Prepared in cooperation with the

New York State Department of Environmental Conservation and Rochester Institute of Technology

Identifying Trout Refuges in the Indian and Hudson Rivers in Northern New York Through Airborne Thermal Infrared Remote Sensing

Open-File Report 2015−1078

U.S. Department of the Interior

U.S. Geological Survey
Cover. The Hudson River upstream of its confluence with the Boreas River. Photograph by Barry P. Baldigo, U.S. Geological Survey.
Identifying Trout Refuges in the Indian 

and Hudson Rivers in Northern New York 

Through Airborne Thermal Infrared Remote 

Sensing

By Anne Gallagher Ernst, Barry P. Baldigo, Fred J. Calef, Douglas A. Freehafer, 

and Robert L. Kremens

Prepared in cooperation with the

New York State Department of Environmental Conservation and 

Rochester Institute of Technology

Open-File Report 2015–1078

U.S. Department of the Interior

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

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2015

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Although this information product, for the most part, is in the public domain, it also may contain copyrighted materials 

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

Suggested citation:

Ernst, A.G., Baldigo, B.P., Calef, F.J., Freehafer, D.A., and Kremens, R.L., 2015, Identifying trout refuges in the Indian 

and Hudson Rivers in northern New York through airborne thermal infrared remote sensing: U.S. Geological Survey 

Open-File Report 2015–1078, 17 p., http://dx.doi.org/10.3133/ofr20151078.

ISSN 2331-1258 (online)
iii

Acknowledgments

The authors extend their appreciation to Martyn Smith and Scott George of the U.S. Geological 

Survey; Beth Boisvert, Cliff Kraft, and Marshall Thomas of Cornell University for technical 

support; and Donald McKeown of Rochester Institute of Technology for providing the thermal 

infrared data. Comments from Christian Torgersen of the U.S. Geological Survey helped to 

improve this manuscript.

v

Contents

Abstract...........................................................................................................................................................1

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

Study Area.......................................................................................................................................................2

Methods...........................................................................................................................................................4

In-Stream Temperature and Stage Loggers.....................................................................................4

Airborne Thermal Infrared Sensing...................................................................................................4

Image Processing.................................................................................................................................5

Image Analysis......................................................................................................................................5

Longitudinal Temperature Profiles............................................................................................5

Refuge Determination .................................................................................................................5

Split 1-Kilometer River Reaches................................................................................................6

Tributary Confluences .................................................................................................................6

Results .............................................................................................................................................................6

Water Stage and Temperature at Data Logger Sites in Relation to Reservoir Releases .........6

Longitudinal Temperature Profiles.....................................................................................................7

Refuge Identification in Split 1-Kilometer Sections ........................................................................7

Cold-Water Contributions From Tributaries....................................................................................11

Discussion.....................................................................................................................................................13

Study Limitations..........................................................................................................................................14

Summary........................................................................................................................................................15

References Cited..........................................................................................................................................15

Figures

1. Map showing locations at seven stream sites where temperature loggers and crest 

stage gages were placed for study of thermal refuge areas along a 27-kilometer 

study reach below the Lake Abanakee Dam on the Indian and Hudson Rivers in 

northern New York in 2005–6 ......................................................................................................3

2. Graphic representation of refuge number, size, and distance calculations.......................6

3. Graphs showing longitudinal thermal infrared temperature profiles along the study 

reach on August 25, 2005, at A, 1012; B, 1239; and C, 1542 eastern standard time 

(EST), with box plots showing temperature range and mean at seven sites on 

release and on nonrelease days from July 21 through September 21, 2005, and 

locations of five cold-water tributaries.....................................................................................8

4. False-color thermal infrared images showing cold-water areas at the confluences 

of Raquette Brook at kilometer 24 and Deer Creek at kilometer 27 with the Hudson 

River in the Adirondack Mountains, New York, during three overhead flights on 

August 25, 2005, at A, 1012 eastern standard time (EST), B, 1239 EST, and C, 1542 EST 

when passage of reservoir release overwhelmed any cooling effect of inflow from 

tributaries.....................................................................................................................................12
vi

Tables

1. Median water temperature for right (R) or left (L) half of each 1-kilometer (km) 

section of river channel; mean size, standard deviation, and maximum size of 

refuge areas in which water temperature was 1 to 2 degrees Celsius (°C), and more 

than (>)2 °C below the median temperature for that section; and mean distance, 

standard deviation, and median and maximum distances between refuges during 

three flights over the 27-km study reach of the Indian and Hudson Rivers in 

northern New York, August 25, 2005..........................................................................................9

2. Median water temperature in five river sections containing a cold-water tributary; 

mean size, standard deviation, and maximum size of refuge areas in which water 

temperature was 1 to 2 degrees Celsius (°C) and more than (>)2 °C below the 

median temperature for that section; and mean distance, standard deviation, and 

median and maximum distances between refuges during three flights over the 

27-kilometer (km) study reach of the Indian and Hudson Rivers in northern 

New York, August 25, 2005 ........................................................................................................11

Conversion Factors

Inch/Pound to International System of Units

Multiply By To obtain

Length

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 4,047 square meter (m2

)

acre 0.4047 hectare (ha)

International System of Units to Inch/Pound

Multiply By To obtain

Length

kilometer (km) 0.6214 mile (mi)

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

°F = (1.8 × °C) + 32.

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

°C = (°F – 32) / 1.8.
vii

Datum

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

(NAVD 88).

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

Altitude, as used in this report, refers to distance above the vertical datum.

Abbreviations

BMT below median temperature

EST eastern standard time

FLIR forward-looking infrared

RIT Rochester Institute of Technology

TIR thermal infrared

USGS U.S. Geological Survey

UTM Universal Transverse Mercator

Identifying Trout Refuges in the Indian and Hudson Rivers 

in Northern New York Through Airborne Thermal Infrared 

Remote Sensing

By Anne Gallagher Ernst,1 Barry P. Baldigo,1 Fred J. Calef,1 Douglas A. Freehafer,1 and Robert L. Kremens2

Abstract

The locations and sizes of potential cold-water refuges 

for trout were examined in 2005 along a 27-kilometer 

segment of the Indian and Hudson Rivers in northern New 

York to evaluate the extent of refuges, the effects of routine 

flow releases from an impoundment, and how these refuges 

and releases might influence trout survival in reaches that 

otherwise would be thermally stressed. This river segment 

supports small populations of brook trout (Salvelinus 

fontinalis), brown trout (Salmo trutta), and rainbow trout 

(Oncorhynchus mykiss), and also receives regular releases 

of reservoir-surface waters to support rafting during the 

summer, when water temperatures in both the reservoir 

and the river frequently exceed thermal thresholds for trout 

survival. Airborne thermal infrared imaging was supplemented 

with continuous, in-stream temperature loggers to identify 

potential refuges that may be associated with tributary inflows 

or groundwater seeps, and to define the extent to which the 

release flows decrease the size of existing refuges. In general, 

the release flows overwhelmed the refuge areas and greatly 

decreased the size and number of the areas. Mean water 

temperatures were unaffected by the releases, but smallscale heterogeneity was diminished. At a larger scale, water 

temperatures in the upper and lower segments of the reach 

were consistently warmer than in the middle segment, even 

during passage of release waters. The inability of remote 

thermal infrared images to consistently distinguish land from 

water (in shaded areas) and to detect groundwater seeps (away 

from the shallow edges of the stream) limited data analysis 

and the ability to identify potential thermal refuge areas.

Introduction

Water temperature is a central component of aquatic 

ecosystems, and plays a pivotal role in determining the 

suitability of stream and river habitat to trout, especially 

1

U.S. Geological Survey

2

Rochester Institute of Technology

with the threat of climate change (Elliott and others, 1995; 

Biro, 1998; Wehrly and others, 2003; de la Hoz Franco 

and Budy, 2005; Caissie, 2006; Flebbe and others, 2006; 

McMahon and others, 2007; Wehrly and others, 2007). Stream 

temperatures not only affect the distribution, behavior, and 

survival of trout (and other species), but also compel these 

species to move toward areas of preferred temperatures, 

known as refuges, to maximize growth, survival, and fitness 

(Peterson and Rabeni, 1996; Torgersen and others, 1999; 

Ebersole and others, 2001). The longitudinal gradient 

of temperatures along a stream has been recognized as 

a factor affecting the distribution of fish (Vannote and 

others, 1980), but lateral and vertical heterogeneity is 

increasingly recognized as an important component of stream 

thermal structure (Torgersen and others, 2001; Ebersole and 

others, 2003b). This heterogeneity can create a patchwork 

of water temperatures that includes cold-water refuges in 

a warm stream. Several studies confirm that salmonids 

can avoid the sublethal stresses when water temperatures 

approach critical limits by relocating to cold-water refuges 

(Bermann and Quinn, 1991; Power, 1997; Torgersen and 

others, 1999; Baird and Krueger, 2003). For example, mature 

Chinook salmon (Oncorhynchus tshawytscha) in the Yakima 

River, Washington, maintained body temperatures that were 

2.5 degrees Celsius (°C) lower than the surrounding stream 

temperatures by sheltering in areas of cooler temperature to 

optimize energy conservation (Bermann and Quinn, 1991). 

