Water Quality Conditions in Upper Klamath and Agency Lakes, 

Oregon, 2005 

Scientific Investigations Report 2008–5026

Prepared in cooperation with the Bureau of Reclamation 

U.S. Department of the Interior

U.S. Geological Survey
Cover: Photograph of algae bloom on surface of Upper Klamath Lake with Mt. McLoughlin in 

background. (Photograph taken by Dean Snyder, U.S. Geological Survey, Klamath Falls, Oregon, 

October 27, 2007.)
Water Quality Conditions in Upper Klamath and 

Agency Lakes, Oregon, 2005

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

Prepared in cooperation with the Bureau of Reclamation

Scientific Investigations Report 2008–5026

U.S. Department of the Interior

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

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2008

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Suggested citation:

Hoilman, G.R., Lindenberg, M.K., and Wood, T.M., 2008, Water quality conditions in Upper Klamath and Agency Lakes, 

Oregon, 2005: U.S. Geological Survey Scientific Investigations Report 2008–5026, 44 p.
iii

Contents

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

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

Purpose and Scope ..............................................................................................................................4

Description of Study Area ...................................................................................................................4

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

Continuous Water Quality Monitors ..................................................................................................4

Water Sample Collection.....................................................................................................................6

Dissolved Oxygen Production and Consumption Experiments .....................................................6

Meteorological Sites............................................................................................................................8

Data Processing..................................................................................................................................10

Meteorological Conditions.........................................................................................................................10

Nutrients and Chlorophyll a .......................................................................................................................14

Bloom Dynamics of Aphanizomenon flos-aquae .........................................................................14

Spatial Variability in Nutrient and Chlorophyll a Concentrations ...............................................22

Dissolved Oxygen Production and Consumption Experiments ............................................................23

Dissolved Oxygen Production and Consumption ..........................................................................23

Depth of Photic Zone..........................................................................................................................25

Water Quality Conditions............................................................................................................................26

Daily Median Water Quality Conditions ..........................................................................................26

Spatial Variability in Dissolved Oxygen Concentrations ..............................................................29

Variability on Monthly to Seasonal Time Scales ..................................................................29

Variability on Short Time Scales..............................................................................................32

Stratification and Wind Speed ........................................................................................................32

Timing of Daily Extremes in Water Quality Conditions..................................................................34

Occurrence and Duration of Water Quality Conditions Potentially Harmful to Fish.........................36

Dissolved Oxygen Concentration, pH, and Temperature .............................................................36

Ammonia...............................................................................................................................................37

Summary and Conclusions.........................................................................................................................39

Acknowledgments.......................................................................................................................................40

References Cited .........................................................................................................................................40

Appendix A. Quality Control and Quality Assurance of Water Samples.........................................43
iv

Figures

Figure 1. Photograph showing algal bloom Aphanizomenon flos-aquae, disturbed by

the wake of the boat, Upper Klamath Lake, Oregon, 2005 .............................. 2

Figure 2. Map showing location of meteorological sites, continuous water quality

monitoring sites, and water quality sampling sites, Upper Klamath and

Agency Lakes, Oregon, 2005 ............................................................... 3

Figure 3. Schematic diagram of a typical mooring used for placement of continuous

water quality monitors in Upper Klamath and Agency Lakes, Oregon ............... 6

Figure 4. Schematic diagram of apparatus for dissolved oxygen production and

consumption experiments in Upper Klamath Lake, Oregon, 2005 ..................... 7

Figure 5. Schematic diagram showing configuration of land-based meteorological

measurement sites around Upper Klamath Lake, Oregon, 2005 ..................... 9

Figure 6. Graphs showing lakewide daily median wind speed, air temperature, relative

humidity, and daytime solar radiation for meteorological sites in and around

Upper Klamath Lake, Oregon, 2005 ...................................................... 11

Figure 7. Map showing water-current velocity predicted by the hydrodynamic model of

Upper Klamath Lake, Oregon, under prevailing wind conditions ..................... 12

Figure 8. Histograms showing wind speed and direction for all meteorological sites in

the vicinity of Upper Klamath Lake, Oregon, 2005 ....................................... 13

Figure 9. Graphs showing weekly measurements of chlorophyll a and dissolved

nutrient concentration in relation to the duration of a dissolved oxygen

concentration of less than 4 milligrams per liter at water samples collected

from site MDN, Upper Klamath Lake, Oregon, 2002–05 ................................. 15

Figure 10. Graphs showing concentrations of chlorophyll a, total phosphorus,

orthophosphate, ammonia, and nitrite-plus-nitrate in water samples collected

from Upper Klamath Lake, Oregon, 2005 ................................................ 16

Figure 11. Graph showing weekly qualitative observations of algal bloom conditions in

Agency Lake, Oregon, 2005 ............................................................... 18

Figure 12. Graph showing relation of chlorophyll a to total phosphorus concentration in

water samples collected from Upper Klamath Lake, Oregon, 2005 .................. 19

Figure 13. Time-series graph showing ratio of chlorophyll a to total phosphorus and

ratio of ammonia and nitrite-plus-nitrate (bioavailable nitrogen) to

orthophosphate (bioavailable phosphorus) concentrations in water samples

collected from Upper Klamath Lake, Oregon, May–October 2005..................... 20

Figure 14. Graphs showing relation of ammonia and orthophosphate concentrations to

chlorophyll a concentrations in water samples collected from Upper Klamath

Lake, Oregon, 2005........................................................................... 21

Figure 15. Graphs showing statistical distribution of ammonia, orthophosphate, total

phosphorus, and chlorophyll a concentrations measured in water samples

collected from Upper Klamath Lake, Oregon, 2005 .................................... 22

Figure 16. Graphs showing rate of change in dissolved oxygen concentration measured

from dissolved oxygen production and consumption experiments at sites in

Upper Klamath Lake, Oregon, 2005 ...................................................... 24
v

Figure 17. Graphs showing relation of the natural logarithm of chlorophyll a concentration

to dissolved oxygen production in the upper and lower incubation racks during

dissolved oxygen production and consumption experiments in Upper Klamath

Lake, Oregon, 2005........................................................................... 25

Figure 18. Graph showing relation of the natural logarithm of chlorophyll a concentration

to the average depth of the photic zone for all dissolved oxygen production and

consumption experiments in Upper Klamath Lake, Oregon, 2005 ..................... 25

Figure 19. Time-series graphs showing daily median temperature, dissolved oxygen

concentration, dissolved oxygen percent saturation, pH, and specific

conductance recorded by continuous monitors in Agency Lake, Oregon, 2005 ... 27

Figure 20. Time-series graphs showing lakewide daily median dissolved oxygen

concentration, dissolved oxygen percent saturation, temperature, pH, and

specific conductance recorded by continuous monitors in Upper Klamath Lake,

Oregon, 2005 ................................................................................. 28

Figure 21. Time-series graphs showing daily dissolved oxygen percent saturation at water

quality monitoring sites in Upper Klamath Lake, Oregon, 2005 ........................ 30

Figure 22. Time-series graphs showing representative hourly vertical variability in pH,

dissolved oxygen, and temperature at sites MDN, MDT, and EPT, and hourly

median wind speed at site MDN, Upper Klamath Lake, Oregon, 2005 ............... 33

Figure 23. Graphs showing daily extreme of dissolved oxygen concentration, pH, and water

temperature from a representative shallow (HDB), middepth (BLB), and deep site

(EPT) in Upper Klamath Lake, Oregon, 2005 ............................................. 35

Figure 24. Graphs showing lakewide measures of conditions potentially harmful to fish in

Upper Klamath Lake, Oregon, 2005: dissolved oxygen concentration less than 

4 milligrams per liter, and pH greater than 9.7 .......................................... 37

Figure 25. Graphs showing (A) chlorophyll a concentration, (B) total ammonia

concentration, (C) un-ionized ammonia concentration, and (D) pH in water

samples collected at all sites, Upper Klamath Lake, Oregon, 2005 .................. 38

Tables

Table 1. Description of continuous water quality monitoring sites used for the 2005

data-collection program, Upper Klamath and Agency Lakes, Oregon ............... 5

Table 2. Depth of incubator racks at each site during dissolved oxygen production and

consumption experiments in Upper Klamath Lake, Oregon, 2005 ..................... 8

Table 3. Description of meteorological sites and parameters measured at each site, 

Upper Klamath Lake, Oregon, 2005 ...................................................... 9

Table 4. Maximum and minimum chlorophyll a concentrations and dates relative to

Aphanizomenon flos-aquae blooms and decline during sampling season, 

Upper Klamath Lake, Oregon, June–October 2005 .................................... 17

Figures—Continued
vi

Conversion Factors, Datums, and Abbreviations

Conversion Factors

Multiply By To obtain

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

square kilometer (km2

) 0.3861 square mile (mi2)

milliliter (mL) 0.03382 fluid ounce (oz)

liter (L) 1.057 quart (qt)

meter per second (m/s) 3.281 foot per second (ft/s) 

milligram per liter per hour [(mg/L)/hr] 1.0 part per million per hour (ppm/hr)

micrometer (μm) 3.937 x 10–5 inch (in.)

