Water-Quality Conditions in Upper Klamath Lake, 

Oregon, 2002-04

Prepared in cooperation with the Bureau of Reclamation and U.S. Fish and Wildlife Service

Scientific Investigations Report 2006-5209

U.S. Department of the Interior

U.S. Geological Survey

Hanks

Marsh

Howard

Bay

Ball

Bay Shoalwater Bay

Wocus

Marsh

Caledonia

Marsh

Pelican

Bay

Link

River

Agency

Lake

Moss Creek

Klamath

Falls

Plum Valley

Eagle

Ridge

Fremont

Bridge

Link

River

Dam

Buck

Island

Bare

Island

140

42°30’

42°15’

Upper

Klamath

Aspen

Lake

Lake

Williamson

Modoc

Point
Cover: Upper Klamath Lake looking west toward Eagle Ridge. (Photograph taken by Mary Lindenberg, 

U.S. Geological Survey, Klamath Falls, Oregon, 2006.) Insets from left to right are:

Inset 1: Photograph of mom and baby Mergansers in Upper Klamath Lake. (Photograph taken by Mary 

Lindenberg, U.S. Geological Survey, Klamath Falls, Oregon, 2006.)

Inset 2: Photograph of Lost River sucker from Upper Klamath Lake. (Photograph taken by Brian Hayes, U.S. 

Geological Survey, Klamath Falls, Oregon, date unknown.)

Inset 3: Photograph of the buoy platform supporting the meteorological and water quality instrumentation 

at U.S. Geological Survey site MDL on Upper Klamath Lake, Oregon. (Photograph taken by Pamela Burns, 

U.S. Geological Survey, Klamath Falls, Oregon, 2005.)

Inset 4: Photograph of Great Blue Heron taking off, Upper Klamath Lake. (Photograph taken by Mary 

Lindenberg, U.S. Geological Survey, Klamath Falls, Oregon, 2006.)
Water-Quality Conditions in Upper Klamath 

Lake, Oregon, 2002–04

By Tamara M. Wood, Gene R. Hoilman, and Mary K. Lindenberg

Prepared in cooperation with the

Bureau of Reclamation and the U.S. Fish and Wildlife Service

Scientific Investigations Report 2006–5209

U.S. Department of the Interior

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

Dirk A. Kempthorne, Secretary

U.S. Geological Survey

P. Patrick Leahy, Acting Director

U.S. Geological Survey, Reston, Virginia: 2006

For sale by U.S. Geological Survey, Information Services

Box 25286, Denver Federal Center

Denver, CO 80225

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

World Wide Web: http://www.usgs.gov/

Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply 

endorsement by the U.S. Government.

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

reproduce any copyrighted materials contained within this report.

Suggested citation:

Wood, T.M., Hoilman, G.R., and Lindenberg, M.K., 2006, Water-quality conditions in Upper Klamath Lake, Oregon, 

2002–04: U.S. Geological Survey Scientific Investigations Report 2006-5209, 52 p. 
iii

Contents

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

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

Datasets and Methods ................................................................................. 3

Continuous Water-Quality Data .................................................................. 3

Meteorological Data .............................................................................. 4

Nutrients and Chlorophyll a........................................................................... 4

Statistical Methods ................................................................................. 5

Physical Description of Upper Klamath Lake ......................................................... 6

Water-Quality Observations ........................................................................... 11

Weekly Nutrients and Chlorophyll a... ............................................................ 11

Continuous Water-Quality Monitors ............................................................ 17

Occurrence and Duration of Water-Quality Conditions Potentially Harmful to Fish ...... 20

Location and Spatial Extent of Water-Quality Conditions Potentially Harmful to Fish ...... 21

Diel Variability ....................................................................................... 23

Factors Contributing to Low Dissolved Oxygen Events ............................................. 29

Water Column Stratification ..................................................................... 29

Bloom Decline ....................................................................................... 33

Wind-Driven Circulation ........................................................................... 34

Historical Context of 2002-04 Data ..................................................................... 37

Temperature ....................................................................................... 37

Wind Speed and Direction ........................................................................ 38

Lake-Wide Water Quality ........................................................................ 39

Water Quality at Indicator Sites .................................................................. 42

Conclusions Regarding Characteristics of Fish Die-Off Years................................. 44

Summary ................................................................................................... 46

Acknowledgments ....................................................................................... 48

References Cited.......................................................................................... 48

Appendix A. Quality-Assurance Data for Water Samples .......................................... 49
iv

Figures

Figure 1. Maps showing Upper Klamath Lake, with locations of continuous

water-quality monitors, acoustic Doppler current profilers, and water

sample-collection sites in (A) 2002 and (B) 2003–04, Klamath County, 

Oregon ....................................................................................... 2

Figure 2. Graphs showing daily maximum range in temperature over the water

column, minimum range in temperature over the water column, maximum

temperature, and minimum temperature, from hourly values collected at 1

meter off the bottom and 1 meter from the surface at sites UKL07 and UKL08 

in Upper Klamath Lake, Oregon, 2002 ................................................... 6

Figure 3. Graphs showing daily maximum range in temperature over the water

column, minimum range in temperature over the water column, maximum

temperature, and minimum temperature, from hourly values collected at 1

meter off the bottom and 1 meter from the surface at sites UKL07 and UKL13 

in Upper Klamath Lake, Oregon, 2003 ................................................... 7

Figure 4. Graphs showing daily maximum range in temperature over the water

column, minimum range in temperature over the water column, maximum

temperature, and minimum temperature, from hourly values collected at 1

meter off the bottom and 1 meter from the surface at sites UKL07 and UKL16 

in Upper Klamath Lake, Oregon, 2004 ................................................... 7

Figure 5. Graph showing depth of the photic zone (the depth where light is 1 percent

of surface value), as a function of chlorophyll a concentration in Upper

Klamath Lake, Oregon ..................................................................... 8

Figure 6. Graphs showing half-hourly current speed and direction recorded at sites

ADCP4 and ADCP8, Upper Klamath Lake, Oregon, 2003 .............................. 9

Figure 7. Graphs showing half-hourly current speed and direction recorded at sites

ADCP1 and ADCP2 (before August 6) and at sites ADCP3 and ADCP4 (after

August 6), Upper Klamath Lake, Oregon, 2004 .......................................... 10

Figure 8. Map showing circulation pattern in Upper Klamath Lake in response to

prevailing wind conditions.................................................................. 11

Figure 9. Graphs showing chlorophyll a concentrations at sites in Upper Klamath

Lake, Oregon, 2002–04 ..................................................................... 12

Figure 10. Graphs showing total phosphorus concentrations at sites in Upper Klamath

Lake, Oregon, 2002–04 ..................................................................... 13

Figure 11. Graphs showing orthophosphate-P concentrations at sites in Upper

Klamath Lake, Oregon, 2002–04............................................................ 14

Figure 12. Graphs showing ammonia-N concentrations at sites in Upper Klamath Lake,

Oregon, 2002–04 ........................................................................... 15

Figure 13. Graphs showing un-ionized ammonia-N concentrations at sites in Upper

Klamath Lake, Oregon, 2002–04............................................................ 16

Figure 14. Graphs showing nitrate/nitrite-N concentrations at sites in Upper Klamath

Lake, Oregon, 2002–04 ..................................................................... 17

Figure 15. Boxplots showing statistical distributions of chlorophyll a, total phosphorus,

and ammonia-N concentrations for the entire field season at individual sites

in Upper Klamath Lake, Oregon, 2002–04 ................................................ 18

Figure 16. Graphs showing daily medians of (A) percent saturation of dissolved

oxygen, (B) dissolved oxygen concentration, (C) pH, and (D) temperature for

sites in Upper Klamath Lake, Oregon, 2002-04 .......................................... 19
Figure 17. Graphs showing percentage of sites recording at least one reading in the

day of conditions potentially harmful to fish in Upper Klamath Lake, Oregon,

2002–04 ....................................................................................... 21

Figure 18. Graphs showing percentage of total site-hours in the day having conditions

potentially harmful to fish in Upper Klamath Lake, Oregon, 2002–04 .................. 21

Figure 19. Maps showing Geographic Information System coverage of an interpolation

of weekly median dissolved oxygen concentrations, Julian weeks 31–34,

Upper Klamath Lake, Oregon, 2002–04 ................................................... 24

Figure 20. Maps showing Geographic Information System coverage of an interpolation

of weekly median pH, Julian week 27, Upper Klamath Lake, Oregon, 2002–04 ...... 25

Figure 21. Maps showing Geographic Information System coverage of an interpolation

of weekly median temperature, Julian week 31, Upper Klamath Lake,

Oregon, 2002–04 ........................................................................... 26

Figure 22. Histograms showing daily extremes in water-quality conditions as a

function of hour in the day, at representative shallow (UKL02) and deep

(UKL07) sites in Upper Klamath Lake, Oregon, 2002–04. Data for 2002-04

have been combined ........................................................................ 28

Figure 23. Graphs showing daily minimum and maximum ranges in dissolved oxygen

over the water column and minimum and maximum dissolved oxygen from

hourly values collected at 1 meter off the bottom and 1 meter from the

surface at sites UKL07 and UKL08 in Upper Klamath Lake, Oregon, 2002 ............ 30

Figure 24. Graphs showing daily minimum and maximum ranges in dissolved oxygen

over the water column and minimum and maximum dissolved oxygen from

hourly values collected at 1 meter off the bottom and 1 meter from the

surface at sites UKL07 and UKL13 in Upper Klamath Lake, Oregon, 2003 ............ 30

Figure 25. Graphs showing daily minimum and maximum ranges in dissolved oxygen

over the water column and minimum and maximum dissolved oxygen from

hourly values collected at 1 meter off the bottom and 1 meter from the

surface at sites UKL07 and UKL16 in Upper Klamath Lake, Oregon, 2004 ............ 31

Figure 26. Graphs showing daily maximum range in dissolved oxygen concentration

over the water column, maximum range in temperature over the water

column, minimum water column dissolved oxygen concentration, and 90th

percentile of hourly wind values in Upper Klamath Lake, Oregon, 2002-04 ......... 32

Figure 27. Graph showing daily median dissolved oxygen concentrations at sites

UKL04, UKL07, UKL13, and UKL14 in Upper Klamath Lake, Oregon, 2003 ............ 34

Figure 28. Graph showing daily median dissolved oxygen concentrations at sites

UKL04, UKL07, UKL13, and UKL14 in Upper Klamath Lake, Oregon, 2004 ............ 35

Figure 29. Graphs showing hourly dissolved oxygen concentrations at sites UKL14 and

UKL16 in Upper Klamath Lake, Oregon, 2004 ............................................. 36

Figure 30. Graph showing hourly dissolved oxygen concentrations at site UKL14 in

Upper Klamath Lake, Oregon, 2003 ...................................................... 36

Figure 31. Graphs showing July–August distributions of concentrations of chlorophyll

a, ammonia, dissolved oxygen, and temperature, and the difference

between the water column maximum and minimum dissolved oxygen, at

three sites located in Upper Klamath Lake, Oregon .................................... 40

Figures—Continued
vi

Tables

Table 1. Water column depths at the beginning of the summer months at sites where

profiling buoys were located, Upper Klamath Lake, Oregon, 2002–04 ............... 8

Table 2. Start dates of Julian weeks, 2002–04...................................................... 22

Table 3. Spatial extent of extreme water-quality conditions in Upper Klamath Lake,

Oregon, 2002–04 ........................................................................... 22

Table 4. Average number of hours per day in Julian weeks 31 to 34 that dissolved

oxygen concentrations less than 4 milligrams per liter were measured at

shallow and deep sites in Upper Klamath Lake, Oregon, 2002-04 ..................... 23

Table 5. Average number of hours per day in Julian week 27 that pH greater than 9.7

was measured at shallow and deep sites in Upper Klamath Lake, Oregon,

2002-04 ....................................................................................... 23

Table 6. Dates of low dissolved oxygen events in the northern part of Upper Klamath

Lake, Oregon, 2002–03 ..................................................................... 29

Table 7. Spearman’s rho correlation coefficients between daily values derived from

hourly data collected at site UKL08 in 2002 and site UKL07 in 2003-04, Upper

Klamath Lake, Oregon ..................................................................... 33

Table 8. Results of analysis of variance (ANOVA) of air temperature at the Klamath

Falls Airport, Oregon, July and August, 1990–2004 .................................... 37

Table 9. Results of analysis of variance (ANOVA) of wind speed at the Klamath Falls

Airport, Oregon, July and August, 1990–2004 .......................................... 38

Table 10. Results of analysis of variance (ANOVA) of the along-lake component of

wind speed at the Klamath Falls Airport, Oregon, July and August, 1990–2004...... 38

Table 11. Results of analysis of variance (ANOVA) of wind speed at the Klamath Falls

Airport and at the Bureau of Reclamation Agrimet site located at Agency

Lake, Oregon, July and August, 1990–2004 ............................................. 39

Table 12. Spearman’s rho correlation coefficients between selected water-quality

and climate variables in Upper Klamath Lake Basin, Oregon, 1990–2004 ............ 41

Table 13. Principal component scores at sites Eagle Ridge and Midnorth in Upper

Klamath Lake, Oregon ..................................................................... 43

Figure 32. Scatter plots showing correlation between the July–August averaged wind

speed at the Klamath Falls Airport and the median of the July–August

distribution of ammonia, dissolved oxygen, and the difference between

water column maximum and minimum dissolved oxygen, Upper Klamath

Lake, Oregon ................................................................................. 42

Figure 33. Scatter plots showing principal component scores for data from Midnorth

site, all July and August sample dates, Upper Klamath Lake, Oregon, 

1990–2004 .................................................................................... 44

Figure 34. Scatter plots showing principal component scores for data from Eagle

Ridge site, all July and August sample dates, Upper Klamath Lake, Oregon,

1990–2004 .................................................................................... 44

Figures—Continued
vii

Table 14. Distribution statistics of water column averages of chlorophyll a,

ammonia-N, dissolved oxygen, and temperature at Eagle Ridge site, based

on July–August sampling dates, Upper Klamath Lake, Oregon, 1990–2004 ......... 45

Table 15. Distribution statistics of water column averages of chlorophyll a,

ammonia-N, dissolved oxygen, and temperature at Midnorth site, based on

July–August sampling dates, Upper Klamath Lake, Oregon, 1990–2004 ............ 45

Conversion Factors, Datums, and Abbreviations and 

Symbols

SI to Inch/Pound

Multiply By To obtain

centimeter per second (cm/s) 0.0328 foot per second

cubic meter per second (m3/s) 70.07 acre-foot per day

kilometer (km) 0.6214 mile

liter (L) 1.057 quart

liter (L) 0.2642 gallon

meter (m) 3.281 foot 

square kilometer (km2) 0.3861 square mile

square meter (m2) 0.0002471 acre 

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

°F=(1.8×°C)+32.

Datums

Vertical coordinate information is referenced to 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.

Tables—Continued
viii

Abbreviations and Symbols

Abbreviations and Symbols Definition

ADCP acoustic Doppler current profiler

AFA Aphanizomenon flos aquae

ANOVA analysis of variance

BOD biological oxygen demand

GIS Geographic Information System

LDOE low dissolved oxygen event

NWIS National Water Information System

NWQL National Water Quality Laboratory

Reclamation Bureau of Reclamation

USFWS U.S. Fish and Wildlife Service

USGS U.S. Geological Survey

° degree

mg/L milligram per liter

mg/L microgram per liter

mm micrometer

Conversion Factors, Datums, and Abbreviations and 

Symbols—Continued
Abstract

Eleven (2002) to 14 (2003 and 2004) continuous waterquality monitors that measured pH, dissolved oxygen, 

temperature, and specific conductance, were placed in Upper 

Klamath Lake to support a telemetry tracking study of 

endangered adult shortnose and Lost River suckers. Samples 

for the analysis of chlorophyll a and nutrients were collected 

at a subset of the water-quality monitor sites in each year. 

The seasonal pattern in the occurrence of supersaturated 

dissolved oxygen concentrations and high pH associated with 

photosynthetic activity, as well as the undersaturated dissolved 

oxygen concentrations associated with oxygen demand 

through respiration and decay in excess of photosynthetic 

production, were well described by the dynamics of the 

massive blooms of Aphanizomenon flos aquae (AFA) that 

occur each year.

Data from the continuous monitors provided a means 

to quantify the occurrence, duration, and spatial extent of 

water-quality conditions potentially harmful to fish (dissolvedoxygen concentration less than 4 milligrams per liter, pH 

greater than 9.7, and temperature greater than 28 degrees 

Celsius) in the northern part of the lake, where the preferred 

adult sucker habitat is found. There were few observations 

of temperature greater than 28 degrees Celsius, suggesting 

that temperature is not a significant source of chronic stress 

to fish, although its role in the spread of disease is harder to 

define. Observations of pH greater than 9.7 were common 

during times when the AFA bloom was growing rapidly, 

so pH may be a source of chronic stress to fish. Dissolved 

oxygen concentrations less than 4 milligrams per liter were 

common in all 3 years at the deeper sites, in the lower part of 

the water column and for short periods during the day. Less 

common were instances of widespread low dissolved oxygen, 

throughout the water column and persisting through the entire 

day, but this was the character of a severe low dissolved 

oxygen event (LDOE) that culminated in the start of a fish 

die-off in 2003.

Documented evidence indicates that LDOEs played a role 

in three fish die-offs in the mid-1990s as well. In the historical 

context of 15 years of climate and water-quality data, 3 out 

of 4 of the recent fish die-off years, 1996, 1997, and 2003, 

were characterized by low winds and high temperatures in 

July or August coincident with the start of the die-off. High 

temperatures accelerate the oxygen demanding processes that 

lead to a LDOE. The role of low winds remains inconclusive, 

but it could include the development of stratification in 

the water column and/or the alteration of the wind-driven 

circulation pattern. 

At a site centrally located in the study area, die-off 

years could be successfully identified in the historical data 

by screening for water characterized by exceptionally low 

chlorophyll a concentration, exceptionally low dissolved

oxygen concentration throughout the water column (not 

just near the bottom), and exceptionally high ammonia 

concentration and water temperature, just prior to or 

coincident with the start of a fish die-off. These conditions 

indicate that a severe decline in the AFA bloom and 

conversion of most of the organic matter into inorganic form 

had taken place.

Introduction

Upper Klamath Lake (fig. 1) is located in southern 

Oregon; about 25 km north of the California-Oregon border 

and 18 km east of the crest of the Cascade Range. It is a large, 

relatively shallow lake with a surface area of 232 km2 and an 

average depth of 2.8 m at full pool. Most of the lake 

(92 percent) is shallower than 4 m, with the exception of a 

narrow trench running parallel to Eagle Ridge, on the lake’s 

western shore. This trench contains the deepest waters of the 

lake, approaching 15 m. Upper Klamath Lake is located in 

the Klamath Graben structural valley, and much of its 

9,415 km2 drainage basin is composed of phosphorus-rich 

volcanically derived soils. The largest single contributor of 

Water-Quality Conditions in 

Upper Klamath Lake, Oregon, 

2002-04

By Tamara M. Wood, Gene R. Hoilman, and Mary K. Lindenberg
or003UK_01_fig01

See table of contents for mapping sources

Hanks

Marsh

Hanks

Marsh Howard Bay

Ball

Bay

Shoalwater

Bay

Wocus

Marsh

Caledonia

Marsh

Pelican

Bay

Link

River

Lake

Ewauna

Agency

Lake

Moss

Creek

Wood

River

Rock

Creek

Sprague

River

97

97

Klamath

Falls

Plum Valley

Eagle Ridge

Fremont

Bridge

Link River 

Dam

Buck

Island

Bare

Island

Bare

Island

140

161

70

66

Howard

Bay

Ball

Bay

Shoalwater

Bay

Wocus

Marsh

Caledonia

Marsh

Pelican

Bay

Link

River

Lake

Ewauna

Agency

Lake

Moss

Creek

Wood

River

Rock

Creek

Sprague

River

97

97

Klamath

Falls

Plum Valley

Eagle Ridge

Fremont

Bridge

Link River 

Dam

Buck

Island

140

161

70

66

42°30’

42°15’

122°00’ 121°45'

42°30’

42°15’

122°00’ 121°45'

Upper

Klamath

Upper

Klamath

Lake

Lake

Aspen

Lake

Aspen

Lake

River

Williamson

River

Williamson

ModocPoint

ModocPoint

UKL16

UKL11

UKL12

UKL08

UKL04

UKL14

UKL03

UKL02

UKL01 UKL05

UKL06

UKL13 UKL07 UKL09 UKL10

ADCP2 ADCP1

ADCP3

ADCP4

ADCP8

AGRIMET_AL

UKL11

UKL08

UKL04

UKL03

UKL02

UKL01 UKL05

UKL06

UKL07

UKL09

UKL10

NOAA_KF

SB

ER

MN

11502500 11502500

0 5 MILES0 5 KILOMETERS

Studyarea

OREGON

EXPLANATIONDepth of Klamath and Agency Lakes—In feet 0 50USGS streamgageContinuous water-quality monitoring sites 2002 2003–2004ADCP location

—

2003 only2004 only2003 and 2004

Klamath Tribes sampling  siteMeteorological site

11502500

A

B

Figure 1. Upper Klamath Lake, with locations of continuous water-quality monitors, acoustic Doppler current profilers, and water sample-collection sites in (A) 2002 and (

B) 2003–04, Klamath County, Oregon.

   Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
inflow to the lake is the Williamson River, which constitutes 

about 46 percent of the lake’s incoming water and enters 

the lake near its northern end (Johnson and others, 1985). 

Agency Lake, just north of Upper Klamath Lake and 

connected to it by a narrow channel, has 37 km2 of surface 

area and an average depth of 2.2 m, and is for the most part 

distinct from Upper Klamath Lake hydrologically and in 

terms of water quality. Upper Klamath Lake was historically 

eutrophic, but over the past several decades has experienced 

nuisance blooms of the blue-green alga Aphanizomenon 

flos‐aquae (AFA) during the summer and autumn, and can 

now be characterized as hypereutrophic.

Upper Klamath Lake is a natural water body, but lake 

surface elevations have been regulated since 1921, when Link 

River Dam was completed at the southern outlet of the lake. 

The dam was built, and is currently operated, by the Bureau 

of Reclamation, and Upper Klamath Lake is now the principal 

water source for the Klamath Project—an irrigation system 

developed to supply water to 970 km2 of farm and ranch land 

in and around the Upper Klamath Basin. During the summer 

months, water is diverted upstream of the lake for agricultural 

use, water is diverted downstream to supply the irrigators of 

the Klamath Project, water is sent downstream through the 

Link River to meet the flow requirements of the National 

Marine Fisheries Service for Klamath River coho salmon, and 

water is lost from the lake through evaporation. As a result, 

the lake level declines by about 1 m between June 1 and 

September 1. Lake elevations during the 3 study years were 

1262.71, 1262.79, and 1262.64 m on June 1 in 2002, 2003, 

and 2004, respectively. On September 1, the elevations were 

1261.44, 1261.76, and 1261.72 m in 2002, 2003, and 2004, 

respectively (on the basis of data for U.S. Geological Survey 

(USGS) site identification No. 11507001, which is a weighted 

average of three gages located around the lake).

Severe water-quality problems in Upper Klamath 

Lake have led to critical fishery concerns for the region, 

including the listing of Lost River and shortnose suckers 

as endangered in 1988. The lake’s algal community has 

shifted to a monoculture of AFA, massive blooms of which 

have been directly related to episodes of poor water quality. 

The growth and decomposition of dense algal blooms in 

the lake frequently cause extreme water quality conditions 

characterized by high pH (9–10), widely variable dissolved 

oxygen (anoxic to supersaturated), and high ammonia 

concentrations (greater than 0.5 mg/L, un-ionized).

In April 2001, the U.S. Fish and Wildlife Service 

(USFWS) released a Biological Opinion regarding the 

endangered suckers in Upper Klamath Lake. As part of 

that document, the USFWS provided several alternatives to 

allow for the continued operation of the Klamath Project. 

One of those alternatives was for the Bureau of Reclamation 

(Reclamation) to develop a study plan to better determine 

the role of “water quality refuge” areas in adult sucker 

survival in Upper Klamath Lake. This led Reclamation and 

U.S. Geological Survey (USGS) to enter into a cooperative 

agreement, the primary objective of which was to tag and track 

with radio telemetry a representative sample of the endangered 

suckers in the lake while simultaneously monitoring water 

quality. Water quality was monitored primarily through a 

network of multiparameter water quality instrumentation. 

The network was designed with the objective of being able 

to provide a “map” of water quality at any point in time, onto 

which the fish tracking information could be overlaid. Such a 

map would provide information about water quality not only 

where fish were located, but also where fish were not located, 

and would allow robust statistical tests of fish movement in 

response to water-quality conditions. The study area was 

limited to roughly the northern one-third of Upper Klamath 

Lake, largely because a previous tracking study done by 

Reclamation had indicated that the endangered suckers were 

located primarily in this area of the lake. The tracking data 

collected during this study has borne out that assumption.

The purpose of this report is to present the water quality 

information collected during the 3 years of the tracking study, 

along with a discussion of what has been learned about the 

factors determining water quality in Upper Klamath Lake. The 

results of the fish tracking in a water-quality context have been 

presented elsewhere (B.J. Adams, U.S. Geological Survey, 

unpub. data, 2005), but the wealth of information provided by 

the monitoring done in support of the tracking study, much of 

which went well beyond the original objectives, merits its own 

report.

Datasets and Methods

Three datasets that were collected by the USGS as 

part of the fish-tracking study have been used in preparing 

this report. The first is continuous dissolved oxygen, pH, 

specific conductance, and water temperature collected from 

a network of continuous water-quality monitors, the second 

is meteorological data (wind, temperature, relative humidity) 

collected at two locations in the study area, and the third is 

chlorophyll a and nutrient data collected on a weekly basis at 

a subset of the sites in the study area. An additional dataset of 

light-meter readings, collected just under the water surface and 

at 0.5-m depth intervals at several sites around the lake as part 

of the ongoing monitoring effort in 2005, was used to generate 

estimates of the depth of the photic zone.

Continuous Water-Quality Data

In 2002, the water-quality monitoring network consisted 

of 11 sites in the study area (fig. 1A). At nine of these sites, the 

monitor was located in a fixed position at 1 m off the bottom. 

At two of these sites, the monitor was installed on a profiling 

buoy, which was programmed to make a profile of the water 

Datasets and Methods   
column on an hourly basis. Starting in 2003, the network was 

modified on the basis of 2002 results. Most of the sites were 

slightly relocated, and three were added (fig. 1B). In 2004, 

one of the profiling buoys was relocated to a position outside 

of the immediate study area, in the middle of the deep trench 

running along the western shoreline of the lake (site UKL16 in 

fig. 1B). 

The water-quality monitors were cleaned and field 

measurements were collected during weekly site visits. 

Deployments generally lasted 3 weeks; at the end of this time, 

the monitor at the site was replaced with a freshly calibrated 

unit. Quality of the data was assured by collecting field 

information at weekly site visits and processing the time series 

according to the procedures in Wagner and others (2000). 

The maintenance procedure for the monitors at the profiling 

buoys was the same as for those at fixed positions, except that 

deployments generally lasted only 2 weeks.

Data collected from the profiling buoys provided 

information on the variability in water-quality constituents 

over the water column at a single geographic location. The 

vertical resolution of the profiles changed over the 3 years 

of the study as the understanding of the system and the 

objectives of the profiling data evolved. Profiling was based 

on a user-supplied uppermost depth and a sampling interval; 

therefore, as the lake was drawn down over the summer, the 

programming needed to be adjusted to compensate for the 

decreasing overall depth. This resulted in some imprecision 

in the location of the sampling depths relative to the bottom, 

but the buoys were consistently programmed to collect data as 

closely as could be achieved to 1 m from the surface and 1 m 

from the bottom, in addition to other points in the profile. In 

2002, the profiles were completed at 0.5-m intervals; in 2003 

and 2004, a single midwater column position completed the 

profile. The profiling mechanism and proprietary computer 

on the profiling buoys proved difficult to maintain in working 

order over the three field seasons of the study, which resulted 

in numerous gaps in the profiling data. When possible, a fixedposition monitor was placed at 1 m off the bottom at the site 

of a nonfunctioning profiling buoy; as a result, the 1-m offbottom dataset at each of the buoy sites is more complete than 

the dataset of water column profiles. The more complete 1-m 

off-bottom dataset was used in computations where the data 

were combined with data from the rest of the network.

Meteorological Data

Both profiling buoys were equipped with a wind compass 

and anemometer. One was additionally equipped with air 

temperature and relative humidity sensors. Because the 

locations of the profiling buoys changed from year to year, 

wind speed and direction was collected at site UKL07 in all 

3 years, and at site UKL08 in 2002, site UKL13 in 2003, and 

at site UKL16 in 2004. Air temperature and relative humidity 

were collected at site UKL08 in 2002, site UKL07 in 2003, 

and at site UKL16 in 2004. Quality assurance of wind speed 

and relative humidity relied on factory calibrations of the 

equipment; air temperature was checked with a National 

Institute of Standards and Technology thermometer in the 

field. Wind direction was checked at the site using a handheld 

compass.

The same equipment problems that hindered the 

collection of complete water-quality profile data affected the 

collection of the meteorological data as well, so there were 

numerous data gaps, particularly in 2002 (68 and 24 percent of 

days were missing at sites UKL07 and UKL08, respectively, 

between June 15 and October 15). Fortunately, the locations 

of the buoys in 2002 were such that the wind data collected at 

sites UKL07 and UKL08 were highly correlated, and could be 

used interchangeably for most purposes. Data collected at sites 

UKL07 and UKL13 in 2003 were slightly less correlated and 

the data collected at sites UKL07 and UKL16 in 2004 were 

only moderately correlated, but the wind datasets were more 

complete in those years (10 percent of days were missing at 

site UKL07 between June 15 and October 15 in 2003, and 

15 percent in 2004). 

Nutrients and Chlorophyll a

Water samples were collected for the analysis of 

dissolved nutrients (ammonia, orthophosphate, and nitrate/

nitrite), total phosphorus and chlorophyll a on a weekly basis. 

In 2002, samples were collected at sites UKL05, UKL06, 

UKL07, and UKL08. In 2003, samples were collected at sites 

UKL05, UKL07, and UKL08, but not at site UKL06. In 2004, 

a fourth site was added at UKL02 (fig. 1). 

Overall, 27 percent of the dissolved nutrient samples 

and 30 percent of the total phosphorus samples collected 

were for quality-assurance purposes, and included equipment 

blanks (first sample collected every week), splits and method 

replicates (each type every other week), spikes (from one 

to three times per season), and a few sequential blanks 

that were designed to test particular procedures during the 

course of the season. Equipment and sequential blanks 

are samples of inorganic blank water collected in the field 

using the same methods and equipment as environmental 

samples. Sequential blanks are a series of blank samples that 

pass through distinct parts of the collection process. Blank 

samples determine if the processes of collection, handling, 

transport and analysis provide measurable contamination. 

Split samples are environmental water samples collected once 

and divided into two. Replicate samples are environmental 

samples collected twice in rapid succession at the same site. 

Split samples determine the variability of sample processing 

and preservation, whereas replicate samples determine 

both the variability of the system and the variability of 

processing and preservation. The results of the qualityassurance sampling indicated that precision and accuracy 

generally were acceptable and the variability in sampling and 

   Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
processing is lower than seasonal variability (Appendix A, 

tables A1-A4, fig. A1). The only area of concern was 

ammonia in equipment blanks, which showed many instances 

of detectable concentration, in some cases quite high in 2003 

and 2004 (table A1). This problem did not occur in 2002, 

when the samples for dissolved nutrients were collected into 

evacuated bottles, even though a VanDorn sampler was used 

to collect the water from depth as in the other years. The 

difference in the sampling process between years suggests 

that the samples were contaminated by air deposition. A 

series of sequential blanks targeted at finding the cause of the 

problem was analyzed in those years, but the source of the 

contamination was never satisfactorily pinpointed, although 

a small amount of contamination seemed to come from the 

filters. The results of equipment blanks may overestimate 

the amount of contamination present in an environmental 

sample because the equipment is flushed with native water 

before an environmental sample is collected, thereby rinsing 

any contaminants. Nonetheless, it should be assumed that 

contamination of the ammonia samples on the order of 

10 μg/L is possible. Although the lowest ammonia 

concentrations may not be as reliable in 2003 and 2004 as 

in 2002, the highest ammonia concentrations are reliable 

and important because ammonia at these concentrations has 

implications for fish health. In 2005, capsule filters were used 

to collect the samples to be analyzed for ammonia. The use of 

these filters does not eliminate all contact between the sample 

and sample bottle and the atmosphere, but it does limit this 

contact. Results indicate that the problem was not eliminated 

entirely but was much reduced by the use of these filters.

Field processing and equipment cleaning protocols 

were designed to procure samples in which concentrations 

at a parts per billion level of concentration could be detected 

(U.S. Geological Survey, variously dated; Horowitz and 

others, 1994). Samples collected for dissolved nutrients 

were collected with a VanDorn sampler at two locations in 

the water column—in the middle of the upper one-half of 

the water column (one-quarter of the water column depth), 

and in the middle of the lower one-half of the water column 

(three-quarters of the water column depth) and passed 

through a 0.45-μm filter. Samples were chilled and shipped 

within 24 hours to the National Water Quality Laboratory 

(NWQL) in Denver, Colorado. In 2002 only, samples for 

dissolved nutrients were collected into an evacuated container 

to minimize any loss of ammonia from a high pH sample 

(C.J. Patterson, U.S. Geological Survey, written commun., 

2002). In 2002 and 2003, samples for total phosphorus 

and chlorophyll a were integrated over the water column 

by collecting water in a large-diameter flexible hose from 

the surface to 0.5 m from the bottom. In 2004, the flexible 

hose was replaced with a cage sampler that was lowered 

with sample collection bottles at a constant rate to 0.5 m 

from the bottom. This cage sampler proved easier to use, 

and the quality-assurance data did not indicate a significant 

change in the median difference between replicate samples 

of total phosphorus from 2003 to 2004 [although the median 

difference between replicates in chlorophyll a increased 

from 2003 to 2004, but remained within acceptable limits 

(table A3)]. In all years multiple subsamples as needed 

from either the VanDorn sampler or the hose/cage sampler 

were composited with a churn splitter, from which splits for 

different analyses were drawn. Total phosphorus samples 

were acidified, chilled, and shipped within 24 hours to the 

NWQL. Finalized data are stored in the USGS National Water 

Information System (NWIS) database (accessible through 

NWISWeb, http://waterdata.usgs.gov/or/nwis/qw).

 Samples for the analysis of chlorophyll a were sent 

to Aquatic Analysts in White Salmon, Washington. The 

chlorophyll a sampling program was designed to measure 

this surrogate for algal biomass in a cost-effective way, with 

good precision, and allow a reliable assessment of relative 

changes in algal biomass. The results of quality-assurance 

sampling and other more qualitative assessments of the dataset 

indicate that the chlorophyll a dataset is well-suited to this 

purpose. Over the 3 years of the study, 20 method replicates 

were collected (7 percent of the total samples) and the median 

percentage of the difference between the replicates was 4, 11, 

and 11 percent in 2002, 2003, and 2004, respectively; 26 split 

samples were collected (10 percent of the total samples) and 

the median percentage of the difference between the splits was 

3, 7, and 10 percent in 2002, 2003, and 2004, respectively. 

The difference between replicate and split samples is low 

and shows that the variability due to collection and analysis 

methods is small compared to the overall temporal variability 

of the data (Appendix A, fig. A1). Chlorophyll a was 

determined fluorometrically for this study. The quantitative 

comparability between this method and the high performance 

liquid chromatography method used by the NWQL to 

determine chlorophyll a in samples prior to October 1, 

2005, has not been established, and the chlorophyll a data 

collected during this study are not stored in the USGS NWIS 

database. Chlorophyll a data collected by the Klamath 

Tribes in their biweekly sampling program were analyzed 

by a spectrophotometric method; therefore the chlorophyll a

data collected during this study should not be assumed to be 

quantitatively comparable to that dataset either.

Statistical Methods

Nonparametric statistics were used in this report in order 

to accommodate data that are not normally distributed. When 

correlations between datasets were calculated, Spearman 

rather than Pearson correlations were used. When analysis 

of variance (ANOVA) was used, the test used was the Tukey 

studentized range test for differences in the means, performed 

on the rank-transformed data. All statistical tests were run 

using SAS System for WindowsTM, Release 8.02, SAS 

Institute Inc., Cary, North Carolina.

Datasets and Methods 
Physical Description of 

Upper Klamath Lake

Upper Klamath Lake is shallow—92 percent of the 

area of the lake is less than 4 m in depth, 65 percent is less 

than 3 m, and 20 percent is less than 2 m. The 4 percent of 

the area of the lake that is greater than 5 m depth is found in 

a narrow trench along the lake’s western shore (fig. 1). The 

southernmost extent of this trench is at roughly the latitude 

of Buck Island; it runs across the entrance to Howard Bay, 

along the western shoreline and then parallel to Eagle Ridge to 

the west of Bare Island. At the tip of Eagle Ridge, the trench 

turns west and runs across the entrance of both Shoalwater 

and Ball Bays before turning north again and gradually fading 

away. Maximum depths in this trench approach 15 m. The 

bathymetry of the lake plays a prominent role in defining 

the wind-driven circulation and has consequences for water 

quality as well.

Within the northern one-third of the lake that constitutes 

the study area, there are less extreme variations in the 

bathymetry that can influence observations at the continuous 

monitors. The deepest part of the study area (excluding the 

trench) is to the south and west, up against Pelican Bay to 

the west and Shoalwater and Ball Bays to the south. The 

lake bottom shoals upward from there to the north and east, 

so much so that site UKL01 could not be maintained for the 

entire field season as the lake level declined. To provide a 

quantitative measure of the difference in depth across the 

study area, the depths at sites UKL10, UKL07, and UKL02 

were 3.8, 4.5, and 2.9 m, respectively, on June 1, 2003. 

Being a shallow lake, Upper Klamath Lake does not 

develop a strong thermocline as would be observed in much 

deeper lakes. Nonetheless, some degree of thermal stability 

can, and often does, develop in areas of Upper Klamath Lake 

that are deeper than about 2.5 m. This thermal stability is most 

resistant to mixing in the trench, but it routinely develops and 

erodes over the course of a day in areas of the lake only 

2.5–3 m deep. During 2002, data from 1 m off the bottom 

and 1 m from the surface were collected with profiling buoys 

at sites UKL07 and UKL08 (fig. 2). The buoy at site UKL07 

remained there during all 3 years of the study, but in 2003, 

the second buoy was moved to site UKL13 (fig. 3), and in 

2004, it was moved to site UKL16 (fig. 4). The depth at site 

UKL07 varied by almost a meter between the 3 years, but was 

comparable to site UKL08 in 2002 and to site UKL13 in 2003. 

In 2004, the depth at site UKL16 was much greater than that at 

site UKL07 (table 1). 

Daily maximum range

Daily minimum range

Daily minimum

Daily maximum

10

15

20

25

30

TEMPERATURE, IN DEGREES CELSIUS

JULY AUGUST SEPTEMBER OCTOBER

1 15 1 15 1 15 1 15

2002

10

15

20

25

30

UKL07

UKL08

Figure 2. Daily maximum range in temperature over the water column, minimum range in temperature over the water 

column, maximum temperature, and minimum temperature, from hourly values collected at 1 meter off the bottom and 1 

meter from the surface at sites UKL07 and UKL08 in Upper Klamath Lake, Oregon, 2002.

 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
Figure 3. Daily maximum range in temperature over the water column, minimum range in temperature over the water column, 

maximum temperature, and minimum temperature, from hourly values collected at 1 meter off the bottom and 1 meter from the 

surface at sites UKL07 and UKL13 in Upper Klamath Lake, Oregon, 2003.

Figure 4. Daily maximum range in temperature over the water column, minimum range in temperature over the water 

column, maximum temperature, and minimum temperature, from hourly values collected at 1 meter off the bottom and 1 meter 

from the surface at sites UKL07 and UKL16 in Upper Klamath Lake, Oregon, 2004.

or003UK_01_fig03

Daily maximum range

Daily minimum range

Daily minimum

Daily maximum

10

15

20

25

30

TEMPERATURE, IN DEGREES CELSIUS

JULY AUGUST SEPTEMBER OCTOBER

1 15 1 15 1 15 1 15

2003

10

15

20

25

30

UKL07

UKL13

Daily maximum range

Daily minimum range

Daily minimum

Daily maximum

10

15

20

25

30

TEMPERATURE, IN DEGREES CELSIUS

JULY AUGUST SEPTEMBER OCTOBER

1 15 1 15 1 15 1 15

2004

10

15

20

25

30

UKL07

UKL16

Physical Description of sUpper Klamath Lake 
Data from the profiling buoys show that a maximum 

daily difference in temperature of 1–3°C between 1 m off the 

bottom and 1 m from the surface is common and, in fact, this 

amount of thermal stability develops nearly every day during 

the summer. These data also show that the daily minimum 

difference in temperature between 1 m off the bottom and 1 m 

from the surface is usually zero (depicted by a thin red line 

in the figures)—that nearly every day the stratification that 

develops is eroded at some point either by wind mixing or 

cooling at the surface or both. Wind speed typically picks up 

in the late morning to early afternoon, reaching a maximum 

in the evening and then dying down in the early morning 

hours, with calm conditions persisting through the morning. 