Similarly, Baird and Krueger (2003) determined that brook 

trout (Salvelinus fontinalis) and rainbow trout (Oncorhynchus 

mykiss) in an Adirondack river occupied sites that were 4 °C 

and 2.3 °C cooler, respectively, than surrounding waters. Coldwater refuges, if available, can therefore allow fish to survive 

in streams that otherwise might be uninhabitable.

Cold-water refuges in streams are a product of thermal 

heterogeneity, which can result from the interaction of 

surface, hyporheic, and groundwater sources along alluvial 

streambeds or from any patchiness in water temperatures 

caused by geomorphology, hydrology, or vegetation. Thermal 

refuge areas may include groundwater seeps, tributaries, 

emerging streambed flow, and vegetative and topographic 

shading (Bilbey, 1984). The development and extent of these 
2 Identifying Trout Refuges in Northern New York Through Airborne Thermal Infrared Remote Sensing

features may be highly spatially variable and reflect a variety 

of landscape characteristics. Refuges can provide resilience to 

fish and other stream organisms under thermal stress, but the 

effectiveness of the refuges at sustaining populations depends 

on the spatial arrangement, frequency, and connectivity of the 

refuge patches, as well as the condition of the refuge itself 

(Dunning and others, 1992; Townsend and others, 1997). 

Determining the spatial distribution and characteristics 

of thermal refuges within stream systems, therefore, is 

critical to understanding the habitat of cold-water fish and 

other organisms.

Airborne thermal infrared (TIR) sensing has recently 

begun to be used in the eastern United States as a remote 

stream-monitoring tool. Applications of airborne TIR sensing 

have been important to both marine and lacustrine systems and 

have more recently been developed for streams in the Pacific 

Northwest of the United States (Belknap and Naiman, 1998; 

Torgersen and others, 1999; Torgersen and others, 2001). 

Several studies have used TIR remote sensing to assess stream 

temperature patterns in relation to habitat use by salmon. For 

example, Belknap and Naiman (1998) indicated that TIR 

remote sensing was effective at detecting wall-base channels, 

a geomorphic habitat essential for juvenile Coho salmon 

refuge and rearing, and Torgersen and others (1999) correlated 

Chinook salmon distribution and cold-water temperature 

patterns using TIR remote sensing.

Airborne TIR sensing can be an effective tool for 

determining the spatial distribution of thermal heterogeneity 

in a stream system. For a large area, TIR can cover hundreds 

of river kilometers, whereas for smaller areas it can reveal 

thermal patterns along short reaches to allow delineation of 

cold-water refuges. It is especially useful for remote streams or 

river reaches with only limited access (Faux and others, 2001; 

Torgersen and others, 2001). This type of imaging can be 

used to map water temperature patterns along streams or 

rivers at multiple scales (Torgersen and others, 1999, 2001) 

and thereby reveal the locations and potential suitability of 

cold-water areas as fish refuges. Torgersen and others (2001) 

analyzed temperature patterns in several rivers in Oregon 

and determined that peaks and troughs in the longitudinal 

profile over short distances were caused by tributary inputs, 

whereas large-scale patterns like warming or cooling trends 

over 5 to 10 kilometers (km) generally reflected watershedscale processes, such as geomorphic, riparian, and hydrologic 

processes. Thus, thermal remote sensing of streams provides 

limited information about the hydrologic processes that 

influence stream temperature, but it can be an effective tool 

for evaluating the patterns caused by those processes. The 

ability of TIR remote sensing to map the spatial distribution 

(patchiness) and detect changing patterns in cold-water 

refuges at multiple spatial scales could be used to effectively 

assess the availability and quality of thermal refuges for 

resident trout at the reach level.

In 2005, the U.S. Geological Survey (USGS), in 

cooperation with the New York State Department of 

Environmental Conservation and Cornell University, began 

a multidisciplinary study to assess natural resources in the 

Indian and Hudson Rivers along a reach that receives regular 

recreational releases from an upstream reservoir to support 

whitewater rafting. The main objective of the study was to 

evaluate the potential effects of these releases on the resident 

and stocked brown trout (Salmo trutta) fishery. A related goal, 

and the focus of this report, was to identify cold-water areas 

that could provide refuges possibly critical to the survival of 

stocked and resident trout during periods of thermal stress 

(the warm summer months). Stream temperature data from 

seven continuous loggers and TIR remote sensing data from 

the 27-km reach affected by release flows were analyzed 

to (1) assess the effectiveness of thermal remote sensing to 

detect spatial patterns in stream temperatures at multiple 

spatial scales, (2) identify potential thermal refuges at base 

flow and during release flows, (3) define how the release flows 

affect the size and temperature of the identified refuges, and 

(4) compare the results of thermal refuge identification made 

at several spatial scales. Analyses evaluate hypotheses that 

the size and number of thermal refuges are diminished by 

recreational flow releases.

Study Area

The study reach is located in the Adirondack Park of 

northeastern New York and includes the lower 5 km of the 

Indian River, from the Lake Abanakee Dam to its confluence 

with the Hudson River, and 22 km of the Hudson River 

from that confluence to North Creek, New York (fig. 1). 

This section of the Hudson River flows through the Hudson 

Gorge Primitive Area, a 17,000-acre New York State Forest 

Preserve. This study reach was selected because it is directly 

affected by the reservoir releases, it covers the entire affected 

section of river that runs through the Hudson Gorge Primitive 

Area, and it is of manageable length for field measurements. 

The drainage area is 505 square kilometers (km2) near the 

top of the reach at station IR01 and increases to 1,626 km2

after its confluence with the Hudson River (station HR02) 

and to 1,968 km2 by the bottom of the reach (station HR05; 

fig. 1). The reach is mainly accessible by foot along several 

hiking trails or by boat, and supports populations of native 

brook trout as well as naturalized and hatchery (stocked) 

brown trout and rainbow trout. Water temperatures in parts 

of the study reach typically exceed lethal thresholds for these 

species (22–24 °C for brook trout, 24–27 °C for brown trout, 

and 24–25 °C for rainbow trout; Raleigh, 1982; Raleigh and 

others, 1984, 1986; Wehrly and others, 2007) for several 

weeks each summer (Baldigo and others, 2010). Extensive 

whitewater in the study reach also provides the setting for a 

commercial rafting industry that operates from April through 

October. The raft-launching site is located on the Indian River 

just downstream from the Lake Abanakee Dam. The dam is 

owned and operated by the Town of Indian Lake. The town 

makes regular top-water releases from the dam daily during 
Study Area 3

#

#

#

#

# #

#

#

#

# #

#

CR04

CR02 CR03

CR01

HR05

HR04

HR03

HR02

HR01

IR03

IR02

IR01

74°6'0"W 74°2'0"W

43°38'0"N

NEW YORK K

Wakely 

Dam

Abanakee 

Dam

Indian 

Lake 

Dam

Indian 

Lake

Indian Lake

Indian River

Hudson River

Cedar River

Hudson River

Hudson River

Cedar River

Shaded relief map from U.S. Geological Survey National 

Hydrography Dataset, 2015

0 2 4 6

42

MILES

0 6 KILOMETERS

74°30' 74°26' 74°22' 74°18' 74°14' 74°10' 74°06' 74°02'

43°38'

43°42'

43°46'

43°50'

43°54'

Area shown

on map

CR01

# Stream site and identifier

Dam

EXPLANATION

Figure 1. Locations at seven stream sites where temperature loggers and crest stage gages were placed for study of thermal refuge 

areas along a 27-kilometer study reach below the Lake Abanakee Dam on the Indian and Hudson Rivers in northern New York in 2005–6. 