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

°F=(1.8×°C)+32.

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

or micrograms per liter (μg/L). One thousand micrograms per liter is equivalent to 1 mg/L. 

Micrograms per liter is equivalent to “parts per billion.”

Datums

Vertical coordinate information is referenced to the Bureau of Reclamation datum, which is 

1.78 feet above National Geodetic Vertical Datum of 1929 (NGVD 29). Horizontal coordinate 

information is referenced to the North American Datum of 1927 (NAD 27).

Abbreviations

Abbreviations Definition

ADAPS

ADCP

AFA

BOD

LDOE

NWIS

NWQL

USGS

Automated Data Processing System

acoustic Doppler current profiler

Aphanizomenon flos-aquae

biological oxygen demand

low dissolved-oxygen event

National Water Information System

National Water Quality Laboratory

U.S. Geological Survey
Abstract

During June–October 2005, water quality data were 

collected from Upper Klamath and Agency Lakes in Oregon, 

and meteorological data were collected around and within 

Upper Klamath Lake. Data recorded at two continuous water 

quality monitors in Agency Lake showed similar temperature 

patterns throughout the field season, but data recorded at the 

northern site showed more day-to-day variability for dissolved 

oxygen concentration and saturation after late June and more 

day-to-day variability for pH and specific conductance values 

after mid-July. Data recorded from the northern and southern 

parts of Agency Lake showed more comparable day-to-day 

variability in dissolved oxygen concentrations and pH from 

September through the end of the monitoring period. 

For Upper Klamath Lake, seasonal (late July through 

early August) lows of dissolved oxygen concentrations 

and saturation were coincident with a seasonal low of pH 

values and seasonal highs of ammonia and orthophosphate 

concentrations, specific conductance values, and water 

temperatures. Patterns in these parameters, excluding water 

temperature, were associated with bloom dynamics of the 

cyanobacterium (blue-green alga) Aphanizomenon flos-aquae

in Upper Klamath Lake. In Upper Klamath Lake, water 

temperature in excess of 28 degrees Celsius (a high stress 

threshold for Upper Klamath Lake suckers) was recorded only 

once at one site during the field season. Large areas of Upper 

Klamath Lake had periods of dissolved oxygen concentration 

of less than 4 milligrams per liter and pH value greater than 

9.7, but these conditions were not persistent throughout days 

at most sites. Dissolved oxygen concentrations in Upper 

Klamath Lake on time scales of days and months appeared to 

be influenced, in part, by bathymetry and prevailing current 

flow patterns. Diel patterns of water column stratification 

were evident, even at the deepest sites. This diel pattern of 

stratification was attributable to diel wind speed patterns and 

the shallow nature of most of Upper Klamath Lake. Timing of 

the daily extreme values of dissolved oxygen concentration, 

pH, and water temperature was less distinct with increased 

water column depth. 

Chlorophyll a concentrations varied spatially and 

temporally throughout Upper Klamath Lake. Location greatly 

affected algal concentrations, in turn affecting nutrient and 

dissolved oxygen concentrations—some of the highest 

chlorophyll a concentrations were associated with the lowest 

dissolved oxygen concentrations and the highest un-ionized 

ammonia concentrations. The occurrence of the low dissolved 

oxygen and high un-ionized ammonia concentrations 

coincided with a decline in algae resulting from cell death, as 

measured by concentrations of chlorophyll a. 

Dissolved oxygen production rates in experiments were 

as high as 1.47 milligrams of oxygen per liter per hour, and 

consumption rates were as much as –0.73 milligrams of 

oxygen per liter per hour. Dissolved oxygen consumption 

rates measured in this study were comparable to those 

measured in a 2002 Upper Klamath Lake study, and a higher 

rate of dissolved oxygen consumption was recorded in dark 

bottles positioned higher in the water column. Data, though 

inconclusive, indicated that a decreasing trend of dissolved 

oxygen productivity through July could have contributed to 

the decreasing dissolved oxygen concentrations and percent 

saturation recorded in Upper Klamath Lake during this time. 

Phytoplankton self-shading was evident from a general inverse 

relation between depth of photic zone and chlorophyll a

concentrations. This shading caused net dissolved oxygen 

consumption during daylight hours in lower parts of the water 

column that would otherwise have been in the photic zone. 

Meteorological data collected in and around Upper 

Klamath Lake showed that winds were likely to come from 

a broad range of westerly directions in the northern onethird of the lake, but tended to come from a narrow range of 

northwesterly directions over the main body of the lake farther 

south.

Water Quality Conditions in Upper Klamath and 

Agency Lakes, Oregon, 2005

By Gene R. Hoilman, Mary K. Lindenberg, and Tamara M. Wood
2 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

Introduction

Water quality degradation in Upper Klamath Lake has 

led to critical fishery concerns for the region, including the 

listing of Lost River and shortnose suckers as endangered 

in 1988. The algal community of the lake has shifted to a 

near monoculture of the cyanobacterium (blue-green algae) 

Aphanizomenon flos-aquae (AFA) during summer (Kann, 

1997; Perkins and others, 2000), massive blooms of which 

have been directly related to episodes of poor water quality in 

Upper Klamath Lake (fig. 1). The growth and decomposition 

of AFA blooms in the lake frequently cause extreme water 

quality conditions characterized by high pH values (9–10), 

widely variable dissolved oxygen conditions (anoxic to 

supersaturated), and high un-ionized ammonia concentrations 

(greater than 0.5 mg/L). Large blooms of AFA and the 

associated water quality concerns also occur in Agency Lake.

Before the U.S. Geological Survey (USGS) began 

monitoring water quality in Upper Klamath Lake in 2002 

in cooperation with the Bureau of Reclamation, continuous 

datasets of temperature, pH, dissolved oxygen, or specific 

conductance spanning spring through fall did not exist. The 

Klamath Tribes have collected biweekly water samples for 

nutrients and chlorophyll a at 10 sites in Upper Klamath and 

Agency Lakes since 1990. Several studies have used this 

dataset, which is the longest consistent record of water quality 

available for Upper Klamath Lake (Wood and others, 1996; 

Kann and Smith, 1999; Kann and Walker, 2001; Kann and 

Welch, 2005; Wood and others, 2006; Morace, 2007). 

During 2002–04, the USGS water quality monitoring 

program study area was limited mostly to the northern onethird of Upper Klamath Lake, where the monitoring supported 

a telemetry tracking study of endangered adult suckers 

(Wood and others, 2006). Data collected during the 3 years 

of monitoring showed that the occurrence and severity of 

poor water quality conditions in Upper Klamath Lake were 

unpredictable from year to year. During each year, however, 

seasonal patterns of low dissolved oxygen concentration and 

high pH coincided with blooms of AFA that occur in the lake. 

A diel pattern of water column stratification was observed 

in the lake, but the data did not indicate a strong association 

between water column stratification and an event of extreme 

low dissolved oxygen concentration and a consequent fish dieoff in 2003.

Water circulation in Upper Klamath Lake is determined 

by wind speed and direction and the bathymetry of the lake. 

