EPA 910-C-12-001
&EPA
United States
Environmental Protection
Agency
Region 10
1200 Sixth Ave.
Seattle, WA 98101
Alaska
Idaho
Oregon
Washington
Water Division
Office of Water and Watersheds
February 2012
Primer for Identifying Cold-Water Refuges to
Protect and Restore Thermal Diversity in
Riverine Landscapes
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EPA 910-C-12-001
for to
and in
Christian E, Torgersen
U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center
Cascadia Field Station, Seattle, Washington
Joseph L. Ebersole
U.S. Environmental Protection Agency
National Health and Environmental Effects Research Laboratory
Western Ecology Division, Corvallis, Oregon
Druscilla M. Keenan
U.S. Environmental Protection Agency, Office of Water and Watershed
Seattle, Washington
This report was prepared for Region 10, U.S. Environmental Protection Agency,
Seattle, Washington under EPA Interagency Agreement No. DW-14-95755001 -0
2012
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The information in this document has been funded wholly or in part by the United States Environmental Protection
Agency under Interagency Agreement DW-14-95755001-0 to the United States Geological Survey. It has been
subjected to the Agency's peer and administrative review and has been approved for publication as an EPA
document. Any use of trade names, commercial products, or contractors is for descriptive purposes only and does
not imply endorsement by the U.S. Government.
Additional copies of this publication may be obtained from the U.S. Environmental Protection Agency, Region 10,
1200 Sixth Ave., Suite 900, M/S: QWW-134, Seattle, WA 98101
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HI
The authors thank Hiram Li (professor emeritus) with the Oregon Cooperative Fish and Wildlife
Research Unit at Oregon State University for introducing us to the concept of a thermal refuge through
his early observations and experimental work in the John Day River basin. In addition, many of the
figures and illustrations in this primer were generously provided by colleagues Russ Faux (Watershed
Sciences. Inc.), Scott O'Daniel (Confederated Tribes of the Umatilla Indian Reservation), Carol Volk
(NOAA Fisheries), John Vaccaro (U.S. Geological Survey, Washington Water Science Center). Brian
Cochran (Confederated Tribes of the Warm Springs Indian Reservation of Oregon). Mark Colcman
(Coleman Ecological. Inc.). Erich Hester (Virginia Tech). Michael Gooseff (Pennsylvania State
University), Mike Deas (Watercourse Engineering, Inc.), Jonny Armstrong (University of Washington),
Greg Nagle, Kent Smith (Insight Consultants), Stan Gregory (Oregon State University), and Dave
Hulse (University of Oregon). The speakers and discussants in the Western Division and Oregon
Chapter American Fisheries Society Special Symposium "Identifying, protecting, and restoring
thermal refuges for coldwater fishes" in Portland, Oregon, May 4-8, 2008, provided insights and much
critical thought that helped to foment the ideas and information presented in this primer. Matthew
McLaughlin (University of Washington) provided videographic sendees and made it possible to share
the symposium over the Internet. Constructive reviews were generously provided by Dcbra Sturdcvant
(Oregon Department of Environmental Quality), Jeff Lockwood (NOAA Fisheries), Don Essig (Idaho
Department of Environmental Quality), Robert Beschta (professor emeritus at Oregon State University),
Jason Dunham (U.S. Geological Survey. Forest and Rangeland Ecosystem Science Center), and Dale
McCullough (Columbia River Inter-Tribal Fish Commission).
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IV
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Acknowledgments iii
Executive Summary[[[ 1
1. Introduction 2
1.1. Why are cold-water refuges important? 2
1.2. Science and management needs 2
1.3. Purpose and intended audience[[[ 2
1.4. How to use this primer[[[ 3
1.5. Objectives 4
2. What is a cold-water refuge? 5
2.1. Scientific definitions[[[ 5
2.2. Proposed terminology[[[ 5
2.3. Management and policy 6
2.4. Conceptual framework[[[ 6
2.4.1. Ecological context 6
2.4.2. Spatial and temporal variability 7
2.4.3. Physical typology 7
3. A 'road map' for identifying cold-water refuges to address water quality standards.............................. 8
3.1. Approach[[[ 8
3.2. Spatial scale 8
3.3. Temporal scale 9
3.4. Stream size and accessibility[[[ 9
3.5. Toolbox[[[ 10
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VI
Contents^Continued
5. Classification and characterization 16
5,1, Hierarchical organization[[[ 16
5,2. Basin and subbasin[[[ 16
5.3. Segment 16
5.4. Reach 17
5,5, Channel unit[[[ 17
5,6, Microhabitat[[[ 17
6. Identification and prediction 18
6.1. Maps 18
6,2, Modeling 18
6,3, Remote sensing[[[ 18
6.3.1. Aerial photography 19
6.3.2. LiDAR 19
6.3.3. Thermal infrared imaging[[[ 19
6.4. Direct measurement 19
6.4.1. Thermocouples and probes 20
6.4.2, Stationary data loggers[[[ 20
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¥11
Figure 2.4.1.1. Performance capacity offish in cold-water refuges 23
Figure 2.4.1.2. Rainbow trout in Joseph Creek in northeastern Oregon exhibit size hierarchy in
occupying a cold-water refuge, with the largest individual in the coldest
thermal zone 24
Figure 2.4.1.3. Adult spring chinook salmon in the Middle Fork John Day River, Oregon, have
been observed behaviorallythermoregulating in mid-summer by locating
cold alcoves 25
Figure 2.4.1.4. Small differences in water temperature over short distance are detected and
used by coldwater fish, such as the rainbowtrout depicted in the image of the
Middle Fork John Day River, Oregon [[[ 26
Figure 2.4.1.5. The effectiveness of a cold-water refuge depends on multiple biological and
physical factors in addition to temperature 27
Figure 2.4.2.1. Hierarchical levels of biological organization for stream salmonids and their
persistence at different spatial scales 28
Figure 2.4.2.2. Variability in the favorableness of cold-water refuges in space and time ............... 29
Figure 2.4.2.3. Cool-water areas that are isolated from the main channel also may be shallow and
lack overhead cover, channel complexity, and water depth due to altered riparian
vegetation, thereby increasing the susceptibility of fish to predation while they are
using these refuges 30
Figure 2.4.2.4. Defining cold-water refuges based on changes in temperature, time,
and distance [[[ 31
Figure 2.4.2.5. Example of a cold-water refuge created by asynchronous temporal variability
among proximal patches in a river 32
Figure 2.4.3.1. Hyporheic exchange in lateral and vertical dimensions in streams 33
Figure 2.4.3.2. Hyporheic connectivity through alluvial deposits of gravel and cobble substrate is
illustrated in a tracer experiment using red dye, which is shown emerging from the
streambank after being released at an upstream location in the floodplain ............ 34
Figure 5.1.1. Ecoregions are based on geology, physiography, vegetation, climate, soils, land
use, and hydrology and provide a landscape context for investigating potential
broad-scale influences on thermal heterogeneity in rivers and streams ............... 36
Figure 5.2.1. EPA Level-IV ecoregions and variation in longitudinal patterns of summer water
temperature derived from airborne TIR remote sensing in the North and Middle
Forks of the John Day River, Oregon 37
Figure 5.3.1. Abounded alluvial valley segment (BAVS) in the Elk Creek drainage, Montana ...... 38
Figure 5.4.1. Reach-level cold-water refuges at the scale of hundreds of meters in an alluvial
floodplain reach may be associated with the combined and interactive effects of
tributary confluences, sinuosity, and floodplain connectivity via multiple surface
and subsurface flow pathways 39
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Figures^Continued
Figure 5.5.2. Cold side channels often emerge from seasonal overflow channels 41
Figure 5.5.3. Up-valley oblique view of a meandering river and wall-base channels in the
Clearwater River on the Olympic Peninsula, Washington, showing examples of
associated cold-water habitat types 42
Figure 5.6.1. Cold alcoves are a common cold-water patch type and are typically observed
emerging from relict channels/swales where stream channels converge with
valley walls downstream from floodplains or large gravel point bars 43
Figure 5.6.2. Lateral seeps are low-volume but relatively common cold-water areas that occur
where the active channel directly intercepts groundwater flow through a terrace,
alluvial fan, or hillslope [[[ 44
Figure 6.1.1. Designated fish use maps include qualitative, broad-scale assessments of thermal
requirements for salmonids in 15 major hydrologic basins in Oregon and provide
spatial context for evaluating thermal potential in riverine landscapes at a
state-wide level 45
Figure 6.1.2. Basin-scale variation in mean water temperature for August (1992-2003) in the
John Day River basin, Oregon [[[ 46
Figure 6.1.3. Observed and predicted zones of cooling and hyporheic potential based on
10-m digital elevation models (OEMs) of floodplain and channel geomorphology
in the Umatilla River, Oregon [[[ 47
Figure 6.2.1. Predicting cold-water refuges at the kilometer scale with spatially explicit,
process-based modeling 48
Figure 6.3.1. High-resolution Google® Earth imagery of a springbrookinthe upper Middle Fork
John Day River, Oregon, illustrates the accessibility and utility of readily available
Internet imagery for identifying potential locations of cold-water refuges in small
to large rivers [[[ 49
Figure 6.3.3.1. Helicopter and gimbal mount for airborne TIR remote sensing of
stream temperature 50
Figure 6.3.3.2. Aerial images in natural color and airborne TIR of a cold-water seepage
area in the Crooked River, Oregon, in a high-desert basalt canyon
(August27,2002)[[[ 51
Figure 6.3.3.3. Aerial images in natural color and airborne TIR of groundwater springs flowing
into the upper Middle Fork John Day River, Oregon, in a montane meadow
(August 16,2003) [[[ 52
Figure 6.3.3.4. Aerial images in natural color and airborne TIR showing thermal heterogeneity
in a complex floodplain of the Willamette River, Oregon, which flows through
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IX
Figures^Continued
Figure 6.4,1.3. Miniature temperature mapping system designed for evaluating fish response
to thermal heterogeneity in wadeable streams 56
Figure 7.1,1. Conceptual model outlining steps for assessing, protecting, and restoring
cold-water refuges and thermal diversity in riverine landscapes 57
Figure 7.4.1. Observed and expected cold-water areas in the middle Willamette River, Oregon,
based on qualitative evaluation of historical and current aerial photographs and
field measurements of stream temperature obtained from digital data loggers 58
Figure 7.5.1. Historical and current aerial photographs of the Oxbow Conservation Area of the
Middle Fork John Day River, Oregon, in 1939 and 2006 59
Figure 7.5.2. Floodplain restoration in the Oxbow Conservation Area of the Middle Fork
John Day River, Oregon, incorporated aerial TIR imagery and digital elevation
models derived from LiDAR to guide channel placement in relation to
subsurface-flow patterns 60
Figure 7.5.3. Channel unit and microhabitat-scale restoration of cool-water areas, such as
seeps and cold tributaries, may include placements of wood and bar deflectors
upstream of cool-water inputs to increase channel complexity and reduce mixing
and effectively increase the size of cold-water refuges .................................... 61
Tables
Table 5.1.1. Hierarchical organization of cold-water refuges and associated geographical and
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Executiwe Summary 1
for to and
in
By Christian E. Torgersen, U.S. Geological Survey; and Joseph L. Ebersole and Druscilla M. Keenan,
U.S. Environmental Protection Agency
In 2003, EPA issued Region 10 guidance for Pacific Northwest state and tribal temperature water quality standards. This
document was the culmination of a multi-agency, multi-disciplinary effort to develop a temperature standard for the protection
of salmon, steelhead, bull trout and redband and Lahontan cutthroat trout (collectively termed coldwater salmonids). Since its
release, Oregon and Washington have adopted the temperature standard for their waters designated for protection of coldwater
salmonids. One of the unique aspects of the temperature standard, which strived to integrate the physical nature of rivers and
streams and the biological requirements of coldwater salmonids. is the requirement to protect and restore cold-water refuges.