The upper, middle, and lower study reaches fall between sites IR01 and IR03, HR02 and HR04, and HR04 and HR05, respectively. An eighth, 

control site (HR01) was upstream from the middle study reach. Modified from Baldigo and others (2010).
4 Identifying Trout Refuges in Northern New York Through Airborne Thermal Infrared Remote Sensing

the spring and on 4 days of each week in the summer and fall 

to augment seasonal low flows. These brief (1.5- to 2-hour) 

recreational releases are vital to the rafting industry.

Methods

In-Stream Temperature and Stage Loggers

Fixed stage and temperature loggers were placed in steel 

pipe extending well above bankfull to roughly 0.67 meter (m) 

below the water surface at each of seven sites along the 27-km 

study reach; three of the sites were on the Indian River, and 

four were on the Hudson River (fig. 1). An eighth (control) 

logger was placed on the Hudson River upstream from the 

confluence with the Indian River and thus was unaffected by 

releases from the impoundment. Loggers along the Hudson 

River were placed in areas that were accessible by hiking 

trails, railroad tracks, and (or) moderate wading. The loggers 

recorded water temperatures and stage at 15-minute intervals 

from approximately June 30 through October 27 in 2005 and 

from approximately April 20 through September 26 in 2006 to 

provide a record of daily and seasonal in-stream temperature 

fluctuations (Baldigo and others, 2010). The gages at each 

site recorded changes in water level (stage), the times of 

day at which stage increases associated with a dam release 

occurred, and the times at which stage returned to its original 

starting level. These data were plotted as a function of distance 

downstream from the Lake Abanakee Dam to estimate the 

start and end times of high water along the river at each gage. 

These times on August 25, 2005, were compared with timestamped TIR images of the river at high and low flows to 

verify their accuracy.

Airborne Thermal Infrared Sensing

Spatially continuous surface water temperatures along the 

study reach were mapped with TIR photography during three 

low-altitude flights (beginning at 1012, 1239, and 1542 eastern 

standard time [EST]) on August 25, 2005, a release day. The 

release began at 0930 EST and lasted 2 hours. Durations 

for the three low-altitude flights of the survey airplane 

were 43 minutes, 37 minutes, and 23 minutes, respectively. 

Airborne TIR remote sensing detects thermal radiation from 

the upper 0.1 millimeter (mm) of the water surface (Wick and 

others, 1996). Because the study reach consists of many rapids 

and riffles, the water in the reach was generally assumed to be 

well mixed and surface water temperatures were assumed to 

be a valid proxy for water temperature profiles along the river. 

Thermal stratification is uncommon in streams with turbulent 

flow (Torgersen and others, 2001), although cold seeps and 

(or) tributaries may alter temperatures locally. The plane was 

equipped with a forward-looking infrared (FLIR) system, 

which detected thermal energy in the 0.7- to 9.2-micrometer 

(μm) waveband (also called thermal infrared). Long-wave 

infrared typically measures a band of 8 to 14 μm, but the 

equipment used in this study measured a smaller band (1.4 to 

8 μm). Short bandwidths are more sensitive to reflection than 

longer bandwidths and thus may have increased the error. 

A separate camera collected visible spectral band imagery 

(0.4–0.7 μm). Thermal and visible cameras covered the same 

ground area; each image frame represented a ground area of 

about 100 × 150 m and had a spatial resolution of about 1 m. 

Each pixel represented 1 square meter (m2) of water surface. 

Thermal images were collected digitally and recorded directly 

from the sensor to an onboard computer and tagged with 

acquisition time and geographic position data. Visible band 

imagery and acquisition time were recorded to an onboard 

digital video recorder.

All flights surveyed the river in a downstream direction. 

These flights recorded data during low and high flows (before, 

during, or after the arrival of the slug from the release) at most 

points along both rivers, although no single flight covered the 

whole study reach under either low or high flow. The datasets 

from all three flights are missing from 0.3 to 0.7 km of data 

near kilometer 16 of the study reach; the first flight also is 

missing 0.5 km of data from kilometer 23.

Thermal radiation measurements can be affected by 

emissivity, atmospheric transmission, view angle, and water 

surface characteristics (Smith and others, 1996; Faux and 

others, 2001; Torgersen and others, 2001). Emissivity is a 

measure of the ability of a material to absorb and radiate 

energy in relation to the energy radiated by a black body at 

the same temperature. Water is a nearly ideal infrared black 

body emitter with an emissivity close to 1; therefore, no 

emissivity corrections were made. Atmospheric transmission 

effects were small because the flying altitude was low; the 

data were corrected through an in-scene calibration from the 

seven temperature-measurement sites and had a resolution of 

approximately 0.1 °C. View-angle effects were minimized by 

flying at a low altitude near vertical incidence and by using 

a narrow field of view (approximately 50-degree full width). 

Rough water surfaces, such as riffles and rapids, have lower 

emissivity than smooth water and therefore can seem slightly 

warmer, although the difference is small (less than [<] 0.1 °C; 

Masuda and others, 1988).

Airborne TIR remote sensing is an effective means of 

detecting cold-water refuges within a large river system, but 

it only gives an instantaneous overview of spatial stream 

temperature patterns, whereas a temperature logger record 

is continuous but limited to a single location. Thermometers 

can be physically moved through streams to detect thermal 

refuges (Ebersole and others, 2003a), but this technique is 

spatially limited. Combining temporally continuous data from 

stationary instruments with spatially continuous data obtained 

through remote sensing provides an integrated database of 

stream temperatures across scales ranging from geomorphic 

channel units (riffles and pools) to an entire drainage basin 

(Torgersen and others, 1999, 2001).
Methods 5

Image Processing

Airborne TIR remote sensing data were processed 

through ERDAS Imagine version 8.4 image-processing 

software and analyzed within the Esri Inc. ArcGIS geographic 

information system (GIS; ESRI Inc., 1995). The FLIR imagery 

was converted into GIS-point coverage to provide a basis for 

integration with other spatial data layers. Each image was 

geometrically corrected to a Universal Transverse Mercator 

(UTM) zone 18N projection, the standard for New York State. 

A linear equation was derived to convert TIR radiance values 

into temperature values based on corresponding temperatures 

at the in-stream loggers. Images were stored in a format in 

which each pixel was assigned a temperature value, rounded 

to the nearest 0.1 °C. Thermal images were color-coded to 

facilitate interpretation of thermal patterns.

Individual thermal image frames (119–188 per flight) 

were aligned with 30 to 40 percent overlap in a downstream 

direction to form a single mosaic image for each of the three 

flights. A separate mask for each flight was digitized by hand 

with the visible-spectrum image data to separate land from 

water. Each mask was then overlaid on the TIR image to 

locate and isolate the water. The edge of water was hidden on 

the visible-spectrum image in places by overhanging riparian 

vegetation; therefore, the location of the water edge in these 

areas was estimated. The total length estimated was 6 to 8 km 

along both banks, or 11 to 15 percent of the water edge. The 

Imagine data profiler was used to interlock temperature data 

from adjacent pixels down the middle of the river channel, 

which served as a substitute for the river thalweg.

Image Analysis

The location of the high-water slug was determined 

through visual inspection of the aerial photographs and by 

the crest stage gages along the study reach. Each of the three 

flights included data from a different section of the 27-km 

reach under high flow from the passage of the slug from the 

reservoir. For this reason, data were interpreted on an entirereach basis as discussed in the “Longitudinal Temperature 

Profiles” section, and in smaller (1-km) sections as described 

thereafter for evaluation of each section at low and high flows. 

Additionally, a smaller scale analysis was used to assess 

aggregations of cold-water pixels at potential refuge locations.

Longitudinal Temperature Profiles

Median temperatures were calculated for each pixel along 

the thalweg (median of 5 pixels above and 5 pixels below 

each pixel) and plotted as a function of distance downstream 

from the top of the reach to obtain a running average of 

temperatures along the 27-km reach for each flight. Median 

temperatures were used because they minimize the effect of 

extreme values. Although longitudinal temperature profiles 

represent absolute temperatures from only the time and day of 

the survey, the spatial temperature patterns are often consistent 

among years and thus can provide a general interpretation of a 

river’s thermal structure (Faux and others, 2001). Longitudinal 

temperature profiles can also reveal thermally unique areas 

that can be linked to specific causes, such as groundwater 

seeps and tributary inflows, if a stream is shallow and (or) 

narrow; however, longitudinal temperature profiles may fail 

to reveal temperature anomalies along the edges of deep, wide 

rivers unless the seeps and inflows are large enough to affect 

the temperature in the center of the channel.