The lake is mostly shallow (less than 3.5-m depth), with 

the exception of a narrow trench (greater than 10-m depth) 

that extends along the western shoreline (fig. 2). Prevailing 

winds over Upper Klamath Lake are westerly (between 

about 250 and 315 degrees) over the northern part of the lake 

and then are constrained by the surrounding topography to 

northwesterly (between about 315 and 360 degrees) over the 

southern part of the lake. Velocity measurements of currents 

made with acoustic Doppler current profilers (ADCPs, Wood 

and others, 2006) and hydrodynamic modeling with the 

three-dimensional UnTRIM model (Cheng and others, 2005) 

have confirmed that circulation is clockwise around the lake 

during periods of prevailing winds, consisting of a broad and 

shallow southward flow through most of the lake and a narrow, 

deep, northward flow through the trench along the western 

shoreline. The direction of the current in the trench is tightly 

constrained by the bathymetry to flow to the northwest at 

about 320 degrees when forced by prevailing winds. Some of 

the water exiting the trench just west of Bare Island continues 

clockwise around the island, and the rest turns west around 

Eagle Point, generating a clockwise circulation within the 

northern one-third of the lake. This understanding of the winddriven currents indicates that poor water quality conditions 

(particularly low dissolved oxygen concentrations) that are 

observed in the northern part of the lake do not originate 

locally. Instead, these conditions originate farther south in the 

lake and are transported to the north along this circulation path 

through the trench and west of Bare Island (Wood and others, 

2006).

OR19_0158_UKL_fig_1

Figure 1. Algal bloom Aphanizomenon flos-aquae, disturbed 

by the wake of the boat, Upper Klamath Lake, Oregon, 2005. 

(Photograph taken by Mary Lindenberg, U.S. Geological 

Survey, September 26, 2006.)
Introduction 3

Figure 2. Location of meteorological sites, continuous water quality monitoring sites, and water quality sampling sites, Upper 

Klamath and Agency Lakes, Oregon, 2005.

OR19_0158_UKL_fig_2

Link

River

Pelican

Bay

Wood

River

Sprague

River

Hank's 

Marsh

Upper

Klamath

Lake

Aspen

Lake

Howard

Bay

Ball

Bay

Shoalwater

Bay

Wocus

Marsh

Caledonia

Marsh

Agency

Lake

Williamson

River

Moss

Creek

BLB

NBI

HDB

AGN

SHB

AGS

MDL

EHB

RPT

MPT

EPT - U

EPT - L

FBS

WMR

MDT - U

MDT - L

MDN - U

MDN - L

WMR Met

BLB Met

HDB Met

SSHR Met

Rattlesnake

Point.

Hagelstein

County Park

Modoc Rim

Agency

Straits

Ball

Point

97

97

ALT

97

97

Buck

Island

Bare

Island

140

140 39

62

Klamath 

Falls

Plum Valley

Eagle

Ridge

Modoc

Point

Link

River 

Dam

Sources: 

Bathymetry: Produced by Glen Canyon Environmental Studies 

in cooperation with U.S. Bureau of Reclamation, Mid-Pacific 

Region, Klamath Basin Area Office, and the Klamath Tribes.

Digital Raster Graphics and Elevation: Produced by U.S. 

Geological Survey, various scales.

Projection: UTM, Zone 10

Meteorological Sites

Water Quality Sampling Sites

0

14.6

Depth, in meters

EXPLANATION

Continuous Water Quality 

Monitoring Sites

MDL

FBS

BLB Met

122°05' 122°0' 121°55' 121°50' 121°45'

42°

35'

42°

30'

42°

25'

42°

20'

42°

15'

OREGON

Study

Area

0 1 2 3 4 5 MILES

0 1 2 3 4 5 KILOMETERS
4 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

In 2005, the existing water quality monitoring program 

expanded to become lakewide in Upper Klamath Lake and 

to include Agency Lake. These changes created a program 

better suited to establishing long-term status and trends of 

water quality dynamics and monitoring the suitability of water 

quality for protection of endangered species of fish living 

within the lakes.

Meteorological sites were established at four locations 

on land around the lake in addition to the two floating 

meteorological sites used in previous years, providing greater 

resolution of wind speed, wind direction, air temperature, and 

relative humidity. Additionally, collection of solar-radiation 

data at SSHR began in 2005. The additional wind data were 

used to improve the hydrodynamic model describing water 

movement in Upper Klamath Lake. The air temperature, 

relative humidity, and solar-radiation data were used to 

calculate heat transfer at the water surface in a heat transport 

model of Upper Klamath Lake (T.M. Wood, U.S. Geological 

Survey, unpub. data, 2006; Wood and Cheng, 2006). 

Purpose and Scope

This report presents the results of water quality 

monitoring in Upper Klamath and Agency Lakes during 2005. 

Meteorological data, including wind speed and direction, 

air temperature, relative humidity, and solar radiation, are 

presented and used to describe wind patterns and their 

influence on circulation in Upper Klamath Lake. Dissolved 

nutrient concentrations are correlated with chlorophyll a

concentrations, which serve as a surrogate for algal biomass. 

Results of dissolved oxygen production and consumption 

experiments are described. Dissolved oxygen concentration 

and saturation, water temperature, pH, and specific 

conductance values of water samples collected from the lakes 

are presented and used to determine water quality conditions 

potentially harmful to fish.

Description of Study Area

Upper Klamath Lake (fig. 2) is located in southern 

Oregon. It is a large, shallow lake with a surface area of 232 

km2 and an average depth of 2.8 m. Most of the lake (about 

90 percent) is shallower than 4 m, except for a narrow trench 

running parallel to Eagle Ridge on the western shore of the 

lake. 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 volcanically derived soils. 

The largest single contributor of inflow to the lake is the 

Williamson River, which contributes, on average, nearly onehalf of the lake’s incoming water and enters the lake near its 

northern end. Upper Klamath Lake historically was eutrophic, 

but over the past several decades has experienced nuisance 

blooms of AFA during the summer and fall and can now be 

characterized as hypereutrophic (Eilers and others, 2004). 

Upper Klamath Lake is a natural water body, but lake-surface 

elevations have been regulated since 1921, when the Link 

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

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

Reclamation. The lake is now the principal water source for 

the Klamath Project, an irrigation system developed to supply 

water to farms and ranches in and around the Klamath basin 

(Bureau of Reclamation, 2000).

Agency Lake, just north of Upper Klamath Lake and 

connected to it by a natural, narrow channel, adds about 

38 km2 of surface area to the Upper Klamath Lake-Agency 

Lake hydrologic entity (Johnson, 1985). Agency Lake also 

is shallow, with a maximum depth approaching 3 m and an 

average depth of 0.9 m. Like Upper Klamath Lake, Agency 

Lake is hypereutrophic and experiences annual blooms of 

AFA. Because the channel connecting Upper Klamath Lake 

and Agency Lake is narrow compared to the two water bodies 

and the amount of flow through it is small, the two lakes are 

largely independent in terms of the seasonal cyanobacterial 

bloom and water quality dynamics. 

Methods

Continuous Water Quality Monitors

YSI model 600XLM, 6920, or 6600 continuous 

multiparameter water quality monitors (sondes) were placed 

at 13 sites in Upper Klamath Lake and 2 sites in Agency Lake 

(fig. 2; table 1). At all these locations, sondes were placed 

vertically at a fixed depth of 1 m from the lake bottom. If 

the depth at a site was less than 2 m, the sonde was placed 

horizontally at the midpoint of the water column. A typical 

sonde mooring is shown in figure 3. The placement depth of 1 

m from the bottom was chosen to provide data relevant to the 

endangered suckers of Upper Klamath Lake, which are bottom 

feeding fish. To observe water quality conditions near the 

water surface and provide comparisons to conditions near the 

lake bottom, a second sonde was placed on the same mooring 

at a fixed depth 1 m from the surface at three of the deepest 

locations, MDT, EPT, and MDN (fig. 2). All sondes recorded 

dissolved oxygen concentration, pH, specific conductance, and 

temperature at the beginning of every hour.
Methods 5

Sondes were cleaned and field measurements of site 

depth were made during weekly site visits to ensure proper 

placement of the instrument in the water column. Separate 

field measurements of dissolved oxygen concentration, 

pH, specific conductance, and temperature at the depth 

of each sonde were made as an additional check of sonde 

performance. During cleanings, measurements were made to 

compensate for the effect of biological fouling. Deployments 

generally lasted 3 weeks; at the end of this time the sonde 

at the site was replaced with a freshly calibrated instrument. 

Calibration of the sonde was checked for each parameter in the 

laboratory after retrieval to account for the effect of calibration 

Table 1. Description of continuous water quality monitoring sites used for the 2005 data-collection program, 

Upper Klamath and Agency Lakes, Oregon.