Thermal stability typically develops and increases throughout 

the morning and afternoon, and then collapses in the evening 

or early morning. Occasionally a period of calm winds will 

result in stratification persisting for several days, particularly 

at deeper sites such as UKL16, which is located in the trench 

(fig. 4). This daily pattern of thermal stability provides ideal 

conditions for the growth of AFA, which is able to take 

advantage of thermal stability to regulate buoyancy in order 

to position cells optimally in the water column (Oliver and 

Ganf, 2000). Thus, the typical pattern of diurnal stratification/

destratification in the lake probably has contributed to the 

ability of AFA to out-compete green algal species in the lake. 

The depth of the photic zone varies with the amount 

of AFA in the water column, but typically is between 

1.5 and 2.5 m during a moderate to heavy bloom (fig. 5). 

Consequently, much of the lake is shallow enough that nearly 

the entire water column is continuously within the photic 

zone. The areas this shallow include Howard Bay and the open 

waters of the lake east of Howard Bay and south to the lake 

outlet, as well as the northern and easternmost parts of the 

study area, including south of Agency Straits and the entrance 

to the Williamson River.

Because observations of water quality, meteorological 

variables, and currents were made simultaneously in this study, 

an increased understanding of the wind-driven circulation in 

the lake has emerged. Two acoustic Doppler current profilers 

(ADCPs) were placed to the east (ADCP8) and west (ADCP4) 

of Bare Island in 2003 by investigators at the USGS National 

Research Program. A basic description of ADCP operation and 

the type of data they collect is provided by Gartner and Ganju 

(2002). During prevailing wind conditions (wind from the west 

to northwest, between about 270 and 300 degrees), currents 

at the trench site (ADCP4) were consistently aligned toward 

about 350 degrees, just west of due north, while currents to 

the east of Bare Island were consistently aligned to between 

120 and 150 degrees, to the southeast (fig. 6). There were 

periods of time lasting from one to several days when the wind 

reversed and came from the east to southeast. These periods are 

seen in the ADCP data as times when the currents also reversed 

direction. 

In 2004, an ADCP was put in the midtrench area at 

ADCP1 from June 16 through August 6, and then it was 

moved to ADCP4 for the next deployment from August 6 to 

September 15 (fig. 7). A second ADCP was put in at ADCP2 

from June 16 through August 6, and then moved to ADCP3 

from August 6 to September 15. The currents at both sites 

in the trench were aligned with the bathymetry in the trench, 

flowing north under prevailing (west to northwest) wind 

conditions, but reversing direction for periods from one to a 

few days when the wind direction changed. Currents at site 

ADCP2 were low and highly variable in direction, flowing 

primarily to the south and southeast, occasionally turning 

northward briefly during a particularly strong wind reversal. 

Currents at ADCP3 were consistently northward, aligned with 

the end of the trench as it turns northward at Ball Bay. There 

were no strong wind reversals during the period of record at 

ADCP3, so it is unclear whether the currents there are likely to 

reverse when the wind changes direction.

Table 1. Water column depths at the beginning of the summer 

months at sites where profiling buoys were located, Upper 

Klamath Lake, Oregon, 2002–04. 

[Symbols: <, less than]

Site Year

Depth at the beginning of the month 

(meters)

July August September

UKL07 2002 3.0 2.8 2.3

2003 3.9 3.5 3.3

2004 3.7 3.3 3.1

UKL08 2002 3.2 3.0 2.5

UKL13 2003 3.9 3.5 3.3

UKL16 2004 14 <14 <14

Figure 5. Depth of the photic zone (the depth where 

light is 1 percent of surface value), as a function of 

chlorophyll a concentration in Upper Klamath Lake, 

Oregon.

0

0.5

1

1.5

2

2.5

3

3.5

4

4.5

5

1 10 100 1000 10,000

CHLOROPHYLL-a CONCENTRATION, IN MICROGRAMS PER LITER

DEPTH OF PHOTIC ZONE, IN METERS

 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
The response of the lake to wind stress under prevailing 

wind conditions (winds from the west to northwest) is 

illustrated conceptually in figure 8. Under these conditions, 

the currents over the broad, shallow part of the lake to the 

east of Bare Island flow down the lake to the southeast. 

Strong currents flowing northwest carry a return flow in the 

narrow trench area to the west of Bare Island. Circulation in 

the study area is clockwise under prevailing wind conditions. 

Preliminary modeling has indicated that most of the water 

in the lake turns around in the southern part of the lake 

between Howard Bay and Buck Island, but this part of the 

circulation is complicated and will require further study to 

refine (R.T. Cheng, U.S. Geological Survey, unpub. data, 

2004). It is clear, however, that the pattern of a broad flow to 

the southeast on the eastern side of the lake and a narrow flow 

to the northwest through the trench on the western side of the 

lake is a persistent feature. When the wind reverses, the basic 

flow pattern reverses as well, to a broad flow to the northwest 

on the east of Bare Island, narrow flow to the southeast in 

the trench, and a counterclockwise circulation through the 

study area. The basic principles of the flow pattern were 

suggested in earlier modeling work (Blank and Juza, 2001), 

but the data to confirm and refine the results were not available 

until the placement of the ADCPs in the lake during this study.

Figure 6. Half-hourly current speed and direction recorded at sites ADCP4 and ADCP8, Upper Klamath Lake, Oregon, 2003. 

Shaded time periods denote times of wind and current reversals. The current direction data range from 100 to 460 degrees 

because 360 degrees have been added to values of current direction less than 100 degrees to avoid the appearance of a 

large shift when the wind direction varies to either side of north. 

0

10

20

30

40

100

200

300

400

500

0

10

20

30

40

100

0

0

200

300

400

500

SPEED, IN CENTIMETERS

PER SECOND

DIRECTION OF CURRENT,

IN DEGREES

SPEED, IN CENTIMETERS

PER SECOND

DIRECTION OF CURRENT,

IN DEGREES

ADCP8

ADCP4

JULY AUGUST SEPTEMBER

1 15 1 15 1 15

2003

Physical Description of sUpper Klamath Lake 
or003UK_01_fig07

0

10

20

30

40

50

100

200

300

400

500

0

0

10

5

15

0

100

200

300

400

500

SPEED, IN CENTIMETERS

PER SECOND

DIRECTION OF CURRENT,

IN DEGREES

SPEED, IN

CENTIMETERS

PER SECOND

DIRECTION OF CURRENT,

IN DEGREES

JUNE AUGUST SEPTEMBER

15 1

JULY

15 1 15 1 15

2004

ADCP2

ADCP1

ADCP3

ADCP4

Figure 7. Half-hourly current speed and direction recorded at sites ADCP1 and ADCP2 (before August 6) and at sites 

ADCP3 and ADCP4 (after August 6), Upper Klamath Lake, Oregon, 2004. Shaded time periods denote times of wind and 

current reversals. The current direction data from ADCP1, ADCP3, and ADCP4 range from 100 to 460 degrees because 360 

degrees have been added to values of current direction less than 100 degrees to avoid the appearance of a large shift when 

the wind direction varies to either side of north.

10 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
An instantaneous measurement of the discharge 

northward through the trench west of Bare Island 

(cross-section A-B in fig. 8) obtained in June 2005 was 

580 m3/s (R.E. Wellman, U.S. Geological Survey, written 

commun., 2005). On the basis of this value and a Geographic 

Information System (GIS) estimate of the volume of the 

lake north of Buck Island of 475×106 m3 (T.L. Haluska, U.S. 

Geological Survey, written commun., 2005), an estimate of the 

traveltime around the entire loop is on the order of 10 days. 

This is not to be confused with residence time in the lake, the 

amount of time between when a parcel of water enters the lake 

and when it leaves, which is likely to be many times longer. 

or003UK_01_fig08

See table of contents for mapping sources

Hanks

Marsh

Howard

Bay

Ball

Bay

Shoalwater Bay

Wocus

Marsh

Caledonia

Marsh

Pelican

Bay

Link

River

Lake

Ewauna

Agency

Lake

Moss Creek

Wood

River

Rock

Creek

Sprague

River

97

97

Klamath

Falls

Plum Valley

Eagle

Ridge

Fremont

Bridge

Link

River

Dam

Buck

Island

Bare

Island

140

161

70

66

42°30’

42°15’

122°00’ 121°45'

Upper

Klamath

Aspen

Lake

Lake

River

Williamson

Modoc

Point

0 5 MILES

0 5KILOMETERS

 EXPLANATION

Depth of Klamath and Agency Lakes—In feet

0

 50

Circulation of water within the lake under

 prevailing wind conditions

Cross-section

A B

A

B

Figure 8. Circulation pattern in Upper Klamath Lake in 

response to prevailing wind conditions.

Water-Quality Observations

Weekly Nutrients and Chlorophyll a

The weekly water samples, while collected at only a 

subset of the sites in the study area, provide valuable context 

for understanding the data from the continuous water-quality 

monitors. Trends and fluctuations in water-quality parameters 

often are associated with bloom dynamics, as reflected in the 

chlorophyll a data. The basic reasons are straightforward: 

a sharp reduction in chlorophyll a indicates a crash in the 

bloom. The spatial extent of the crash may be small enough 

to be captured at only one site, or it may be large enough that 

the crash is evident at several sites. A crash in the bloom is 

characterized by a shutdown or sharp reduction in oxygen 

production through photosynthesis, which is manifested as 

a decrease in dissolved oxygen, generally to values below 

saturation as ongoing sediment and water column demands 

continue to operate unabated. Periods of growth in the bloom 

are, in contrast, generally manifested as supersaturated 

dissolved oxygen and high pH, as photosynthesizing algae 

consume carbon dioxide and produce oxygen. 

The chlorophyll a data collected in all 3 study years 

are presented in figure 9. These 3 years present interesting 

contrasts and demonstrate that the 3 study years were quite 

different. In 2002, the chlorophyll a in samples collected at 

three of the four weekly sampled sites indicated that a crash 

in the bloom occurred around mid-July; the chlorophyll a

concentration at site UKL06 decreased from 630 μg/L on 

July 15 to 29 μg/L on July 22. At all sites except UKL08, 

chlorophyll a concentration remained low for two weekly 

samples. The best estimate of the dates encompassing the 

bloom crash are June 19 to August 1, which was arrived at 

by projecting backward 3 days (approximately one-half of 

the weekly sampling interval) from the first sample date on 

which the crash was observed, and forward 3 days from the 

last sample date on which the bloom was observed. A second 

crash, evident on only one sample date, occurred later in the 

season, and the best estimate of the dates encompassing that 

crash are September 6–12. 

The sample collected on July 29, 2002, in Shoalwater 

Bay was an anomaly—a value of 1,410 μg/L was measured 

there at the same time that the bloom appears to have crashed 

at the other sites. Such exceptionally high values have, on 

occasion, been measured in Shoalwater Bay and Howard Bay 

in the past 15 years (Klamath Tribes, unpub. data), and may 

be an indication that AFA can become physically concentrated 

in these embayments by the action of wind and currents. The 

high chlorophyll a concentration in Shoalwater Bay when 

concentrations elsewhere in the lake were at a minimum 

also is evidence that the blooms in the embayments tend be 

localized, and that the bloom dynamics in the embayments are 

often independent of the bloom dynamics in the open waters 

of the lake. 

Water-Quality Observations 11
Chlorophyll a in samples collected in 2003 at all 

three weekly sampled sites indicated that a crash in the 

bloom occurred near the end of July, when chlorophyll a

concentration decreased from 397 μg/L on July 15 to 17.5 

μg/L on July 23. The estimated dates of the crash are July 19 

to August 1. Secondary crashes lasting only one sample date 

were observed in the second and fourth weeks of September; 

estimated dates are September 6–12 and September 20–26. 

There is no evidence that the fact that the dates of the July and 

first September crash coincide exactly with those in 2002 is 

anything other than a coincidence, although it is possible that 

some natural cycle in the bloom was responsible.

Data from 2004 provide an interesting contrast to the 

other 2 years. The chlorophyll a data did not indicate a 

dramatic bloom crash at any point in the season that affected 

all sites, although very low chlorophyll a values were 

measured at individual sites at various times throughout the 

season. On the basis of low chlorophyll a concentrations at 

four of the five sites, a minor bloom crash may have occurred 

between August 7 and 13.

UKL05

UKL06

UKL07

UKL08

UKL02

Estimated dates of bloom decline

JUNE AUGUST SEPTEMBER OCTOBER

1 15

JULY

1 15 1 15 1 15 1 15

200

400

600

800

200

400

600

800

CHLOROPHYLL-a CONCENTRATION, MICROGRAMS PER LITER

0

200

400

600

800

0

0

2002

2003

2004

1410

Figure 9. Chlorophyll a concentrations at sites in Upper Klamath Lake, Oregon, 2002–04.

12 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
The crashes in the AFA blooms are not prominent in the 

total phosphorus data (fig. 10), indicating that when the cells 

senesce, they tend to recycle nutrients to the water column, 

rather than carrying nutrients to the lake bottom. This is also 

evident in the plots of dissolved nutrients (orthophosphate and 

ammonia), which show a roughly inverse relation overall with 

chlorophyll a (figs. 11 and 12). 

When high ammonia concentrations occur coincident 

with high pH and high temperatures, a significant fraction of 

the total concentration will be present in the un-ionized form, 

which is particularly toxic to aquatic life. The dependence on 

pH is stronger than the dependence on temperature—at 22°C 

and a pH of 9, 31 percent of the ammonia will be in un-ionized 

form, but at a pH of 9.5 that fraction increases to 60 percent 

(U.S. Environmental Protection Agency, 1998). Because 

ammonia tends to peak when the bloom declines, the peaks in 

ammonia are often mismatched in time with the highest pH 

values. That is why the peak in un-ionized ammonia preceded 

the peak in total ammonia concentration at most sites in the 3 

study years (fig. 13). The highest concentration of un-ionized 

Figure 10. Total phosphorus concentrations at sites in Upper Klamath Lake, Oregon, 2002–04.

0

100

200

300

400

0

100

200

300

400

TOTAL PHOSPHORUS CONCENTRATION, IN MICROGRAMS PER LITER

0

100

200

300

400

521 2002

2003

2004

JUNE AUGUST SEPTEMBER OCTOBER

1 15

JULY

1 15 1 15 1 15 1 15

UKL05

UKL06

UKL07

UKL08

UKL02

Estimated dates of bloom decline

Water-Quality Observations 13
or003UK_01_fig11

JUNE AUGUST SEPTEMBER OCTOBER

1 15

JULY

1 15 1 15 1 15 1 15

2002

2003

2004

0

50

100

150

200

250

0

50

100

150

200

250

ORTHOPHOSPHATE-P CONCENTRATION, IN MICROGRAMS PER LITER

0

50

100

150

200

250

UKL05

UKL06

UKL07

UKL08

UKL02

Figure 11. Orthophosphate-P concentrations at sites in Upper Klamath Lake, Oregon, 2002–04.

14 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
or003UK_01_fig12

JUNE AUGUST SEPTEMBER OCTOBER

1 15

JULY

1 15 1 15 1 15 1 15

200

400

600

800

1,000

200

400

600

800

1,000

AMMONIA-N CONCENTRATION, IN MICROGRAMS PER LITER

0

200

400

600

800

1,000

0

0

2002

2003

2004

UKL05

UKL06

UKL07

UKL08

UKL02

Estimated dates of bloom decline

Figure 12. Ammonia-N concentrations at sites in Upper Klamath Lake, Oregon, 2002–04.

Water-Quality Observations 15
ammonia occurred in 2003 just prior to the bloom crash at 

the end of July. Concentrations peaked at nearly 300 μg/L at 

two sites. Experimentally derived 96-hr LC50 (median lethal 

concentration) values for un-ionized ammonia were 780 and 

530 μg/L for Lost River and shortnose suckers, respectively 

(Saiki and others, 1999), well above the peak concentrations 

observed in this study. Nonetheless, exposure to lower 

concentrations cannot be dismissed as a source of chronic 

stress to fish. 

The lack of detectable nitrate/nitrite concentrations 

through much of 2002 and 2003 and very low nitrate/

nitrite concentrations overall in comparison to ammonia, 

suggest that, in spite of very high ammonia concentrations, 

nitrification is not a rapid or effective process for removal of 

ammonia from the water column (fig. 14).

In addition to the temporal patterns through the June to 

October season, the chlorophyll a and nutrient data showed 

site-specific trends (fig. 15). The median chlorophyll a and 

JUNE AUGUST SEPTEMBER OCTOBER

1 15

JULY

1 15 1 15 1 15 1 15

0

100

200

300

400

0

100

200

300

400

0

100

200

300

400

UN-IONIZED AMMONIA-N CONCENTRATION, IN MICROGRAMS PER LITER

2002

2003

2004

UKL05

UKL06

UKL07

UKL08

UKL02

Figure 13. Un-ionized ammonia-N concentrations at sites in Upper Klamath Lake, Oregon, 2002–04.

16  Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
total phosphorus values were higher at site UKL07 in all 

3 years than at sites UKL05, UKL02 (2004 only), or UKL06 

(2002 only). Thus, there is a tendency for the deeper part of 

the study area to the south to experience higher concentrations 

of chlorophyll a, total phosphorus, and ammonia than the 

shallower part of the study area to the north and northeast. 

There also is a slight tendency for concentrations at site 

UKL08, which is in Shoalwater Bay, to be lower than those at 

site UKL07, which is centrally located in the study area.

Continuous Water-Quality Monitors

In order to provide a sense of the overall seasonal and 

interannual variability in water quality in the study area, it 

was useful to consolidate the datasets into a single statistical 

median that would be broadly representative of the entire 

study area. Because the sampling design changed between 

2002 and 2003, this median was computed using only sites 

that were common (or nearly so) to all 3 years: UKL01–

Figure 14. Nitrate/nitrite-N concentrations at sites in Upper Klamath Lake, Oregon, 2002–04. 

JUNE AUGUST SEPTEMBER OCTOBER

1 15

JULY

1 15 1 15 1 15 1 15

0

50

100

150

200

0

50

100

150

200

0

50

100

150

200

2002

2003

NITRATE/NITRITE CONCENTRATION, IN MICROGRAMS PER LITER

2004

UKL05

UKL06

UKL07

UKL08

UKL02

Water-Quality Observations 17
UKL11. Two sites, UKL07 and UKL08, were located at the 

same latitude and longitude in all 3 years; the rest of the sites 

included in the median were located at a different latitude 

and longitude between 2002 and 2003, but were judged to 

represent generally similar locations in the lake. A study-area 

daily median was only computed when a daily median could 

be computed for 8 of the 11 individual sites. Daily medians 

were calculated at a site only for those days on which at least 

20 hours of data were available.

The study-area daily median of dissolved oxygen, 

percent saturation of dissolved oxygen, temperature, and 

pH for 2002–04 is presented in figure 16. The percent 

saturation of dissolved oxygen provides a convenient way 

to assess the seasonal trends in each year and to make yearto-year comparisons. A value of 100 percent saturation 

indicates that the water column is in equilibrium with the 

atmosphere. Values greater than 100 percent indicate that 

oxygen production through photosynthesis is in excess of 

oxygen consumption through respiration and decay processes. 

Values less than 100 percent saturation indicate the opposite 

situation—oxygen consumption is in excess of oxygen 

production. Surface exchange processes always act to move 

the system toward 100 percent saturation from either a 

supersaturated or an undersaturated condition. 

Over much of the summer and autumn in all 3 years 

the rate of photosynthetic production of oxygen in the water 

was enough to keep the study-area daily median dissolved 

oxygen concentrations well above saturation, even though 

chlorophyll a concentrations indicate that the bloom was 

highly variable, both spatially and temporally. This was the 

case even though concurrent oxygen demanding processes 

such as sediment oxygen demand and water column biological 

oxygen demand can consume large amounts of oxygen 

(Wood, 2001; Lieberman and others, 2003). In each year, or003UK_01_fig15

1,000

UKL02 UKL05 UKL06 UKL07 UKL08

800

600

400

200

0

1,000

800

600

400

200

0

MICROGRAMS PER LITER

1,000

800

600

400

200

0

2002

2003

2004

75th percentile

90th percentile

Median

25th percentile

10th percentile

Lower outlier

Upper outlier

Ammonia

Total phosphorus

Chlorophyll-a

EXPLANATION 

Figure 15. Statistical distributions of chlorophyll a, total phosphorus, and ammonia-N concentrations for the entire field 

season at individual sites in Upper Klamath Lake, Oregon, 2002–04.

18  Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
however, there were periods when the balance changed 

and photosynthetic production abated or stopped and/or 

oxygen demands increased, and the study-area daily median 

concentration of dissolved oxygen in the water column 

decreased to well below saturated conditions. Understanding 

what happens during these periods is of interest because 

dissolved oxygen can become low enough to produce chronic 

or acute stress on fisheries. These conditions were more 

common in 2003 than in 2002 or 2004, and notably the percent 

saturation and concentration of dissolved oxygen trended 

downward through the entire month of July 2003. The studyarea median concentration approached 2 mg/L and 20 percent 

saturation at the end of July 2003. 