Refuge Determination

Cold-water refuges were defined as any group of two or 

more consecutive pixels at least 1, 2, or 3 °C below median 

temperature (BMT), although no pixels in this study were 

more than 3 °C BMT. Previous studies have defined “coldwater refuge” as water that is at least 3 oC colder than the 

surrounding water (Garrett and Bennett, 1995; Ebersole 

and others, 2003a). Even minor differences between fish 

body temperature and river temperature denote active 

thermoregulation, however, and can be important for fish 

health and survival (Somero and Hoffman, 1997); therefore, 

the classification of a thermal refuge as being as little as 1 oC 

colder than surrounding water reflects this importance.

Individual pixels at least 1 oC BMT were identified in 

ArcGIS. Pixels that shared an edge (but not a corner) were 

considered connected (fig. 2). Individual, unconnected pixels 

at least 1 oC BMT were not included in any refuge calculations 

in case they were false results, and because individual, isolated 

pixels may not represent a usable refuge area for local fish. 

For all other pixels at least 1 oC BMT, the number of groups 

of connected pixels (refuges) and number of pixels in each 

group were calculated for pixels between 1 and 2 oC BMT and 

for pixels greater than (>) 2 oC BMT. Figure 2 illustrates how 

refuges were determined.

Distances between refuges were calculated by counting 

the minimum number of pixels from a refuge to the next 

nearest refuge. This calculation included all refuges where 

the median temperature was at least 1 oC BMT rather than 

separate calculations for pixels where the median temperature 

was 1 to 2 oC BMT and for pixels where the median 

temperature was >2 oC BMT. For example, a refuge with a 

median temperature 1 to 2 oC BMT that shared an edge with a 

refuge with a median temperature >2 oC BMT was considered 

to have a distance of 0 m separating the first from the second 

refuge. Refuges that were connected by corners (rather than 

by a shared edge) were also considered to have a distance 

between them of 0 m. Figure 2 illustrates how distances 

between refuges were determined. The decision to treat 

refuges of 1 to 2 oC BMT and >2 oC BMT separately may have 

underestimated median (and to a lesser extent mean) distances 

between refuges. Thus, although potentially conservative, 

mean values may be the best estimate of distances between 

refuges in most sections.
6 Identifying Trout Refuges in Northern New York Through Airborne Thermal Infrared Remote Sensing

1 2

3

4

4

5

EXPLANATION

Pixel greater than 2 degrees Celsius below median temperatue

Refuge and number

Pixel 1 to 2 degrees Celsius below median temperature

Figure 2. Graphic representation of refuge number, size, and 

distance calculations. In this example, there are two refuges 1 to 

2 degrees Celsius (°C) below median temperature (BMT; sizes: 

5 and 2 pixels) and three refuges at least 2 °C BMT (sizes: 2, 3, 

and 1 pixels). The distance between refuges 1 and 2 is 0 pixels, 

the distance between refuges 3 and 4 is 0 pixels, and the distance 

from refuge 5 to refuge 3 is 6 pixels.

Split 1-Kilometer River Reaches

For analysis of water temperatures, the study reach was 

divided into 27 sections along the thalweg, each 1 km long. 

The east banks of river sections that ran north to south were 

shaded in the morning by riparian vegetation that allowed 

exposed rocks within the river to remain cooler than the 

water during the morning flight. The shading created two 

potential problems: first, exposed rocks in the morning TIR 

images appeared as thermal refuges that were absent in the 

later images when they had become warm from the sun; and 

second, this shading lowered the water temperature locally 

and thereby may have obscured genuine refuges, whose 

temperature is relative to the ambient water temperature. 

Therefore, each 1-km river section was split in half along the 

thalweg, and only the temperature data for the half with the 

lesser amount of morning shade were compiled. Median water 

temperature, number of refuges, average and maximum refuge 

size, and average and maximum distance between refuges 

were calculated for each split 1-km section.

Tributary Confluences

Five tributaries entering the lower one-third of the study 

reach (fig. 1) were cooler than the river during at least one 

flight, as indicated by a large aggregation of cold-water pixels 

in the TIR images: Boreas River, Raquette Brook, Aldous 

Brook, Deer Creek, and Thirteenth Lake Outlet. Several other 

tributaries enter the river as well, but did not have a cooling 

effect on the Hudson River water temperatures. Small areas 

around the five cold-water confluences were delineated by 

hand to isolate the effects of these tributaries on the river 

temperature at a small scale. Area polygons were drawn such 

that the cold tributary water represented 15 to 25 percent of 

their area at base flow. For each confluence, the median water 

temperature, number of refuges, average and maximum refuge 

size, and average and maximum distance between refuges 

were calculated.

Results

Water Stage and Temperature at Data Logger 

Sites in Relation to Reservoir Releases

River stage at each of the seven data-logger sites 

followed a uniform pattern in the monitoring periods of 2005 

and 2006: on release days, river stage increased sharply as 

the slug of water arrived at each site, then dropped below the 

starting stage once the slug had passed. On nonrelease days, 

river stage rose slowly throughout the day as a continued 

rebound from the sharp rise and decline that followed the 

previous release. Average increases in stage during releases 

in June, July, August, and September at the three Indian River 

sites ranged from 0.36 to 0.65 m in 2005 and from 0.24 to 

0.59 m in 2006; stage increases at the four Hudson River sites 

ranged from 0.35 to 0.96 m in 2005 and from 0.20 to 0.40 m 

in 2006 (Baldigo and others, 2010). The increase in river stage 

generally decreased with distance downstream as the river 

widened, except at HR03, which is in a narrow section of 

the Hudson River gorge. The return to base flow also slowed 

downstream as the slug spread out; the high-water period 

lasted for less than 2.5 hours at the top of the reach (IR01), 

and nearly 5.5 hours at the lower end (HR05; Baldigo and 

others, 2010).

Baldigo and others (2010) also compared water 

temperatures during the release day (August 25, 2005) 

with those during the previous, nonrelease day to evaluate 

differences in water temperature patterns. Water temperature 

at all seven data-logger sites along the reach rose on release 

days and nonrelease days through the day until 3 or 4 p.m., 

then began to drop, although the temperature range was 

larger at most sites on the release day (1.2–8.7 oC) than on 

the preceding day (1.2–4.4 oC) and was larger at the Hudson 

River sites than at the Indian River sites. No consistent 
Results 7

relation between temperature and stage was noted; water 

temperature tended to rise less from start to peak of the release 

than during the same time period on nonrelease days, but 

this difference between release and nonrelease days was only 

significant (P < 0.05) at three of the seven sites (IR01, IR02, 

and HR04; Baldigo and others, 2010). Water temperatures 

did not differ significantly between release and nonrelease 

days except at HR02 during the first flight (mean difference 

= –1.5 °C, P=0.042) and at HR03 during the second flight 

(mean difference = +0.8 °C, P=0.093). Between July 1 

and August 1, 2005, means of the daily maximum water 

temperatures on release days did not differ significantly 

(P>0.05) from those on nonrelease days at any site.

Longitudinal Temperature Profiles

The longitudinal temperature profiles constructed for the 

three flight periods on August 25, 2005, indicate that river 

temperatures increased unevenly during the day. The three 

flights are as follows:

• First flight (1012 EST).—The high-water slug 

entered kilometers 1 through 5 during this flight. The 

temperature along most of the thalweg was below 

22 oC and generally decreased downstream (fig. 3A).

• Second flight (1239 EST).—The high-water slug 

entered kilometers 4 through 19 during this flight. 

The temperature of most of the river was around 

22 °C, although the middle part of the study reach 

(kilometers 6–18) was cooler than the upper 

(kilometers 1–4) and lower (kilometers 20–27) 

parts (fig. 3B).

• Third flight (1542 EST).—The high-water slug 

entered kilometers 16 through 27 during this flight. 

The temperature of most of the river was above 

22 oC, although the upper part of the study reach 

(kilometers 3–8) was much warmer than the rest, and 

the middle part of the study reach (kilometers 15–21) 

was cooler (fig. 3C).

Radiant temperatures along the thalweg were generally 

warmer than the median temperatures of the split 1-km 

sections (fig. 3; table 1), but followed the same general 

patterns. Thalweg temperatures tended to be cooler than the 

data-logger values along the banks during the first two flights, 

but the two were similar during the last flight (fig. 3). The 

thalweg temperatures correlated moderately well with the 

data-logger values (R2

=0.93), although this correlation may 

have been lowered because overhanging vegetation made 

it difficult to locate radiant temperatures exactly at several 

data-logger sites. Differences between radiant temperatures 

and in-stream measurements tend to be systematic, but the 

similarity of trends indicates that radiant temperatures depict 

the same longitudinal patterns (Cherkauer and others, 2005; 

Hancock and others, 2005). All three flights showed many 

spikes and dips in temperature along the thalweg; although 

either may reflect spurious data (such as possible from 

exposed rocks), analyses focused only on the low dips, which 

might indicate cold-water refuges for fish. None of the five 

tributary confluences below the Boreas River (fig. 1) were 

associated with a dip in the longitudinal temperature profile 

(fig. 3), probably because any cold-water inflows along the 

bank were too small to affect temperatures in the thalweg.