This requirement is incorporated into the temperature criterion for the protection of migration corridors in the Willamette,
Columbia, and Snake rivers. The intent of this provision is the recognition that some coldwater salmonids migrate through
waters during thermally stressful months of summer and most likely are able to do so by using features in the rivers that provide
cold water spatially or temporally. The challenge is to ensure that these features are identified, protected, and restored in order
for these waters to meet the temperature standard. This primer is intended to assist Region 10 states, tribes, and local watershed
groups in meeting this goal and thereby further the protection and restoration of coldwater salmonids. It provides an up-to-
date summary with easily referenced information and illustrations on the scientific advances and management applications
of research on cold-water refuges and can be used as a 'roadmap' for identifying cold-water refuges and learning more about
processes that create thermal diversity in riverine landscapes. The specific objectives are to
1. Define cold-water refuge in scientific and management contexts,
2. Outline an approach for identifying cold-water refuges to address water quality standards,
3. Classify and characterize the types and physical processes that create cold-water refuges,
4. Review methods and tools for identifying cold-water refuges in small streams to large rivers, and
5. Describe ecological perspectives and on-the-ground approaches for protecting and restoring thermal diversity in
rivers.
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Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
1.
1.1. Why are
1.2.
1.3.
Cold-water refuges in rivers and streams have physiological and
ecological significance because temperature is the driving factor that
determines the metabolic rates of cold-blooded animals, such as fish and
the organisms on which they feed. Because fish and invertebrates have
specific ranges of thermal tolerance, increases in water temperature as a
result of human modification of the natural thermal regime may require
fish and invertebrates to move to areas that are more thermally suitable.
91, 39, 27, 61, 19, 77, 155, 184
In order to protect the beneficial uses of rivers and streams, which
include promoting a favorable environment for salmon and trout,
cold-water refuges require specific consideration in the regulation of
water quality through standards developed by state and federal
agencies. 12S-12°-18S
The social and economic importance of wild salmon and trout in the
Pacific Northwest and their dramatic decline over the last century has
brought the issue of water temperature to the forefront in fisheries
science and management because of its significance as a habitat
requirement under current conditions and in the broader context of
climate change. 89'137' '"•182'15-153
Although scientific understanding offish and their fundamental
physiological responses to elevated water temperature was well
developed in a laboratory setting prior to the 1990s, application of
this understanding in the field to address management needs has been
and remains a significant challenge. This is due to the difficulty of
replicating spatially and temporally complex thermal environments
in the laboratory and relating observations of domesticated fish to the
behavior of wild fish in natural environments. The need for science and
applications of relevant technology has driven rapid advances in the
last 15 years in identifying and predicting both the physical drivers of
thermal heterogeneity in streams and the responses of aquatic organisms
to these patterns.
The purpose of this primer is to provide an overview of cold-water
refuges in river systems for the protection of salmon and trout. The
primer provides instruction on what cold-water refuges are, how to
identify them, how they function, and how they can be protected
and restored. The following sections include the latest resources and
references to assist in this work and are specifically designed to support
state and tribal water quality standards for temperature. This primer is an
outgrowth of the Environmental Protection Agency Region 10 Guidance
for Pacific Northwest State and Tribal Temperature Water Quality
Standards. 82
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1. Introduction
1.4. How to use this primer
EPA's temperature guidance was the culmination of a multi-agency,
multi-disciplinary effort to develop a temperature standard for
the protection of coldwater salmonids. Since its release, Oregon
and Washington have adopted the temperature standard. One of
the unique aspects of the temperature standard, which strived to
integrate the physical nature of rivers and streams and the biological
requirements of coldwater fish, is the requirement to protect and restore
cold-water refuges.
The challenge is to ensure that these features are identified, protected,
and restored in order for these waters to meet the temperature standard.
This primer is intended to assist Region 10 states, tribes, and local
watershed groups in meeting this goal and thereby further the protection
and restoration of salmon and trout populations.
This document is organized to provide information concisely and in a
manner that facilitates navigation forward or backward as a handbook
without requiring the reader to progress sequentially through each
section to find information. The figures and table are numbered so that
they can be associated with their corresponding sections and references
in the main text. Detailed annotations and textual clarification are
included with each figure and table so that they can be interpreted
independently from the main text. To facilitate the flow and readability
of the text, references are cited at the end of the paragraph to which
they refer and are indicated with a corresponding number in the list of
references.
Section 2 provides an overview of important ecological concepts
in a management context. Sections 3 and 4 provide step-by-step
instruction for identifying cold-water refuges to address water quality
standards. Sections 5. 6, and 7 outline the scientific underpinnings
and methodological approaches for understanding and identifying the
processes that create and maintain cold-water refuges for the purposes
of protection and restoration. Detailed information on any one topic
is best acquired through the cited references that range from broad in
scope to very specific.
Additional materials are provided in the appendices, including streaming
video of scientific presentations on cold-water refuges and summaries
and maps of remotely sensed stream temperature data, which are
available online and on request from the authors.
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4 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
1.5. ObjectiweS The primer has the following objectives:
* Define 'cold-water refuge' in scientific and management contexts.
• Outline an approach for identifying cold-water refuges to address water
quality standards.
• Classify and characterize the types and physical processes that create
cold-water refuges.
* Review methods and tools for identifying cold-water refuges in small
streams to large rivers.
« Describe ecological perspectives and on-the-ground approaches for
protecting and restoring thermal diversity in rivers.
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2. What is a cold-water refuge?
2. What is a cold-water refuge?
2.1. Scientific definitions
The terms refugium, refugia, and refuge have been used widely in
the scientific literature, but they have different connotations and
denotations and require clarification in order to avoid confusion. In
the field of biogeography, refugia (plural for refugium in Latin) are
distinct geographic areas, or 'islands' in a figurative sense, in which
flora and fauna have been able to survive in isolation from surrounding
unfavorable environmental conditions. For example, glacial refugia
are areas in which plants and animals were able survive during the
Pleistocene Epoch (the Great Ice Age). Fire refugia are areas of various
sizes ranging from a microhabitat to a portion of a landscape that is not
burned in wildfire. An important aspect of refugia in a biogeographical
sense is that they are considered refugia only if they are occupied by
species that were already present in an area, as opposed to areas of
retreat used by migratory species. 176- 233- 205- 53- 52- 2
In community ecology, refugium and refuge generally refer to areas
occupied by organisms to avoid predation and competition, or human
impacts, such as angling, harvest, or land use. 233-52-2-55
Aquatic ecologists also apply the concept of refuge in regard to species
interactions, but more frequently, refugia and refuges are used to
identify local-scale areas or 'shelters' in which organisms are protected
from unfavorable physical conditions, such as streamflow, flood-related
disturbance, and temperature. Aquatic organisms may take refuge in
warm water in winter or cold water in summer, depending on ambient
conditions and the thermal tolerances of the species. 97- 13°-192-101' 64'206'
174, 177, 56, 144, 158, 107, 12, 181, 164, 5, 55, 8J
Applications of the concept of refuges in aquatic systems have not
always been explicit regarding scale. As we will elaborate in 5.
thermal refuges can be understood to operate at spatial scales ranging
from microhabitats to entire river basins. Regardless of scale, refuges
will always be defined as discrete patches within some larger spatial
context.
2.2. Proposed terminology
To avoid possible confusion about (1) the biogeographical definition of
refugia and (2) the spelling of its singular form refugium, this primer
uses refuge and refuges, which may be either cold or warm in relation
to surrounding water and are collectively termed thermal refuges. For
example, a thermal refuge in the winter is a place that is warmer than the
surrounding water (i.e., a "warm-water" refuge). Conversely, a thermal
refuge in the summer is a place that is colder than the surrounding water
(i.e., a "cold-water" refuge). This primer focuses on cold-water refuges
as pertains to water quality standards and the effects of elevated water
temperature on salmonids (see 1.3).
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Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
2.3. Management and policy
Due to the inherent physical and ecological complexity of cold-water
refuges, explicit terminology is required in order to minimize varying
interpretations. 235-128- 37
The EPA has determined that "Critical aspects of the natural thermal
regime that should be protected and restored include the spatial extent of
cold-water refugia (generally denned as waters that are 2°C colder than
the surrounding water), the diurnal temperature variation, the seasonal
temperature variation (i.e., number of days at or near the maximum
temperature), and shifts in the annual temperature pattern." 82
Based on EPA guidance, the Oregon Department of Environmental
Quality developed a more specific definition: "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°C colder than
the daily maximum temperature of the adjacent well-mixed flow of the
water body." (OAR 340-041-0002 [10]). 17°- 36- 46-171
http://www.dea. state .or.us/wa/standards/temperature .htm
2.4. Conceptual framework
2.4.1. Ecological context
Fish are capable of detecting differences in temperature of <0.1°C
and respond to these fine-scale differences in both space and time by
moving to areas that are more favorable. Movement by an organism
to occupy more favorable thermal environments is termed behavioral
thermoregulation. Observations offish using cold-water refuges in
the Pacific Northwest provided direct evidence of thermal effects on
salmon and trout and raised awareness of the importance of these
habitats. Understanding how fish respond to cold-water refuges requires
information on the ecological context, spatial and temporal variability,
and physical typology of the refuge itself.142-163- 248- 23°- 77- 201- 202-149
The upper and lower limits of all environmental conditions within which
a species can persist have been described as a multidimensional space or
"fundamental niche" for that species. Although abstract in a theoretical
sense, the idea of the fundamental niche is important because it provides
an avenue for understanding the multiple factors at play in determining
the capacity of a species to perform in the natural environment
(Figure 2.4.1.1). "*• 235' 204
For example, there are physical and biological tradeoffs for a fish
that moves to a cold-water refuge. Although the water temperature
may be favorable, conditions may be less than optimal for dissolved
oxygen, depth, cover, and isolation from the mainstem. Feeding and
species interactions, such as predation and competition, all affect
the favorability of a cold-water refuge and may be compromised in
order for the fish to maintain immediate physiological homeostasis
(Figures 2.4.1.2. 2.4.1.3. and 2.4.1.4V 142-197> 32' 48' 80' 75>134' 78' 243' 65- 94-
38, 157
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2. What is a cold-water refuge?
2.4.2. Spatial and
temporal variability
2.4.3. Physical typology
For the purposes of this primer, a refuge is first defined in relation to
temperature. To be effective in providing the conditions necessary for
persistence within an otherwise hostile matrix, a refuge also must meet
all minimal habitat requirements for a given species. Evaluations of
thermal refuge effectiveness will require consideration of accessibility,
chemical environment, and other trade-offs that may be associated with
predation risk or foraging efficiency within refuges (Figure 2.4.1.5).