Study-area median pH conditions for 2002 and 2004 had 

a similar pattern. The pH increased early in the season and 

slowly decreased until mid-to-late August, following the same 

pattern of expansion and decline in the AFA bloom that is 

evident in the dissolved oxygen data. The pH then increased 

to greater than 9.0 and remained there for the rest of these 

field seasons. The study-area daily median pH for 2003 had 

or003UK_01_fig16

A

B

C

D

160

140

120

100

80

60

40

20

12

10

8

6

4

2

0

10.0

9.5

9.0

8.5

8.0

7.5

7.0

26

24

22

20

18

16

14

12

10

JUNE JULY AUGUST

MONTH

SEPTEMBER OCTOBER

TEMPERATURE, IN DEGREES CELSIUS pH DISSOLVED OXYGEN,

IN MILLIGRAMS PER LITER

DISSOLVED OXYGEN,

IN PERCENT SATURATION

2002

2003

2004

Figure 16. Daily medians of (A) percent saturation of dissolved oxygen, (B) dissolved oxygen concentration, (C) 

pH, and (D) temperature for sites in Upper Klamath Lake, Oregon, 2002-04.

Water-Quality Observations 19
the same pattern of higher pH in the early field season, but 

then showed large departures from those in the other 2 years. 

The pH decreased more abruptly in mid-to-late July than in 

the other 2 years of the study, mirroring the steep decrease 

in dissolved oxygen during this time. The study-area daily 

median pH then increased sharply in early August, hovered 

around 9.5 until late August, and then decreased for the rest of 

the field season to values in October that were much less than 

those in the other years of the study.

Temperatures increased from late June through late July, 

and then began a steady, decreasing trend from early August 

until the end of the field season. This general pattern is seen in 

all years, with the result that the highest temperatures in each 

of the 3 years of the study occurred around the end of July. 

Notable, however, is the fact that the highest temperatures 

of the 3 study years were observed at the end of July 2003. 

These temperatures exceeded the peak temperatures in the 

other 2 years by 2 to 3°C. This may be significant because the 

July 2003 time period coincided with the lowest study-area 

median dissolved oxygen. High temperatures accelerate 

oxygen demanding processes and may have contributed to the 

low dissolved oxygen during this time.

Occurrence and Duration of Water-Quality 

Conditions Potentially Harmful to Fish

In order to identify periods when water-quality conditions 

potentially harmful to fish were present in the study area, and 

the spatial extent of these conditions, the hours when dissolved 

oxygen was less than 4 mg/L, temperature was greater than 

28oC, or pH was greater than 9.7 were enumerated at each site. 

These values were based on high stress thresholds established 

to calculate stress indices for Upper Klamath Lake suckers 

(Reiser and others, 2000). The numbers of hourly occurrences 

of these conditions per day were summed over all of the sites 

to provide a count of “site-hours” per day of these conditions. 

To compare these counts of site-hours across years, the counts 

per day were divided by the total possible site-hours in the 

day (24 hours multiplied by the number of sites), giving a 

percentage of site-hours in the day that had potentially harmful 

conditions. This statistic provided a concise measure of the 

severity of the water-quality conditions across the study area 

during each day. To get a measure of the spatial extent of these 

potentially harmful conditions, the percentage of sites at which 

a potentially harmful condition was recorded at least 1 hour 

in a day was calculated. The study-area statistic was only 

computed when a daily statistic could be computed for 8 of 

the 11 individual sites, and the daily statistics were calculated 

at a site only for days on which at least 20 hours of data were 

available (figs. 17 and 18). Temperature is not included in the 

plots because temperature did not exceed 28°C in 2002 or 

2004, and exceeded 28°C at only one site for a few hours on 

3 days in 2003.

During several periods in 2002, at least one instance of 

potentially harmful dissolved oxygen conditions per day was 

recorded at 10 percent or more of the sites in the study area. 

Before mid-August, there were several days during which 

almost 20 percent of the sites recorded a dissolved oxygen 

concentration less than 4 mg/L; on one day in early August, 

40 percent of the sites recorded dissolved oxygen 

concentration less than 4 mg/L (fig. 17A). During the second 

week in July and again during the second week in August, 

the percentage of site-hours during which concentrations less 

than 4 mg/L were recorded exceeded 60 percent, indicating 

that for a few days at a time the occurrence of these conditions 

was widespread and persistent throughout the day (fig. 18A). 

Occurrences of potentially harmful pH conditions were less 

common, but during a few days in late July, 10 percent or 

more of the sites recorded at least one pH reading greater than 

9.7 (fig. 17B). There were, however, relatively few site-hours 

for which conditions potentially harmful to fish were recorded 

for any parameter in 2002, indicating that the duration of these 

conditions at any one site generally was only a few hours 

during the day (fig. 18B).

The year 2003 was unique among the 3 study years in 

both the extent and daily duration of low dissolved oxygen 

conditions. From July 22 through July 31, 2003, a large 

fraction of the study area (as much as 60 percent of sites) 

had at least one dissolved oxygen measurement less than 

4.0 mg/L in a day. During the same period, consistently high 

percentages (more than 60 percent) of the daily site-hours 

were characterized by concentrations less than 4.0 mg/L. 

The combination of a large fraction of the study area having 

at least one dissolved oxygen reading per day less than 

4.0 mg/L and a high percentage of daily site-hours having 

these conditions indicates that the spatial extent of this low 

dissolved oxygen event was large and that potentially harmful 

dissolved oxygen conditions persisted through most of the day 

during the event. The large percentage of sites (40–50 percent) 

and the consistently high percentage of site-hours (50 percent 

or greater for nearly 2 weeks) recording dissolved oxygen 

concentrations less than 4 mg/L in late September and early 

October also was unique (figs. 17A and 18A). Figures 17B

and 18B show that potentially harmful pH conditions in 

July and again in August and early September were, like the 

low dissolved oxygen conditions in late July, widespread 

throughout the study area and persistent throughout the day 

during these periods.

The 2003 statistics show that low dissolved oxygen 

conditions were more widespread throughout the study 

area and more persistent throughout the day for about 

10 consecutive days between mid-July and early August 

than during any period in any of the other years. These 

water-quality conditions coincided with the beginning of 

a significant fish die-off event in 2003. In the period from 

July 22 to September 30, 2003, 108 endangered suckers 

were found dead in Upper Klamath Lake (B.J. Adams, U.S. 

Geological Survey, written commun., 2006). Widespread and 

20 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
persistent pH conditions greater than 9.7 through much of 

the rest of the field season provided further potential to stress 

fish during 2003 and likely contributed to fish mortality in the 

latter part of the summer of that year.

Potentially harmful dissolved oxygen conditions were 

recorded at more than 20 percent of sites in 2004 during a few 

days in mid-August (fig. 17A), and the percentage of sitehours indicates that the conditions were widespread during 

those days (fig. 18A). A pH greater than 9.7 was recorded 

during more than 20 percent of the site-hours nearly every 

day over a 2-week period starting in late June of 2004, and 

the percentage peaked at more than 40 percent (fig. 17B). 

The potentially harmful pH conditions were widespread in 

the study area during this period, as indicated by the high 

percentage (more than 60 percent) of site-hours affected 

(fig. 18B). 

Location and Spatial Extent of Water-Quality 

Conditions Potentially Harmful to Fish

The previous discussions have provided an overview 

of the occurrence and daily duration of poor water-quality 

conditions across the study area. It is also of interest to 

determine more specifically where these conditions occur, 

whether they tend to occur at the same sites in every year, 

whether the spatial extent is defined by a single, contiguous 

area or whether occurrences are scattered around the study 

area, and to get a quantitative estimate of the spatial extent. 

To answer these questions, two-dimensional spline 

interpolations of the weekly median values at each site 

in each study year were generated using ArcGIS Spatial 

Analyst. The weekly time step was used because it allowed 

enough averaging to smooth the data while still capturing 

the important temporal changes during the season. The 

interpolations have limitations, however. First, the spacing of 

the sites in the network provides a lower limit on the length 

scale of spatial variability that can be resolved. At various 

times in each year, an effort was made to complete higher 

resolution transects between established sites in order to 

determine whether the dominant spatial scales were being 

resolved by the network. The results were inconclusive, as 

sometimes the transects showed little small-scale variability 

between network sites, although at other times there was more 

small-scale variability. A complicating factor seems to be that 

it is impossible to get a truly synoptic set of measurements, 

and the temporal variability in lake conditions is sometimes 

so great that what appears to be spatial variability is simply 

Figure 17. Percentage of sites recording at least one 

reading in the day of conditions potentially harmful to 

fish in Upper Klamath Lake, Oregon, 2002–04.

Figure 18. Percentage of total site-hours in the day 

having conditions potentially harmful to fish in Upper 

Klamath Lake, Oregon, 2002–04.

A. Dissolved oxygen less than 

 4 milligrams per liter

B. pH greater than 9.7

JUNE JULY AUGUST

MONTH

SEPTEMBER OCTOBER

0

20

40

60

80

100

PERCENTAGE OF SITE-HOURS

0

20

40

60

80

100

or003UK_01_fig18

2002

2003

2004

A. Dissolved oxygen less than 4 milligrams per liter

B. pH greater than 9.7

or003UK_01_fig17

2002

2003

2004

JUNE JULY AUGUST

MONTH

SEPTEMBER OCTOBER

0

20

40

60

80

100

PERCENTAGE OF SITES

0

20

40

60

80

100

Water-Quality Observations 21
temporal variability over the traveltime along the transect. 

Nonetheless, the fact that the interpolations generally show 

smooth trends over the dimensions of the study area suggests 

that the dominant patterns are being resolved by the network. 

Second, the spline interpolation is a mathematical algorithm 

that fits a smooth surface through known values at known 

locations, but it does not incorporate equations describing the 

physics of the situation. For example, geographic features like 

Eagle Ridge that are real physical barriers are not seen as such 

by the interpolation. Another example is that physical features 

of the lake bathymetry that influence the water circulation 

and the distribution of water quality, like the trench, do not 

affect the interpolation. In this sense, the GIS interpolations 

are different from, for example, the visualization of the output 

of a numerical transport model. Even with these limitations, 

however, the GIS interpolations are a useful means of 

visualizing the spatial patterns in water quality and estimating 

the spatial extent of extreme conditions. 

On the basis of GIS coverages of the interpolations, the 

spatial extent of dissolved oxygen concentrations less than 

4 mg/L was estimated for each Julian week in each study 

year. From these results, it was determined that the maximum 

spatial extent of these conditions occurred between week 31 

and 34 in all 3 years. (The dates corresponding to Julian weeks 

in each year are provided in table 2 for reference.) The results 

from these 4 weeks show how uniquely severe the conditions 

were in 2003, when the spatial extent of the weekly median 

of dissolved oxygen less than 4 mg/L reached a maximum 

of 39 km2 in Julian week 31 (table 3). In comparison, the 

maximum spatial extent of these conditions in 2004 was 2 km2

and in 2002 was 11 km2. 

Even though there was a big difference in the severity of 

the lowest dissolved oxygen conditions between the 3 years 

of the study, the interpolations show consistency in the 

patterns of weekly median dissolved oxygen (fig. 19). Recall 

that the water-quality monitors are located at 1 m from the 

bottom, so the interpolations represent the concentrations on 

a surface that follows the bathymetry of the lake, 1 m from 

the bottom, rather than concentrations at or near the surface of 

the lake. The patterns that are evident, therefore, are a result 

of vertical as well as geographic differences in the location 

of the monitors. The highest concentrations generally occur 

toward the northern boundary of the study area, although the 

lowest concentrations tend to occur toward the southern end 

of the study area, along the segments of the trench that cross 

the entrances of Ball and Shoalwater Bays, and sometimes 

extend into the bays themselves. The patterns demonstrate that 

the lowest concentrations occur most often at the deeper sites 

(table 4). 

Spatially, the range in values is quite large, from 

highly supersaturated (indicating photosynthetic production 

of dissolved oxygen in excess of consumption) to very 

undersaturated (indicating that respiratory and other 

consumptive processes exceed production). The 2003 map for 

week 31 shows a particularly large range in dissolved oxygen 

from north to south (from the shallower areas to the deeper 

areas) in the study area. This period coincides with the major 

bloom decline in that year and reflects a steep decrease in 

dissolved oxygen in the deeper part of the study area that is 

associated with that decline. In all 3 years, the blooms tended 

to peak at higher values at the deeper sites, as evidenced 

by the general increase in median seasonal chlorophyll a

concentrations from the northern to the southern sites (fig. 15), 

and the effects of the bloom declines on dissolved oxygen 

were more severe at the deeper sites as well (fig. 19).

In contrast, both the peaks of the bloom and the decreases in 

dissolved oxygen associated with a crash were moderated at 

the shallower sites toward the north and east in the study area.

The spatial extent of pH greater than 9.7 was at a 

maximum in late June in each study year, but among the 

3 study years the extent was by far the greatest in 2004, 

encompassing as much as 47 km2 (table 3). Overall, bloom 

intensity was moderate in 2004 compared with that in the 

other 2 years (fig. 9), but the June peaks in chlorophyll a were 

higher and apparent at more of the sites in 2004 than in 2002 

or 2003. As a result, the spatial extent of extreme pH in June, 

2004, was large, and the extreme values occurred with nearly 

the same frequency and daily duration at deep and shallow 

Table 2. Start dates of Julian weeks, 2002–04.

Julian 

week 2002 2003 2004

26 06-23 06-21 06-19

27 06-30 06-29 06-27

28 07-07 07-06 07-04

29 07-14 07-13 07-11

30 07-21 07-20 07-18

31 07-28 07-27 07-25

32 08-04 08-03 08-01

33 08-11 08-10 08-08

34 08-18 08-17 08-15

Table 3. Spatial extent of extreme water-quality conditions in 

Upper Klamath Lake, Oregon, 2002–04.

[Abbreviations: mg/L, milligram per liter. Symbol: <, less than]

Julian 

week

Spatial extent of extreme conditions

(square kilometers)

2002 2003 2004

Median dissolved oxygen <2 mg/L

29 0 0 0

30 0 0 0

31 0 22 0

32 0 0 0

33 0 0 <1

34 0 0 1

Median dissolved oxygen <4 mg/L

29 0 3 0

30 0 0 <1

31 11 39 2

22 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
Table 4. Average number of hours per day in Julian weeks 31 to 34 that dissolved oxygen concentrations less than 4 milligrams per 

liter were measured at shallow and deep sites in Upper Klamath Lake, Oregon, 2002-04.

[Abbreviations: NA, insufficient data to make an estimate]

Site Julian 

week

Average number of hours per day

2002 2003 2004

Shallow sites

UKL01 31 NA 0 0

32 10 10 10

33 1.9 0 NA

34 10 4.7 NA

UKL02 31 0 10.1 0

32 0 0 0

33 0 0 2.6

34 NA 0 0

UKL03 31 0 0 0

32 0 0 0

33 0.6 0 4.7

34 0 0 0

UKL04 31 7.1 0 0

32 1.7 0 NA

33 15.3 0 0

34 2.7 0 1

UKL05 31 0 3.4 0

32 NA 0 0

33 .3 0 1.6

34 NA 0.3 0

UKL09 31 5.7 13.1 NA

32 2 0 10

33 3 0 4.7

34 0 .7 .4

Site Julian 

week

Average number of hours per day

2002 2003 2004

Deep sites

UKL06 31 1.9 19.4 0

32 10 0 .4

33 1.3 0 .6

34 10 0 4

UKL07 31 10.7 22.3 10

32 10.7 0 0

33 3.7 0 .4

34 1.3 0 1.1

UKL08 31 14.1 19 7.3

32 9.6 5.4 8.9

33 10.9 0 11.3

34 4.1 1.1 18.9

UKL10 31 8.4 19.7 2.9

32 8 1.3 .9

33 10.7 0 0

34 2 1.3 3

UKL11 31 18.9 20.1 3.6

32 10 .4 5

33 1.9 0 17.6

34 0 0 13.9

sites (table 5). At times, the spatial pattern in pH trended from 

higher values toward the north to lower values toward the 

south (fig. 20). This trend was particularly evident in 2004, 

and reflects the greater photosynthetic activity in the shallower 

areas to the north, where the entire water column is in the 

photic zone. 

Temperatures greater than 28°C did not have a 

measurable spatial extent in any week of any year (fig. 21). 

Although there were a few periods in 2003 when temperatures 

exceeded 28°C, those periods were extraordinary and of 

short duration, lasting less than half a day. The fact that 

temperatures greater than 28°C are rarely observed suggests 

that extreme temperature is not a significant contributor to 

chronic stress on fish health in at least the northern part of 

Upper Klamath Lake. 

Diel Variability

Histograms showing the timing of daily minimum 

dissolved oxygen, daily maximum pH, and daily maximum 

temperature at a representative deep site (defined as having a 

full pool depth greater than 2.5 m) and shallow site (defined 

Table 5. Average number of hours per day in Julian week 27 that 

pH greater than 9.7 was measured at shallow and deep sites in 

Upper Klamath Lake, Oregon, 2002-04.

[Abbreviations: NA, insufficient data to make an estimate]

Site

Average number of hours per day

2002 2003 2004

Representative shallow sites

UKL01 0 10.7 12.6

UKL02 1.7 8.6 118.8

UKL03 3.3 2.9 18.1

UKL04 .1 6.3 23.3

UKL05 NA 11 7.9

UKL09 0 .4 11.3

Representative deep sites

UKL06 NA 6.4 6.3

UKL07 NA 10 14.4

UKL08 1.4 0 0

UKL10 0 3.4 9.4

UKL11 0 0 0

1

Value based on less than six fully sampled (20 out of 24 hours) days.

1

Value based on less than six fully sampled (20 out of 24 hours) days.

Water-Quality Observations 23
Figure 19. Geographic Information System coverage of an interpolation of weekly median dissolved oxygen 

concentrations, Julian weeks 31–34, Upper Klamath Lake, Oregon, 2002–04.

or003UK_01_fig19

122°05' 122°00' 121°55'

42°25'

42°30'

0 1 2 3 4 5 MILES

0 1 2 3 4 5 KILOMETERS

DISSOLVED OXYGEN, IN MILLIGRAMS PER LITER

0 - 1

1 - 2

2 - 3

3 - 4

4 - 5

5 - 6

6 - 7

7 - 8

8 - 9

9 - 10

10 - 11

11 - 12

12 - 13

13 - 14

14 - 15

EXPLANATION

WEEK 32

2002

WEEK 33

2002

WEEK 34

2002

WEEK 30

2003

WEEK 31

2003

WEEK 32

2003

WEEK 33

2004

WEEK 34

2004

WEEK 35

2004

24 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
or003UK_01_fig20

122°05' 122°00' 121°55'

42°25'

42°30'

WEEK 26

2002

WEEK 27

2002

WEEK 28

2002

WEEK 26

2003

WEEK 27

2003

WEEK 28

2003

WEEK 26

2004

WEEK 27

2004

WEEK 28

2004

0 1 2 3 4 5 MILES

0 1 2 3 4 5 KILOMETERS pH

8.6 - 8.7

8.7 - 8.8

8.8 - 8.9

8.9 - 9.0

9.0 - 9.1

9.1 - 9.2

9.2 - 9.3

9.3 - 9.4

9.4 - 9.5

9.5 - 9.6

9.6 - 9.7

9.7 - 9.8

9.8 - 9.9 10.1 - 10.2

9.9 - 10.0

10.0 - 10.1

EXPLANATION

Figure 20. Geographic Information System coverage of an interpolation of weekly median pH, Julian week 27, Upper 

Klamath Lake, Oregon, 2002–04.

Water-Quality Observations 25
or003UK_01_fig21

122°05' 122°00' 121°55'

42°25'

42°30'

0 1 2 3 4 5 MILES

0 1 2 3 4 5 KILOMETERS

TEMPERATURE, IN DEGREES CELSIUS

20.0 - 20.5

20.5 - 21.0

21.0 - 21.5

21.5 - 22.0

22.0 - 22.5

22.5 - 23.0

23.0 - 23.5

23.5 - 24.0

24.0 - 24.5

24.5 - 25.0

25.0 - 25.5

25.5 - 26.0

EXPLANATION

WEEK 28

2002

WEEK 29

2002

WEEK 30

2002

WEEK 30

2003

WEEK 31

2003

WEEK 32

2003

WEEK 30

2004

WEEK 31

2004

WEEK 32

2004

Figure 21. Geographic Information System coverage of an interpolation of weekly median temperature, Julian week 31, 

Upper Klamath Lake, Oregon, 2002–04.

26  Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
as having a full pool depth less than 2.5 m) are shown in 

figure 22. These histograms display the normalized frequency 

of occurrence of the daily extreme water-quality reading as 

a function of the hour of day the most extreme water-quality 

reading occurred. Data from all 3 years were combined to 

create these histograms after determining that data from 

each of the 3 years showed the same patterns. Histograms 

for shallow sites were similar to each other, as were the 

histograms for the deeper sites. A representative shallow site 

(UKL02) and a representative deep site (UKL07) were chosen 

to illustrate the results. It is helpful to recall that the monitors 

used in this study were located at 1 m off the bottom, so at 

shallow sites they are located within the photic zone, whereas 

at deep sites they are located below the photic zone.

