main channel

and off-channel feature, in degrees Celsius

2016—Independence monitoring reach (continued)

Off-channel feature warmer than the main channel during July and August

EXPLANATION
66 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/25/1605/30/1606/05/1606/10/1606/16/1606/21/1606/27/1607/02/1607/08/1607/13/1607/19/1607/24/1607/30/1608/04/1608/10/1608/15/1608/21/1608/26/1609/01/1609/06/1609/12/1609/17/1609/23/1609/28/1610/04/1610/09/1610/15/16

Side channel at river mile (RM) 161.3 minus main channel at RM 164.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/25/1605/30/1606/05/1606/10/1606/16/1606/21/1606/27/1607/02/1607/08/1607/13/1607/19/1607/24/1607/30/1608/04/1608/10/1608/15/1608/21/1608/26/1609/01/1609/06/1609/12/1609/17/1609/23/1609/28/1610/04/1610/09/1610/15/16

Alcove at RM 161.7 minus main channel at RM 164.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/25/1605/30/16

06/05/1606/10/1606/16/1606/21/1606/27/1607/02/1607/08/16

07/13/1607/19/1607/24/1607/30/1608/04/1608/10/1608/15/1608/21/1608/26/16

09/01/1609/06/1609/12/1609/17/1609/23/1609/28/1610/04/1610/09/1610/15/16

Alcove at RM 162.2 minus main channel at RM 164.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/25/1605/30/1606/05/1606/10/1606/16/1606/21/1606/27/1607/02/1607/08/1607/13/1607/19/1607/24/1607/30/1608/04/1608/10/1608/15/1608/21/1608/26/1609/01/1609/06/1609/12/1609/17/1609/23/1609/28/1610/04/1610/09/1610/15/16

Alcove at RM 162.9 minus main channel at RM 164.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/25/16

05/30/1606/05/1606/10/16

06/16/16

06/21/1606/27/1607/02/16

07/08/1607/13/1607/19/16

07/24/1607/30/16

08/04/1608/10/1608/15/16

08/21/1608/26/1609/01/1609/06/16

09/12/1609/17/1609/23/16

09/28/1610/04/1610/09/1610/15/16

Alcove at RM 164.1 minus main channel at RM 164.2

−10

−8

−6

−4

−2

0

2

4

6

8

10

05/25/1605/30/1606/03/1606/08/1606/13/1606/18/1606/23/1606/27/1607/02/1607/07/1607/12/1607/16/1607/21/1607/26/1608/19/1608/24/1608/28/1609/02/1609/07/1609/12/1609/17/1609/21/1609/26/1610/01/1610/06/1610/11/1610/15/16

Side channel at RM 164.8 minus main channel at RM 164.2

Date

Difference in temperature between main channel and off-channel feature, in degrees Celsius

2016 – Harrisburg monitoring reach

Off-channel feature warmer than the main channel during July and August

Off-channel feature cooler than the main channel during July and August

Off-channel feature that fluctuates between warmer and cooler than the main 

channel during July and August

EXPLANATION
Appendix 2. Aerial Imagery from 1994 and 2016 for Select Off-Channel Features 67

Appendix 2. Aerial Imagery from 1994 and 2016 for Select Off-Channel Features

July 23, 2016

May 22, 1994

Base map data from Google, 2018

Location of water-quality monitor at

Fairfield alcove (river mile 67.1)

0 500 METERS

0 1,000 FEET

Willamette River N

flow direction

River mile 67

River mile 68

This appendix shows aerial imagery from 1994 and 2016 for the five off-channel features that were intensively monitored 

in 2016. Such imagery is useful in ascertaining the stability of the channel and its gravel bars and features, as well as the presence and absence of vegetation over time.
68 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

July 23, 2016

June 18, 1994

Location of water-quality monitor at

Windsor Bar side channel

(river mile 74.6)

Base map data from Google, 2018 0 250 METERS

0 500 FEET

N

Willamette River

flow direction

River mile 75
Appendix 2. Aerial Imagery from 1994 and 2016 for Select Off-Channel Features 69

July 23, 2016

May 6, 1994

Base map data from Google, 2018

Location of water-quality monitor at

Murphy Bar alcove (river mile 97.7)

0 500 METERS

0 1,000 FEET

N

Willamette River

flow direction

River mile 98
70 Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16

May 29, 2016

May 6, 1994

Base map data from Google, 2018

Location of water-quality monitor at

Harpers Bend side channel 

(river mile 164.8)

Location of water-quality monitor 

at Blue Ruin alcove

(river mile 164.1)

0 500 METERS

0 1,000 FEET

Willamette River N

flow direction

River mile 164

River mile 165
Publishing support provided by the U.S. Geological Survey

Science Publishing Network, Tacoma and Rolla 

Publishing Service Centers

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

Director, Oregon Water Science Center

U.S. Geological Survey

2130 SW 5th Avenue

Portland, Oregon 97201

https://www.usgs.gov/centers/or-water 
Smith and Others—Temperature and Water-Quality Diversity and Effects of Surface-Water Connection, Willamette River, Oregon, 2015–16—SIR 2020–5068

ISSN 2328-0328 (online)

https://doi.org/10.3133/sir20205068