Guidance on evaluation of these factors is beyond the scope of this
primer, but we urge users to collect supplemental data on other factors
that may influence refuge effectiveness to help advance the state of the
science (see Figure 2.4.1.5 for examples of these supplemental data).
Changes in the size and persistence of cold-water refuges have
corresponding effects at various spatial and temporal scales and levels
of biological organization for a given fish species (Figure 2.4.2.1).
Moreover, the favorableness of a given cold-water refuge varies
depending on the degree of isolation between refuge habitats and
the distance to other habitats required for survival and growth
(Figures 2.4.2.2 and 2.4.2.3). 211,193' 66' 74' 103' 72
Fish may use cold-water refuges at various temporal and spatial
scales. This particular aspect of the thermal ecology offish is poorly
understood due, in part, to the difficulty of quantifying the dimensions
of cold-water refuges that can be constantly changing in space and
time (Figure 2.4.2.4). The literature on cold-water refuges primarily
addresses spatial heterogeneity in water temperature as opposed to
temporal variability. Although this primer focuses more on spatial
patterns, it is important to stress that more information is needed
on how coldwater fish use both spatial and temporal variability in
water temperature to survive in thermally stressful environments
(Figure 2.4.2.5). Improved technology for tracking movements of
fish, as discussed in Section 6.4.3. has great potential for addressing
problems of spatial and temporal scale and behavioral thermoregulation
by fish 163- 86-188- 23°
Hydrologic processes that create cold-water refuges may be broadly
defined as either point sources (e.g., tributaries and groundwater seeps)
or as non-point sources (e.g., 'gaining' or 'losing' reaches). Direct
measurement of gaining or losing reaches requires the use of mini-
piezometers installed in the streambed, or highly precise stream gaging.
Indirect methods also are effective for identifying potential gaining
and losing reaches and are easier to apply over large areas because
indirect methods do not involve installing equipment in the field. These
indirect methods can be used to identify floodplain features, channel
morphology, and thermal patterns that are associated with groundwater/
streamwater exchange (see Sections 5 and 6) (Figures 2.4.3.1 and
2.4.3.2) 42- 60-187-109-17- 58- 51-186
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8 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
3. A 'road map' for identifying cold-water refuges to address water
quality standards
3.1. Approach
3.2. Spatial scale
The process of identifying cold-water refuges in riverine landscapes and
using this information to address management objectives is complex.
However, the process can be divided into a series of steps to make the
task more manageable. This section outlines these steps in general terms
and provides a framework for addressing EPA Region 10 temperature
water quality guidance to protect and restore cold-water refuges. This
framework also provides a 'road map' for navigating to subsequent
sections of the handbook with more detailed information, references,
and illustrations.
Step 1. Define the spatial context of interest in terms of resolution
and extent.
The resolution is the scale (also described as 'grain' in the ecological
literature) at which cold-water refuges are quantified, whereas the extent
is the geographic area (e.g., basin size or length of stream) over which
an assessment of cold-water refuges is conducted.
The resolution and extent may not be defined explicitly in the objectives
that call for an assessment of cold-water refuges. Therefore, it may be
necessary to review, and perhaps revise, the overall goals of a project in
order to focus the questions regarding the spatial characteristics of the
cold-water refuges of interest. Information for a given extent may be
needed on cold-water refuges at several different resolutions.
Section 5 of this primer provides information to assist the user on
selecting the appropriate spatial scale(s) of interest in an assessment
of cold-water refuges (e.g., basins and subbasins, segments, reaches,
channel units, and microhabitats). Table 5.1.1 lists these scales and
provides dimensions in space (length and area) and time (months,
decades, etc.) that typically are associated with processes that create
cold-water refuges. Note that the actual dimensions of streams and rivers
vary depending on stream size (i.e., Strahler order; see Section 3.4V
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3. A 'road map' for identifying cold-water refuges to address water quality standards
3.3. Temporal scale
3.4. Stream size and
accessibility
Step 2. Define the temporal context of interest in terms of resolution
and extent.
The temporal resolution of a temperature measurement is denned as
the interval in time between measurements in seconds, minutes, hours,
days, weeks, or other predefined intervals. The temporal extent is the
length of time over which temperature measurements are collected. For
evaluating stream temperature, typical extents range from months and
years to decades, or greater, depending on the frequency of the natural
and human disturbances of interest.
The concept of temporal scale as applied to cold-water refuges is
abstract, so it helps to think in terms of different sampling methods.
For example, measuring temperatures in a stream with a hand-held
thermometer typically has a temporal resolution of seconds, based
on the time it takes to obtain a reading. The temporal extent of this
method typically is on the order of minutes. The temporal resolution
of a digital temperature data logger is the interval at which the logger
is programmed to record measurements, and the temporal extent is the
duration of the deployment.
The various methods discussed in Section 6 have different capabilities
in terms of temporal resolution and extent. An assessment of cold-water
refuges may require data at multiple temporal resolutions.
Step 3. Evaluate the range of stream sizes that will be encountered in the
river segment of interest.
Methods for identifying cold-water refuges vary with respect to their
effectiveness in streams of different sizes and their accessibility by
foot, boat, or car (Section 6). Knowing the approximate stream sizes
likely to be encountered will help guide planning efforts for conducting
surveys of cold-water refuges. Stream size is measured in terms of
discharge, which is a function of wetted width, depth, and water
velocity. Discharge and/or channel widths can be visually estimated
from remotely sensed imagery or obtained from on-line data repositories
(USGS gaging station data:
http://or.water.usgs.gov/.
http://waterdata.usgs.gov/nwis.
http://or.water.usgs.gov/projs_dir/will_tmdl/main_stem_bth.htmD.
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10 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
3.5. Toolbox Step 4. Select the appropriate tools based on the scales of interest,
logistical constraints, and available resources.
A variety of tools exist for identifying cold-water refuges and the areas
in which they are likely to occur (Section 6). As a general rule, maps,
models, and imagery are most effective for evaluating where cold-water
refuges are likely to occur at medium to large spatial scales, whereas
methods for measuring cold-water refuges directly are more appropriate
at medium to small spatial scales.
The order of methods presented below highlights the importance of
using publically available data prior to conducting fieldwork. Even
when resources exist for data collection in the field, a priori evaluation
of maps, models, existing data, and airborne/satellite imagery ensures
that resources will be used efficiently.
3.5.1. Maps When the spatial extent of an area of interest is large, maps are an
essential screening tool for focusing field data collection. Maps of
ecoregions, geology, and topography provide readily accessible
information on potential locations of cold-water refuges at basin,
subbasin, segment, and reach scales (Sections 5.1. 5.2. 5.3. 5.4. and
6.1). Historical maps may provide an important temporal context
(Section 7.4). These maps depict channel locations and morphology
prior to human alteration and could illustrate areas where cold-water
refuges have been lost and potentially could be restored (Section 7.5).
Maps are effective for identifying potential locations of cold-water
refuges in large rivers (i.e., non-wadeable streams) that are difficult
to sample exhaustively in the field, and in remote areas that are
inaccessible by car or boat.
3.5.2. ModGling During the initial phase of identifying cold-water refuges, various
models and data may be used to fine-tune map-based predictions
of potential cold-water refuge locations. Spatially explicit stream
temperature models have been developed by natural resource agencies
for many rivers throughout the Pacific Northwest (Section 6.2V
Model output consists of longitudinal profiles and maps depicting
variability in stream temperature at relatively high spatial resolutions
(<1 km) for entire river segments tens of kilometers in length. Cold-
water refuges detected in stream temperature models at basin, subbasin,
segment, and reach scales include tributary inputs, effects of riparian
shading, and groundwater/surface-water interactions (Sections 5.2. 5.3.
and 5A).
-------
3. A 'road map' for identifying cold-water refuges to address water quality standards 11
3.5.3. Remote sensing
3.5.4. Direct measurement
Airborne and satellite imaging (Section 6.3) can be an invaluable tool
for predicting where cold-water refuges are likely to occur under present
conditions and where they may have occurred historically and where
they potentially could be restored (Sections 7.4 and 7.5). These tools are
most useful for identifying features associated with cold-water refuges
at segment, reach, and channel unit scales (Sections 5.3. 5.4. and 5.5V
In medium- and large-sized rivers, aerial photographs also can be used
to identify riverine features associated with cold-water refuges at the
microhabitat scale (Section 5.6). When available, thermal infrared
imagery collected from an aircraft or on the ground provides a means
to locate and map cold-water areas with a high degree of precision
(Section 6.3.3). A limitation of imagery is that it can be used effectively
only in river systems in which the view of the stream channel and
floodplain is not obstructed by trees.
If the spatial extent of the area of interest is small or involves small
stream sizes, it may be appropriate to forgo maps, models, and airborne/
satellite imagery and proceed directly to measuring cold-water refuges
in the field (Section 6.4). An example of this situation would be in
headwater streams, for which (1) available maps are too coarse in scale
to detect channel characteristics and (2) aerial views of the stream are
obscured by riparian vegetation. In most cases, direct measurement is
used only after a thorough investigation of maps, imagery, models, and
existing field data.
3.6. Assessment
Appropriate spatial and temporal scales for direct measurement of cold-
water refuges vary among methods. For example, stationary temperature
data loggers can be deployed throughout entire basins and throughout
segments to create maps of broad-scale patterns of stream temperature
(Section 6.1). However, stationary data loggers typically cannot be
deployed at densities high enough to detect cold-water refuges at reach,
channel unit, and microhabitat scales. Hand-held thermocouples and
towed digital temperature data loggers can be used to identify cold-
water anomalies at segment, reach, channel unit, and microhabitat scales
(Sections 5.3. 5.4. 5.5. and 5.6). but these techniques do not provide a
synoptic assessment, or 'snapshot', of thermal patterns.
Step 5. Identify and map cold-water refuges with respect to their
typology.
Assessment involves map-, model-, image-, and field-based
identification (Section 6) of existing cold-water refuges as well as the
locations where they may have occurred prior to human alteration of the
riverine landscape. Cold-water refuges are classified and characterized
as described in Section 5.
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12 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
3.7. Data Compilation Step 6. Generate tables and maps.
and documentation .
Cold-water refuges are coded by type (Section 2.4.3). hierarchical
level (Sections 5.2. 5.3. 5.4. 5.5. and 5.6). location by river kilometer
(referenced to the USGS National Hydrography Dataset), method
of assessment (Sections 6.1. 6.2. 6.3. and 6.4). data source (i.e., if
publically available maps, data, models, and imagery are used), and time
and date of measurement.
3.8. Evaluation and Step 7. Evaluate the distribution of cold-water refuges with respect to
implementation EPA Region 10 temperature water quality guidance.
The current distribution, including size, frequency, and spacing of
cold-water refuges, provides (1) information needed to protect existing
habitats, (2) clues to the historical distribution of such habitats that
can be used as a baseline for determining targets for restoration, and
(3) evidence to help evaluate the sufficiency of these habitats for
supporting successful migration and/or rearing of juvenile and adult
salmonids (Section 7V An example of a process by which managers can
use this combined information to make informed management decisions
for protecting and restoring cold-water refuges is provided in Section 7
(see Figure 7.1.1).