Daily minimum dissolved oxygen concentration at the 

shallow sites tended to occur around 7 a.m. (fig. 22A). Daily 

maximum pH and temperature occurred most frequently in the 

early evening between the hours of 4 p.m. and 8 p.m. (fig. 22B

and 22C). This pattern reflects the strong influence of the diel 

cycle of photosynthesis and respiration on the water column, 

which is almost entirely within the photic zone at these sites.

At deep sites, however, there was no distinct period of the 

day when daily minimum dissolved oxygen conditions tended 

to occur (fig. 22D). The maximum pH at the deep sites tended 

to occur in late afternoon, but over a much broader window of 

time than at the shallow sites, lasting from the hours of about 

4 p.m. to 2 a.m. the next morning (fig. 22E). Temperature at 

the deep sites behaved much like temperature at the shallow 

sites, usually peaking in a narrow window between the hours 

of about 5 p.m. and 9 p.m. in the late afternoon (fig. 22F). 

At the deep sites, only the surface (roughly the top 

2 m) of the water column is in the photic zone. In the lower 

part of the water column, below the photic zone, the rate of 

consumption of dissolved oxygen by metabolic respiration 

and other oxygen demanding processes within the water 

column is greater than the rate of production of oxygen by 

photosynthesis. Near the bottom, sediment oxygen demand 

also consumes dissolved oxygen from the water. Temperature 

differences between the upper and lower water column can 

produce some degree of thermal (density) stratification, which 

isolates the lower from the upper water column. If the water 

column develops even a small degree of stratification, it then 

becomes possible for dissolved oxygen to reach minimum 

daily conditions in the lower part of the water column (where 

site monitors were located) at any time during the day, even 

during daylight hours. This is because dissolved oxygen below 

the photic zone will continue to decrease until a mixing event 

erodes the thermal stratification and mixes the lower layer with 

the upper layer, which is at a relatively higher concentration. 

At a deep site, therefore, the minimum in dissolved oxygen 

does not always occur in the early morning hours just before 

dawn, but rather can occur throughout the day depending on 

when the wind picks up and mixes the water column.

At the shallow sites, a secondary maximum in pH and 

temperature occurs at midnight (figs. 22B and 22C). On close 

inspection of individual time series, it was determined that this 

secondary maximum occurs on a significant subset of days 

when the parameter (pH or temperature) is trending strongly 

downward. In that case, the change in the parameter over the 

day from midnight to midnight is greater than the upward and 

downward movement due to solar radiation during the day, 

with the result that the maximum occurs at the beginning of 

the day instead of some other time during the day. Similarly, 

when dissolved oxygen is trending strongly downward, the 

minimum of the day occurs at 11 p.m. for the same reason 

(fig. 22A). When the parameters are trending strongly upward, 

the opposite (maximum in pH and temperature at 11 p.m.; 

minimum in dissolved oxygen at midnight.) does not occur 

as often because of the asymmetry in the diel cycle, which is 

heavily skewed toward the late afternoon, thus making it less 

likely that a value at the end of the day will end up being an 

extreme value. A strong secondary maximum in temperature at 

midnight also is seen at the deep site (fig. 22F). The trends and 

diel cycle in temperature in the lower layer of the deep water 

column develops in response to the same atmospheric forcing 

that operates at the shallow sites, so the timing of extreme 

values is similar, but the magnitude of the diel fluctuations 

generally is dampened in comparison to that at the shallow 

site.

Water-Quality Observations 27
or003UK_01_fig22

FRACTION OF MAXIMUM TEMPERATURE READINGS

FRACTION OF MAXIMUM pH READINGS

FRACTION OF MINIMUM DISSOLVED OXYGEN READINGS

0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25

0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25

0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25

A. UKL02 daily minimum 

 dissolved oxygen

B. UKL02 daily 

 maximum pH

C. UKL02 daily maximum 

 temperature

D. UKL07 daily minimum 

 dissolved oxygen

E. UKL07 daily 

 maximum pH

F. UKL07 daily maximum 

 temperature

12 am

11 pm

10 pm

9 pm

8 pm

7 pm

6 pm

5 pm

4 pm

3 pm

2 pm

1 pm

12 pm

11 am

10 am

9 am

8 am

7 am

6 am

5 am

4 am

3 am

2 am

1 am

HOUR OF DAY

12 am

11 pm

10 pm

9 pm

8 pm

7 pm

6 pm

5 pm

4 pm

3 pm

2 pm

1 pm

12 pm

11 am

10 am

9 am

8 am

7 am

6 am

5 am

4 am

3 am

2 am

1 am

12 am

11 pm

10 pm

9 pm

8 pm

7 pm

6 pm

5 pm

4 pm

3 pm

2 pm

1 pm

12 pm

11 am

10 am

9 am

8 am

7 am

6 am

5 am

4 am

3 am

2 am

1 am

12 am

11 pm

10 pm

9 pm

8 pm

7 pm

6 pm

5 pm

4 pm

3 pm

2 pm

1 pm

12 pm

11 am

10 am

9 am

8 am

7 am

6 am

5 am

4 am

3 am

2 am

1 am

12 am

11 pm

10 pm

9 pm

8 pm

7 pm

6 pm

5 pm

4 pm

3 pm

2 pm

1 pm

12 pm

11 am

10 am

9 am

8 am

7 am

6 am

5 am

4 am

3 am

2 am

1 am

12 am

11 pm

10 pm

9 pm

8 pm

7 pm

6 pm

5 pm

4 pm

3 pm

2 pm

1 pm

12 pm

11 am

10 am

9 am

8 am

7 am

6 am

5 am

4 am

3 am

2 am

1 am

Figure 22. Daily extremes in water-quality conditions as a function of hour in the day, at representative shallow (UKL02) 

and deep (UKL07) sites in Upper Klamath Lake, Oregon, 2002–04. Data for 2002-04 have been combined. 

28  Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
Factors Contributing to Low Dissolved 

Oxygen Events

To this point the presentation of the data has focused on 

three aspects of water quality that contribute to chronic stress 

on endangered suckers when they exceed or fall below certain 

limits—dissolved oxygen, pH, and temperature. An analysis of 

all possible causes of mortality during fish die-offs in the mid1990s concluded, however, that mortality was ultimately the 

result of hypoxia, even considering that substantial mortality 

occurred after hypoxic conditions had abated, because hypoxia 

had compromised the immune systems of the fish and left 

them vulnerable to infection (Perkins and others, 2000). 

Observations of the fish die-off in 2003 were consistent with 

this conclusion, in that they indicated that the role of hypoxia 

was to force fish into crowded conditions in the vicinity of 

Pelican Bay, where many eventually succumbed to disease 

(B.J. Adams, U.S. Geological Survey, oral commun., 2005). 

For that reason, the following discussion focuses on the 

probable causes for the occurrence of a low dissolved oxygen 

event (LDOE) in the study area, which encompasses the area 

of the lake that is the preferred habitat of adult suckers. 

For the purposes of discussion it is useful to define an 

LDOE quantitatively. There are several ways to do this; four 

were chosen, and the time periods that emerge in each year 

as a result of those four definitions are compiled in table 6. 

A few dates consistently emerge in each year when all but 

the most stringent definition is used—August 1–2 in 2002, 

July 23 to August 2 in 2003, October 1–8 in 2003, and August 

13 in 2004. When an LDOE is defined as 50 percent or more 

of site-hours having a dissolved oxygen concentration less 

than 4 mg/L, then only the period July 23–30 in 2003 meets 

the definition. By combining the various datasets collected 

during this study, including weekly chlorophyll a samples, 

meteorological data, water-quality profiles from the profiling 

buoys, and, in 2003 and 2004, the ADCP current data, it has 

been possible to evaluate three of the factors that contribute to 

an LDOE—thermally stable conditions, a bloom decline, and 

the wind-driven circulation.

Water Column Stratification

The profiling buoys collected observations of dissolved 

oxygen concentration over the water column between 1 m 

off the bottom and 1 m from the surface (figs. 23–25). 

Even though the degree of stratification in Upper Klamath 

Lake is moderate compared with that of deeper lakes, it 

has implications for water quality. Stratification isolates a 

near-bottom layer of water, allowing oxygen demanding 

processes to deplete this layer of oxygen and potentially 

creating unsuitable conditions for endangered suckers. These 

oxygen depleted conditions do not usually extend throughout 

the water column, however, because stratification also tends 

to create favorable conditions for AFA in the upper layer. The 

AFA cells can regulate their buoyancy and thereby maintain 

a position close to the surface; consequently, the upper water 

column tends to become supersaturated with respect to 

dissolved oxygen during periods of stratification. 

Because stratification rarely persists from day to day, 

the relatively oxygen-rich upper water column and the 

relatively oxygen depleted lower water column are usually 

mixed together on a daily basis. That is why the maximum 

concentration of the day at the profiling buoys was usually 

greater than the value of concern of 4 mg/L (figs. 23–25) even 

when the minimum of the day was less than this value, and 

why the concentration in the mixed water column (indicated 

by the daily minimum difference between the upper and lower 

monitors) usually was greater than 4 mg/L even on days when 

the minimum of the day was less than this value. The daily 

maximum range in dissolved oxygen concentration between 

the upper and lower water column generally was such that 

the upper water column was characterized by concentrations 

tolerable to fish (greater than 4 mg/L) even when the lower 

water column was characterized by concentrations severely 

stressful to fish or even lethal. These observations from the 

profiling buoys suggest that periods when habitat is limited by 

water quality to only part of the water column and to less than 

a full day are common. Observations of fish behavior during 

2002–04 suggest that the endangered suckers are, for the most 

part, able to survive through these periods, although the effects 

of the chronic stress that accompanies these conditions cannot 

be determined from tracking studies.

Table 6. Dates of low dissolved oxygen events in the northern 

part of Upper Klamath Lake, Oregon, 2002–03.

[Dates were determined using four criteria: 1, percentage of site-hours 

with dissolved oxygen concentrations < (less than) 4 mg/L (milligrams per 

liter) was greater than or equal to 20 percent; 2, percentage of site-hours 

with dissolved oxygen concentrations <4 mg/L was greater than or equal to 

25 percent; 3, study area median dissolved oxygen concentration was 

<80 percent of saturation; and 4, percentage of site-hours with dissolved 

oxygen concentration <4 mg/L was greater than or equal to 50 percent]

Criterion

Dates

2002 2003 2004

1 07-10–07-11

07-31

08-02–08-3

08-12

07-18–08-02

09-20–10-09

10-11–10-13

08-12–08-13

08-17–08-19

08-22

2 08-02–08-03 07-19–08-02

09-21–09-29

10-01–10-08

08-13

3 07-10

07-23

07-29–08-13

07-21–08-02

09-19–10-14

08-11–08-13

4 None 07-23–07-30 None

Factors Contributing to Low Dissolved Oxygen Events 29
or003UK_01_fig23

Daily maximum range

Daily minimum range

Daily minimum

Daily maximum

10

15

20

25

DISSOLVED OXYGEN CONCENTRATION, IN MILLIGRAMS PER LITER

JULY AUGUST SEPTEMBER OCTOBER

1 15 1 15 1 15 1 15

2002

10

15

0

5

0

5

20

25

UKL07

UKL08

Stress threshold

for suckers

Stress threshold

for suckers

Figure 23. Daily minimum and maximum ranges in dissolved oxygen over the water column and minimum and maximum 

dissolved oxygen from hourly values collected at 1 meter off the bottom and 1 meter from the surface at sites UKL07 and UKL08 

in Upper Klamath Lake, Oregon, 2002.

Daily maximum range

Daily minimum range

Daily minimum

Daily maximum

2003

UKL07

10

15

20

25

DISSOLVED OXYGEN CONCENTRATION, IN MILLIGRAMS PER LITER

JULY AUGUST SEPTEMBER OCTOBER

1 15 1 15 1 15 1 15

10

15

0

5

0

5

20

25

UKL13

Stress threshold

for suckers

Stress threshold

for suckers

Figure 24. Daily minimum and maximum ranges in dissolved oxygen over the water column and minimum and maximum 

dissolved oxygen from hourly values collected at 1 meter off the bottom and 1 meter from the surface at sites UKL07 and UKL13 

in Upper Klamath Lake, Oregon, 2003.

30 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
The periods of increased surface-to-bottom difference 

in dissolved oxygen were related to periods of enhanced 

stratification, as indicated by an increased surface-to-bottom 

difference in temperature (fig. 26). These two quantities were 

highly correlated on a daily basis in all 3 years (table 7). 

This did not, however, translate into a high correlation 

between enhanced stratification, as measured by either 

increased surface-to-bottom difference in temperature or 

increased surface-to-bottom difference in dissolved oxygen 

concentration, and the minimum daily dissolved oxygen 

(fig. 26). These quantities were only significantly and 

negatively correlated in 2002 (table 7). Thus, the occurrence 

of the lowest minimum dissolved oxygen concentrations 

is not necessarily associated with a high degree of water 

column stratification, although some LDOE dates appear to 

coincide with a stratified water column—July 10, July 23, 

July 30, August 8–13 in 2002, September 25–29 in 2003, and 

August 11–12 and August 19 in 2004.

The relation between wind speed, water column 

stratification, and daily minimum dissolved oxygen was not 

straightforward. On a daily basis, wind speed was significantly 

and negatively correlated with water column stratification, as 

measured by the surface-to-bottom difference in temperature, 

in 2002 and 2004, but not in 2003. The correlation between 

wind speed and daily surface-to-bottom difference in dissolved 

oxygen concentration was significant in all 3 years (fig. 26 and 

table 7). Kann and Welch (2005) noted an inverse correlation 

between wind speed and the surface-to-bottom difference in 

dissolved oxygen when profile data collected from 1990 to 

2000 were averaged over the entire July–August period; in 

this study the relation appears to hold on a daily basis as well. 

The correlation between daily wind speed and daily minimum 

dissolved oxygen, however, was insignificant in 2002, weakly 

positive in 2003, and weakly negative in 2004 (table 7). 

So, although wind speed clearly influences the degree of 

stratification in the water column, it has less influence over 

when the lowest dissolved oxygen concentrations occur. Some 

of the LDOE dates were associated with low wind speeds; 

many were not.

Significantly, the most severe LDOE of the 3 study 

years, which occurred in July 2003, was not associated with 

stratification of the water column. Concentrations during 

the last week in July were about 3 mg/L or less during the 

entire day and throughout the water column at site UKL07 

(fig. 24). Data from the other monitoring sites showed that 

low concentrations were widespread during a period of 

several days (fig. 19), meaning that habitat in the entire 

southwestern part of the study area was unsuitable throughout 

the water column and throughout the day for several days. The 

distinction between the severity of the LDOE of July 2003 

and times during 2002–04 when water quality was perhaps 

chronically stressful but not lethal appears to have been 

important to the endangered suckers in the lake. The suckers 

responded to the 2003 event by leaving the area (B.J. Adams, 

U.S. Geological Survey, oral commun., 2004), whereas they 

generally remained in place in other years during times when 

the lowest dissolved oxygen concentrations were less than 4 

mg/L near the bottom but moderated slightly both closer to the 

surface and at intervals during the day. 

or003UK_01_fig25

Daily maximum range

Daily minimum range

Daily minimum

Daily maximum

UKL07

10

15

20

25

DISSOLVED OXYGEN CONCENTRATION, IN MILLIGRAMS PER LITER

JULY AUGUST SEPTEMBER OCTOBER

1 15 1 15 1 15 1 15

2004

10

15

0

5

0

5

20

25

UKL16

Stress threshold

for suckers

Stress threshold

for suckers

Figure 25. Daily minimum and maximum ranges in dissolved oxygen over the water column and minimum and maximum 

dissolved oxygen from hourly values collected at 1 meter off the bottom and 1 meter from the surface at sites UKL07 and 

UKL16 in Upper Klamath Lake, Oregon, 2004.

Factors Contributing to Low Dissolved Oxygen Events 31
or003UK_01_fig26

Daily 90th percentile wind speed

Daily maximum range in temperature 

Daily minimum dissolved oxygen

Daily maximum range in dissolved oxygen

EXPLANATION

0

5

10

15

0

5

10

15

DAILY 90TH PERCENTILE WIND SPEED, IN METERS PER SECOND

DAILY MAXIMUM RANGE IN TEMPERATURE, IN DEGREES CELSIUS

DAILY MINIMUM DISSOLVED OXYGEN CONCENTRATION, IN MILLIGRAMS PER LITER

DAILY MAXIMUM RANGE IN DISSOLVED OXYGEN CONCENTRATION, IN MILLIGRAMS PER LITER

0

5

10

15

JULY AUGUST SEPTEMBER OCTOBER

1 15 1 15 1 15 1 15

2004

UKL07

2003

UKL07

2002

UKL08

Stress

threshold

for suckers

Stress

threshold

for suckers

Stress

threshold

for suckers

Figure 26. Daily maximum range in dissolved oxygen concentration over the water column, maximum range in 

temperature over the water column, minimum water column dissolved oxygen concentration, and 90th percentile of 

hourly wind values in Upper Klamath Lake, Oregon, 2002–04.

32 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
Sites UKL07 and UKL08 were in similar water depths 

(table 1), and the 2002 data from these sites show that the 

periods when very low dissolved oxygen was observed and 

the periods of maximum vertical variability in dissolved 

oxygen over the water column were similar as well (fig. 23). 

Data collected by profiling buoys in 2003 from sites UKL07 

and UKL13, sites that were in similar water depths, show 

a corresponding similarity in periods when low dissolved 

oxygen was observed in the lower water column (fig. 24). 

In 2004, however, one of the profiling buoys was moved to 

site UKL16, a site in the middle of the trench on the western 

side of the lake (fig. 1). This site was much deeper than any 

of the sites where profiling buoys were located previously, 

and the data show that very low near-bottom dissolved 

oxygen developed more readily at this site than at any of the 

shallower sites. There was very little evidence of low nearbottom dissolved oxygen at site UKL07 in 2004, but there 

were several periods when low concentrations developed 

in the trench at UKL16 (July 12–20, July 30–August 3, 

and August 13–19, fig. 25). The causes and implications of 

the development of these conditions in the trench area are 

discussed below in the context of the wind-driven circulation.

Bloom Decline

In a hypereutrophic water body like Upper Klamath Lake, 

a shutdown or sharp decline in the rate of photosynthesis can 

cause a rapid decrease in dissolved oxygen concentration. 

This decrease occurs because the rate of oxygen demanding 

processes, which can be high in lakes with large amounts of 

labile organic matter in the water column and the surficial 

sediments, continue unabated while the rate of oxygen 

production ceases or slows markedly. Senescing cells also 

add to the oxygen demand in the water column. During the 3 

years of this study, bloom declines seem to have contributed to 

several LDOEs. 

In 2002, the bloom decline, as estimated from weekly 

chlorophyll a, occurred between about July 19 and August 1, 

so it preceded and then overlapped the LDOE between July 31 

and August 3 (table 6). By one definition, this LDOE lasted 

until August 13, but chlorophyll a concentrations largely 

recovered, although not to prebloom concentrations, during 

the first 2 weeks in August, so it seems unlikely that the bloom 

decline could be the primary cause of the undersaturated 

dissolved oxygen conditions that lasted until August 13. The 

timing of the LDOE was coincident with elevated particulates 

in the air caused by the smoke from forest fires in 2002, most 

notably the Biscuit Fire, which began in the Siskiyou National 

Forest west of Upper Klamath Lake on July 13 and ultimately 

burned nearly 500,000 acres. The first burst of 10- and 2.5-μm 

particulates entered the area on July 25, and the particulates 

remained elevated in concentration through August (U.S. 

Environmental Protection Agency, 2006). Solar radiation data 

collected during the same period at the Bureau of Reclamation 

Agrimet site on Agency Lake does not show a reduction in 

incident radiation associated with the elevated concentration 

of particulates in the air, however, so the evidence linking the 

LDOE between August 2 and August 13, 2002, directly to 

reduced photosynthetic activity caused by smoke in the air 

from the Biscuit fire is not conclusive.

In the 3 years of this study, the period when the 

connection between the bloom decline and the occurrence of 

a LDOE was most direct was between July 21 and August 2, 

2003. This severe LDOE, which culminated in a fish die-off, 

was coincident with a sharp decrease in chlorophyll a

concentrations, indicating that a major decline in the bloom 

had occurred (fig. 9); the dates estimated to bracket the 

decline were July 19 and August 1, 2003. Even so, the bloom 

decline does not appear to be the entire explanation for the 

LDOE because dissolved oxygen began to trend downward 

early in July 2003, well before the marked decrease in 

the weekly chlorophyll a concentrations. This apparent 

discrepancy suggests that although the bloom decline may 

have exacerbated and perhaps accelerated the downward 

trend in dissolved oxygen, a larger set of circumstances also 

contributed to the event.

Table 7. Spearman’s rho correlation coefficients between daily 

values derived from hourly data collected at site UKL08 in 2002 

and site UKL07 in 2003-04, Upper Klamath Lake, Oregon.