[Sites are shown in order of decreasing depth.]

Site name Site name 

abbreviation

USGS site 

identification No. Latitude (north) Longitude (west)

Full-pool 

measured 

depth (meters)

Middle of trench (lower)

Middle of trench (upper)

Eagle Point (lower)

Eagle Point (upper)

Entrance to Howard Bay

Midlake

Midnorth (lower)

Midnorth (upper)

Modoc Point

Ball Bay

Rattlesnake Point

Shoalwater Bay

Agency North

Fish Banks

North Buck Island

Upper Klamath Lake at 

Williamson River outlet

Agency South

Howard Bay

MDT-L

MDT-U

EPT-L

EPT-U

EHB

MDL

MDN-L

MDN-U

MPT

BLB

RPT

SHB

AGN

FBS

NBI

WMR

AGS

HDB

422305121553800

422305121553803

422559121574400

422559121574403

421935121530600

422312121515900

422622122004000

422622122004003

422523121525100

422431122010100

422042121513100

422444121580400

423335121564300

422808122024400

421838121513900

422719121571400

423124121583400

421933121550000

42° 23' 5.09''

42° 23' 5.09''

42° 25' 59.2''

42° 25' 59.2''

42° 19' 35.4''

42° 23' 12''

42° 26' 21.5''

42° 26' 21.5''

42° 25' 23.2''

42° 24' 31''

42° 20' 41.6''

42° 24' 26.1''

42° 33' 35''

42° 28' 8.8''

42° 18' 38''

42° 27' 19.4''

42° 31' 24.9''

42° 19' 33''

121° 55' 38.2''

121° 55' 38.2''

121° 57' 44.1''

121° 57' 44.1''

121° 53' 5.9''

121° 51' 59.1''

122° 0' 40.0''

122° 0' 40.0''

121° 52' 50.8''

122° 1' 1''

121° 51' 31.4''

121° 57' 47.1''

121° 56' 43''

122° 2' 43.5''

121° 51' 39''

121° 57' 13.6''

121° 59' 3.4''

121° 55' 0''

15.00

15.00

12.50

12.50

5.20

4.50

4.20

4.20

3.70

3.50

3.40

3.30

3.00

2.80

2.80

2.50

2.50

2.50

drift. Data internally logged during deployment in the field 

were downloaded from retrieved sondes in the laboratory. 

These raw data were then loaded into the USGS Automated 

Data Processing System (ADAPS). Quality of the data was 

assured by the field information collected at weekly site visits 

and by processing the time series according to the procedures 

in Wagner and others (2000). Data corrections resulting from 

biological fouling and calibration drift were entered into 

ADAPS, which calculated the corrected values. 
6 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

Water Sample Collection

Of the 15 continuous water quality monitoring sites, 

6 sites, MDN, WMR, EPT, MDT, HDB, and MDL (fig. 2), 

were selected for nutrient and chlorophyll a analyses. Water 

samples were collected on a weekly basis according to 

established protocols (U.S. Geological Survey, variously 

dated). Samples were analyzed for chlorophyll a, total 

phosphorus, total ammonia (ammonia plus ammonium), 

orthophosphate, and nitrite-plus-nitrate concentrations. To 

protect samples from contamination during the collection 

process, quality control protocols were followed as described 

Figure 3. Schematic diagram of a typical mooring used for 

placement of continuous water quality monitors in Upper 

Klamath and Agency Lakes, Oregon.

OR19_0158_UKL_fig_3

Chain

Tension Buoy (maintains position

of sonde at 1 meter from bottom)

Ring (to help haul sonde into boat)

Brass Lock

Sonde

1 meter

Weight Bucket

NOT TO SCALE

Lake Sediment

Buoy

in the National Field Manual for the Collection of WaterQuality Data (U.S. Geological Survey, variously dated). Two 

sampling methods were used relative to the type of constituent 

measured. Water samples analyzed for dissolved nutrients, 

including total ammonia, orthophosphate and nitrite-plusnitrate, were collected from either one or two points in the 

water column, depending on the depth at the site. At the deep 

sites MDT and EPT, dissolved nutrient samples were collected 

from two points in the water column—one-quarter and threequarters of the total water column depth—to investigate the 

difference between the upper and lower sections of the water 

column. At the shallow sites MDN, WMR, HDB, and MDL, 

dissolved nutrient samples were collected from middepth of 

the water column. Dissolved nutrient samples were collected 

by pumping through a hose (lowered to the appropriate 

depth in the water column) connected to a 0.45-μm capsule 

filter. Whole (unfiltered) water samples analyzed for total 

phosphorus and chlorophyll a constituted an equal integration 

over the depth of the water column. To collect depth-integrated 

samples, a weighted cage holding two 1-L bottles was 

lowered at a constant rate into the water to 0.5 m from the 

bottom at sites less than 10.5 m depth and to 10 m from the 

surface at sites greater than 10.5 m depth. Each bottle had two 

small ports, one for water to flow in and one for the escape 

of displaced air. The contents of the bottles from multiple 

collections of the cage sampler were combined in a churn 

splitter from which samples were collected for determination 

of total phosphorus and chlorophyll a concentration. Samples 

to be analyzed for total phosphorus were preserved with 1 mL 

of 4.5N (4.5 normal) H2S04, and chlorophyll a samples were 

fixed with MgCO3. Samples to be analyzed for dissolved 

nutrients and total phosphorus were chilled onsite and sent to 

the National Water Quality Laboratory (NWQL) in Denver, 

Colorado, for analysis. Finalized data were stored in the 

USGS National Water Information Systems (NWIS) database. 

Samples to be analyzed for chlorophyll a concentration were 

chilled onsite and sent to Aquatic Analysts in White Salmon, 

Washington. Results of the 2005 quality assurance program 

are discussed in the appendix.

Dissolved Oxygen Production and 

Consumption Experiments

Experiments were conducted to provide measurements 

of dissolved oxygen production and consumption rates in 

Upper Klamath Lake (fig. 4). Biological oxygen demand 

(BOD) bottles, with a volume of 300 mL and made of type 

1 borosilicate glass, were filled with lake water integrated 
Methods 7

OR19_0158_UKL_fig_4

Buoy

Clear

Biological Oxygen

Demand Bottles

Opaque

Biological Oxygen

Demand Bottle

Upper Incubator Rack

Lower Incubator Rack

Eyebolt

Rope

5 Pound

Weight

NOT TO SCALE

Figure 4. Schematic diagram of apparatus for dissolved oxygen 

production and consumption experiments in Upper Klamath Lake, 

Oregon, 2005.

over the entire water column. BOD bottles were filled 

from the churn splitter with the same collection of lake 

water as chlorophyll a samples. This procedure allowed the 

chlorophyll a data to be used in the analysis of data from the 

dissolved oxygen production and consumption experiments. 

After filling, initial dissolved oxygen concentration and 

temperature were measured in the bottles with a YSI model 

52 dissolved oxygen meter. Three bottles were attached to rest 

horizontally on racks at each of two depths. One bottle out 

of each group of three was dark (made so by wrapping it and 

its stopper with black electrical tape). Once attached to the 

incubator rack, the bottles were lowered into the water. 

The experiment apparatus was moored at the site for at 

least 1 hour and typically retrieved before 3 hours. Dissolved 

oxygen concentration and temperature were again measured 

in each bottle, and incubation time was noted. The change 

in dissolved oxygen concentration was calculated in each 

bottle, and the incubation time was used to express the rate of 

dissolved oxygen change in milligrams of oxygen per liter per 

hour. Most experiments were conducted between the hours of 

10:00 a.m. and 3:00 p.m. Logistical constraints did not allow 

for this experiment to be done at every water sample collection 

site during every week of sampling, but an attempt was made 

to collect the dissolved oxygen rate data at each of the six sites 

throughout the season, if not on a weekly basis (table 2). The 

upper rack generally was positioned 0.5 m below the water 

surface. Early in the season experimentation was done with 

the position of the lower rack before settling on 2 m depth 

to give sufficient contrast with the upper rack. As the season 

progressed, the lower rack was raised to 1.5 m, and toward 

the end of the season the lower rack was raised to 1 m at the 

shallow sites. Some sites became too shallow toward the 

end of the field season to incorporate the lower rack into the 

experiment. 