Refuge Identification in Split 1-Kilometer 

Sections

Few cold-water refuges were present along the study 

reach, regardless of whether or not the high-water slug 

was present, and most of the refuges were 1–2 oC BMT. Of 

the 27 1-km sections, 15 sections did not provide refuge 

>2 oC BMT during any of the 3 flights, and only 5 sections 

provided refuge >2 oC BMT during more than 1 flight. No part 

of the study reach was >3 oC BMT (table 1).

The greatest number and size of cold-water refuges were 

present during the first and third flights, whereas few refuges 

were present during the second flight. Overall, the study reach 

had 254 refuges >1 oC BMT covering 4,572 m2 during the 

first flight, and slightly more refuge area during the third flight 

(262 refuges covering 6,962 m2). More than 10 percent of 

the refuge area was >2 oC BMT during both of these flights. 

During the second flight, however, there were only 91 refuges 

covering 2,825 m2, and only 2 refuges (covering 66 m2) were 

>2 oC BMT (table 1).

The middle section of the study reach (kilometers 6–18) 

had the fewest available refuges, although this pattern is 

clearer for refuges >2 oC BMT than for refuges >1 oC BMT. 

The lack of refuges is partly a result of the lower median 

temperatures present in the middle section; refuges are 

defined to local water temps, so cold water is less likely to 

create a refuge in a cooler section of river, even if its absolute 

temperature is lower than other refuges.

The number of cold-water refuges was positively related 

to the median temperature of each 1-km section. Although the 

scatter of available refuges had a wedge-shaped distribution, 

the upper boundary of the scatter plot indicates that sections 

with higher median temperatures tended to have more refuges, 

which probably is mostly an artifact of the nature of defining 

cold-water refuges to surrounding water temperatures; 

however, the presence of many or large refuges may also 

indicate the presence of a source of cold water.

The high-water slug did not have a uniform effect 

on cold-water refuges. During the first flight, when river 

temperatures were coolest, more than one-third of refuges 

were located in the area of the high-water slug, and all 1-km 

sections within the slug had some refuge present; however, 

during the second and third flights, most of the 1-km sections 

within the high-water slug had no available refuge area. The 

1-km sections that had been inundated with the high-water 

slug for longer were less likely to have refuges present, 
8 Identifying Trout Refuges in Northern New York Through Airborne Thermal Infrared Remote Sensing

B. 1239 eastern standard time

C. 1542 eastern standard time

A. 1012 eastern standard time

EXPLANATION

Location of cold-water tributary along river

Temperature (± standard error) during high-flow water slug Thalweg temperature ( ̊C) during release period 

Thalweg temperature ( ̊C) during nonrelease period

IR01

Temperature (± standard error) during base flow

Temperature-measurement site identification number and location

IR01

IR01

IR01

HR05

HR05

HR05

HR04

HR04

HR04

HR03

HR03

HR03

HR02

HR02

HR02

IR02

IR02

IR02

IR03

IR03

IR03

Boreas River inlet

Raquette Brook inlet

Aldous Brook inlet

Thirteenth lake outlet

Deer Creek inlet

Boreas River inlet

Raquette Brook inlet

Aldous Brook inlet

Thirteenth lake outlet

Deer Creek inlet

Boreas River inlet

Raquette Brook inlet

Aldous Brook inlet

Thirteenth lake outlet

Deer Creek inlet

18

20

22

24

26

28

18

20

22

24

26

28

18

20

22

24

26

28

River water temperature, in degrees Celsius ( ̊C)

0 5 10 15 20 25 30

Distance downstream from Lake Abanakee Dam, in kilometers 

Figure 3. Longitudinal thermal infrared temperature profiles along the study reach on August 25, 2005, at A, 1012; B, 1239; and 

C, 1542 eastern standard time (EST), with box plots showing temperature range and mean (plus or minus [±] standard error) 

at seven sites on release and on nonrelease days from July 21 through September 21, 2005, and locations of five cold-water 

tributaries. Temperature measurement sites and tributary locations are shown in figure 1.
Results 9

Table 1. Median water temperature for right (R) or left (L) half of each 1-kilometer (km) section of river channel; mean size, standard 

deviation, and maximum size of refuge areas in which water temperature was 1 to 2 degrees Celsius (°C), and more than (>)2 °C below 

the median temperature for that section; and mean distance, standard deviation, and median and maximum distances between refuges 

during three flights over the 27-km study reach of the Indian and Hudson Rivers in northern New York, August 25, 2005.

[Sections were divided into halves to avoid effects of shading. Release from upstream reservoir began at 0930 eastern standard time (EST). Shading denotes 

high-water conditions during passage of release from the Lake Abanakee Dam (fig. 1). temp, water temperature; m2, square meter; m, meter; no., number; 

SD, standard deviation; Max, maximum; --, no data]

Km Half

Median 

temp 

(°C)

Refuge areas below median temperature (m2

) Distances between refuges (m)

1 degree 2 degrees

No. Size SD Max No. Size SD Max Mean SD Median Max

First flight (1012 EST)

1 L 20.8 10 23 45 154 1 13 0 13 42 132 0 440

2 L 20.0 20 6 4 15 0 -- -- -- 10 16 7 74

3 L 20.2 16 14 24 100 2 5 3 7 30 118 1 503

4 L 20.7 32 12 18 84 6 7 5 15 1 2 0 10

5 L 20.6 2 3 1 3 0 -- -- -- 4 0 4 4

6 L 20.1 0 -- -- 0 0 -- -- -- -- -- -- --

7 L 19.8 24 3 2 8 0 -- -- -- 3 3 1 14

8 L 19.7 11 40 117 410 1 7 0 7 17 30 1 85

9 L 20.0 16 6 7 28 0 -- -- -- 19 67 1 271

10 R 19.7 2 5 3 7 0 -- -- -- 3 0 3 3

11 L 19.5 19 22 37 144 3 5 3 10 4 8 1 38

12 L 19.5 6 13 10 34 0 -- -- -- 125 256 9 644

13 L 19.8 0 -- -- 0 0 -- -- -- -- -- -- --

14 L 19.7 1 19 0 19 0 -- -- -- 0 . 0 0

15 L 19.7 2 4 2 5 0 -- -- -- 2 0 2 2

16 L 20.2 0 -- -- 0 0 -- -- -- -- -- -- --

17 L 20.2 5 10 11 32 0 -- -- -- 118 199 6 464

18 L 20.0 2 4 1 4 1 2 0 2 0 0 0 0

19 L 19.9 4 268 380 917 9 36 51 163 28 100 0 359

20 R 19.9 3 15 17 38 0 -- -- -- 1 0 1 1

21 R 20.0 4 84 50 164 2 36 33 69 7 9 4 23

22 R 20.0 43 4 5 37 0 -- -- -- 8 39 1 256

23 R 19.6 0 -- -- 0 0 -- -- -- -- -- -- --

24 R 19.4 0 -- -- 0 0 -- -- -- -- -- -- --

25 R 19.7 0 -- -- 0 0 -- -- -- -- -- -- --

26 R 19.4 4 61 86 208 3 8 9 21 2 2 1 4

27 R 19.2 0 -- -- 0 0 -- -- -- -- -- -- --

Overall: 19.9 226 18 71 917 28 18 34 163 16 72 1 644

Second flight (1239 EST)

1 L 22.3 5 3 1 5 0 -- -- -- 35 63 1 145

2 L 22.1 0 -- -- -- 0 -- -- -- -- -- -- --

3 L 21.9 0 -- -- -- 0 -- -- -- -- -- -- --

4 L 22.1 0 -- -- -- 0 -- -- -- -- -- -- --

5 L 21.9 0 -- -- -- 0 -- -- -- -- -- -- --

6 L 22.0 0 -- -- -- 0 -- -- --

7 L 21.8 0 -- -- -- 0 -- -- -- -- -- -- --

8 L 21.9 0 -- -- -- 0 -- -- -- -- -- -- --

9 L 21.7 1 2 0 2 0 -- -- -- -- . -- --

10 R 21.4 0 -- -- -- 0 -- -- -- -- -- -- --

11 L 21.0 0 -- -- -- 0 -- -- -- -- -- -- --

12 L 20.9 0 -- -- -- 0 -- -- -- -- -- -- --

13 L 21.2 0 -- -- -- 0 -- -- -- -- -- -- --

14 L 21.3 1 360 0 360 0 -- -- -- -- . -- --
10 Identifying Trout Refuges in Northern New York Through Airborne Thermal Infrared Remote Sensing