[Wind speed: daily 90th percentile of hourly values. Max ∆T, daily 

maximum range in temperature based on hourly values collected at 1 m 

(meter) from the bottom and 1 m from the surface. Max ∆DO, daily 

maximum range in dissolved oxygen based on hourly values collected at 1 m 

from the bottom and 1 m from the surface. Min DO, daily minimum dissolved 

oxygen of hourly values collected at 1 m from the bottom and 1 m from the 

surface. Boldface type indicates significant correlation (p<0.001). Boldface 

italicized type indicates significant correlation (p<0.05)]

Year Wind 

speed Max. ∆T Max. ∆DO Min. DO

Wind speed 2002 1.00 -0.45 -0.28 -0.03

2003 1.00 -0.11 -0.28 0.32

2004 1.00 -0.36 -0.43 -0.28

Max. ∆T 2002 1.00 0.63 -0.37

2003 1.00 0.64 -0.17

2004 1.00 0.78 0.03

Max.∆DO 2002 1.00 -0.44

2003 1.00 0.05

2004 1.00 -0.06

Min. DO 2002 1.00

2003 1.00

2004 1.00

Factors Contributing to Low Dissolved Oxygen Events 33
In 2004, an LDOE occurred between August 11 and 

August 13, which coincides with the estimates of the dates 

of a bloom decline in that year (fig. 9). This bloom decline 

was less definitive than in the other 2 years, and the dates 

were difficult to estimate, but chlorophyll a concentrations 

on August 11 were very low at sites UKL07 and UKL02 (5.8 

μg/L at UKL07 and 1 μg/L at UKL02, respectively). It seems 

likely, therefore, that a bloom decline, perhaps more localized 

than in the other 2 years, accompanied by a reduction in 

photosynthesis, is part of the explanation for the LDOE during 

mid-August in 2004. 

Wind-Driven Circulation

Under prevailing wind conditions, the wind-driven 

circulation moves water northward in the lake through the 

trench along the western shoreline (fig. 8). The immediate 

source of water to the study area, therefore, is the cross-section 

between Bare Island and Eagle Ridge (A-B in fig. 8). Direct 

observations of the water leaving the trench were made as part 

of this study starting in 2003, when sites UKL13 and UKL14 

were established. Upon leaving the trench, water circulating 

in the prevailing clockwise direction first passes through site 

UKL14, then UKL13. Site UKL07, centrally located in the 

study area, can be considered “downstream” of site UKL13. 

The traveltime between UKL14 and UKL07 is short—about 

1.4 days, on the basis of a current velocity of 5 cm/s as 

representative of the currents measured at ADCP3 (fig. 1). 

From these observations, it is apparent that the water 

that enters the area from the trench often is depleted of 

dissolved oxygen compared to other parts of the lake (figs. 27

and 28). Under some circumstances there is very little 

change in the dissolved oxygen concentration of the water 

as it progresses from sites UKL14 to UKL07, as during the 

entire month of July 2003 (fig. 27). At other times, however, 

nonconservative processes alter the dissolved oxygen 

concentration substantially between the time that the water 

leaves the trench and when it passes through site UKL07. 

This was the situation through much of July and August 

2004, when concentrations at site UKL07 were consistently 

higher than those at sites UKL14 and UKL13 by several 

milligrams per liter (fig. 28). In mid-August in particular, a 

pulse of water low in dissolved oxygen was observed at sites 

UKL14 and UKL13, but by the time this pulse of water passed 

through site UKL07, the dissolved oxygen concentration had 

increased substantially. Whether nonconservative processes 

can alter the characteristics of the water leaving the trench 

substantially as it passes through the study area depends on the 

actual traveltime, which varies with wind speed and direction, 

and the intrinsic oxygen-producing and oxygen-consuming 

capacities of the water. Neither of these can be estimated with 

the datasets presented in this report, but a better understanding 

of both in the future may be key to understanding the 

development of a severe LDOE in the northern part of the 

lake.

UKL14

UKL13

UKL07

UKL04

0

5

10

15

DAILY MEDIAN DISSOLVED OXYGEN

CONCENTRATION, IN MILLIGRAMS PER LITER

JULY

2003

AUGUST SEPTEMBER OCTOBER

1 15 1 15 1 15 1 15

Figure 27. Daily median dissolved oxygen concentrations at sites UKL04, UKL07, UKL13, and UKL14 in Upper Klamath Lake, 

Oregon, 2003.

34 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
The wind-driven circulation must be considered when 

evaluating the causes of long-term trends (on weekly to 

monthly time scales) in water quality, such as the steady 

decrease in dissolved oxygen in July 2003 that culminated 

in a severe LDOE. Because the wind-driven circulation 

moves much of the volume of the lake around a closed loop 

in about 10 days, trends in water quality on time scales that 

long or longer must be understood as the cumulative effect 

of nonconservative processes as water moves in its flow path 

around the lake. A steady decrease in dissolved oxygen, such 

as was seen in July 2003, therefore, indicates that, when 

integrated over the entire flow path, the oxygen demands 

exceeded oxygen production through photosynthesis. Given 

that is the case, further investigation of oxygen consumption 

and production rates around the lake, particularly in areas not 

monitored in this study, will be helpful. It also is important 

to understand how changes in wind speed and direction are 

manifested as changes in the wind-driven circulation, and 

how changes in circulation around the lake interact with 

the spatially varying oxygen consumption and production 

rates. Changes in the circulation pattern could be part of the 

explanation for why severe LDOEs develop in some years but 

not in others.

Because of the proximity of the trench to the study area, 

and because it is the immediate source of water to that area, 

the wind-driven circulation pattern, and in particular short 

reversals or stalls in that pattern, affect water quality in the 

study area on the short 1–2-day time scale that represents the 

residence time in the trench, as well as on longer time scales 

as discussed above. Passage through the trench results in a 

net loss of dissolved oxygen in the water column because 

the depth of the narrow flow through the trench is much 

greater than the photic zone, and the respiratory and decay 

processes that consume oxygen over the entire water column 

overwhelm the photosynthetic production in the photic zone. 

The magnitude of the loss will depend on the rates of oxygen 

demanding processes, which vary in space and time. The 

magnitude of the loss also depends on the traveltime through 

the trench, which under routine conditions probably is on the 

order of 1.2 days [based on a GIS estimate of the volume of 

the trench of 61.6 m3 (T.L. Haluska, U.S. Geological Survey, 

unpub. data, 2005), and an estimate of the discharge through 

cross-section A-B (fig. 8) based on synoptic measurements 

in June 2005 of 580 m3/s (R.E. Wellman, U.S. Geological 

Survey, unpub. data, 2005)]. 

There are periods lasting from one to several days when 

the wind reverses and comes from the east to southeast. These 

periods are seen in the ADCP data as times when the currents, 

still in alignment with the trench bathymetry, reverse direction 

(figs. 6 and 7). The effect of these shifts is to reverse or stall 

the prevailing circulation pattern. One of the consequences of 

a reversal in the wind, or even a period of lower-than-normal 

wind stress, is that the traveltime in the trench is increased. 

Depending on how long the reversal or low-wind period 

lasts, the increase in traveltime can be substantial. When this 

happens, oxygen demanding processes have a longer time 

to act, and the effect on the quality of water in the trench 

can be substantial. This effect can be seen in the dissolved 

oxygen data collected at site UKL16, which was located in 

the midtrench area in 2004 (fig. 29). The hourly dissolved 

oxygen measurements at site UKL14, which is the first study 

site encountered by a water parcel leaving the trench heading 

north, also are shown. 

The wind reversed for a day or more nine times during 

this 3-month record. Nearly every time there was a reversal in 

the wind, there was a rapid decrease in the dissolved oxygen 

at site UKL16; sometimes the effect was limited to the 1-m 

off-the-bottom measurement, and sometimes the effect was 

Figure 28. Daily median dissolved oxygen concentrations at sites UKL04, UKL07, UKL13, and UKL14 in Upper Klamath Lake, 

Oregon, 2004.

or003UK_01_fig28

JULY

2004

AUGUST SEPTEMBER OCTOBER

1 15 1 15 1 15 1 15

0

5

10

15

DAILY MEDIAN DISSOLVED OXYGEN

CONCENTRATION, IN MILLIGRAMS PER LITER

UKL14

UKL13

UKL07

UKL04

Factors Contributing to Low Dissolved Oxygen Events 35
seen in the mid-water-column measurement as well. The pulse 

of low dissolved oxygen water through site UKL14 occurred 

after currents returned to the prevailing direction, delayed by 

the traveltime between sites UKL16 and UKL14. When the 

pulse of low dissolved oxygen water passed by site UKL14, 

it generally was moderated compared to conditions at site 

UKL16, and it was superimposed on the trends in the data 

at longer time scales. Sometimes there was no discernible 

signal at site UKL14, even after a long period of reversal, 

such as occurred from July 12–18, 2004. During the reversal, 

the effect at site UKL14 was often to generate widely 

fluctuating measurements, and sometimes a rapid increase 

in concentration, as water farther away from the trench (the 

“downstream” direction under prevailing conditions) was 

pulled into the site.

In 2003, there was no profiling buoy at the midtrench 

site, but data were collected at site UKL14 (fig. 30). As in 

2004, the immediate effect of the wind reversals was usually 

an increase in the dissolved oxygen concentration and larger 

fluctuations, but this was usually followed by a decrease in 

concentration as the pulse of low dissolved oxygen water from 

the trench passed by. Between August 5 and August 27, there 

was a series of reversals that appear to build on each other 

such that the concentration at site UKL14 decreased a little 

more with each short event, finally resulting in a period of 

several days between August 23 and 29 when concentrations 

fluctuated below 5 mg/L, often dipping below 2 mg/L. The 

LDOE of 2003 that led to a fish die-off, however, occurred 

during the last 2 weeks in July, and there were no reversals in 

the period leading up to it. There was a reversal event between 

July 24 and 26, which caused concentrations at both sites to 

approach zero. This effect was superimposed on a longer-term 

trend, however, that resulted in concentrations in the 2–3 mg/L 

range before the reversal occurred, so a wind reversal does not 

appear to be the sole explanation for the July 2003 LDOE. It 

does, however, appear to have caused already low dissolved 

oxygen concentrations to decrease even further. 

Bottom

Surface

Mid-water column

0

5

10

15

0

5

10

15

20

DISSOLVED OXYGEN CONCENTRATION,

IN MILLIGRAMS PER LITER

UKL14

UKL16

JULY

2004

JUNE AUGUST SEPTEMBER

15 1 15 1 15 1 15

Figure 29. Hourly dissolved oxygen concentrations at sites UKL14 and UKL16 in Upper Klamath Lake, Oregon, 2004. 

Shaded periods denote current reversals.

0

5

10

15

DISSOLVED OXYGEN

CONCENTRATION, IN

MILLIGRAMS PER LITER

UKL14

JULY

2003

AUGUST SEPTEMBER

1 15 1 15 1 15 1

Figure 30. Hourly dissolved oxygen concentrations at site UKL14 in Upper Klamath Lake, Oregon, 2003. Shaded 

periods denote current reversals.

36  Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
Historical Context of 2002-04 Data

It is of interest to know whether the data collected during 

the 3 years of this study and the resulting insights into water 

quality generally are applicable, or whether 2002–04 were 

in some way extraordinary in a historical context. Equally 

important, because there was a small fish die-off in 2003, 

was to investigate whether, in the context of 15 years of data, 

certain conditions distinguish the years when fish die-offs 

occurred. In addition to the die-off that occurred in 2003, 

severe die-offs occurred in 1996 and 1997, and a smaller 

die-off occurred in 1995. The comparison of the numbers of 

dead fish collected during die-offs is compromised by the lack 

of reliable estimates of the effort expended in collecting the 

fish, so these comparisons should not be considered reliable 

quantitative measures of the relative severity of the die-offs in 

the mid-1990s. Nonetheless, based on the number of dead fish 

collected, the most severe die-offs occurred in 1996 and 1997, 

and the 1995 die-off was more severe than the 2003 die-off 

[472 dead suckers were collected in 1995; 4,453 in 1996; 

2,335 in 1997 (Perkins and others, 2000)], and 113 in 2003 

(B.J. Adams, U.S. Geological Survey, written comm., 2006). 

It is possible, however, that the low number of fish collected 

in 2003 reflects the devastating loss to the population caused 

by the mid-1990s die-offs, and that from a water-quality 

perspective the 2003 die-off was as severe an event as occurred 

in the mid-1990s. The die-off in 1995 differed from the other 

three in that it did not begin until September 1, whereas 

each of the other three began in July [July 16 in 1996, July 

23 in 1997, and July 22 in 2003 (Perkins and others, 2000)]. 

Because of the need to limit the scope of the analyses, a focus 

was placed on the July/August time period, and the 1995 fish 

die-off was not considered. 

The datasets that are long enough and of adequate quality 

for such an investigation are limited, but this discussion makes 

use of four. The first is the water-quality dataset collected by 

the Klamath Tribes since 1990. This dataset consists of water 

samples collected every 2 weeks and analyzed for nutrient and 

chlorophyll a concentrations, and accompanying water-quality 

profiles of dissolved oxygen, pH, temperature, and specific 

conductance. The second dataset is a weather dataset (wind 

speed and direction, and air temperature ) obtained from the 

National Climatic Data Center (NCDC, 2006) collected since 

1990 at the Klamath Falls airport. Both of these datasets are 

used to look at a 15-year length of record. The third dataset 

is a wind dataset collected by the Bureau of Reclamation 

(1997) at an Agrimet site near Agency Lake; the length of 

record is only the 5 years since 2000, but the comparison with 

the NCDC data for that 5-year period is informative. The last 

dataset is the discharge collected at the Williamson River 

gaging station maintained by the USGS , 10.3 mi upstream of 

where the Williamson River discharges into the lake (fig. 1; 

USGS site identification No. 11502500; U.S. Geological 

Survey [no date]).

Temperature

One of the distinguishing characteristics of 2003 was 

water temperature. The median study-area water temperatures 

peaked at the end of July in 2003 at 24.9°C, which was higher 

than the highest temperatures observed in 2002 (23.3°C) or 

2004 (23.5°C). High water temperatures can contribute to an 

LDOE by accelerating oxygen demanding processes, and can 

contribute to a fish die-off by facilitating the spread of disease. 

Historic water-temperature records are not available, but water 

temperature is largely a function of air temperature, and so it 

is logical to look for years that stand out in the air-temperature 

record. The median air temperature for the months of July 

and August were determined from hourly values in the NCDC 

dataset, and subjected to an ANOVA (table 8). Fish die-offs in 

1996, 1997, and 2003 began in mid- to late July, although the 

majority of dead suckers that were collected in 1996 and 1997 

were collected later—between August 26 and September 12 

in 1996, and between August 20 and September 8 in 1997 

(Perkins and others, 2000)—so both July and August 

temperatures were used in this analysis. The years 1994, 1996, 

and 2003, although statistically indistinguishable from each 

other in this analysis, as a group had the highest median air 

temperature in July of the entire 15-year record. In August, the 

years 1992, 1996, 1997, 1998, and 2001 ranked as the hottest 

group of years, while 2003 was cooler. It seems appropriate 

to conclude that 3 of the 4 fish die-off years were among the 

warmest years in July and August of the 15-year record.

Table 8. Results of analysis of variance (ANOVA) of air 

temperature at the Klamath Falls Airport, Oregon, July and August, 

1990–2004.

[Medians were calculated from hourly values obtained from the National 

Climatic Data Center. Years that share a letter are not statistically 

distinguishable (p<0.05) from each other using this test. Years that do 

not share a letter are statistically distinguishable (p<0.05) using this test. 

Abbreviations: °F, degree Fahrenheit]

July August

Median 

temperature 

(°F)

Year Tukey 

grouping

Median 

temperature 

(°F)

Year Tukey 

grouping

73 1994 A 69 1992 A

72 1996 A 68 1997 A,B

70 2003 A,B 68 1996 A,B

70 1998 B,C 68 1998 A,B

69 1991 B,C 66 2001 A,B,C

70 2004 B,C,D 66 1991 B,C

70 2002 B,C,D 64 2004 B,C

68 1990 B,C,D 66 1994 C

68 1997 B,C,D 64 2003 C

67 1992 C,D 64 2000 C,D

66 1999 D,E 64 1999 C,D

66 1995 D,E 64 1995 C,D

64 2001 E,F 62 1993 D

63 2000 F 63 2002 D

60 1993 G 61 1990 D

Historical Context of 2002-04 Data 37
Wind Speed and Direction

An ANOVA also was done on the wind-speed data 

collected at the Klamath Falls Airport (table 9). Because of the 

way wind speeds are distributed throughout the day, peaking 

for a relatively brief period but being much lower over the 

rest of the day, it was difficult to see important differences by 

looking at the entire distributions, which were dominated by 

the lowest wind speeds. Under the assumption that it is the 

peak wind speeds that are most important, only wind speeds 

that exceeded 50 percent of the distribution for the entire 

month were extracted for this analysis. In July, the years 

1996 and 1997 ranked as the lowest wind speed group of the 

15-year dataset; 2003 ranked slightly higher. In August, all 

3 die-off years ranked higher than they did in July; 1996 and 

2003 ranked in the second lowest group, but 1997 ranked in 

the middle of the 15-year record. Low July and August wind 

speed, therefore, seems to be a distinguishing characteristic of 

fish die-off years.

Because short-term wind reversals were observed to 

cause oxygen concentration to decrease in the study area, an 

attempt was made to identify years in which wind reversals 

might have been relatively numerous compared to other years, 

thus increasing the average traveltime in the trench. To do 

this, the vector wind data from the NCDC were projected onto 

a set of axes rotated 60° clockwise, such that one axis was 

aligned along the length of the lake. The resulting “alonglake” component of the wind is positive for a northwest 

wind. An ANOVA was performed on this component of the 

wind (table 10). The analysis shows clearly the reversals in 

August of 2003, as evidenced by a slightly negative alonglake component, but these reversals occurred after the peak of 

the July LDOE that precipitated the fish die-off. August 1997 

also had a slightly negative median along-lake component, 

indicating that there were several wind reversals in August 

of that year, when the wind speed was moderate. Three 

die-off years—1996, 1997, and 2003—rank in the middle of 

the 15-year record in the magnitude of the July along-lake 

component, indicating that the number of reversals in July of 

those years was not exceptional compared to the entire 15-year 

record. Fish die-off years were not, therefore, characterized 

by a higher-than-average number of wind reversals in July or 

August.

Table 9. Results of analysis of variance (ANOVA) of wind speed 

at the Klamath Falls Airport, Oregon, July and August, 1990–2004.

[Medians were calculated from hourly values obtained from the National 

Climatic Data Center after first selecting those that fell in the upper one-half 

of the distribution for the month, as determined by combining all 15 years 

of the record. Years that share a letter are not statistically distinguishable 

(p<0.05) from each other using this test. Years that do not share a letter are 

statistically distinguishable (p<0.05) using this test. Abbreviations: m/s, 

meter per second]

July August

Median 

wind 

speed 

(m/s)

Year Tukey 

grouping

Median 

wind 

speed 

(m/s)

Year Tukey 

grouping

4.9 2001 A 4.5 1993 A

4.9 1993 A,B 4.5 2001 A

4.5 1994 A,B 4 1994 B

4.5 1992 B 4 1992 B,C

4.5 1991 B 4.5 1991 B,C

4.5 1990 B 3.6 1997 B,C

4 1995 C 3.6 1995 B,C,D

3.6 2000 C,D 3.6 2000 C,D,E

3.6 2004 D,E 3.6 1990 C,D,E,F

3.6 1999 E 3.6 2003 D,E,F,G

3.6 2002 E 3.6 2004 D,E,F,G

3.6 1998 E 3.6 2002 E,F,G

3.1 2003 E 3.1 1996 F,G

2.7 1997 F 3.1 1999 G

2.7 1996 G 2.2 1998 H

Table 10. Results of analysis of variance (ANOVA) of the 

along-lake component of wind speed at the Klamath Falls Airport, 

Oregon, July and August, 1990–2004.

[Medians were calculated from hourly values obtained from the National 

Climatic Data Center after first selecting those that fell in the upper one-half 

of the distribution for the month, as determined by combining all 15 years of 

the record. The along-lake component was obtained by projecting the vector 

data onto a set of axes rotated 60° clockwise. Years that share a letter are not 

statistically distinguishable (p<0.05) from each other using this test. Years that 

do not share a letter are statistically distinguishable (p<0.05) using this test. 