Light intensity was measured in a vertical profile from 

the water surface to a depth of 2.5 m (or the lake bottom) in 

0.5-m increments by using a LiCor LI-193SB underwater 

spherical quantum sensor. These measurements were used to 

estimate the depth of the photic zone, defined here as the point 

at which 99 percent of incident light is absorbed (or, 1 percent 

of incident light is transmitted), by using Beer’s law, which 

describes the penetration of solar radiation through the water 

column as an exponential relation (Welch, 1992):

I I e

z

I

z

z

z

= −

0

α

where

is depth, in meters,

is radiation at depth , in micromoles per second 

per square meter,

is surfac

z

Io e radiation, in micromoles per second per 

square meter, and

α is the extinction coefficient.

(1)

α was estimated for each set of measurements by fitting 

equation (1) to the vertical profile of the light meter readings. 

The depth of the photic zone zp was then calculated as:

 z p = − ln( . 0 01) / ( ) α (2)

Measurements were made at each site on each date at the 

beginning of the incubation period (“early” measurements) 

and immediately after the incubation period (“late” 

measurements). The early and late measurements were 

then combined to provide the average depth of photic zone 

throughout the duration of each experiment at each site.
8 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

Meteorological Sites

The location of meteorological measurement sites in the 

Upper Klamath Lake basin is shown in figure 2 and listed in 

table 3. Floating meteorological sites have been part of the 

Upper Klamath Lake monitoring program in previous years. 

Land-based meteorological sites were a new addition to the 

monitoring effort in 2005.

A schematic diagram of the typical land-based 

meteorological site is shown in figure 5. Wind speed and 

direction data were collected by an RM Young model 05103 

wind monitor. Air temperature and relative humidity data were 

collected by a Campbell Scientific CS500 or HMP35C relative 

Table 2. Depth of incubator racks at each site during dissolved oxygen production and consumption experiments in Upper Klamath 

Lake, Oregon, 2005.

[Description of sites are shown in table 1; location of sites shown in figure 2. Abbreviations: n/a, site became too shallow to incorporate the lower rack into the 

experiment. –, no data were collected]

Depth, in meters below water surface

Rack location

First day of sampling in week

June July August September October

14 21 28 6 12 19 26 2 9 15 22 29 6 19 26 3

Howard Bay (HDB)

Upper 0.5 – – – – – – – – 0.5 0.5 0.5 0.5 0.5 0.5 0.5

Lower 1 – – – – – – – – 1.5 1.5 1 1 n/a n/a n/a

Average photic zone 2.35 – – – – – – – – 0.62 1.42 1.07 1.04 1.08 1.60 2.17

Upper Klamath Lake at Williamson River Outlet (WMR)

Upper 0.3 – – 0.5 – – – – – 0.5 0.5 0.5 0.5 0.5 0.5 0.5

Lower 1 – – 2 – – – – – 1.5 1 1 1 n/a n/a n/a

Average photic zone 2.47 – – 2.84 – – – – – 2.01 1.89 1.09 1.55 2.29 2.80 1.8

Midlake (MDL)

Upper 0.5 0.5 0.5 0.5 – 0.5 – 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5

Lower 2 2 2 2 – 1.5 – 1.5 1.5 1.5 1.5 1.5 1 1 1.5

Average photic zone 2.12 1.87 1.78 2.06 – 3.92 – 2.61 2.71 1.06 2.40 1.87 1.15 1.70 1.88

Midnorth (MDN)

Upper 0.5 0.5 – – 0.5 – 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5

Lower 2 2 – – 2 – 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1 1.5

Average photic zone 1.83 1.69 – – 2.15 – 4.31 2.76 2.86 1.52 1.61 1.90 1.45 1.51 1.44

Eagle Point (EPT)

Upper – – – 0.5 – 0.5 – – 0.5 0.5 0.5 – 0.5 0.5 0.5

Lower – – – 2 – 1.5 – – 1.5 1.5 1.5 – 1.5 1 1.5

Average photic zone – – – 2.29 – 3.01 – – 1.90 1.86 1.76 – 1.99 1.52 1.72

Middle of trench (MDT)

Upper – – – – 0.5 – 0.5 – 0.5 0.5 0.5 – 0.5 0.5 0.5

Lower – – – – 2 – 1.5 – 1.5 1.5 1.5 – 1.5 1.5 1.5

Average photic zone – – – – 0.87 – 1.90 – 0.71 1.07 1.25 – 0.91 1.44 1.42

humidity and air temperature sensor. Additionally, solar 

radiation data were collected only at the WMR MET station 

by using a Li-Cor LI200SZ pyranometer. Floating sites were 

configured similarly to the land-based sites, although the mast 

attached to the buoy provided a height, measured from the 

surface of the water, of 2 m for wind monitors and 1.5 m for 

relative humidity and temperature sensors. Relative humidity 

and temperature data were not collected at the MDN MET, 

BLB MET, or SSHR MET sites during the 2005 field season. 

Data collected from all sensors at a site were stored every 

15 minutes by a Campbell Scientific CR510, CR10, or CR10X 

datalogger located at the station. Power was provided by a 

12-volt battery at the station charged by a solar power array. 
Methods 9

Table 3. Description of meteorological sites and parameters measured at each site, Upper Klamath Lake, Oregon, 2005.

[USGS site identification No.: Unique number for each site based on the latitude and longitude of the site. First six digits are the latitude; next eight digits are 

longitude; and final two digits are a sequence number to uniquely identify each site. Abbreviations: USGS, U.S. Geological Survey]

Meteorological site 

name

Site name 

abbreviation

USGS site 

identification No. Latitude (north) Longitude (west) Parameters measured

Ball Bay BLB MET 422341122003800 42° 23' 40.9'' 122° 0' 38.4'' Wind speed/direction

Howard Bay HDB MET 421846121542800 42° 18' 46.2'' 121° 54' 28'' Wind speed/direction, air temperature, 

relative humidity

Midlake1 MDL MET 422312121515900 42° 23' 12'' 121° 51' 59.1'' Wind speed/direction, air temperature, 

relative humidity

Midnorth1 MDN MET 422622122004000 42° 26' 21.5'' 122° 0' 40'' Wind speed/direction

South Shore SSHR MET 421402121491400 42° 14' 2.76'' 121° 49' 14.38'' Wind speed/direction

Williamson River WMR MET 422809121574800 42° 28' 9'' 121° 57' 48.5'' Wind speed/direction, air temperature, 

relative humidity, solar radiation

1

Floating site.

NOT TO SCALE

Wind Speed/Direction Sensor

2.5 cm Pipe

Relative Humidity and

Reducer Temperature Sensor

Solar Power Array

3.8 cm Pipe

3 meter

2 meter

Concrete Footing

Datalogger

Figure 5. Configuration of land-based meteorological 

measurement sites around Upper Klamath Lake, Oregon, 2005.
10 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

Data were collected during site visits, about every 2 weeks 

during the field season. During these visits, sensors were 

checked for proper function by comparison with hand-held 

instruments and were cleaned and maintained if necessary. 

Information necessary to correct data that may have been 

corrupted by fouling or drifts from proper calibration was 

collected as needed. Raw meteorological data were loaded 

into ADAPS and processed in the same manner as the water 

quality data.

Data Processing

Before calculating any statistics, data recorded by 

continuous water quality monitors were screened using 

temporal and, when appropriate for the statistic, spatial 

criteria. In this report, daily statistics are used for continuous 

water quality monitoring data. For a day’s worth of data to be 

acceptable for computing daily statistics, at least 80 percent of 

the day’s possible measurements were necessary, constituting 

a “qualifying day” of data. A spatial criterion was applied 

when data over the entire lake were compiled to compute a 

statistic, such as lakewide daily median dissolved oxygen 

concentration. This criterion specified that at least 7 percent of 

the lake’s water quality monitoring sites had to have qualifying 

daily data to in order to compute the lakewide statistic for a 

particular day. 

For statistics at individual meteorological sites, the 

temporal criterion ensured that at least 80 percent of the 

day’s possible measurements were available to constitute a 

qualifying day of data. To compute lakewide meteorological 

statistics, the SSHR MET site was not included in calculations 

because this site was not established until August 18, 

2005. Different levels of spatial acceptability were applied 

depending on the parameter because not all parameters 

were collected at all sites, and there were relatively few 

meteorological sites around the Upper Klamath Lake basin. 