Table 1. Median water temperature for right (R) or left (L) half of each 1-kilometer (km) section of river channel; mean size, standard 

deviation, and maximum size of refuge areas in which water temperature was 1 to 2 degrees Celsius (°C), and more than (>)2 °C below 

the median temperature for that section; and mean distance, standard deviation, and median and maximum distances between refuges 

during three flights over the 27-km study reach of the Indian and Hudson Rivers in northern New York, August 25, 2005.—Continued

[Sections were divided into halves to avoid effects of shading. Release from upstream reservoir began at 0930 eastern standard time (EST). Shading denotes 

high-water conditions during passage of release from the Lake Abanakee Dam (fig. 1). temp, water temperature; m2, square meter; m, meter; no., number; 

SD, standard deviation; Max, maximum; --, no data]

Km Half

Median 

temp 

(°C)

Refuge areas below median temperature (m2

) Distances between refuges (m)

1 degree 2 degrees

No. Size SD Max No. Size SD Max Mean SD Median Max

Second flight (1239 EST)—Continued

15 L 21.3 0 -- -- -- 0 -- -- -- -- -- -- --

16 L 21.5 0 -- -- -- 0 -- -- -- -- -- -- --

17 L 22.2 56 35 202 1,513 0 -- -- -- 4 11 1 63

18 L 21.8 0 -- -- -- 0 -- -- -- -- -- -- --

19 L 21.9 3 95 120 265 0 -- -- -- 3 3 1 7

20 R 22.0 0 -- -- -- 0 -- -- -- -- -- -- --

21 R 22.1 2 4 1 5 0 -- -- -- 8 0 8 8

22 R 22.2 10 4 3 11 0 -- -- -- 4 3 2 9

23 R 22.3 0 -- -- -- 0 -- -- -- -- -- -- --

24 R 22.0 2 2 0 2 0 -- -- -- 7 0 7 7

25 R 22.1 0 -- -- -- 0 -- -- -- -- -- -- --

26 R 22.4 9 11 12 34 2 33 27 59 2 5 0 16

27 R 22.2 0 -- -- -- 0 -- -- -- -- -- -- --

Overall: 21.9 89 31 167 1,513 2 33 27 59 5 17 1 63

Third flight (1542 EST)

1 L 23.2 24 22 40 195 3 107 148 317 11 47 2 247

2 L 23.2 33 17 22 103 0 -- -- -- 6 14 1 74

3 L 23.5 44 45 114 756 13 10 15 60 4 9 0 38

4 L 24.1 53 36 70 409 14 7 7 23 3 7 1 41

5 L 24.0 10 6 5 20 1 2 0 2 50 113 8 381

6 L 24.1 9 5 5 16 1 2 0 2 22 68 0 215

7 L 23.4 7 3 1 4 0 -- -- -- 97 248 4 660

8 L 23.1 20 42 149 688 3 16 2 19 2 7 1 33

9 L 23.2 4 34 50 120 2 8 4 11 2 2 2 4

10 R 22.8 9 9 5 20 0 -- -- -- 93 231 3 699

11 L 23.1 0 -- -- -- 0 -- -- -- -- -- -- --

12 L 22.9 0 -- -- -- 0 -- -- -- -- -- -- --

13 L 23.2 0 -- -- -- 0 -- -- -- -- -- -- --

14 L 23.1 0 -- -- -- 0 -- -- -- -- -- -- --

15 L 22.4 10 6 5 21 0 -- -- -- 3 3 2 6

16 L 22.4 0 -- -- -- 0 -- -- -- -- -- -- --

17 L 22.4 0 -- -- -- 0 -- -- -- -- -- -- --

18 L 22.1 0 -- -- -- 0 -- -- -- -- -- -- --

19 L 22.2 0 -- -- -- 0 -- -- -- -- -- -- --

20 R 22.2 0 -- -- -- 0 -- -- -- -- -- -- --

21 R 22.3 0 -- -- -- 0 -- -- -- -- -- -- --

22 R 22.6 0 -- -- -- 0 -- -- -- -- -- -- --

23 R 22.9 0 -- -- -- 0 -- -- -- -- -- -- --

24 R 23.2 0 -- -- -- 0 -- -- -- -- -- -- --

25 R 23.5 0 -- -- -- 0 -- -- -- -- -- -- --

26 R 23.9 0 -- -- -- 0 -- -- -- -- -- -- --

27 R 24.0 2 10 5 14 0 -- -- -- 3 0 3 3

Overall: 23.1 225 28 78 756 37 17 51 317 13 67 1 699
Results 11

compared to sections farther downstream that were more 

recently inundated at the time of the flight. In addition, several 

of the 1-km sections just upstream from the high-water slug 

(and therefore, most recently returning to base flow) also had 

no available refuge area.

Mean distances between refuges within a section ranged 

widely, but median distances were generally small for all 

three flights (table 1). Overall median distance was 1 m for all 

three flights, and ranged from 0 to 9 m for the first flight, and 

from 0 to 8 m for the second and third flights. Overall mean 

distance was smallest for the second flight (5 m) and higher 

for the first (16 m) and third (13 m) flights. Maximum distance 

between refuges was also smallest during the second flight 

(63 m) compared with the first and third flights (644 m and 

699 m, respectively). Distance between refuges can be related 

to refuge number: the more refuges in an area, the shorter the 

distance between any of them, especially if they are distributed 

randomly; however, small distances between many refuges 

can also indicate a cold-water source that is contributing to the 

creation of several larger refuges in a particular location.

Cold-Water Contributions From Tributaries

All five cold-water tributaries in the lower part of the 

study reach (fig. 1) seemed to have a local cooling effect on 

river water temperatures during the first flight. Two of these 

tributaries (Boreas River at kilometer 19 and Deer Creek at 

kilometer 27) enter the Hudson River from the east bank, 

where the confluences were shaded during the morning flight. 

For these tributaries, the appearance of more refuge area 

during the first flight than during the second flight (table 2) 

can probably be attributed to the shading of exposed rocks. 

The three other tributaries (Raquette Brook at kilometer 24, 

Aldous Brook at kilometer 25, and Thirteenth Lake Outlet at 

kilometer 26) enter from the west bank, and therefore were 

not shaded during any flight. These three tributaries provided 

more refuge during the second flight than during the first 

(table 2). None of the five confluences provided much refuge 

during the third flight, when the high-water slug was passing 

through (fig. 4; table 2). Two of the tributaries each provided 

one refuge >1 oC BMT (12 m2 and 47 m2, respectively) and 

Table 2. Median water temperature in five river sections containing a cold-water tributary; mean size, standard deviation, and maximum 

size of refuge areas in which water temperature was 1 to 2 degrees Celsius (°C) and more than (>)2 °C below the median temperature for 

that section; and mean distance, standard deviation, and median and maximum distances between refuges during three flights over the 

27-kilometer (km) study reach of the Indian and Hudson Rivers in northern New York, August 25, 2005.