Abbreviations: m/s, meter per second]

July August

Median 

wind 

speed 

(m/s)

Year Tukey 

grouping

Median 

wind 

speed 

(m/s)

Year Tukey 

grouping

4.2 2001 A 2.7 2002 A

4 1994 A,B 3.4 1993 A,B

3.8 1993 A,B 2.9 2001 A,B,C

3.8 1991 A,B,C 2.5 1992 A,B,C

3.5 1992 B,C 2.4 2000 B,C,D

3.4 1990 C,D 2.5 1995 B,C,D

2.5 2002 D,E 2.3 1999 C,D,E

2.2 2003 E,F 2.2 1996 C,D,E

2.1 2000 E.F 1.8 1994 D,E,F

2.2 1996 F,G 1.2 1998 E,F,G

2 1999 F,G 1.2 2004 E,F,G

2 1997 F,G 1.3 1990 F,G

1.7 1995 F,G .9 1991 G

1.4 2004 F,G .9 1997 G,H

1.6 1998 G -1.3 2003 H

38  Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
There were indications that the NCDC wind dataset 

was not ideally suited to highly quantitative analysis. There 

was clear evidence, for example, of “binning” in the NCDC 

wind dataset—values always fell on discrete values rather 

than being continuous. In addition, wind speeds of zero were 

numerous, so it is likely that all values below a threshold 

became zero. As a means of assessing the quality of the 

data and the confidence one should have in the ANOVA 

analysis, an analysis of only 2000–04 data was compared for 

consistency to the same analysis for those 5 years of wind 

data collected at the Agency Lake Agrimet site (table 11). 

Among other discrepancies, the year 2003 ranks in the lowest 

wind speed group in the NCDC data, but ranks second highest 

in the Agrimet data. The relative ranking among the 2002, 

2003, and 2004 wind datasets collected at the profiling buoys 

in this study are consistent with the Agrimet data but not the 

NCDC data, the 2003 July wind data being the highest of the 

three. The significance of this comparison is that the NCDC 

wind data probably should be interpreted qualitatively. It is 

appropriate, for example, to conclude that wind speed in the 

years 1996, 1997, and 2003 ranks toward the low end of the 

entire 15-year period, but the quantitative differences between 

any pair of years is not reliable, and the characterization 

of 2003 as a very low wind speed year should be viewed 

skeptically because it is inconsistent with data collected over 

the 3 years of this study, and with the 5 years of Agrimet data.

Lake-Wide Water Quality

An ANOVA similar to that used to rank the wind and 

air temperature datasets was used to rank the years of the 

15-year water quality dataset collected by the Klamath Tribes 

(fig. 31). Only data from seven lake sites that were consistent 

through 1990–2004 were used in the analysis. The variability 

between sites and within a 2-month time frame largely 

swamps interyear variability in chlorophyll a and dissolved 

oxygen, making the distributions nearly indistinguishable 

from each on a yearly basis. This type of aggregate analysis 

over several sites and the entire July–August time frame 

averages out important distinctions, and no characteristics 

emerge to distinguish the fish die-off years of 1995, 1996, 

1997, and 2003. Attempts to relate the Klamath Tribes waterquality variables to NCDC wind speed over the 15 years 

of record available in both datasets yielded nonsignificant 

relations as well (fig. 32), in spite of the fact that significant 

correlations were obtained by others on a shorter period of 

record (Kann and Welch, 2005).

In contrast to chlorophyll a and the other nutrients, 

large multiyear trends in the distribution of the July–August 

ammonia concentration have been observed over the 15-year 

record; these multiyear trends strongly suggest that climatic 

factors are involved. In order to test this, correlations were 

calculated among two climate variables, July–August NCDC 

wind speed and the October–May cumulative discharge in the 

Williamson River, May–June and July–August median values 

of ammonia and chlorophyll a concentration, and the median 

of the difference between the water column maximum and 

minimum dissolved oxygen (denoted ∆ dissolved oxygen) 

(table 12). July–August median chlorophyll a concentration 

and ∆ dissolved oxygen were not correlated with either 

climate variable, indicating that year-to-year variability 

in these variables is not climate-driven. Nor are year-toyear changes in chlorophyll a concentration, ammonia 

concentration, or ∆ dissolved oxygen correlated with each 

other. July–August median ammonia concentrations were, 

however, highly correlated with both climate variables, 

confirming that the interannual variability in ammonia 

probably is climate related. Because the two climate 

variables—July–August wind speeds and discharge from 

the Williamson River for the previous October–May—are 

themselves correlated, it could be difficult to sort out which, if 

either of these, represents a causal relation. Because, however, 

the July–August wind speed median also was correlated 

with the ammonia concentration in the previous months of 

May and June, it is more likely that the correlation between 

ammonia and Williamson River discharge represents some 

kind of causal relation. 

Table 11. Results of analysis of variance (ANOVA) of wind speed 

at the Klamath Falls Airport and at the Bureau of Reclamation 

Agrimet site located at Agency Lake, Oregon, July and August, 

1990–2004.

[Medians were calculated from hourly values obtained from the National 

Climatic Data Center (NCDC) after first selecting those that fell in the upper 

one-half of the distribution for the month, as determined by combining 

all 15 years of the record. Medians at the Agency Lake Agrimet site were 

calculated from hourly values that fell in the upper one-half of the distribution 

for the month, as determined by combining 5 years of the record from 2000 

to 2004. Years that share a letter are not statistically distinguishable (p<0.05) 

from each other using this test. Years that do not share a letter are statistically 

distinguishable (p<0.05) using this test. Abbreviations: m/s, meter per 

second]

NCDC AGRIMET

Median 

wind 

speed 

(m/s)

Year Tukey 

grouping

Median 

wind 

speed 

(m/s)

Year Tukey 

grouping

4.9 2001 A 2.2 2000 A

3.6 2000 B 1.9 2003 B

3.6 2004 B,C 1.8 2001 C

3.6 2002 C 1.8 2002 C

3.1 2003 C 1.5 2004 D

Historical Context of 2002-04 Data 39
or003UK_01_fig31

0

100

200

300

400

500

CHLOROPHYLL a

CONCENTRATION,

IN MICROGRAMS PER LITER 

0

1000

2000

3000

AMMONIA CONCENTRATION,

IN MICROGRAMS PER LITER

0

5

10

15

20

25

15

20

25

30

35

TEMPERATURE,

IN DEGREES CELSIUS 

1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 0

5

10

15

20

RANGE IN DISSOLVED OXYGEN

CONCENTRATION, IN

MILLIGRAMS PER LITER

DISSOLVED OXYGEN

CONCENTRATION, IN

MILLIGRAMS PER LITER

D,E D,E E D,E E D,E B,C,D A C,D A,B A A,B,C D,E

A D,E

A,B A A,B A,B B A,B A A,B A,B A,B B A,B A,B A,B B

A,B B A,B A,B B A,B A,B A,B A,B A A,B A,B B A,B A,B

A,B E,F D,E F A,B,C,D E C,D,E D,E A E B,C,D,E E C,D,E A,B A

75th percentile

90th percentile

Median

25th percentile

10th percentile

Upper outlier

EXPLANATION 

Figure 31. July–August distributions of concentrations of chlorophyll a, ammonia, dissolved oxygen, 

and temperature, and the difference between the water column maximum and minimum dissolved 

oxygen, at three sites located in Upper Klamath Lake, Oregon. Data collected biweekly by the Klamath 

Tribes (K. Fischer, written commun., 2005). Years that share a letter are not statistically distinguishable 

(p<0.05) from each other using this test. Years that do not share a letter are statistically distinguishable 

(p<0.05) using this test. There were no significant differences in the yearly distributions of chlorophyll a. 

40 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
A straightforward explanation for this relation would be 

that higher discharge from the Williamson River during the 

winter and spring delivers more organic material that acts as 

a source of ammonia when it decays in the summer. Although 

the climate connection to ammonia appears solid, ammonia 

concentration alone is not a predictor of fish die-off years. 

Table 12. Spearman’s rho correlation coefficients between selected water-quality and climate variables in Upper Klamath Lake 

Basin, Oregon, 1990–2004.

[Water-quality data are biweekly values of chlorophyll a and nutrient concentrations, and biweekly profiles of dissolved oxygen concentration collected by 

the Klamath Tribes at seven sites in Upper Klamath Lake. Means at the Klamath Falls Airport were calculated from hourly values obtained from the National 

Climatic Data Center (NCDC) after first selecting those that fell in the upper one-half of the distribution for the month, as determined by combining 15 years 

of the record from 1990 to 2004. Correlations that are significant (p<0.05) are in boldface type. Median July-Aug. ∆DO: median difference between water 

column maximum and minimum dissolved oxygen concentration. Mean July-Aug. wind speed: mean of July and August wind speed at the Klamath Falls 

Airport. Cumulative Oct.-May discharge: discharge at U.S. Geological Survey station 11502500 from October of the previous calendar year through May of 

the current year. Symbols: <, less than]

Concentrations

Spearman’s rho correlation coefficient

Concentrations

Mean 

July–Aug. 

wind speed

Cumulative 

Oct.–May 

Williamson River 

discharge

Median 

July–Aug. 

chlorophyll a

Median 

May–June 

chlorophyll a

Median 

July–Aug. 

ammonia

Median 

May–June 

ammonia

Median 

July–Aug. 

∆DO

Median July–Aug. 

chlorophyll a

1.00 -0.32 0.00 0.23 -0.10 -0.08 0.11

Median May–June 

chlorophyll a

1.00 .12 .24 .15 .33 -.32

Median July–Aug. 

ammonia

1.00 .81 -.01 -.52 .75

Median May–June 

ammonia

1.00 -.10 -.54 .52

Median Jul–Aug 

∆DO 

1.00 -.14 .32

Mean July–Aug. 

wind speed

1.00 -.71

Cumulative Oct.–May 

Williamson River 

discharge

1.00

Concentrations in 1997 were among the highest on record, but 

other years had similarly high concentrations. Concentrations 

in 1996 were in the midrange, and concentrations in 2003 

were among the lowest of the record, comparable to the early 

1990s. 

Historical Context of 2002-04 Data 41
Water Quality at Indicator Sites

The aggregate analysis of the Klamath Tribes’ dataset 

based on July–August distributions at the sites in the northern 

part of the lake did not yield an obvious way of identifying 

the fish die-off years in the 15-year record. Another approach 

taken was to focus on individual sites and test the idea of an 

“indicator site”—a particular site that could be reliably used 

to indicate the onset of an LDOE in the study area. Because 

the water quality in the study area is largely a function of the 

quality of the water entering the study area through the trench 

between Bare Island and Eagle Ridge, the onset of an extreme 

event should be accompanied by the transport of a large 

volume of water with a low concentration of dissolved oxygen 

through the trench. One of the Klamath Tribes’ sampling sites 

is located in the area of the trench between Bare Island and 

Eagle Ridge; this site is known as Eagle Point, or EP. Another 

site located roughly between the 2003–04 UKL06 and UKL07 

sites is Midnorth, or MN (fig. 1). The latter site is, like 

UKL07, broadly representative of the conditions in the deeper 

part of the study area that is preferred habitat for adult suckers 

and is bounded by the remnants of the trench and the entrances 

to Ball and Shoalwater Bays to the south. Data from these two 

sites were used in a principal component (PC) analysis to test 

the “indicator site” idea.

Seven variables were included in the PC analysis—

chlorophyll a concentration, ammonia concentration, average 

water column dissolved oxygen concentration, minimum 

water column dissolved oxygen concentration, the difference 

between maximum and minimum water column dissolved 

oxygen concentration, maximum water column temperature, 

and the difference between maximum and minimum water 

column temperature. At site MN, the first three eigenvalues 

were able to explain 36, 28, and 12 percent of the total 

variance, respectively; at site ER the first three eigenvalues 

were able to explain 39, 31, and 14 percent of the total 

variance, respectively. The loadings of the first three principal 

components on each variable are given in table 13, and 

the scores on each July–August sample date are shown in 

figures 33 and 34. The first principal component at each site 

largely captures variability in average water column dissolved 

oxygen concentration and chlorophyll a concentration, 

fluctuating opposite to water temperature and ammonia, 

although the contribution from variability in ammonia is 

relatively small. The second principal component captures 

primarily the variability in the water column stratification, and 

the third principal component is dominated by the variability 

in ammonia concentration. 

The sample date July 28, 2003, has the largest negative 

PC1 score, reflecting a low average water column dissolved 

oxygen concentration and low chlorophyll a concentration, in 

combination with high water temperature and relatively high 

ammonia concentration. In this analysis, July 2003 appears 

unique in the context of a 15-year record. The 1996 and 

or003UK_01_fig32

3 4 5 6

MEAN JULY/AUGUST WIND SPEED,

IN METERS PER SECOND

0

2

4

6

8

10

MEDIAN DELTA DISSOLVED OXYGEN,

IN MILLIGRAMS PER LITER

4

6

8

10

MEDIAN DISSOLVED OXYGEN,

IN MILLIGRAMS PER LITER

0

500

1000

1500

AMMONIA CONCENTRATION,

IN MICROGRAMS PER LITER

Figure 32. Correlation between the July–August averaged 

wind speed at the Klamath Falls Airport and the median of 

the July–August distribution of ammonia, dissolved oxygen, 

and the difference between water column maximum and 

minimum dissolved oxygen, Upper Klamath Lake, Oregon. 

Wind data are from the National Climatic Data Center 

(2006), and the means are calculated on only the upper 

50 percent of the distribution. Ammonia and dissolved 

oxygen data were obtained from the Klamath Tribes.

42 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
Table 13. Principal component scores at sites Eagle Ridge and Midnorth in Upper Klamath Lake, Oregon.

[Water-quality data are biweekly values of chlorophyll a and nutrient concentrations, and biweekly profiles of dissolved oxygen concentration 

collected by the Klamath Tribes at two sites in Upper Klamath Lake during July and August, 1990–2004. Concentrations: ∆DO: difference 

between water column maximum and minimum dissolved oxygen concentration. Water column temperature: ∆T, difference between maximum 

and minimum water column temperature]

Principal 

component

Concentrations

Water column temperature

Chlorophyll a Ammonia-N

Dissolved oxygen

Mean Minimum ∆DO Maximum ∆T

Principal component score at Eagle Ridge

1 0.32 -0.16 0.56 0.58 -0.19 -0.42 -0.07

2 .4 -.06 .19 .04 .59 .28 .61

3 .2 .97 .07 .08 -.05 .04 -.03

Principal component score at Midnorth

1 0.32 -0.36 0.6 0.48 0.27 -0.17 0.28

2 .22 .07 -.1 -.39 .53 .5 .5

3 .63 .74 .03 .08 -.06 -.2 -.04

1997 points that have a relatively high PC2 score and stand 

out from the cloud of other data points are from late July, 

reflecting the exceptional stratification during that time period. 

This characteristic of those 2 years has been documented by 

others (Perkins and others, 2000; Kann and Welch, 2005) 

in the context of a shorter length of record; in this analysis 

the exceptional stratification in those years stands out in the 

context of a longer 15-year record. 

In this analysis, the fish die-off years do not group 

together in obvious separation from the other years on record. 

This suggests that 2003 does not have a lot in common, in 

terms of the variables included in this analysis and their 

correlations, with the other 2 fish die-off years, 1996 and 

1997. There are two possible reasons for this. The first is that 

the years really were different in important ways, and that 

there is more than one set of circumstances that lead to a fish 

die-off. The second is that the two-week interval of the sample 

dates resulted in the most relevant conditions of 1996 and 

1997, immediately preceding the die-off, being missed.

The statistics of the distribution of dissolved oxygen, 

ammonia, and chlorophyll a concentrations, and water 

temperature for the entire July and August time period were 

compiled separately for sites ER and MN in tables 14 and 15, 

respectively. The values of these variables on the sample 

dates most closely associated with the onset of the fish dieoffs in 1996, 1997, and 2003 also are compiled in the tables. 

Samples were collected on July 28, 2003, at the peak of the 

low dissolved oxygen event. The description of this period as 

characterized by very low dissolved oxygen concentrations in 

combination with very high ammonia concentrations, as well 

as high temperatures and low chlorophyll a, reappears in this 

analysis. At both sites, dissolved oxygen and chlorophyll a

fall within the first quartile, and ammonia and temperature fall 

within the fourth quartile, of all sample dates for the July–

August period in the 15 years of data. 

Data collected on the 1996 and 1997 sampling dates are 

more difficult to interpret because there are no continuous 

datasets with which to identify when the worst conditions 

actually occurred. These sample dates probably missed 

the time period of lowest dissolved oxygen at site ER. 

Nonetheless, the August 20, 1996 and August 12, 1997 values 

at site MN generally are consistent with a low dissolved 

oxygen/high temperature/low chlorophyll a/high ammonia 

combination, with the exception that the temperature fell in 

the third rather than fourth quartile. Consistent among all fish 

die-off dates at site MN is the combination of average water 

column dissolved oxygen concentration and chlorophyll a

concentration in the first quartile (less than 6 mg/L and less 

than 65 μg/L, respectively) and ammonia concentration in the 

fourth quartile (greater than 520 μg/L). If these same criteria 

are used to screen data collected at site MN during all July–

August sample dates in the 15-year dataset, then only four 

additional dates (out of a total of 71 dates) pass the screening, 

from 3 non-die-off years: August 12, 1998; August 9 and 22, 

2000; and August 29, 2001. It appears, therefore, that there 

is some validity to screening for die-off conditions based on 

these criteria at only site MN. These screening criteria offer 

no predictive capability, of course; their utility is in being able 

to better describe the set of conditions that appear to have a 

greater risk of leading to a die-off, and they point to some 

commonality among the die-off years.

Historical Context of 2002-04 Data 43
Figure 33. Principal component scores for data from 

Midnorth site, all July and August sample dates, Upper 

Klamath Lake, Oregon, 1990–2004. Data were obtained 

from the Klamath Tribes (K. Fischer, written commun., 

2005).

Figure 34. Principal component scores for data from 

Eagle Ridge site, all July and August sample dates, 

Upper Klamath Lake, Oregon, 1990–2004. Data were 

obtained from the Klamath Tribes (K. Fischer, written 

commun., 2005).

or003UK_01_fig33

Sample date closest to fish die-off

 2002

 2003

 2004

All sample dates

-3

-1

1

3

5

SCORE OF PC2

-5 -3 -1 1 3

SCORE OF PC1

-2

-1

0

1

2

3

4

SCORE OF PC3

or003UK_01_fig34

-5 -3 -1 1 3

SCORE OF PC1

-3

-1

1

3

5

7

SCORE OF PC2

-2

-1

0

1

2

3

4

5

SCORE OF PC3

Sample date closest to fish die-off

 1996

 1997

 2003

All sample dates

Conclusions Regarding Characteristics of Fish 

Die-Off Years

The evidence for a correspondence between low wind 

speeds and fish die-off years is compelling; all 3 years—1996, 

1997, and 2003—stand out in the historical record has having 

lower-than-average July wind speeds. The connection that has 

been made between low wind speeds and fish die-off years is 

increased density stratification and the low dissolved oxygen 

in the lower water column that often accompanies it. Yet, low 

wind speeds did not correlate well with high dissolved oxygen 

stratification on either a daily basis within a single year or on 

the basis of a 2-month average over 15 years of data, nor were 

all fish die-off years characterized by exceptional dissolved 

oxygen stratification. Furthermore, strong dissolved oxygen 

stratification in the water column was not directly the cause 

of the recent, more well-documented, fish die-offs. This was 

noted by Perkins and others (2000) regarding fish die-offs in 

1996 and 1997, when the great majority of dead suckers were 

44 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
Table 14. Distribution statistics of water column averages of 

chlorophyll a, ammonia-N, dissolved oxygen, and temperature at 

Eagle Ridge site, based on July–August sampling dates, Upper 

Klamath Lake, Oregon, 1990–2004.

[Water-quality data are biweekly values of chlorophyll a and nutrients, and 

biweekly profiles of dissolved oxygen collected by the Klamath Tribes at 

Eagle Ridge in Upper Klamath Lake during July and August 1990–2004. 

Quartile: Q1, first quartile; Q2, second quartile; Q3, third quartile; Q4, fourth 

quartile. Abbreviations: mg/L, milligram per liter; oC, degree Celsius; μg/L, 

microgram per liter]

Water column averaged value

Dissolved 

oxygen

 (mg/L)

Temperature 

(°C)

Chlorophyll a

(μg/L)

Ammonia-N 

(μg/L)

Percentile

95th 8.03 23.4 314 1,170

90th 7.51 22.9 256 1,090

75th 6.54 21.8 148 898

50th 4.72 20.4 100 313

25th 3.72 19 60 86

10th 2.16 17.9 24 29

5th 1.21 17.3 14 19

Values on dates closest to fish die-offs

07-28-03 0.6 24.3 28 907

Quartile Q1 Q4 Q1 Q4

08-20-96 5.16 19.7 64 979

Quartile Q3 Q2 Q2 Q4

08-12-97 4.3 21.1 44 803

Quartile Q2 Q3 Q1 Q3

Table 15. Distribution statistics of water column averages of 

chlorophyll a, ammonia-N, dissolved oxygen, and temperature 

at Midnorth site, based on July–August sampling dates, Upper 

Klamath Lake, Oregon, 1990–2004.

[Water-quality data are biweekly values of chlorophyll a and nutrients, and 

biweekly profiles of dissolved oxygen collected by the Klamath Tribes at 

Eagle Ridge in Upper Klamath Lake during July and August 1990–2004. 