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4. Application to EPA guidance on migration corridors for salmon and trout 13
4. Application to EPA guidance on migration corridors for salmon and trout
4.1. Background The EPA recommends a 7-day average daily maximum water
temperature of 20°C in portions of rivers through which salmon
and trout migrate during maximum summer temperatures. This
recommendation includes the provision to protect and restore cold-water
refuges where they currently exist and where they may have occurred
historically prior to human alteration of the landscape (see Section 2.3
for the definition of a cold-water refuge based on EPA guidance). 82
The following steps are provided to assist states and tribes in identifying
cold-water refuges in migration corridors for salmon and trout. The
lower Willamette River in Oregon is used as an example because it is
designated by the Oregon Department of Environmental Quality as
a migration corridor for salmon and trout. This use also occurs in the
lower parts of other rivers in the Pacific Northwest (e.g., John Day
River, Columbia River, and Snake River; see website below). The lower
Willamette River contains a wide range of channel forms and sizes and
provides an illustration of how the following steps may be applied in
other river systems of similar size and complexity.
http://www.deq.state.or.us/wq/rules/divQ41tblsfigs.htmtft2
Details regarding the lower Willamette River are provided only as
an example; adaptations of this approach by states and tribes will be
required to meet their specific needs, objectives, and budget constraints.
The Willamette River has been studied extensively and therefore has
the benefit of a wealth of data from remote sensing and intensive
investigation in the field. Many of these techniques may not be
available to resource managers in less-studied basins; however, low-cost
approaches using publically available data and Internet resources also
are effective for identifying areas of potential thermal heterogeneity.
These low-cost techniques are illustrated and described in Sections 5
and 6.
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14 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
4.2. Spatial and
temporal scales
4.3. Stream size and
accessibility
Steps 1 and 2
The spatial and temporal extents of inquiry are set by EPA guidance and
by the State water quality standard that refer to migration corridors for
salmon and trout during the warmest two months of summer. The lower
80 km of the Willamette River is designated as a migration corridor
for salmon and trout in the summer. Thus, the spatial and temporal
extents of this assessment are 80 km and two months (July-August),
respectively. For a river segment this long, quantifying cold-refuges at
a very fine spatial resolution may not be logistically feasible. Therefore,
an entire pool or riffle (channel unit), or a portion thereof (microhabitat:
e.g., 10 m2), is an appropriate scale at which to examine cold-water
refuges in this river segment. Cold-water refuges smaller than the stated
resolution would not be considered in the assessment.
An appropriate temporal resolution for examining cold-water refuges
in the lower Willamette River is 1 day, in which a potential metric
of interest is daily maximum water temperature. Because the stated
temporal resolution is 1 day, cold-water refuges would be considered
only in the assessment if their daily maximum temperature is 2°C less
than the surrounding waters (see Section 2.4.2 for guidance on how the
spatial boundaries of a cold-water refuge are defined).
Step 3
The lower Willamette River segment is a large, floodplain river with
stream widths greater than 100 m and depths greater than 3 m. The
river segment is not wadeable but is navigable by boat; access by car
to specific riverbank locations is limited by adequate roads and private
land. Aerial photography available from Google® Earth (http://earth.
google.com) or other high-resolution sources can be an invaluable tool
for evaluating stream size (i.e., width) and the accessibility of specific
river reaches from roads. Because water depth is more difficult to
evaluate from aerial photography, it is recommended that reconnaissance
be conducted on foot or by boat before surveys of cold-water refuges are
conducted.
4.4. Toolbox
Step 4
Maps, models, and imagery are appropriate tools (Sections 6.1. 6.2. and
6.3) for an initial assessment of cold-water refuges at segment, reach,
and channel unit scales in the lower Willamette River (Sections 5.3. 5.4.
and 5.5).
Methods for in situ identification of cold-water refuges could include
(1) surveys by boat with hand-held thermocouples and towed digital
temperature data loggers, (2) deployment of stationary data loggers,
and (3) tracking offish with temperature-sensitive tags and data loggers
(Section 6.4).
-------
4. Application to EPA guidance on migration corridors for salmon and trout 15
4.5. Assessment
Step 5
The Oregon Department of Environmental Quality used airborne
thermal infrared remote sensing and temperature models to develop total
maximum daily loads (TMDLs) for temperature in the Willamette River.
Thermal infrared images can be used to help identify cold-water refuges
associated with river confluences and thermal heterogeneity at segment,
reach, and channel unit scales. The TMDL models provide information
on cold-water refuges at segment and reach scales.
http: //www. deq. state. or.us/wq/tmdls/tmdls .htm
http://or.water.usgs.gov/proi/will temp/
4.6. Data compilation
and documentation
4.7. Evaluation and
implementation
Maps and imagery for the lower Willamette River are publically
available over a range of spatial scales and can be used to assess
landscape features associated with zones of potential and historical
groundwater/surface-water interactions. These areas are where
cold-water refuges are likely to occur at segment, reach, and channel
unit scales (Section 7.4).
Direct measurement of cold-water refuges in the lower Willamette
River is best accomplished by deploying stationary data loggers at point
locations based on patterns observed in maps, models, and imagery
to target areas likely to contain cold-water refuges. Data loggers may
be used to confirm the locations of cold-water refuges and to monitor
variability in their size seasonally and with different flow conditions.
If resources are not sufficient to deploy stationary data loggers at a
density commensurate with the spatial resolution and extent of interest,
additional surveys with towed data loggers may be required to quantify
thermal patterns in gaps between data loggers.
Step 6
Generate tables and maps as outlined in Section 3.7.
Step?
Evaluate the distribution of cold-water refuges to address EPA Region
10 guidance and Oregon Department of Environmental Quality
water quality standards for the lower Willamette River as outlined in
Section 3.8.
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16 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
5. Classification and characterization
5.1. Hierarchical organization
This section builds on the simple typology introduced in Section 2.4.3
by discussing the various processes that are associated with creating
point and non-point cold-water refuges at different spatial scales.
Landscapes, watersheds, and streams are organized hierarchically in
space and time, and this structure provides a useful framework for
classifying and characterizing cold-water refuges (Table 5.1.1). For the
purposes of this primer, the EPA level-II and -IV ecoregions provide
the landscape context of geology, physiography, vegetation, climate,
soils, land use, and hydrology (Figure 5.1.1). Subsequent levels in the
hierarchy include basins, subbasins, segments, reaches, channel units
(pool/riffle), and microhabitats, which form the templates upon which
cold-water refuges and the processes that create them are shaped. 90-172-
175, 70, 79, 223, 146, 186
5.2. Basin and subbasin
5.3. Segment
Understanding cold-water refuges at lower levels in the hierarchy
requires knowledge of the basin-scale context. For example, cold-water
refuges at the basin and subbasin level are often driven by elevation,
topography, geology, channel slope, and interactions with surface and
subsurface hydrology. Hydrologic landscapes and ecoregions integrate
these patterns and make it possible to draw conclusions about which
basins and subbasins will be cooler than others (Figure 5.2.1). Patterns
of vegetation, soils, and land use provide additional clues about the
thermal potential of watersheds.194'244' n-218-246-125-126-157-164-40-219-242
Cold-water refuges at scales of 0.5-1 km in small rivers and 5-10 km in
large rivers occur at confluences where large tributaries (Strahler order
>4) enter the mainstem and where bounded alluvial valley segments
(BAYS) 'funnel' cooler subsurface water upward into the stream channel
(Figure 5.3.1V Abrupt changes in channel slope also are potential
indicators of thermal heterogeneity associated with downwelling and
upwelling zones at the valley-segment level.16-159-183-20-21-132-14- 23-33-
81, 99, 113, 34, 131, 238
Hypolimnetic releases downstream of dams create segment-scale
thermal discontinuities that are predictable based on the structure and
timing of releases, whereas segment-scale changes in temperature
related to sediment dynamics and differences in thermal loading
(Kent Smith, Yoncalla.net, personal commun., September 10, 2009)
are difficult to differentiate from other processes without developing
process-based models (see Section 6.2) (Figure 5.2.1V 147
htto://www. voncalla.net/Temperature 10.htm
-------
5. Classification and characterization 17
5.4. Reach
Medium-sized tributaries (Strahler order: 3-4) with relatively constant,
cool flow throughout the summer may create reach-scale cold-water
refuges at confluences where the tributaries enter the mainstem.10- 69-98-
216
5.5. Channel unit
Floodplain connectivity in alluvial valleys with high sinuosity, multiple
subsurface pathways, and alluvial fans with glacial meltwater can
create thermal diversity at a reach scale (Figure 5.4.1). but studies that
have investigated how these areas may be used as cold-water refuges
are rare. Reach-scale studies offish and groundwater, hyporheic and
surface-water exchange primarily have focused on spawning site
selection by salmonids where upwelling creates warm-water refuges for
eggs and fry in the winter. 7-16-145-183-16°- 41-14°-186
Where the channel is confined laterally by steep valley walls, thermal
heterogeneity may be associated with vertical as opposed to lateral
exchange of hyporheic and surface water. These upwelling and
downwelling zones may occur at discontinuities, or "steps", in the
longitudinal elevational profile of headwater streams at the reach and
valley scale. Within bedrock-dominated reaches, thermal heterogeneity
may be minimal due to a lack of vertical and lateral hyporheic exchange
through the streambed and floodplain. Alluvial valleys are more likely
to have reach-scale cold-water refuges formed by hyporheic processes,
whereas bedrock canyons primarily may be limited to tributary sources
(see Section 5.3V 127- 247- 238
Cold-water refuges at the scale of pools and riffles are associated
with small tributary confluences (Strahler order: 1-2), springbrooks
(Figure 5.5.1). side channels (Figure 5.5.2). and wall-base channels
(Figure 5.5.3) that occur in a wide variety of stream types throughout
the Pacific Northwest. Cold-water patches also occur at smaller spatial
scales (see Section 5.6) and are created by similar processes where
groundwater and subsurface flow emerges from the streambank into the
main stream channel. "8- 22- 78- 45-7- 44- 6- 47- 213
5.6. Microhabitat
Cold-water refuges and their use by salmonids at the microhabitat level
are well described in the literature. Microhabitat cold-water refuges
occur in thermally stratified pools and where bedform topography
creates strong vertical hydraulic gradients. Alcoves and lateral seeps
also are commonly found along riverbanks (Figures 5.6.1 and 5.6.2).
but they may not be in locations that are easily accessible to fish. 28'173'
151, 162, 166, 150, 29, 95, 104, 54, 8, 77, 96, 9, 79, 78, 106, 85, 222
Shade from overhanging vegetation or steep valley walls can affect
cold-water refuges at the microhabitat scale by preventing warming.
214, 127, 200, 249, 161, 251
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18 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
6. Identification and prediction
6.1. Maps
Publicly available paper and digital maps are useful for determining
the landscape context and hydrologic characteristics of rivers prior
to identifying cold-water refuges at segment, reach, and channel unit
SCaleS. 172.43.175.244.246
http://www.epa.gov/wed/pages/ecoregions/level_iv.htm
http://water.usgs. gov/GIS/metadata/usgswrd/XML/hlrus .xml
The Oregon Department of Environmental Quality has created
1:100,000-scale fish use designation maps that provide assessments of
habitat for coldwater fish based on field surveys (Figure 6.1.1). 21°
http://www.dea.state.or.us/wa/rules/div041tblsfigs.htmtft2
6.2. Modeling
6.3. Remote sensing
Although these maps are not based directly on temperature, the spatial
patterns of cold-water areas correspond remarkably well with large-scale
database records of actual stream temperature (Figure 6.1.2).