Statistics of solar radiation were computed only with data 

collected during daylight hours. Solar radiation data were 

collected at only one site, so no spatial criterion was applied 

to these data. Air temperature and relative humidity data 

were collected at three sites, so the spatial criterion for these 

parameters ensured that two of the three sites (67 percent) had 

daily qualifying data to compute a lakewide daily statistic. 

Wind speed data were collected at all meteorological sites, so 

the spatial criterion for wind speed ensured that four of the 

five sites (80 percent) had daily qualifying data to compute a 

lakewide daily statistic. Lakewide statistics were not computed 

for wind direction. Statistics of direction can be potentially 

misleading or uninformative. For example, a mean wind 

direction may indicate a direction that was not an actual wind 

direction during the time the statistic was computed, and 

because wind direction is a value between 0 and 359, daily 

minimum and maximum values of direction tend to be 0 and 

359, respectively. 

Meteorological Conditions

The graphs of lakewide daily median meteorological 

conditions (fig. 6) provide information about the general 

behavior of these environmental parameters in the vicinity of 

the lake throughout the field season. Daily median wind speed 

generally was constant throughout the study. Some particularly 

windy periods occurred in mid-June, late August, and midSeptember, when lakewide daily median wind speed exceeded 

5 m/s. Air temperature gradually increased from June through 

July and then gradually decreased from August through 

October. Relative humidity generally followed the inverse 

of air temperature patterns. Variability in solar radiation 

was low through July and August; indicating that conditions 

during these months were mostly sunny. Greater variability in 

mid-June and again from September onward indicates more 

periods of cloudiness during these times. These patterns of air 

temperature, relative humidity, and solar radiation are typical 

of the hot, dry summers of the Upper Klamath Lake basin. 

Wind speed and direction ultimately determine the 

circulation of the water in Upper Klamath Lake. This 

phenomenon has been verified with a hydrodynamic model 

of the lake (Cheng and others, 2005) and with the placement 

of acoustic Doppler current profilers in the lake (Wood and 

others, 2006). The hydrodynamic model describes a general 

clockwise circulation pattern of water in Upper Klamath Lake 

under northwesterly winds (fig. 7), which are prevalent during 

the summer.

Because the wind and the currents are so closely related, 

the preliminary modeling effort also demonstrated the need 

to collect spatially accurate wind data, rather than data from 

a single site. Before meteorological measurements were 

collected at several sites on and around the lake (fig. 2), little 

was understood about wind characteristics in the vicinity of 

the lake. 

Wind histograms (fig. 8) provide a summary of wind 

direction and speed at each site. These histograms show 

the relative frequency of occurrence of wind in four speed 

categories from each 5-degree direction category around 

360 degrees of direction. The wind speed histogram bars are 

stacked in each 5-degree direction category, with bars for the 

strongest winds on top. The histograms display simple counts 

of direction readings categorized by wind speed; no temporal 

filters were applied to the data used in these plots. 
Meteorological Conditions 11

Figure 6. Lakewide daily median wind speed, air temperature, relative humidity, and daytime solar radiation for 

meteorological sites in and around Upper Klamath Lake, Oregon, 2005.

OR19_0158_UKL_fig_6

WIND SPEED

0

1

2

3

4

5

6

7

8

DAYTIME SOLAR RADIATION

 1 JUNE 1 JULY 1 AUGUST

 2005

 1 SEPTEMBER 1 OCTOBER

0

200

400

600

800

RELATIVE HUMIDITY

RELATIVE HUMIDITY,

IN PERCENT

40

50

60

70

80

90

100

AIR TEMPERATURE

AIR TEMPERATURE,

IN DEGREES CELSIUS

0

5

10

15

20

25

30

SOLAR RADIATION, IN WATTS

PER SQUARE METER

WIND SPEED, IN METERS

PER SECOND

The histograms reveal that wind characteristics in the 

northern part of the lake, represented by MDN MET, differed 

from those in the main body of the lake, represented by MDL 

MET. In the northern part of the lake, winds were likely to 

come from the southwest-to-northwest sector, including 

most winds greater than 5 m/s, which have more potential to 

drive lake currents. In the main body of the lake, most winds 

in all speed categories came from a relatively narrow band 

to the northwest, because the topographic ridges to the east 

and west funnel the winds into a narrow range of direction 

over the main body of the lake. This same narrow band of 

northwesterly winds was observed for most winds greater 

than 5 m/s at the land-based HDB MET and SSHR MET sites 

farther south, although winds less than 5 m/s came primarily 

from the northeast and south at HDB MET and primarily from 

the south at SSHR MET. This observation indicates that strong 

winds blowing from the northwest over the main body of 

the lake typically continue in this direction over the southern 

part of the lake. At the land-based meteorological sites in the 

northern part of the lake, the strongest winds typically came 

from the northwest at BLB MET and from the west at WMR 

MET, reinforcing the inference drawn from the MDN MET 

histogram that westerly winds dominate in the northern part of 

Upper Klamath Lake.
12 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

OR19_0158_UKL_fig_7

EXPLANATION

Current velocity and direction 

predicted for July 29, 2005 at

4:00 PM. Arrow length 

represents relative current

speed. Arrow shown here 

represents a speed of 10 

centimeters per second. 

Figure 7. Water-current velocity predicted by the hydrodynamic model of Upper 

Klamath Lake, Oregon, under prevailing wind conditions. 
Meteorological Conditions 13

OR19_0158_UKL_fig_8

0 0.02 0.04 0.06 0.02 0.04 0.06

0 0.02 0.04 0.06 0.02 0.04 0.06

0 0.03 0.06 0.09 0.06 0.09

0

45

90

135

180

225

270

315

0

45

90

135

180

225

270

315

0

45

90

135

180

225

270

315

0

45

90

135

180

225

270

315

0

45

90

135

180

225

270

315

0

45

90

135

180

225

270

315

0 0.02 0.04

0.02

0.04

0 0.02 0.04 0.06 0.08 0.02 0.04 0.06 0.08

0 0.02 0.04 0.02 0.04

<=1

>1 - 2.5

>2.5 - 5

>5

Relative frequency

Compass azimuth

EXPLANATION

Wind speed categories—

values in meters per second

MDN-MET WMR-MET

MDL-MET

HDB-MET SSHR-MET

BLB-MET

270

Upper

Klamath

Lake

Agency

Lake

MDL-MET

MDN-MET

WMR-MET

BLB-MET

HDB-MET

SSHR-MET

Figure 8. Wind speed and direction for all meteorological sites in the vicinity of Upper Klamath Lake, Oregon, 2005. The histogram bars 

are stacked in each 5-degree direction category. (The SSHR meteorological site was installed midway through the study and recorded 

only 38 days of data).
14 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

Nutrients and Chlorophyll a

Bloom Dynamics of Aphanizomenon flos-aquae 

Photosynthetic pigments, like chlorophyll a, are 

measured as a surrogate for algal biomass because the cost and 

time required to collect and analyze chlorophyll a is less than 

that for measurements of algal biomass. In this report, algal 

biomass will be represented by chlorophyll a concentration. 

Between May and November, 90–100 percent of the total 

phytoplankton biomass in Upper Klamath Lake consists of 

AFA (Kann, 1997). The weekly water samples, although 

collected at only a subset of the sites in the study area, 

provided valuable context for understanding the data recorded 

by the continuous water quality monitors. 

Trends and fluctuations in water quality parameters 

commonly were associated with algal trends and 

fluctuations, as reflected in the chlorophyll a data. Maximum 

concentrations of chlorophyll a, coinciding with similar 

maximum concentrations of dissolved oxygen and pH 

values, indicated an algal bloom. Week-to-week variation in 

chlorophyll a concentrations indicated that either populations 

were periodically blooming and declining (as a result of 

algal cell death) or that there was an inherent patchiness 

of algal growth and that the patches were moving around 

the lake. Indicators of cell death are low dissolved oxygen 

concentration and increased dissolved nutrient concentration. 