Quartile: Q1, first quartile; Q2, second quartile; Q3, third quartile; Q4, fourth 

quartile. Abbreviations: mg/L, milligram per liter; oC, degree Celsius; μg/L, 

microgram per liter]

Water column averaged value

Dissolved 

oxygen

 (mg/L)

Temperature 

(°C)

Chlorophyll a

(μg/L)

Ammonia-N 

(μg/L)

Percentile

95th 10.1 23.1 252 982

90th 9.3 22.7 240 952

75th 8.8 21.8 159 520

50th 7.8 20.4 107 121

25th 6.2 19 65 21

10th 4.5 17.6 37 5

5th 4 17.2 13 5

Values on dates closest to fish die-offs

07-28-03 1.86 24.36 7 873

Quartile Q1 Q4 Q1 Q4

08-20-96 5.33 20.05 52 757

Quartile Q1 Q3 Q1 Q4

08-12-97 4.49 21.51 36 640

Quartile Q1 Q3 Q1 Q4

counted after stratification had collapsed. It also was apparent 

in the difference between 2002 and 2003 in this study. 

Although 2003 probably was a lower-than-average wind speed 

year, it was not a year characterized by an exceptional degree 

of dissolved oxygen stratification, particularly in July, when 

the most severe LDOE occurred. Indeed, one of the things 

that made the event exceptional was the fact that stratification 

was weak and dissolved oxygen was low throughout the water 

column. In 2002, which also was a lower-than-average wind 

speed year, the water column was more consistently stratified 

in dissolved oxygen and to a greater degree than in 2003, and 

for the most part endangered suckers persisted in the study 

area and, apparently, survived. 

An extended period of dissolved oxygen stratification 

in the early to mid-summer could increase the risk of a fish 

die-off several weeks later. For example, low dissolved oxygen 

in the lower water column could present chronic stress to 

fish that weakens them and makes them more susceptible 

to adverse conditions later in the summer. Low winds also 

may play a role in bloom dynamics, in that even moderate 

stratification tends to provide favorable conditions for AFA, 

thus leading to higher biomass and more dramatic bloom 

declines. From what we can determine from the available data, 

these possibilities seem applicable to the 1996 and 1997 fish 

die-offs, but the fact remains that in 2003, when the die-off 

began at the end of July, it was not preceded by a period of 

several weeks of exceptional dissolved oxygen stratification. 

If there is a common set of conditions that link all 

the fish kill years, it seems possible, if not likely, that the 

correspondence between low wind speeds and fish die-off 

years has a different significance. One possibility is that 

interannual variability in wind stress influences interannual 

variability in water quality through the wind-driven 

circulation. Oxygen production and consumption varies 

around the lake, in part as a consequence of the changes in 

bathymetry that water encounters along a flow path. Because 

the wind-driven circulation is responsive to wind stress, lower 

wind speeds slow down the overall wind-driven circulation 

relative to higher wind speeds and increase residence time in 

different areas of the lake, providing, in general, more time 

for both oxygen demanding and oxygen producing processes 

to act in different areas of the lake. Understanding how the 

nonconservative processes interact along a flow path as water 

circulates around the lake faster or slower in response to 

wind stress is difficult using data from a fixed-site sampling 

strategy, and likely will require the use of a computer model.

Historical Context of 2002-04 Data 45
In addition to the role that low winds may play in the 

development of an LDOE, it is clear that any severe LDOE, 

and consequently any fish die-off, will be coincident with a 

dramatic decline in the AFA bloom. Not only do the senescing 

cells provide water column oxygen demand, but the shutdown 

in photosynthetic production also is significant, as water 

column and sediment oxygen demanding processes continue to 

consume oxygen. Because, however, the trigger for a dramatic 

bloom decline is not well understood, we are still unable to 

determine the root cause of a severe LDOE. An important 

area of future research will be to try to better understand what 

causes the AFA bloom to decline, especially when it does 

so precipitously. Although the cause of AFA bloom declines 

remains undetermined, we have been able to determine some 

characteristics of a severe LDOE that all fish die-off years 

have in common with each other, but with few other nondie-off years. Water coming through the trench and into the 

northern part of the lake during these events was characterized 

by exceptionally low water-column averaged dissolved oxygen 

and chlorophyll a in combination with exceptionally high 

ammonia, indicating that nearly all AFA biomass had already 

been converted to inorganic form, in the process consuming 

nearly all available oxygen. An additional characteristic seems 

to be high temperature, which can accelerate the respiratory 

and decay processes that consume oxygen. 

Summary

Monitoring data collected during a 3-year study of sucker 

behavior in response to water quality provided an opportunity 

to describe water quality in the study area (approximately 

the northern one-third of Upper Klamath Lake) at a spatial 

and temporal resolution that was unavailable prior to 2002. 

Several questions were addressed using these data: What is the 

seasonal and interannual variability in water quality? Are there 

any aspects of seasonal variability that are predictable? If poor 

water quality is defined as conditions that would be potentially 

harmful to endangered suckers, where do these conditions 

tend to occur and how are they distributed throughout the day? 

What is the spatial extent of poor water quality conditions? 

Are there predictable differences in water quality between 

deep and shallow sites?

Each of the 3 years of the study was unique in terms 

of the seasonal patterns in water quality and the occurrence 

and severity of poor water-quality conditions, indicating that 

little predictability can be expected in these from year to 

year. Potentially harmful pH conditions, defined as greater 

than 9.7, occurred in late June and early July of all 3 years, 

coincident with a rapid expansion of the first bloom of the 

season. When averaged by Julian week, the spatial extent 

of these conditions was the greatest in the first or second 

week in July in all 3 years, reaching 0, 8, and 47 km2 (square 

kilometers) to less than 9.7 around mid-July in all 3 years, 

and only in 2003 did pH increase again to values greater than 

9.7, coincident with a second bloom from the second week 

in August through the first week in September. Temperatures 

peaked in late July in all 3 years, but the spatial extent of 

potentially harmful temperatures, defined as greater than 

28 degrees Celsius, was negligible in all 3 years. Dissolved 

oxygen was the most variable of the three continuously 

monitored water-quality constituents, as it is determined in 

large part by bloom dynamics, which also are highly variable 

from year to year. In each year, there were several periods that 

could be termed “low dissolved oxygen events” (LDOE) on 

the basis of the occurrence of concentrations less than 4 mg/L 

(milligrams per liter). Concentrations less than 4 mg/L in the 

lower water column for part of the day were common during 

the 3 study years, but did not result in a fish die-off. The most 

severe LDOE, which did culminate in a fish die-off, occurred 

in 2003. This LDOE was characterized by concentrations 

that were 3 mg/L or less throughout the water column and 

that persisted throughout the day, for 8 days, at a site located 

centrally in the study area and the area of the lake that was 

preferred adult sucker habitat. The maximum spatial extent of 

weekly averaged concentrations less than 4 mg/L occurred in 

the week starting on July 27, 2003, and was 39 km2. The next 

highest spatial extent of these potentially harmful dissolved 

oxygen conditions was 17 km2 and occurred in the week 

starting on August 15 in 2004.

There were differences between deep (defined roughly as 

deeper than 2.5 meters) and shallow sites in the daily timing 

of the most extreme values of temperature, pH, and dissolved 

oxygen, although the timing at both deep and shallow sites 

was consistent from year to year. At shallow sites, temperature 

and pH tended to peak in the late afternoon, primarily 

between the hours of 5 p.m. and 7 p.m. The daily minimum in 

dissolved oxygen tended to occur in the early morning hours, 

before the sun was high in the sky and when dark respiration 

had been operating the longest, between the hours of about 

6 a.m. and 8 a.m. At deep sites, the timing of extreme 

values of temperature and pH was in the late afternoon, as 

at the shallow sites, but the timing of the extreme values of 

dissolved oxygen was less well defined than at the shallow 

sites. This is because the deeper sites often experience some 

degree of thermal stability during the day. Dissolved oxygen 

can continue to decrease in the lower water column beyond 

the early morning hours due to ongoing respiratory and 

other oxygen demanding processes in the water column and 

sediments, until at some point the water column mixes when 

the wind picks up or the water surface cools sufficiently. As 

a result, there was no well-defined time window in which 

the minimum daily dissolved oxygen concentration tended 

to occur at the deeper sites. Because low dissolved oxygen 

conditions tend to be more extreme at the deeper sites, and 

concentrations potentially harmful to fish are most likely to 

occur at the deeper sites, the assumption, sometimes made, 

that the worst conditions of the day for fish (in terms of 

dissolved oxygen) occur in the early morning hours probably 

is not justified in this lake. 

46  Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
Because hypoxia was determined to be an important 

trigger of recent, documented fish die-offs, a section of this 

report was devoted to discussing the factors contributing to 

an LDOE. Exceptional stratification in dissolved oxygen and 

low wind stress were not consistent features of the observed 

LDOEs, but the most severe LDOEs were coincident with a 

bloom decline. 

Because the cause for bloom declines is unknown, the 

fundamental cause of a severe LDOE remains undetermined, 

but it was determined that severe LDOEs in the northern part 

of the lake for the most part do not develop there, but rather 

develop to the south and are transported into the area by the 

wind-driven circulation. The placement of acoustic Doppler 

current profilers in the lake in conjunction with the collection 

of wind data showed decisively the close coupling between 

the currents in the lake and the surface wind stress, and the 

fact that under prevailing wind conditions most of the volume 

of the lake moves in a clockwise loop that is completed in 

about 10 days. Water enters the northern part of the lake, 

where the preferred sucker habitat is found, almost entirely 

through a small cross-section between Eagle Ridge and 

Bare Island. Water coming through that cross section during 

the most severe LDOE, in July 2003, was characterized by 

exceptionally low water-column averaged dissolved oxygen, 

exceptionally low chlorophyll a, and exceptionally high 

temperature and ammonia.

The concentration of dissolved oxygen observed at 

a fixed site on the lake is a complicated function of the 

wind-driven circulation. Reversals or stalls in the wind 

increase the residence time in the deep trench along the 

western shoreline, thus allowing more time for oxygen 

demanding process to deplete the water passing through of 

oxygen. These stalls or reversals increase residence time along 

the northern and eastern broad shallow areas of the lake as 

well, thus giving oxygen producing photosynthesis more time 

to increase dissolved oxygen concentration in those areas. 

Short-term pulses of water low in dissolved oxygen coming 

through the trench were linked directly to brief wind reversals. 

Long-term trends in water quality, on a time scale greater than 

about 10 days, integrate the net effect of all oxygen demanding 

and oxygen producing processes along the flow path. It was 

such a trend that culminated in the severe July 2003 LDOE.

An attempt was made to place the 3 study years into a 

more historical context and, in particular, to the characteristics 

that distinguish the three most severe recent fish die-off years 

(1996, 1997, and 2003). A 15-year record of meteorology (air 

temperature and wind speed collected at the Klamath Falls 

airport, obtained from the National Climatic Data Center) 

and water quality (biweekly water-quality profiles collected 

at three sites in the northern part of the lake by the Klamath 

Tribes) were used to provide the historical context. Air 

temperature was used as a surrogate for water temperature, 

as no long-term continuous records of water temperature 

exist. Two of the three fish die-off years, 1996 and 2003, 

ranked at the high end of the range in July temperature, 

and 1996 and 1997 ranked at the high end of the range in 

August temperature, on the basis of an analysis of variance 

test (ANOVA). Thus, high temperatures may contribute to 

the conditions leading to a fish die-off. The same test ranked 

all 3 fish die-off years at the low end of the range in July 

wind speeds. An attempt to correlate wind stress with the 

degree of dissolved oxygen stratification or with dissolved 

oxygen concentration using the 15 years of climate data 

yielded insignificant relations, so the contribution of lowerthan-average wind stress to a severe LDOE or a fish die-off 

probably is not through stratification, but rather something 

else, possibly the wind-driven circulation. 

Attempts were made to rank July–August median 

water-quality variables in the biweekly dataset collected by 

the Klamath Tribes with an ANOVA. Most water-quality 

variables had short term and spatial variability comparable 

to interannual variability, making it difficult to statistically 

distinguish July–August distributions between years. The 

exception was ammonia concentration, which showed 

year-to-year trends in the July–August distributions suggestive 

of a climatic signal. The ammonia concentration was highly 

correlated with two climate variables—mean July–August 

wind speed, and October to May cumulative discharge in 

the Williamson River. Because both climate variables were 

also correlated with May–June ammonia concentration, the 

correlation with Williamson River discharge is more likely to 

represent a causal relation, such as high spring runoff bringing 

in more readily decomposed material, resulting in a higher 

water column ammonia concentration in late spring and early 

summer. It is unclear, however, that there is any connection 

between the climate signal in ammonia concentration and the 

occurrence of fish die-offs. One of the three fish die-off years, 

1997, was characterized by some of the highest ammonia 

concentrations on record, one year, 1996, was characterized 

by more moderate, but still high (relative to the entire 15-year 

record) concentrations, and one year, 2003, was characterized 

by some of the lowest concentrations in the 15-year record.

Even though fish die-off years were not all years of 

exceptionally high ammonia concentration, high ammonia 

concentration (in the fourth quartile of the entire historical 

distribution of July–August values) at a single index site 

located in the study area was one of three factors that, 

in combination, could be used to successfully screen the 

historical water-quality dataset for those dates which most 

closely preceded the fish die-offs. The other two factors were 

dissolved oxygen and chlorophyll a concentration, both in the 

first quartile. Dates preceding the fish die-offs in all 3 years 

were passed by the screening, and dates from only three other 

non die-off years were passed by this screening. Therefore, the 

idea that one site could act as an “indicator” site was deemed a 

success, which might be information that could be used in the 

design of a long-term monitoring program for the lake.

Summary 47
Acknowledgments

The commitment of Rip Shively and Scott Vanderkooi 

from the USGS Klamath Falls Field Station to facilitating 

the water quality field program is gratefully acknowledged. 

Jeff Gartner from the USGS National Research Program was 

responsible for the deployment of the ADCPs in the lake. 

Ralph Cheng from the USGS National Research Program 

provided the hydrodynamic modeling results that greatly 

improved our interpretation of the water quality observations. 

Many people contributed to the field work over the 3 years of 

this study, and their efforts are gratefully acknowledged: Jason 

Cameron, Michael Berg, and Jessica Asbill from the Bureau 

of Reclamation in Klamath Falls; Daniel Gambetta, Anna 

Glass, April McKellar, Michael Altmayer, Anthony Ordway, 

Pamela Burns, Jim Harris, Melissa Berhardt, and Christine 

Adelsberger, from the USGS in Klamath Falls; Matt Johnston 

and Micelis Doyle from the USGS in Portland. Reviews by 

Greg Fuhrer, Dale Robertson, Tara Shraga, and John Williams 

greatly improved the first draft of the manuscript.

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Williams and Associates, Ltd., report no. 1507 prepared for 

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C.A., Oberg, K.A., and Vermeyen, T.B., eds., Proceedings 

of the Hydraulic Measurements and Experimental Methods 

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oxygen concentrations in Upper Klamath Lake—Model 

development and application: Redmond, Wash., 

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lake level on the biology and habitat of selected fish species 

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role of poor water quality and fish kills in the decline of 

endangered Lost River and shortnose suckers in Upper 

Klamath Lake: Klamath Falls, Oreg., U.S. Geological 

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48  Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
Appendix A. Quality-Assurance Data for Water Samples

Table A1. Blank sample results for the water-quality sample collection program.

[Abbreviations: mg/L, milligram per liter; NA, not applicable]

Analyte

Number of samples Percentage 

of blank 

samples

Minimum

reporting

level 

(mg/L)

Number of blank 

samples 

greater or

less than 

minimum 

reporting level

Value of blank samples 

greater than minimum 

reporting level (mg/L)

Blank Total Maximum Median

2002

Orthophosphate-P 18 218 8 0.01 10 0.03 0.02

Ammonia-N 18 218 8 .02 18 NA NA

Nitrate/nitrite-N 18 218 8 .03 18 NA NA

Total phosphorus 19 114 17 .004 18 .007 NA

Chlorophyll a 1 101 1 NA NA 2.4 NA

2003

Orthophosphate-P 24 130 18 0.007 20 NA NA

Ammonia-N 24 130 18 .015 9 0.202 0.032

Nitrate/nitrite-N 24 130 18 .022 17 .038 .032

Total phosphorus 16 81 2 .004 11 .005 NA

Chlorophyll a 2 62 3 NA NA 0 NA

2004

Orthophosphate-P 21 191 11 0.006 0 NA NA

Ammonia-N 29 199 15 .01 7 0.188 0.034

Nitrate/nitrite-N 21 191 11 .016 17 .037 .022

Total phosphorus 22 133 17 .004 17 NA NA

Chlorophyll a 0 106 0 NA NA NA NA

Appendix A. Quality-Assurance Data for Water Samples 49
Table A2. Split sample results for the water-quality sample collection program, 

2002–04.

[Abbreviations: mg/L, milligram per liter]

Analyte

Number of samples Percentage 

of split 

samples

Difference between split 

samples

Split Total Median

(mg/L)

Median

(percent)

2002

Orthophosphate-P 19 218 9 0.01 7.4

Ammonia-N 19 218 9 .02 22.2

Nitrate/nitrite-N 19 218 9 0 0

Total phosphorus 8 114 7 .014 5.2

Chlorophyll a 14 101 14 1.6 3.4

2003

Orthophosphate-P 11 130 8 0.004 10

Ammonia-N 11 130 8 .02 16.9

Nitrate/nitrite-N 11 130 8 0 0

Total phosphorus 7 81 9 .011 7.7

Chlorophyll a 5 62 8 5 6.6

2004

Orthophosphate-P 17 191 9 0.001 6.2

Ammonia-N 17 199 9 .002 2.9

Nitrate/nitrite-N 17 191 9 .004 10.5

Total phosphorus 7 133 5 .006 4.6

Chlorophyll a 7 106 7 11 10.3

50 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
Table A3. Replicate sample results for the water-quality sample collection program, 

2002–04.

[Abbreviations: mg/L, milligram per liter]

Analyte

Number of samples Percentage 

of replicate

samples

Difference between 

replicate samples

Replicate Total Median

(mg/L)

Median

(percent)

2002

Orthophosphate-P 12 218 6 0.009 10.5

Ammonia-N 12 218 6 .011 3.8

Nitrate/nitrite-N 12 218 6 0 0

Total phosphorus 6 114 5 .004 2.7

Chlorophyll a 6 101 6 4.5 4.3

2003

Orthophosphate-P 8 130 6 0.014 34.2

Ammonia-N 8 130 6 .046 19.4

Nitrate/nitrite-N 8 130 6 .005 7.2

Total phosphorus 5 81 6 .014 5.6

Chlorophyll a 4 62 6 4.5 11.2

2004

Orthophosphate-P 15 191 8 0.001 13.3

Ammonia-N 15 199 8 .016 38.6

Nitrate/nitrite-N 15 191 8 .004 12.2

Total phosphorus 10 133 8 .01 9.8

Chlorophyll a 10 106 9 11 10.5

Table A4. Spiked sample results for the water-quality sample 

collection program, 2002–04.

[Abbreviations: NA, not applicable (no analysis)]

Analyte

Average percentage recovery 

of spiked samples

2002 2003 2004

Orthophosphate-P 112 106 92

Ammonia-N 114 94 98

Nitrate/nitrite-N 100 90 97

Total phosphorus NA 100 104

Appendix A. Quality-Assurance Data for Water Samples  51
or003UK_01_figA1

1410

Median of the difference between 

splits or replicates

Minimum, maximum, and median 

values of environmental samples

EXPLANATION

0.6

0

0.05

0.10

0.15

0.20

0.6

0.8

1.0

0

0.2

0.4

0.04

0.08

0.12

0.16

0

0.2

0.4

CHLOROPHYLL a,

IN MICROGRAMS PER LITER

NITRATE + NITRITE,

IN MILLIGRAMS PER LITER

AMMONIA,

IN MILLIGRAMS PER LITER

TOTAL PHOSPHORUS,

IN MILLIGRAMS PER LITER

ORTHOPHOSPHORUS,

IN MILLIGRAMS PER LITER

0

200

400

600

800

0

Min, max,

Min and

and median

median

SPLIT SAMPLES REPLICATE SAMPLES

2002 2003 2004 2002 2003 2004

Figure A1. Median of the difference between replicate and split 

samples, compared to the distribution of the environmental samples.

52 Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04
Manuscript approved for publication, August 15, 2006

Prepared by the USGS Publishing Network, 

Publishing Service Center, Tacoma, Washington

Donita Parker

Linda Rogers

Sharon Wahlstrom

Bobbie Jo Richey

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

Director, Oregon Water Science Center

U.S. Geological Survey

10615 SE Cherry Blossom Drive 

Portland, Oregon 97216

http://or.water.usgs.gov
SIR 2006–5209 Wood and others

Printed on recycled paper

Water-Quality Conditions in Upper Klamath Lake, Oregon, 2002-04