[Release from upstream reservoir began at 0930 eastern standard time (EST). Shading denotes high-water conditions during passage of release from the Lake 

Abanakee Dam (fig. 1). temp, water temperature; m2, square meter; m, meter; SD, standard deviation; Max, maximum; --, no data]

Km Tributary

Median 

temp 

(°C)

Refuge areas below median temperature (m2

) Distances between refuges (m) 1 degree 2 degrees

No. Size SD Max No. Size SD Max Mean SD Median Max

First flight (1012 EST)

19 Boreas River 19.6 7 179 324 940 6 13 8 24 0 1 0 1

24 Raquette Brook 19.5 0 -- -- -- 0 -- -- -- -- -- -- --

25 Aldous Brook 19.9 1 8 0 8 0 -- -- -- 0 -- 0 0

26 Thirteenth Lake Outlet 19.4 3 113 136 305 5 12 9 24 2 2 1 4

27 Deer Creek 18.8 4 87 144 336 1 11 0 11 0 0 0 0

Second flight (1239 EST)

19 Boreas River 21.9 4 72 113 268 0 -- -- -- 20 33 4 69

24 Raquette Brook 22.3 7 12 11 32 2 4 2 5 1 1 0 4

25 Aldous Brook 22.3 5 9 14 37 1 21 0 21 0 0 0 0

26 Thirteenth Lake Outlet 22.4 16 9 9 33 5 27 28 65 0 1 0 5

27 Deer Creek 22.1 7 27 35 109 3 5 0 5 1 1 0 3

Third flight (1542 EST)

19 Boreas River 22.4 0 -- -- -- 0 -- -- -- -- -- -- --

24 Raquette Brook 23.4 1 47 0 47 0 -- -- -- 0 -- 0 0

25 Aldous Brook 23.5 1 12 0 12 0 -- -- -- 0 -- 0 0

26 Thirteenth Lake Outlet 24.0 0 -- -- -- 0 -- -- -- -- -- -- --

27 Deer Creek 23.8 0 -- -- -- 0 -- -- -- -- -- -- --
12 Identifying Trout Refuges in Northern New York Through Airborne Thermal Infrared Remote Sensing

50 METERS

164 FEET

0

0

A. 1012 eastern standard time

B. 1239 eastern standard time

C. 1542 eastern standard time

Raquette

Brook

Deer

Creek

EXPLANATION

Warmer (+3 C°)

Mean temperature

Potential cold-water refuge boundary

Cooler (–3 C°)

Hudson River

Hudson River

Figure 4. False-color thermal infrared images showing cold-water areas at the confluences of 

Raquette Brook at kilometer 24 and Deer Creek at kilometer 27 with the Hudson River in the Adirondack 

Mountains, New York, during three overhead flights on August 25, 2005, at A, 1012 eastern standard 

time (EST), B, 1239 EST, and C, 1542 EST when passage of reservoir release overwhelmed any cooling 

effect of inflow from tributaries. Tributary locations are shown in figure 1.
Discussion 13

no refuges >2 oC BMT, and the three other tributaries did not 

provide any refuge >1 oC BMT (table 2). During the third 

flight, the northernmost tributary (Boreas River) was warmer 

at its mouth than the Hudson River; the other four tributaries, 

which were cooler at their mouths than the Hudson River, 

had only a negligible effect on Hudson River temperatures 

at their confluence. Distances between refuges were small in 

the areas below these confluences, indicating that cold-water 

refuges are clumped around the cooler water entering from 

respective tributaries.

Discussion

The study reach did not provide much suitable habitat 

or cold-water refuges for resident cold-water fish species 

such as brown trout. Only a few areas of the study reach 

were 1 oC BMT at any scale, and there were even fewer and 

smaller areas that were 2 oC BMT, which indicates that the 

availability of refuges from critically warm temperatures 

along the 27-km study reach is severely limited, regardless 

of release flows. A concurrent study on fish movement 

determined that survival of stocked Brown Trout within the 

Indian and Hudson Rivers was poor (Boisvert, 2008). Almost 

no study trout persisted within the Indian and Hudson study 

reaches for an entire summer, compared to half of the tracked 

trout in the nearby control system (Cedar River; fig. 1) which 

was unaffected by recreational releases. This loss of trout 

in the study reach during the warm summer period supports 

the finding that suitable cold-water habitats for Brown Trout 

are scarce. Although a small number of trout may survive 

and possibly overwinter, it is unlikely that a substantial 

population of brown trout hold over through the summer in 

these reaches. Coutant (1985) proposed a similar explanation 

for summer dieoffs and poor condition of adult striped bass 

(Morone saxatilis) in several North American river basins and 

reservoirs. Similarly, Sutton and others (2007) determined 

that main-stem flows in a northern California river could 

not sustain its salmonid population without the presence of 

adequate thermal refuges. High temperatures can fragment fish 

populations within a watershed by isolating suitable thermal 

habitats (Matthews and Zimmerman, 1990). The entire study 

reach contains very few and small thermal refuge areas, so it 

seems to be unable to sustain viable brown trout populations 

regardless of the releases. Other trout species, which are less 

tolerant of warm temperatures than brown trout, would also 

not be expected to maintain resident (year-round) populations.

Recreational flow releases generally decreased the 

number and size of several small, main-channel refuges by 

diluting the cold-water areas at tributary mouths in the study 

reach. In a concurrent study on fish movement, temperature 

loggers were anchored 6 inches above the stream bottom 

in the mixing zone of three cold-water tributaries. Water 

temperatures were generally 4 to 6 oC lower than surface 

temperatures at base flow, but this temperature difference 

disappeared during releases (Boisvert, 2008). These changes 

illustrate how warm-water releases can temporarily eliminate 

thermal refuges. Sutton and others (2007) identified a similar 

scenario in a stream where localized cold-water patches 

were diluted by water discharged from upstream reservoirs. 

This effect may last longer than the period of high-water 

passage; for example, in Sutton and others (2007), the 16 river 

sections inundated by high water during the second flight 

had little refuge area, but only the 8 upstream sections had 

a greatly increased refuge area during the third flight. Such 

a delay in the recovery of refuge areas after a release could 

affect local trout and other species that have a tolerance for 

high temperature decreases with increasing exposure time 

(Galbreath and others, 2004). This difference between surface 

water and stream bottom temperatures also indicates that 

surface temperatures cannot always accurately identify coldwater refuges, especially if they are at tributary confluences.

The middle part of the study reach (kilometers 6–18) 

provided more cold-water habitats than many of the refuges 

in the upper and lower parts of the reach. Water temperatures 

were cooler in many of the 1-km sections of the middle part 

of the reach than in some of the refuges in the upper and 

lower parts of the reach. Thermal remote sensing data from 

an Oregon river basin indicated that large-scale patterns in 

the longitudinal temperature profile, such as downstream 

warming trends and dips in temperature that extended at 

least 5 km, reflected basin-scale processes (Torgersen and 

others, 2001). In the study detailed in this report, the lower 

temperatures in the middle sections of the study reach 

compared with the upper and lower sections may have resulted 

from local physical and geomorphic anomalies. The middle 

sections run east to west and therefore may be more shaded 

from afternoon sun by riparian vegetation than the upper and 

lower reaches, which run north to south. The TIR imagery 

revealed no cold-water tributaries or groundwater seeps in 

this reach. The drainage area through the Hudson Gorge 

(middle section) increases by only 65 km2, from 1,626 km2

just below the Indian River confluence to 1,691 km2 just above 

the Boreas River confluence, and indicates that a large coldwater inflow is unlikely. Any cold-water tributaries may sink 

in this region and be undetected by remote thermal sensing, 

because the banks in this middle reach are steeper than in 

the lower reaches, and the channel is narrower and deeper 

(Boisvert, 2008). Alternatively, this greater channel depth 

could increase hyporheic flow exchange, which in turn could 

buffer temperature increases (Loheide and Gorelick, 2006), 

although these explanations are speculative.

The spatial distribution of refuges and trout movement 

patterns (Boisvert, 2008) in the upper and lower study 

reaches indicate that brown trout were probably limited in 

their ability to find refuges and behaviorally thermoregulate. 

Many studies indicate that salmonids move often, sometimes 

over long distances (Gowan and Fausch, 1996; Mellina and 

others, 2005). Garrett and Bennett (1995) found that brown 

trout in a Michigan reservoir migrated more than 1.7 km 

upstream into a cold-water tributary to thermoregulate during 
14 Identifying Trout Refuges in Northern New York Through Airborne Thermal Infrared Remote Sensing

high summer temperatures. In the current study, such longdistance movements would allow trout to access cold waters 

in the middle study reach; however, although brown trout may 

be capable of long-range movements, they may be less likely 

to do so during the day when the high-water slug is present, 

or during the warm summer months. For example, brown 

trout in a southern Appalachian stream did not seek available 

thermal refuge in nearby tributaries despite summer water 

temperatures that approached lethal limits, which increased 

their mortality (Burrell and others, 2000).

Burrell and others (2000) noted that the study fish had 

long spawning runs during the fall (up to 7.7 km upstream), 

but stayed within a small home range during summer, possibly 

because the stress of high-water temperatures decreased 

their energy. Matthews and others (1994) also determined 

that brown trout in a California river commonly limit their 

movements to a much smaller range during summer low 

flows, possibly because the elevated temperatures force them 

to decrease their energy expenditures. In addition, brown 

trout tend to move significantly less during the day than at 

night (Young and others, 1997; Diana and others, 2004) and 

the recreational releases in the Indian and Hudson River 

only occur during the day. Brown trout in the lower reaches 

generally used refuges that only occurred within 50 m of their 

daily position (Boisvert, 2008). The mean distance between 

adjacent thermal refuges in the upper and lower study reaches 

was 5 to 16 m during all three flights, and the maximum 

distance exceeded the 150-m limit for less than one-third of 

the refuges. In comparison, fish tracked in the middle reach 

were generally several kilometers away from the nearest 

refuges. Thus, even though the refuges were within their home 

range, brown trout may not have used refuges often because of 

limited access or inadequate energy for movement.