USGS l:24,000-scale topographic quadrangles and the 30- and 10-m
digital elevation models derived from these maps have been used
very effectively to identify segment- and even reach-level patterns of
hyporheic exchange corresponding to cool-water areas (Figures 5.3.1
and 6.1.3). ", m 14
A wide variety of process-based and statistical models have been
developed to predict stream temperature at basin, segment, and reach
levels (Figure 6.2.1). These tools have become more accessible to
resource managers as geographic information system (GIS) software
has improved and the available pool of employees with programming
experience has increased.2S-13-136'U2-71-3S-93-19S-92-169-3'62'4-63-123'm
The availability of high-quality, high-resolution satellite imagery has
increased dramatically in the last decade through Internet mapping
services, which provide a spatial resolution that is sufficient even
for detecting cold-water areas, such as springbrooks in small rivers
(Figure 6.3.1):
TerraServer: http ://www.terraserver.com
Google6 Earth: http://earth.google.com
Google® Maps: http://maps.google.com
-------
6. Identification and prediction 19
6.3.1. Aerial photography
6.3.2. LiDAR
6.3.3. Thermal infrared
imaging
High-resolution color digital orthophotography is now available for
most of the Pacific Northwest and Oregon.
National Agriculture Imagery Program (NAIP):
http://165.221.201.14/NAIP.html
Oregon Imagery Explorer:
http://oregonexplorer.info/imagery
Even higher resolution (<1 m) airborne color imagery is becoming
more affordable and has been used to map fine-scale channel features
associated with channel complexity and subsurface flow paths. 241-148
Current methods for detecting groundwater with remote sensing are still
in development but are likely to be increasingly used in the future. 31- n4-
18, 67, 68, 179
Technology that uses airborne light detection and ranging (LiDAR) to
map the elevation of the water surface and surrounding floodplain with
sub-meter accuracy currently offers the greatest potential for identifying
floodplain features associated with cold-water refuges and groundwater
inputs at segment, reach, and channel unit scales. LiDAR that utilizes
the blue-green portion of the electromagnetic spectrum is capable of
mapping the streambed by penetrating the water.156
Airborne thermal infrared (TIR) remote sensing has been used
extensively throughout the Pacific Northwest to map cold-water refuges
and thermal heterogeneity in rivers at channel unit to basin scales using
helicopters and fixed-wing aircraft (Figures 6.3.3.1. 6.3.3.2. 6.3.3.3. and
6.3.3.4: Appendix B). In some cases, airborne TIR imagery has been
related directly to field surveys offish locations and cold-water refuges,
but more work is needed in this area. Limitations of the approach are
that (1) dense riparian canopy and overhanging streambanks can block
the sensor's view of the water, and (2) in deep, slow-moving rivers,
the surface temperature may not be indicative of the overall water
temperature or of cold-water areas near the river bottom. 229-227-22- 23°-84-
83, 228, 138, 141, 225, 47, 63, 226, 105
Recent advances in sensor technology have led to the development of
relatively low-cost (about $2,000) hand-held TIR imagers that could be
used for ground-based assessments of thermal heterogeneity in small,
wadeable streams.
http://www.professionalequipment.com/flir-i7-infrared-camera-i7/
thermal-infrared-camera/
6.4. Direct measurement
Techniques for locating cold-water refuges directly with hand-held
sensors or probes that are towed through the river also have improved
and become more accessible in the last decade with the improved
accuracy of portable global positioning systems (GPS) and the small
size and high storage capacity of digital temperature data loggers.
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20 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
6.4.1. Thermocouples and
probes
6.4.2. Stationary data loggers
6.4.3. Tagged fish
A fast-response, hand-held thermocouple mounted on a telescoping
rod is one of the least expensive and most precise ways to detect
thermal anomalies and map cold-water refuges in wadeable streams
(Figure 6.4.1.1). Because the digital readout displays near instantaneous
changes in temperature, the spatial extent of small- to medium-
sized cold-water refuges can be mapped before ambient temperature
has changed. 78'1
In large, deep rivers where a spatially continuous transect of water
temperature, depth, conductivity, or resistivity is needed to detect
groundwater inputs, a 'profiling' technique can be used (Figure 6.4.1.2V
In this approach, the temperature sensor is towed behind a boat or
on foot (i.e., in wadeable streams) (Figure 6.4.1.3): data logging of
temperature (or conductivity, depth, etc.) and geographic coordinates
occurs simultaneously. Localized decreases in temperature (i.e.,
'troughs' in the longitudinal profile) indicate possible cold-water areas
(Figure 6.4.1.2V 224- 217-133-14- 231- 50- 24°-199
Stationary data loggers include digital temperature data loggers and
distributed fiber optic temperature sensing. Digital temperature data
loggers have been used in fisheries and water quality monitoring since
the 1990s and are useful for characterizing the temporal patterns of
cold-water refuges once they have been located with other methods.
Digital temperature data loggers are useful for quantifying spatial
patterns in stream temperature at reach, segment, and watershed scales
but are less effective for locating cold-water refuges at microhabitat
and channel unit scales because of their small spatial 'footprint' (about
10 cm). Digital temperature data loggers can be deployed in spatially
dense arrays (i.e., spaced at 1-2 m intervals) to evaluate thermal
heterogeneity in small areas, but this approach typically is not extended
over many kilometers due to the cost and logistical difficulties of
deploying thousands of data loggers 7S-208-209
Recent developments in distributed temperature sensing (DTS)
have made it possible to map spatial and temporal heterogeneity of
groundwater, hyporheic, and surface-water interactions because the
fiber optic cable can measure water temperature at a spatial resolution
of less than 1 cm over multiple kilometers. Temperature measurements
at this fine spatial resolution also are recorded at a very fine temporal
resolution. A present disadvantage of the method is that the cable may
not be able to withstand high water velocities and may break, making
deployment in remote locations problematic. 57-116
Methods for monitoring the internal temperature offish in the wild
also have dramatically improved, such that it is possible to log their
temperatures continuously overtime. This method, when combined
with radio telemetry or passive integrated transponder (PIT) tags, offers
an unprecedented view into the thermal ecology offish in the natural
environment. In order to determine whether fish are using cold-water
refuges, other methods of direct measurement must be used to quantify
the spatial and temporal variability of water temperatures available to
the fish 24'188-30' 220'190'215' n5
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7. Protection and restoration 21
7. Protection and restoration
7.1. Scientific guidance for
policy decisions
7.2. The shifting mosaic of
thermal landscapes
7.3. Ecological complexity
To provide the science necessary for making policy decisions regarding
cold-water refuges, a conceptual framework is needed that is consistent
in terminology and provides a means to (1) quantitatively monitor
the distribution of cold-water refuges in a spatially explicit manner,
(2) prioritize areas for protection, and (3) restore the processes that
create and maintain thermal diversity in riverine landscapes. An example
of such a framework is provided in Figure 7.1.1.168-154-189- 59-196- 236
The fact that thermal landscapes are dynamic in time and space
indicates that they can not be easily summarized in metrics that can
be translated into water quality criteria. However, this challenge is
not insurmountable and can be addressed by explicitly considering
temporal dynamics as an integral part a functioning and resilient
riverine landscape. 234-183-203-108-18°-102
Given the complexity of human and natural systems that have reduced
thermal diversity in river systems, restoration will require consideration
of cold-water refuges within a broad context including (1) physical
factors, such as riparian condition and hydrologic connectivity in the
floodplain, (2) biological interactions with native and non-native species
that may influence the effectiveness of cold-water refuges for coldwater
fish, (3) effects on other aquatic species and life history stages, and
(4) unanticipated human effects, such as climate change. 88-232- n9-239-
139, 167, 250, 191, 49
7.4. Predictive modeling in
space and time
Advances in qualitative and quantitative modeling to predict the
locations of current cold-water refuges and prioritize areas for
restoration will continue to make it easier for scientists to provide the
kind of information that managers need in order to make informed
decisions that are based on the best available science.135'169-im-138'221-
207, 121
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22 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
7.5. Restoration as
experimentation
7.6. Conclusion
Are current distributions of cold-water refuges sufficient to support
migration and rearing of juvenile and adult salmonids within a given
riverscape? If not, what improvements will be necessary in the size,
frequency, or characteristics of refuges to achieve goals for salmonid
management in the future? To answer these questions, approaches are
needed to assess the suitability of current or future thermally diverse
riverscapes for the successful completion of salmonid life histories.
For example, combining field data collection, predictive modeling
with validation, and landscape scenarios of alternative futures has
much to offer for protecting and restoring cold-water refuges at scales
from localized reaches to entire floodplain segments (Figure 7.4.1).
By reconnecting the river with the floodplain and restoring riparian
vegetation, potential hydrologic processes that create thermal
heterogeneity may be restored. This integrated approach certainly will
be required to address the challenges posed by climate change, which
will put additional constraints on the capacity of rivers to maintain the
processes that create thermal diversity.143-137-124-15- 117-165
To effectively restore the hydrologic processes that create thermal
diversity, manipulation of entire riverine landscapes may be required,
not just of distinct reaches or channel units. Hyporheic processes occur
laterally, longitudinally, and vertically and do not have easily defined
boundaries. Thus, active approaches to restoring these processes by
installing instream structures and engineering new channels may be
difficult to apply and test in the field. When passive restoration and
reestablishment of riparian vegetation are not enough to reconnect the
river with the floodplain, re-engineering may be used as an experiment,
with monitoring in place to adapt the approach as needed. For example,
the current Upper Middle Fork John Day Restoration Project being
conducted by the Confederated Tribes of the Warm Springs Indian
Reservation, the Bureau of Reclamation, and the U.S. Forest Service
is one such program and provides a case study on restoring cold-water
refuges (Figures 7.5.1. 7.5.2. and 7.5.3V 26-129- 85- no' n6-1U- m
A goal of this primer is to help bridge the gap between research and
management of cold-water refuges through outreach and technology
transfer. The many references to completed and on-going work in
this area demonstrate that much of the research on cold-water refuges
is closely tied to on-the-ground issues and questions brought up in
discussions between scientists and managers. In providing a more
complete view of cold-water refuges across a range of spatial and
temporal scales, this document will lead to more discussions between
scientists and managers about the complexity of river systems.
Maintaining thermal diversity across multiple spatial scales—not just
small-scale cold-water refuges in wadeable streams that are most easily
detected—is essential for long-term viability of coldwater stream fish.
This complexity, although daunting, reflects the potential capacity of
riverine landscapes to recover thermal diversity through restoration and
ultimately provide the habitats required for the long-term viability of
coldwater fish. 212-76-245- 70-237
-------
8. Figures and table 23
8. Figures and table
Movement
to cold-water
refuge
n,™,,,th /^ Predator
Growth (G) avoidance (P)
Figure 2.4.1.1. Performance capacity of fish in cold-water refuges (adapted from
Schreck and Li, 1991). The performance phenotype (e.g., disease resistance [D], growth
[G], and predator avoidance [P]; see triangle on left) of a fish is set by the genotype,
which itself is the result of genetics, environment, history, and ontogeny. When a fish
moves along arrows A, B, or C to a cold-water refuge, the performance vectors indicating
the capacity to resist disease, avoid predators, and grow (see vectors D, P, and G) may
increase or decrease, creating a new realized performance capacity based on the unique
physical and biological conditions of the cold-water refuge. For example, cold-water
areas may increase (A) or decrease (B) all performance capacities equally, or more often
than not there will be tradeoffs (C) where the capacity for growth increases, disease
resistance is unaffected, but predator avoidance decreases, or any combination thereof.