During an event of massive cell death, the magnitude of 

the increase in dissolved nutrient and decrease in dissolved 

oxygen concentrations can be variable and is related to the 

chlorophyll a concentrations before the event. Variation 

in chlorophyll a concentration caused by patchiness is not 

associated with increased nutrient or decreased dissolved 

oxygen concentration. Many blue-green algae, such as AFA, 

contain gas vesicles that allow cells to regulate their position 

in the water column by floating to the surface or sinking to 

the bottom. The sampling protocols used in this study may be 

insufficient to detect chlorophyll a very near the lake bottom, 

thereby falsely indicating a lack of chlorophyll a at a site. 

In addition, algae floating to the surface can form mats that 

are moved around by the wind, possibly resulting in a low 

chlorophyll a concentration at the site of measurement when 

in fact a bloom is in progress elsewhere in the lake. 

A bloom decline is characterized by a sharp reduction in 

oxygen production through photosynthesis and is manifested 

as a decrease in dissolved oxygen concentration, generally 

to values potentially harmful to fish, as oxygen demand in 

the water column or sediments caused by decomposition of 

organic material continues. In contrast, periods of growth 

in the bloom are generally manifested as supersaturated 

dissolved oxygen concentrations and high pH values, as 

photosynthesizing algae consume carbon dioxide and produce 

oxygen. 

At site MDN, data were collected from 2002 through 

2005, allowing direct interyear comparison. In each year, the 

algal bloom expanded rapidly to an initial peak sometime 

between mid-June to mid-July, as measured by a maximum 

in chlorophyll a concentration (fig. 9). Between late July 

and mid-August in each year, chlorophyll a concentrations 

decreased concurrent with increased dissolved nutrient and 

decreased dissolved oxygen concentrations, indicating an algal 

bloom decline associated with large-scale cell death. Dissolved 

oxygen concentrations of less than 4 mg/L lasting between 

several hours and several days were measured at site MDN 

in association with this type of bloom decline from as early 

as late July to as late as mid-October during 2002–05 (fig. 9). 

The most severe (longest duration) low dissolved oxygen 

events occurred mid-season in 2003 and in 2005, and were 

associated with the largest decreases in chlorophyll a from the 

previous peak and the highest peaks in nutrient concentrations, 

particularly ammonia (note difference in the vertical scales 

among the years). The occurrence of a low dissolved oxygen 

event in October 2003, however, demonstrates that this type of 

event is not limited to occurring at mid-season, and can occur 

more than once in a single season. 

The variability of chlorophyll a concentrations measured 

in 2005 suggests the occurrence of multiple summer 

chlorophyll a maximums, with concentrations at some sites 

reaching two or more maximums during the season (fig. 10). 

The highest chlorophyll a concentrations occurred after the 

mid-season bloom decline at sites HDB, MDL, MDT, and 

WMR (table 4). Data collected during previous years also 

indicated late-summer blooms of AFA (Kann, 1997; Wood 

and others, 2006). Measured reductions in bloom-related 

chlorophyll a concentrations at all sites except HDB in 

late July 2005 were notable because of the associated low 

dissolved oxygen events (LDOE) and increased un-ionized 

ammonia concentrations that were potentially harmful to fish. 

Chlorophyll a concentrations were lowest after the June–July 

bloom and were measured between July 18 and August 3, 

2005, with most of the lowest concentrations in early August 

(table 4). The decrease in chlorophyll a concentrations was 

measured at site HDB in early August, a week later than 

the onset of decline at other sites. Howard Bay is largely 

disconnected from the circulation in the main body of the lake, 

and as a result the bloom there probably developed its own 

seasonal dynamics in response to localized nutrient, wind, 

and circulation patterns within the bay. During the widespread 

bloom decline, measurements recorded by the continuous 

water quality monitors showed that dissolved oxygen 

concentrations decreased to less than 6 mg/L at all sites, less 

than 4 mg/L at site MDN, and less than 2 mg/L at sites HDB, 

MDT, and EPT. Dissolved oxygen concentration at sites MDL 

and WMR did not decrease to such low levels, indicating that 

oxygen consumption was not as extreme at those two sites. 
Nutrients and Chlorophyll a 15

Figure 9. Weekly measurements of chlorophyll a and dissolved nutrient concentration in relation to the duration of 

a dissolved oxygen concentration of less than 4 milligrams per liter at water samples collected from site MDN, Upper 

Klamath Lake, Oregon, 2002–05. Note the difference in the scale of the chlorophyll a and nutrient axes among years.

OR19_0158_UKL_fig_9

2003

0

200

400

600

800

1,000

0

100

200

300

400

500

2002

0

100

200

300

400

0

50

100

150

200

250

300

2004

0

100

200

300

400

500

600

700

0

100

200

300

400

500

2005

0

200

400

600

800

1,000

0

200

400

600

800

CHLOROPHYLL a CONCENTRATION, IN MICROGRAMS PER LITER

AMMONIA AND ORTHOPHOSPHATE CONCENTRATION, IN MICROGRAMS PER LITER

 2005

20 MAY 1 JUNE 1 JULY 1 AUGUST 1 SEPTEMBER 1 OCTOBER

12

24

72

96

144

168

NO NUTRIENT DATA

AMMONIA

ORTHOPHOSPHATE

CHLOROPHYLL a

EXPLANATION

CHLOROPHYLL a DECLINE RESULTING

 FROM CELL DEATH

CHLOROPHYLL a DECLINE RESULTING

 FROM PATCHINESS

DURATION OF DISSOLVED OXYGEN CONCENTRATION

 LESS THAN 4 MILLIGRAMS PER LITER, IN HOURS
16 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

OR190158UKLfig10

0

200

400

600

800

0

200

400

600

800

0

20

40

60

80

100

120

140

0

200

400

600

800

1,000

1,200

10 JUNE 1 JULY 1 AUGUST

2005

1 SEPTEMBER 1 OCTOBER 0

20

40

60

80

A

B

C

D

E

BLOOM

DECLINE

TOTAL PHOSPHORUS CONCENTRATION,

IN MICROGRAMS PER LITER

CHLOROPHYLL a CONCENTRATION,

IN MICROGRAMS PER LITER

NITRITE-PLUS-NITRATE

CONCENTRATION, IN 

MICROGRAMS PER LITER

AMMONIA CONCENTRATION,

IN MICROGRAMS PER LITER

ORTHOPHOSPHATE CONCENTRATION,

IN MICROGRAMS PER LITER

MDT on Sept. 20; 2,055 Mg/L

MDT on Sept. 13; 1,121 Mg/L

HDB on Sept. 19; 1,354 Mg/L

MDN

WMR

MDL 

HDB 

MDT (Graph A and B only) 

EPT (Graph A and B only) 

Sampling site

MDT Upper

Graphs C, D, AND E

EPT Upper

MDT Lower

EPT Lower

Figure 10. Concentrations of chlorophyll a, total phosphorus, orthophosphate, ammonia, and nitrite-plus-nitrate in 

water samples collected from Upper Klamath Lake, Oregon, 2005. 
Nutrients and Chlorophyll a 17

Table 4. Maximum and minimum chlorophyll a concentrations and dates relative to 

Aphanizomenon flos-aquae blooms and decline during sampling season, Upper Klamath Lake, 

Oregon, June–October 2005.

[NA, not available]

Chlorophyll a concentrations, in micrograms per liter

Week of Howard Bay 

(HDB)

Midlake 

(MDL)

Middle 

of trench 

(MDT)

Eagle Point 

(EPT)

Upper Klamath 

Lake at 

Williamson 

River outlet 

(WMR)

Midnorth 

(MDN)

June 13–17 12 58 NA 38 22 29

June 20–24 64 175 70 13 56 88

June 27–July 1 152 35 175 111 134 110

July 5–8 700 61 49 26 88 701

July 11–15 78 50 315 35 152 188

July 18–22 257 32 38 38 50 71

July 25–29 504 10 76 21 30 28

Aug. 1–5 105 117 38 9 18 9

Aug. 8–12 111 58 140 18 64 55

Aug. 15–19 560 41 280 79 158 76

Aug. 22–26 110 122 105 58 292 304

Aug. 29–Sept. 2 337 76 164 73 490 158

Sept. 6–9 455 71 210 88 105 114

Sept. 12–16 350 149 1,121 24 113 105

Sept. 19–23 1,354 607 2,055 73 93 292

Sept. 26–30 264 175 175 79 29 228

Oct. 3–7 28 86 70 93 58 99

Maximum concentrations at each site before algae decline resulting from cell death

Minimum concentrations at each site during algae decline resulting from cell death

Sample dates during algae decline resulting from cell death
18 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

Decreases in chlorophyll a concentrations after late-season 

blooms generally were not coupled with low dissolved oxygen 

concentrations, except at the trench sites MDT and EPT, and 

to a lesser extent at site HDB in October, as discussed below 

in the context of the water quality monitors. Dissolved oxygen 

concentrations at the trench sites probably were affected more 

by the respiration processes associated with bloom declines 

than concentrations at the shallow sites because most of the 

water column was below the photic zone at the deep sites, 

whereas most of the water column was within the photic 

zone at the shallow sites. One notable aspect of the sudden 

decrease in chlorophyll a concentrations at the end of July 

was that it occurred nearly simultaneously at all of the water 

quality sampling sites. A simultaneous change in chlorophyll a

concentrations at each site indicates that algal production was 

affected by factors extending throughout the area, such as 

temperature or irradiance or a combination of the two. 