Local thermal refuges near tributaries seem to provide 

more available habitats to brown trout in the lower study 

reach. Whether or not periodic decreases in this refuge area 

caused by the flow releases adversely affect local trout (or 

other species) depends on the use of refuges by trout during 

thermally stressful periods and the amount of refuge area 

that is lost during the releases. If most fish rely on smallscale refuges to escape thermal stress, then the reservoir 

releases may have a strongly negative effect on their survival. 

Transmitter-implanted trout in a concurrent study on fish 

movement exploited thermal refuges, but the low rate of 

use indicates that these areas of cold water were limited 

(Boisvert, 2008). Small, infrequent thermal refuges may be 

difficult for stressed individuals to locate, or they may simply 

be inadequate to support a self-sustaining (naturalized) brown 

trout population.

Study Limitations

Logistics and funding and time constraints created 

several limitations that could have affected some findings in 

the present study. The main limitation of this study was the 

lack of a control flight on a nonrelease day to separate the 

effects of increased daytime solar radiation from the dam 

release on water temperature. The dam release clearly affected 

refuge areas because the top of the reach (kilometers 1–9) 

showed more refuge area during the afternoon flight than the 

flight at 1239 EST, which is inconsistent with the idea that 

solar radiation was the only impact on river temperature. 

Comparisons showing that (1) water temperatures did not 

differ substantially between release and nonrelease days and 

(2) the peaks in river stage associated with the high-water slug 

were not correlated with water temperature changes (Baldigo 

and others, 2010) indicate that the high-water slug does not 

affect the overall temperature patterns of the river, which 

helped compensate for the lack of control flight. Despite these 

compensations, the utility of remote thermal sensing in this 

study was limited by two characteristics of the TIR images.

The first characteristic was the inability to consistently 

differentiate land from water where riparian vegetation was 

abundant and crowded the edge of the water; overhanging 

riparian vegetation obscured 11 to 15 percent of the stream 

banks in the visible-spectrum and TIR images, and therefore 

required visual estimation techniques for these areas. Given 

that all thermal refuges identified in this study were small 

and were located along a stream bank (primarily at tributary 

confluences), the estimated location of the edge of the water 

may have skewed the measurement of thermal refuge area.

The second major limitation of thermal remote sensing 

in this study was the inability to detect groundwater seeps. 

Remote sensing measures only surface water temperatures, 

and cold groundwater upflow into a stream channel is denser 

than warmer main-stem water and not likely to rise to the 

surface. Both of these limitations could be decreased or 

eliminated if additional thermal remote sensing data were 

collected during late fall or early spring when deciduous 

stream-edge vegetation is absent and groundwater flowing 

into streams is warmer than the river and more easily detected 

(Torgersen and others, 2001). Such cold-weather data would 

not have addressed the primary objective of this study, which 

was to quantify the effect of summer recreational releases 

on the number, size, and distribution of thermal (cold-water) 

refuge areas.

Some study methods may have also increased the error 

rate of the data. For example, estimates of mean distances 

between refuges were probably underestimated in most 

sections. Although refuge-interval (distance) measures are 

fairly straightforward, other techniques used to evaluate water 

temperature patterns (mask out the land on TIR images, and 

then calculate averages from all pixels within the stream 

boundary) vary across similar studies, which involve a 

visual inspection of TIR images (for example, Torgersen and 

others, 1999, 2001). Visual inspection can be used to exclude 

rocks and large woody debris when selecting sample points 

in the main stream. The methods used in this study may have 

increased the error rate, affecting the longitudinal profile more 

than the calculation of section medians, as evidenced by the 

spiky longitudinal profile patterns. Black and others (2003) 
References Cited 15

analyzed stream temperatures in a Washington stream using 

methods similar to those of this study and determined that 

remote thermal sensing of streams in which some areas were 

obscured by vegetation and other areas had open canopy 

might promote misinterpretation, with higher temperatures 

throughout the reach rather than solely within the open 

canopy areas. Thus, shaded sections of stream in the present 

study may have lower temperatures than indicated by thermal 

remote sensing data. If so, parts of the reach may actually 

provide more cold-water habitats, but because cooler water 

tends to have fewer refuges, the number and size of refuges 

(and distances between refuges) could differ from those 

described herein.

Summary

In 2005, the U.S. Geological Survey, in cooperation 

with the New York State Department of Environmental 

Conservation and Cornell University, initiated an assessment 

of the natural resources in the Indian and Hudson Rivers along 

a reach that receives regular recreational releases from an 

upstream reservoir to support whitewater rafting. The main 

objective of the study was to evaluate the potential effects of 

these releases on the resident and stocked brown trout (Salmo 

trutta) fishery. A related goal, and the focus of this report, 

was to identify cold-water areas that could provide refuges 

possibly critical to the survival of stocked and resident trout 

during periods of thermal stress (the warm summer months). 

Stream temperature data from seven continuous loggers 

and TIR remote sensing data from the 27-kilometer (km) 

reach affected by release flows were analyzed to (1) assess 

the effectiveness of thermal remote sensing to detect spatial 

patterns in stream temperatures at multiple spatial scales, 

(2) identify potential thermal refuges at base flow and during 

release flows, (3) define how the release flows affect the size 

and temperature of the identified refuges, and (4) compare the 

results of thermal refuge identification made at several spatial 

scales. We evaluated hypotheses that the size and number of 

thermal refuges were diminished by recreational flow releases.

Although high temperatures can fragment fish 

populations within a watershed by isolating suitable thermal 

habitats, the TIR data indicate that thermal (cold-water) 

refuges may be too small and widely distributed to have any 

real effect on local trout populations in the study reach. The 

identification of only a few potential thermal refuge areas 

in the Hudson Gorge probably reflects the typically warm, 

low-flow summer conditions that would prevail even in the 

absence of recreational releases from the warm reservoir. 

Although indirect effects of the releases probably increased 

trout stress and mortality (for example, by physically 

displacing individuals or temporarily eliminating low-velocity 

resting areas), summer temperatures along the study reach 

were stressful, regardless of the pulsed discharge events. Adult 

brown trout living under these thermally stressful conditions 

may not be able to fulfill normal metabolic needs. Remote 

thermal sensing can be an effective way to map spatial patterns 

and variations in river temperatures; however, the drawbacks 

of the method require consideration when small thermal 

refuges are to be characterized. Choosing an appropriate scale 

is critical and depends on both stream-system geomorphology 

and the movement patterns (and thermal requirements) of the 

fish that potentially use cold-water refuges. The 27-km river 

reach in this study provided both small-scale thermal refuges 

at tributary confluences and large-scale refuges that extended 

along several kilometers of river that remain cooler than 

the rest of the study reach. In summary, the limited size and 

number of thermal refuges (and the inability of brown trout 

to utilize cold-water refuges that are more than 50 meters [m] 

away) indicates that self-sustaining (naturalized) brown trout 

populations are unlikely to persist in the lower Indian and 

upper Hudson Rivers.

In general, the release flows overwhelmed the small 

number of thermal refuges that were detected and greatly 

decreased their numbers and their sizes. Mean water 

temperatures were unaffected by the releases, but small-scale 

heterogeneity was diminished. At the river-reach scale, water 

temperatures in the upper and lower segments of the reach 

were consistently warmer than in the middle segment, even 

during passage of release waters. Most important, the limited 

number of thermal refuges may be inadequate to sustain local 

brown trout populations in the upper Hudson and Indian 

Rivers considering findings from published literature and 

academic research indicate trout must have nearby (within 

about 50 m) cold-water refuges to survive extended periods 

of thermal stress. The inability of remote thermal images to 

consistently distinguish land from water (in shaded areas) and 

to detect groundwater seeps (away from the shallow edges 

of the stream), however, hampered our ability to identify and 

assess potential thermal refuge areas in this report.

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Ernst and others—Identifying Trout Refuges in the Indian and Hudson Rivers, N.Y., Through Airborne Thermal Infrared Remote Sensing—OFR 2015−1078

ISSN 2331-1258 (online)

http://dx.doi.org/10.3133/ofr20151078