204
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24 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Figure 2.4.1.2. Rainbow trout in Joseph Creek in northeastern Oregon exhibit size hierarchy in occupying a cold-water
refuge, with the largest individual in the coldest thermal zone (see Ebersole and others, 2001). When the availability and
size of cold-water areas is limited, fish may elect habitats that are less desirable for growth and disease resistance (i.e.,
through crowding) in order to minimize deleterious physiological effects of high water temperature. Photograph taken by
J. Ebersole in 1994.77
-------
8. Figures and table 25
Figure 2.4.1.3. Adult spring chinook salmon (right) in the Middle Fork John Day River, Oregon, have been observed
behaviorally thermoregulating in mid-summer by locating cold alcoves (left). Such habitats may provide temporary thermal
refuge but may be insufficient in size or frequency throughout a river to promote long-term persistence at elevated water
temperatures. Cold alcoves typically are shallow and offer limited cover for adult salmon. Photographs taken in 1993 by T.
Reeve (Bonneville Environmental Foundation).
-------
26 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Xnbutary
26°C
,, .- 2<
Marn tihatmef
,
Su bsurface J nputs -25°C
' ^-V - ?3r"-r ,-' ** X"»^" "' -- • v- *"' -- ' - *^VVS
r*s^£fcO£* mfl^
WA <.^v s •-: _ ^w-' .'-•T*.
^^f t-MV^
^X>*
Figure 2.4.1.4. Small differences in water temperature over short distance are detected and used by coldwater fish, such
as the rainbow trout depicted in the image of the Middle Fork John Day River, Oregon. Subsurface inputs originating in
the tributary emerged from the cobble bar and constituted a cold-water refuge approximately 2°C cooler than the main
channel, but the refuge lacked size and other characteristics (cover and food) necessary for survival and growth. The
temperature was 2-3°C greater than the thermal tolerances for this species, and the fish elected thermal refuge over
predator avoidance in allowing the photograph to be taken at close range. Photographs taken in 1994 by C. Torgersen.
-------
8. Figures and table 27
Coldwater patch
thermal regime
Z
Within-patch fish
assemblage structure
Physico-
chemical
suitability
Competition and
predation risks
Water
chemistry
(dissolved
oxygen,
toxics)
Refuge
for
during
Coldwater patch
depth
Foraging
opportunities
Riparian canopy
composition and
density
Coldwater patch
isolation distance
Coldwater patch
frequency
Figure 2.4.1.5. The effectiveness of a cold-water refuge depends on multiple biological and physical factors in addition
to temperature. Direct physical impacts (wide arrows) on the fish are in turn affected by a suite of indirect factors (narrow
arrows) that determine the capacity of a given refuge to provide protection during periods of thermal stress.
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28 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diwersity in ftiwerine Landscapes
CO
_o
'CT>
o
,Qo
-Q =
<+- CO
O.N
o
Species
Major evolutionary
group
Geographic race
Population
Individual
Pool / riffle
Reach
Segment
Figure 2.4.2.1. Hierarchical levels of biological organization for stream salmonids and their persistence
at different spatial scales (adapted from Frissell and others, 1986, Currens 1997, and Gresswell 1999),
Cold-water refuges occur at similar spatial and temporal scales and affect fish at corresponding levels
of biological organization. For example, refuges at reach, pool/riffle, and smaller spatial scales influence
individuals over short time scales, whereas populations respond to thermal heterogeneity at segment or
larger spatial scales. Maintaining thermal diversity across multiple spatial scales—not just small-scale
cold-water refuges in wadeable streams that are most easily detected—is essential for long-term viability
of coldwater stream fish. 90-se'm
-------
8. Figures and table 29
Large patch / long duration
(a)
V)
CD
c
o
CO
Small patches / short duration
Isolated patch
(c)
Isolated patch
unfavorable
unfavorable
x102
x103
Space
Time
Figure 2.4.2.2. Variability in the favorableness of cold-water refuges in space and time (adapted from
Southwood, 1977). For a given species, the favorableness of a cold-water refuge (cross-hatched area) varies
spatially (length, area, or volume) from large (a) to small (b). In a fluctuating thermal environment, favorableness
also varies temporally from long (a) to short (b) in duration. Cold-water refuges vary in degree of isolation (c) if
movement between patches is impeded by unfavorable conditions or if an organism is only able to move between
patches while conditions are favorable (i.e., at night when stream temperatures may be lower). 211
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30 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Figure 2.4.2.3. Cool-water areas that are isolated from the main channel also may be shallow and lack overhead
cover, channel complexity, and water depth due to altered riparian vegetation (left channel), thereby increasing the
susceptibility of fish to predation while they are using these refuges (inset) (Grande Ronde River, Oregon). Photographs
taken in 1998 by J. Ebersole.
-------
8. Figures and table 31
Less mixed
(a)
0
Summer (high elevation)
(b)
'/
Summer (low elevation) Ns\
Early
Late
Time of day
Figure 2.4.2.4. Defining cold-water refuges based on changes in temperature, time, and
distance. Change in temperature (At) divided by change in distance (Ad) is plotted versus
distance (d) along a transect from the coldest part of the refuge (f0)to the point at which
temperature (f,) no longer changes with distance;this graphical approach provides a
quantitative means for determining the spatial boundaries of a cold-water refuge (a). The
two curves illustrate hypothetical differences between 'less mixed' (solid line) and 'more
mixed' (dashed line) hydraulic environments (a). These temperature changes as a function of
distance may be evaluated at a point in time, or by using standard temperature metrics (e.g.,
daily maximum, mean, or 7-day average daily maximum). For measurements at a given time,
an appropriate time of day for delineating the spatial extent of cold-water refuges can be
estimated by determining the time at which the difference between f0 and t} is at a maximum
(b). These times may vary among geographic locations and elevations (long- versus short-
dashed lines) depending on the time of day of maximum ambient water temperature (b).
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32 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
OJ
O3
-------
8. Figures and table 33
Riffle
Flow
direction
benthic zone
concentration, Eh, temperature
Figure 2.4.3.1. Hyporheic exchange in lateral (upper left) and vertical (upper right) dimensions in streams (adapted
from Hester and Gooseff, 2010). Hyporheic exchange occurs laterally (upper left) through point bars and meander bends.
The cross-sectional view in the upper right diagram illustrates down- and up-welling (white and grey bars, respectively)
zones at the pool/riffle scale as water flows through topographic relief in the streambed. Vertical zones of stream surface
flow, hyporheic flow, and groundwater flow (lower left) correspond with gradients in dissolved oxygen, redox state, and
temperature associated with increasing depth (lower right). Hyporheic exchange occurs over a range of spatial scales
from channel units and microhabitats (depicted above) to entire river segments (see Section 5.3). '"
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34 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Figure 2.4.3.2. Hyporheic connectivity through alluvial deposits of gravel and cobble substrate is illustrated in a tracer
experiment using red dye (rhodamine WT), which is shown emerging from the streambank (left inset) after being released
at an upstream location in the floodplain (right inset). The blue dashed arrow in the central image indicates the direction
of subsurface flow. The experiment was conducted in the northern foothills of the Brooks Range, Alaska. Cool water flows
along hyporheic pathways, such as those shown above can emerge at varying temperatures depending on the depth and
distance of subsurface connections. Photographs taken by Breck Bowden (University of Vermont) and Michael Gooseff
(Pennsylvania State University) are from Hester and Gooseff (2010).'"
-------
8. Figures and table 35
Table 5.1.1. Hierarchical organization of cold-water refuges and associated geographical and physical drivers in the
Pacific Northwest,
System
I ewe I
Spatial
scale
Driwers
Type of cold-water refuge
Time scale
(fears)
Ecorcgion 104~105km2 Geology and climate (e.g..giaciation,
volcanism. uplift), latitude
Basin and 102-103km2 Elevation, air temperature,
subbasin precipitation, snowpack,
hydrogeology
Segment 103 m
Reach
102m
Channel unit 10' m
Microhabitat
Valley segment type, groundwatcr/
surface-water interactions,
hyporheic exchange, longitudinal
position, land use (timber harvest,
grazing, mining), land cover type
(urban, forest, grassland)
Surface and groundwater inflow.
sediment type, grain size and
sorting, floodplain connectivity
Channel morphology, horizontal
and vertical mixing (thermal
stratification)
Hydraulic head differential caused
by structural features (wood and
boulders) and bedrock fractures
Relict habitats from Pleistocene
giaciation
Alluvial valley segment with
high groundwater/surface-water
exchange; topographic shading
and vegetation (e.g., canyons and
riparian gallery forests)
Springbrooks. side channels, and
tributary junctions
Alcoves and stratified pools
Springs and groundwater seeps
>104
Summer streamflow derived from 103
sustained, cold groundwater inputs
or snowmelt
102
101
10°
<104
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36 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Level-Ill ecoregions of PNW
Blue Mountains
Cascades
Central Basin and Range
Coast Range
Columbia Plateau
Eastern Cascades
Slopes and Foothills
Idaho Batholith
Klamath Mountains
Middle Rockies
North Cascades
Northern Basin and Range
Northern Rockies
Puget Lowland
Snake River Plain
Wasatch and
Uinta Mountains
Willamette Valley
Wyoming Basin
Level-IV ecoregions of Oregon
50
100
200km
Figure 5.1.1. Ecoregions are based on geology, physiography, vegetation, climate, soils, land use, and hydrology and provide a
landscape context for investigating potential broad-scale influences on thermal heterogeneity in rivers and streams. The diversity of
landscapes in EPA level-Ill and level-IV ecoregions in the Pacific Northwest includes a corresponding varied array of riverscapes.
-------
8. Figures and table 37
Basin and subbasin scale
John Day Basin
Level-IV ecoregions
Cold Basins
Continental Zone Foothills
Continental Zone Highlands
Deschutes/John Day Canyons
John Day/ Clarno Highlands
John Day/Clarno Uplands
Maritime-Influenced Zone
Melange
Mesic Forest Zone
Pleistocene Lake Basins
Subalpine-Alpine Zone
Umatilla Dissected Uplands
Umatilla Plateau
28 -i
U
o
CD
•i-*
£
CD
Q.
E
CD
26 -
24 -
22 -
20 -
18 -
16 -
Middle Fork John Day R.
5 August 1998
North Fork John Day R.
4 August 1998
10 20 30 40 50 60
Distance upstream (km)
70
80
Figure 5.2.1. EPA level-IV ecoregions and variation in longitudinal patterns of summer water
temperature derived from airborne TIR remote sensing in the North and Middle Forks of the John Day
River, Oregon. The more pronounced rate of increase in temperature in a downstream direction in the
North Fork is associated with the rapid succession in a downstream direction of landscape transitions
through which the river flows (i.e., subalpine, mesic forest, melange, cold basins, and John Day/Clarno
highlands). The Middle Fork in comparison has a flatter longitudinal profile and originates at lower
elevation and in more xeric conditions. Overall longitudinal change in temperature in the Middle Fork is
less than in the North Fork over the same distance, but the Middle Fork still exhibits spatial variability at a
5-10 km scale due to local effects, such asthermal loading and hydrologic connectivity with hillslope and
floodplain processes.
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38 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Segment scale
Figure 5.3.1. A bounded alluvial valley segment (BAVS) in the Elk Creek drainage, Montana. The dimensions of
the BAVS were measured directly from USGS topographic 7.5 quadrangle maps (1: 24,000 scale) (A-A' = length,
B-B = maximum valley bottom width). The cross-sectional diagram (A-A) illustrates how reach-scale (large
arrow) and bedform-scale (small arrows) hyporheic exchange typically occurs within a BAVS. The stippling
denotes the alluvial valley fill (adapted from Baxter and Hauer, 2000). Cold-water areas are most likely to occur at
the downstream terminus (A ) of the BAVS.!6
-------
8. Figures and table 39
•Y
*••»..;' '\
Tributary
confluence
' , „
•• <. .-^; ;"''•••••'•••'
TV "<^ rr^fc/^
Figure 5.4.1. Reach-level cold-water refuges at the scale of hundreds of meters in an alluvial floodplain reach (depicted
above) maybe associated with the combined and interactive effects of tributary confluences, sinuosity, and floodplain
connectivity via multiple surface and subsurface flow pathways (dashed arrows). The illustration above depicts potential
locations of cold-water refuges where field-based measurements could be collected. Source: Queets River, Olympic
Peninsula, Washington (Google® Earth).
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40 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Channel unit scale
Springbrook
Figure 5.5.1. Floodplain springbrooks have steady, shallow, spring-like flow (blue fill in the diagram at left) emerging
downstream from bars (stippling) near floodplain depressions and abandoned channels. The black circle (left inset) shows
the area depicted in the photograph (right). Springbrooks are most common in river systems with active transport of coarse
sediment and high hydraulic transmissivity associated with recent glaciation (e.g., the Flathead basin in Montana and the
Olympic Peninsula in Washington) but may occur at a smaller scale in lower-energy rivers and streams (see Figure 3b in
Torgersen and others, 2001) (adapted from Ebersole and others, 2003a). Photograph taken in 1993 by J. Ebersole.78-228
-------
8. Figures and table 41
Channel unit scale
Cold side
channel
Figure 5.5.2. Cold side channels (blue fill in the diagram at right) often emerge from seasonal overflow channels. The
black circle (right inset) shows the area depicted in the photograph (left). Flow may become intermittent or remain
continuous at the downstream end of the channel, depending on the bar surface morphology (stippling in diagram on right)
and cold-water source (e.g., hillslope groundwater) (adapted from Ebersole and others, 2003a). Photograph taken in 1993 by
J. Ebersole.7S
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42 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Channel unit scale
Figure 5.5.3. Up-valley oblique view of a meandering river and wall-base channels (circled) in the Clearwater River on
the Olympic Peninsula, Washington, showing examples of associated cold-water habitat types (adapted from Peterson
and Reid, 1984). m
-------
8. Figures and table 43
Cold alcove
Microhabitat scale
Figure 5.6.1. Cold alcoves (blue in diagram at left) are a common cold-water patch type and are typically observed
emerging from relict channels/swales where stream channels converge with valley walls downstream from floodplains or
large gravel point bars (stippling on diagram at left) (adapted from Ebersole and others, 2003a). The black circle (left inset)
shows the area depicted in the photograph (right). Photograph taken in 1998 by J. Ebersole.7S
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44 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Lateral
seep t£
Microhabitat scale
. .
Figure 5.6.2. Lateral seeps (blue) are low-volume but relatively common cold-water areas that occur where the active
channel directly intercepts groundwater flow through a terrace, alluvial fan, or hillslope.The black circle (left inset) shows
the area depicted in the photograph (right). When these areas are located near the main flow downstream of point bars
(stippling), they may be difficult to detect, except during low-flow conditions when the surrounding water is warm (adapted
from Ebersole and others, 2003a). Photograph taken in 1998 by J. Ebersole. n
-------
8. Figures and table 45
Designated Fish Use*:
f~\ I Bull Trout Spawning
/ \_7 &Juvenile Hearing
s~\ I Core Cold-Water
/ \J Habitat
Salmon & Trout"
Rearing & Migration
r\ j Salmon & Steel he ad
/ \J Migration Corridors
Figure 6.1.1. Designated fish use maps include qualitative, broad-scale assessments of thermal requirements for
salmonids in 15 major hydrologic basins in Oregon and provide spatial context for evaluating thermal potential in riverine
landscapes at a state-wide level. In the John Day River Basin (depicted above), the coldest sections of stream are
represented by the year-round distribution of bull trout (<12°C) (blue), followed by "core cold-water habitat" (<16°C)
(green), salmon and trout rearing and migration (<18°C) (orange), and salmon and steelhead migration corridors (<20°C)
(magenta), which generally are too warm during the summer to support coldwater salmonids (see Figure 5.2.1 for
additional information on map orientation, scale, and the names of the main forks). Water temperatures associated with the
designated fish use categories refer to the 7-day average daily maximum as outlined in the Oregon water quality standards.
Source: Oregon Department of Environmental Quality, Water Quality Program, http://www.deq.state.or.us/wq/rules/
div041tblsfiqs.htm#t2
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46 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Water
temperature (°C)
« <12
O 12-14
O 14-16
O 16-18
O 18-20
>20
Figure 6.1.2. Basin-scale variation in mean water temperature for August (1992-2003) in the John Day River basin,
Oregon. Multi-agency coordination in digital temperature data logger deployment and data analysis facilitates spatially
explicit modeling and the identification of cold-water refuges at a subbasin scale from a stream network perspective.
Broad-scale databases provide the spatial context necessary for identifying cold-water refuges at multiple spatial scales
(see Table 5.1.1). Sources: Carol Volk and Chris Jordan (NOAA Fisheries, Seattle, Washington and Corvallis, Oregon; Ruesch
and others, in review). m
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8. Figures and table 47
Figure 6.1.3. Observed and predicted zones of cooling and hyporheic potential based on 10-m digital elevation models
(OEMs) of floodplain and channel geomorphology in the Umatilla River, Oregon. Geomorphic parameters were derived
from OEMs and included in the model predicting hyporheic potential based on sinuosity, stream gradient, floodplain
width, and valley width (O'Daniel, 2005). Source: Scott O'Daniel, GIS Program, Confederated Tribes of the Umatilla Indian
Reservation, Pendleton, Oregon).1B9
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48 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
30 T
0)
3 22
-i-j
CO
o> 20 f
Q.
E
0)
CO
18:-
16:-
14
12 }
10
o
o Kinetic temperature (ground truth)
— Radiant temperature (TIP)
— Predicted temperature (model)
132 147 162 177 192 207 222 237
Distance upstream (km)
252
267 282
Figure 6.2.1. Predicting cold-water refuges at the kilometer scale with spatially explicit, process-based modeling. The
above longitudinal profile of water temperature in the upper Grande Ronde River (Oregon) depicts radiant temperature
acquired during an airborne thermal IR overflight (August 20,1999), in-stream measurements of kinetic temperature,
and calibrated model predictions. Distance upstream (x-axis) was determined from the river mouth (Oregon Department
of Environmental Quality Upper Grande Ronde Subbasin Total Maximum Daily Load [TMDL], April 2000, Appendix A:
Temperature Analysis, p. A-86) (adapted from Handcock and others, in press).105
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8. Figures and table 49
Figure 6.3.1. High-resolution Google® Earth imagery of a springbrook in the upper Middle Fork
John Day River, Oregon, illustrates the accessibility and utility of readily available Internet imagery
for identifying potential locations of cold-water refuges in small to large rivers. Riparian canopy
may obscure precise locations of cold-water areas but also can provide an indication of subsurface
flow pathways leading to cool-water areas as indicated above by different levels of greens in
floodplain vegetation.
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50 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Figure 6.3.3.1. Helicopter and gimbal mount (inset) for airborne TIR remote sensing of stream temperature. The thermal
imager (8-14 urn wavelength) and paired daylight video camera (lower left inset) are controlled from inside the aircraft and
are georeferenced with a global positioning system (GPS) (for more detail see Torgersen and others, 2001228 and Handcock
and others, in press). Photographs taken in 1995 by C. Torgersen. W5
-------
8. Figures and table 51
cool
coldwater
seep
warm
13°C
17°C
Figure 6.3.3.2. Aerial images in (a) natural color and (b) airborne TIR of a cold-water seepage area in the Crooked River,
Oregon, in a high-desert basalt canyon (August 27, 2002). The colored portion of the TIR temperature scale spans the
approximate range in water-surface temperature in the image; land and vegetation surface temperature are depicted in
shades of gray. Lateral cold-water seeps, such as the one depicted above, are relatively small in area but provide important
cold-water refuges for salmonids (Bureau of Land Management; Watershed Sciences, Inc., Corvallis, Oregon) (adapted
from Handcock and others, in press).105
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52 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
subsurface
flow
(b)
cool
warm
15°C
20°C
25°C
Figure 6.3.3.3. Aerial images in (a) natural color and (b) airborne TIR of groundwater springs flowing into the upper Middle
Fork John Day River, Oregon, in a montane meadow (August 16, 2003). See Figure 6.3.3.2 for an explanation of the color
and grayscale thermal classification. Complex subsurface hydrologic flow paths and areas of increased soil moisture
adjacent to the wetted channel are revealed by lower temperatures compared to the surrounding landscape (Bureau of
Reclamation; Watershed Sciences, Inc., Corvallis, Oregon) (adapted from Handcock and others, in press). W5
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8. Figures and table 53
(a)
(b)
cool
125m
15°C
sprng-
brook
warm
20°C
25°C
Figure 6.3.3.4. Aerial images in (a) natural color and (b) airborne TIR showing thermal heterogeneity in a complex
floodplain of the Willamette River, Oregon, which flows through a large, low-elevation agricultural valley (July 22, 2002).
See Figure 6.3.3.2 for an explanation of the color and grayscale thermal classification. Radiant water temperature varies
laterally from the cooler and relatively homogeneous thalweg and main channel to warmer backwaters and disconnected
channels. A springbrook is indicated with a black arrow where relatively cooler hyporheic flow emerges from the
unconsolidated substratum of a large riverine island (Oregon Department of Environmental Quality; Watershed Sciences,
Inc., Corvallis, Oregon) (adapted from Handcock and others, in press). m
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54 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Figure 6.4.1.1. Rapid temperature assessment in wadeable streams with fast-response thermocouple probes. Locations
of cold-water areas can be identified by walking through or along the stream and sweeping the extendable probe along the
stream bottom. The near instantaneous response of the thermocouple and digital readout of the instrument (Atkins, Inc.,
Models 35200 and 39658) are essential for identifying thermal anomalies with the pole-mounted probe. Photographs taken
by J. Ebersole in 1997, Mark Coleman in 2009 (Coleman Ecological, Inc., personal commun.), and Nancy Raskauskas in 2004
(Oregon State University). http://www.techinstrument.com/acatalog/Digital Thermometers Thermocouple.html
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8. Figures and table 55
Distance downstream (mi)
Figure 6.4.1.2. Towable temperature/pressure transducer probe for mapping thermal anomalies and water depth in large,
deep rivers that are navigable by raft or inflatable kayak. The user tows the probe downstream and maps spatial variation
in temperature (lower right: temperature in black and depth in green) at 1-2 second intervals by synchronizing the data
logger time stamps with geographic coordinates collected simultaneously using an on-board global positioning system
(GPS). Spatial variation in water temperature depicted in the lower right panel was measured in the upper Yakima River,
Washington, in September 2001. Source: John Vaccaro, U.S. Geological Survey, personal commun. (see Vaccaro and
Maloy,2006).23'
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56 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
500 1000 1500 2000 2500 3000 3500
Distance Upstream (m)
Figure 6.4.1.3. Miniature temperature mapping system designed for evaluating fish response to thermal heterogeneity
in wadeable streams. The user pulls the external-probe digital temperature data logger (lower left) downstream and
maps the longitudinal temperature profile (lower right) at 1-second intervals by synchronizing the temperature data with
geographic coordinates collected simultaneously using the track-log function of a hand-held global positioning system
(GPS). Photographs taken and data collected in 2009 by Jonny Armstrong, University of Washington, unpublished data (see
also Ruff and others, 2011).'33
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8. Figures and table 57
1. Assess - Characterize cold-water refuges via direct and indirect methods
Design an assessment approach using a combination of the following tools
based upon needs and available resources (Sections 3, 5, and 6)
A. Ground-based surveys
• Labor and time intensive for field
crews
• Enables identification and mapping of
physical and chemical characteristics of
cold-water refuges at small scales
(1-100 m)
B. Temperature
data loggers
• Point measure-
ments require many
sensors to detect
spatial pattern
• Characterizes
C. Airborne remote
sensing
• Spatially extensive
snapshot
• Characterizes spatial
pattern at small and large
scales(10°-105m)
D. Models and maps
• Empirical associations and
statistical relationships or
process-based models
• Can be widely extrapolated with
error estimates
• Enables prediction and projection
of change overtime
2. Protect - Ensure continued functioning of processes creating and maintaining refuges
Identify critical processes responsible for creating and maintaining thermal diversity and consider these
processes in an ecological context (Sections 1.1, 1.2, 2.1, 2.4, and 5)
A. Evaluate physical
processes
• Flow regime and seasonality
• Channel form and ground- and
surfacewater exchange
• Riparian vegetation and shade
• Floodplain connectivity
B. Determine ecological
context
• Physiological requirements of spp.
• Performance vs. realized capacity:
growth, predation, disease,
competition
C. Protect and maintain key
structures and functions
identified in Steps 1, 2a, and
2b.
3. Restore - Rehabilitate structure and function of refuges
Use understanding gained in Steps 1 and 2 to rebuild and regain lost
system capacity for creating thermal diversity (Section 7)
Figure 7.1.1. Conceptual model outlining steps for assessing, protecting, and restoring cold-water refuges and thermal
diversity in riverine landscapes. Sections are specified at each step and indicate locations in this document where
relevant information, illustrations, and citations can be found.
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58 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Observed Cold Areas
Areas colder than 2 degrees C
below mainstem average
maximum determined by
interpolation of 2005 and
2006 field collected data
Expected Cold Areas
Areas colder than 2 degrees C
below mainstem average
maximum determined using
geomorphic type and temperature
distributions from 2005 and 2006
field collected data
Eugene
Figure 7.4.1. Observed and expected cold-water areas in the middle Willamette River, Oregon, based on qualitative
evaluation of historical and current aerial photographs and field measurements of stream temperature obtained from
digital data loggers. Thermal reach types (e.g., floodplain alcoves, bar alcoves, and side channels depicted above) were
determined from channel morphology, riparian vegetation, and floodplain structure. Slices at 1-km intervals spanning the
floodplain indicate areas with high ecological potential and social constraints (gray), low ecological potential and high
social constraints (tan), high ecological potential and low social constraints (green), and low ecological potential and low
social constraints (brown) (adapted from Hulse and others, 2007). m
-------
8. Figures and table 59
1939
Original mam
Figure 7.5.1. Historical and current aerial photographs of the Oxbow Conservation Area of the Middle Fork John Day
River, Oregon, in 1939 and 2006. Tan dots provide a spatial reference in the 1939 photograph for the approximate location
of the current main channel, which is located north of the original main channel. Source: Brian Cochran, Restoration
Ecologist, Confederated Tribes of the Warm Springs Indian Reservation of Oregon; Oxbow Conservation Area, Middle Fork
John Day River Dredge Mining Restoration Project, http://www.usbr.gov/pn/programs/fcrps/thp/lcao/index.html
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60 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
Proposed restored channel
reconnecting cold tributary
to original main channel.
Current mam channel
created after mining
will be blocked and filled.
Original main channel
Locations of potential
restored cold-water
refuges
Subsurface flow
pathways and potential
cold-water sources
Figure 7.5.2. Floodplain restoration in the Oxbow Conservation Area of the Middle Fork John Day River, Oregon,
incorporated aerial TIR imagery (above) and digital elevation models derived from LiDAR to guide channel placement
(solid black line) in relation to subsurface-flow patterns (red and yellowtones in thermal image). The cold tributary (solid
blue line) will be reconnected with the floodplain of the original main channel (blue and green tones) located in the lower
portion of the image. An objective of restoration is to create cold-water refuges (small white arrows) where relatively
cool subsurface flow (dotted lines) from the reconnected tributary enters the main channel. Cold water from the tributary
currently flows into the isolated north channel created after the floodplain was dredge mined in the 1940s and 1950s.
Source: Brian Cochran, Restoration Ecologist, Confederated Tribes of the Warm Springs Indian Reservation of Oregon;
Oxbow Conservation Area, Middle Fork John Day River Dredge Mining Restoration Project.
http://www.usbr.aov/pn/proarams/fcrps/thp/lcao/index.html
-------
8. Figures and table 61
Lateral Seep
. cool water
Lateral Seep
with Deflector
seep
seep
cool wateM
Tributary Mouth
Tributary Mouth
with Deflector
Figure 7.5.3. Channel unit and microhabitat-scale restoration of cool-water areas, such as seeps
(top) and cold tributaries (bottom), may include placements of wood (top right) and bar (bottom right)
deflectors upstream of cool-water inputs to increase channel complexity and reduce mixing and
effectively increase the size of cold-water refuges (adapted from Bilby, 1984).2S
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62 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diwersity in ftiwerine Landscapes
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76 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diwersity in ftiwerine Landscapes
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10. Appendix A. Streaming video of a symposium on cold-water refuges 77
10. Appendix A. Streaming video of a symposium on cold-water refuges
Special Symposium: "Identifying, protecting, and restoring thermal refuges for coldwater fishes" at the Joint Annual Meeting of
the Western Division and Oregon Chapter American Fisheries Society, Portland, Oregon, May 4-8, 2008.
Conveners: Christian E. Torgersen and Joseph L. Ebersole
Streaming video available online http://www.ruraltech.org/video/2008AVDAFS/index.asp
Videographer: Matthew McLaughlin, School of Forest Resources, University of Washington, Seattle.
Presentation and Speaker Information
Policy and regulatory context for cold-water refugia
Dru Keenan - EPA Region 10; Office of Water and Watersheds
Cold-water refuges in the Willamette River: Implications for conservation and restoration
Stan Gregory - Oregon State University
Combining spatial and temporal stream temperature measurements to investigate surface/
groundwater exchange across a semi-arid alluvial floodplain
Scott O'Daniel - Confederated Tribes of the Umatilla Indian Reservation; UC Santa Barbara
Influence of hyporheic flow and geomorphology on temperature of a large, gravel-bed river,
Clackamas River, Oregon, USA
Barbara Burkholder - GeoEngineers, Inc.
Assessing thermal suitability of streams for establishment of native trout conservation
populations in high-elevation streams
Mark Coleman - Principal Scientist for Coleman Ecological, Inc.
A thermal profile method for long river reaches to identify potential areas of ground-water
discharge and preferred salmonid habitat and to document the longitudinal temperature regime
John Vaccaro - USGS Washington Water Science Center
Remote sensing techniques for mapping aquatic habitat river channel morphology and thermal
heterogeneity
Russ Faux - Watershed Sciences, Inc.
The effect of landscape topography and in-stream habitat on the distribution, growth, and
survival of Lahontan cutthroat trout (Oncorhynchus clarki henshawi) in a high desert watershed
George Boxall - Oregon State University
Behavioral thermoregulation by adult Chinook: Beneficial thermoregulation or ecological trap?
Chris Peery - University of Idaho
Assessing thermal rearing restrictions of juvenile coho, Redwood Creek, CA
Mary Ann Madej - USGS Western Ecological Research Center
Klamath River thermal refugia: physical and biological characterization
Ron Sutton - Bureau of Reclamation; Mike Deas - Watercourse Engineering, Inc.
Coldwater fishes and thermal refuges in hot water: Synthesis and future directions
Christian Torgersen - USGS Forest and Rangeland Ecosystem Science Center
Panel Discussion:
• Jim Sedell - National Fish and Wildlife Foundation
• Debra Sturdevant - Oregon Dept. of Environmental Quality
• Jeff Lockwood - NOAA, National Marine Fisheries Service, NW Region
• Gordie Reeves - U.S. Forest Service, Pacific Northwest Research Station
• Stan Gregory - Oregon State University
General Discussion
Questions and answers discussed among the panel and symposium attendees.
Time
18:07
18:15
16:43
21:54
20:29
19:03
17:30
12:27
18:03
16:12
23:36
18:11
29:58
14:14
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78 Primer for Identifying Cold-Water Refuges to Protect and Restore Thermal Diversity in Riverine Landscapes
11. Appendix B. Airborne thermal infrared surveys of stream temperature (DVD)
Contractors
Surveys were conducted from 1994 to 2007 by Environmental Research Institute of Michigan (ERIM), and Russ Faux,
Watershed Sciences, Inc., http://www.watershedsciences.com/
Locations: Oregon, Washington, Idaho, Nevada, California, Utah, and Wyoming
Database
Metadata on surveyed sections include: date of survey, river/stream name, description of longitudinal extent (start and end
points), length (miles), location (state), permission to distribute (yes, no, or with permission), client and point of contact
(address). This database is intended to be publically available.
Maps
ESRI GIS shapefiles if available are included on DVD. These data include the actual surface-water temperatures sampled from
thermal imagery and their associated geographic locations and times of acquisition, with notes on tributary junctions, landmarks,
and thermal anomalies. Raw thermal imagery in raster format is not included. Shapefiles may be available to the public on
request from the authors.
Reports
In some cases, reports describing the methodology, results, and preliminary interpretation of thermal surveys are available.
These reports are associated with their respective map and survey data in the compact disk. Reports may be available to the
public on request from the authors.
Additional resources
Extensive airborne thermal infrared surveys of rivers and streams in Idaho were conducted by the Idaho Department of
Environmental Quality from 1999 to 2001. More information on these surveys is available online from the Idaho Department of
Environmental Quality: http://www.deq.idaho.gov/water-quality/surface-water/temperature.aspx
The Washington Department of Ecology provides (1) lists of rivers and streams surveyed with airborne thermal infrared remote
sensing by Watershed Sciences, Inc., and (2) links to online reports with preliminary analyses of the data. More information on
these surveys is available online from the Washington Department of Ecology:
http ://www. ecv. wa. gov/apps/watersheds/temperature/
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