Although samples were not collected in Agency Lake, 

qualitative weekly observations of bloom conditions were 

made at the Agency Lake sites (fig. 11). Trends in these 

observations closely match trends in chlorophyll a data 

gathered biweekly by the Klamath Tribes at sites AGN and 

AGS in 2005 (Klamath Tribes, unpub. data, 2005). From 

mid-June through August, bloom conditions cycled through 

extremes (between “very light” and “very heavy”) on a weekly 

to biweekly basis at site AGN when bloom conditions at site 

AGS were observed to be less variable (between “medium” 

and “heavy”). Bloom conditions above “light” were not 

observed past mid-August at either site in Agency Lake. This 

is in contrast to the bloom in Upper Klamath Lake, where the 

late-season bloom recovered to at least predecline levels at 

most sites (fig. 11). 

Unlike deep lakes in which summertime chlorophyll a

can often be predicted based on the phosphorus available at 

spring turnover (Dillon and Rigler, 1974), shallow lakes are 

not necessarily well-described by simple relations between 

phosphorus and biomass (Havens and others, 2001). Total 

phosphorus and chlorophyll a in UKL tend to increase 

simultaneously in spring, as determined within the resolution 

of weekly or bi-weekly sampling (Kann 1997; Wood and 

others, 2006). Mass balance studies have confirmed that the 

source of phosphorus is internal loading from lake sediments 

(Kann and others, 2001), although the precise mechanism for 

phosphorus loading is as yet unknown (Jacoby and others, 

1982; Barbiero and Kann, 1994; Laenen and LeTourneau, 

1996; Fisher and Wood, 2004). Initial results using porewater profilers suggest that diffusive flux in combination 

with bioturbation is a possible mechanism for internal 

phosphorus loading (Kuwabara and others, 2007). Maximums 

in chlorophyll a concentrations in 2005 corresponded loosely 

with maximums in total phosphorus concentration (fig. 10), 

and total phosphorus concentrations correlated positively 

with chlorophyll a concentrations (fig. 12). Application of 

the Spearman Rank Order Correlation test to the data resulted 

in a correlation coefficient of 0.59 (p < 0.05, n = 101) for 

the relation between total phosphorus and chlorophyll a

concentration in samples from combined sites. Management 

of the lake’s watershed has focused primarily on reducing 

phosphorus loads to the lake (Walker, 2001), but the evidence 

for phosphorus limitation seems inconclusive. A ratio of 

chlorophyll a to total phosphorus concentration around 1 or 

greater indicates that phosphorus was potentially limiting, 

whereas ratios much less than 1 indicate that phosphorus 

was not a limiting nutrient (White, 1989; Graham and others, 

Figure 11. Weekly qualitative observations of algal bloom conditions in Agency Lake, Oregon, 2005.

0

1

2

3

4

5

6

7

8

 1 JUNE 1 JULY 1 AUGUST

 2005

 1 SEPTEMBER 1 OCTOBER

BLOOM GROUP NUMBER

AGN

AGS

1 = Very light

2 = Light

3 = Light/medium

4 = Medium

5 = Medium/heavy

6 = Heavy

7 = Very heavy

EXPLANATION

Bloom Group Number Sampling site
Nutrients and Chlorophyll a 19

Figure 12. Relation of chlorophyll a to total phosphorus concentration in water 

samples collected from Upper Klamath Lake, Oregon, 2005. 

OR19_0158_UKL_fig_12

TOTAL PHOSPHORUS CONCENTRATION, IN MICROGRAMS PER LITER

CHLOROPHYLL 

a CONCENTRATION,

IN MICROGRAMS PER LITER

1

10

100

1,000

10,000

10 100 1,000

MDL 

WMR 

MDN 

 EPT 

MDT 

HDB 

SAMPLING SITE

2004). Ratios of chlorophyll a to total phosphorus in the 2005 

data ranged from 0.05 to 5.28, with 63 percent of samples 

less than 0.8, indicating that during most of June through 

October, phosphorus was not potentially limiting (fig. 13). The 

concentration of bioavailable phosphorus was higher during 

late-season blooms in comparison to the early-season bloom 

(fig. 10), and the ratio of bioavailable nitrogen to bioavailable 

phosphorus decreased between the early season bloom and 

late-season blooms (fig. 13), both of which suggest that 

phosphorus limitation was not consistent from June through 

October. In general, it is necessary to evaluate nitrogen as a 

potentially limiting nutrient (for example, TN:TP less than 10 

indicates potential nitrogen limitation; Forsberg and Ryding, 

1980), but because AFA can fix nitrogen, it seems unlikely 

that nitrogen is limiting. Other potential limiting factors 

include micronutrients such as iron, or light energy. Kuwabara 

and others (2007) noted that the trends of phosphorus in UKL 

were not as expected for a limiting nutrient, whereas the 

trends in iron were. It seems prudent at this point to leave the 

question of what is limiting the bloom in UKL open for further 

research. 

Concentrations of the dissolved nutrients orthophosphate 

and ammonia were slightly negatively correlated with 

chlorophyll a concentrations (fig. 14). Correlations using the 

Spearman Rank Order Correlation test were –0.21 (p < 0.05, 

n = 101) and –0.31 (p < 0.05, n = 101) for orthophosphate 

and ammonia, respectively. The greatest maximums of 

orthophosphate and ammonia coincided with minimums in 

chlorophyll a concentrations at the end of July into early 

August. Low dissolved oxygen concentrations coincided 

with the decrease in chlorophyll a concentrations and the 

increase in dissolved nutrient concentrations in late July 

through early August, indicating that the nutrient maximums 

resulted from decomposition of senescing cells, which 

converts organic nutrients to inorganic form while consuming 

dissolved oxygen. Nitrite-plus-nitrate concentrations were 

low in comparison to ammonia concentrations, indicating that 

nitrification is not a rapid or effective process for removal of 

ammonia from the water column in Upper Klamath Lake.
20 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

OR19_0158_UKL_fig_13

MDL 

MDT 

 EPT 

HDB 

WMR 

MDN 

SAMPLING SITE

RATIO OF CHLOROPHYLL a

TO TOTAL PHOSPHORUS

RATIO OF AMMONIA AND NITRATEPLUS-NITRITE TO ORTHOPHOSPHATE

10 JUNE 1 JULY 1 AUGUST 1 SEPTEMBER 1 OCTOBER

10 JUNE 1 JULY 1 AUGUST 1 SEPTEMBER 1 OCTOBER

2005

0

1

2

3

4

5

6

0

10

20

30

40

50

Figure 13. Ratio of chlorophyll a to total phosphorus and ratio of ammonia and nitrite-plus-nitrate (bioavailable 

nitrogen) to orthophosphate (bioavailable phosphorus) concentrations in water samples collected from Upper Klamath 

Lake, Oregon, May–October 2005. 
Nutrients and Chlorophyll a 21

OR19_0158_UKL_fig_14

AMMONIA CONCENTRATION, IN MICROGRAMS PER LITER

0 200 400 600 800 1000 1200 1400

0

500

1,000

1,500

2,000

ORTHOPHOSPHATE CONCENTRATION, IN MICROGRAMS PER LITER

0 50 100 150 200

0

500

1,000

1,500

2,000

MDN

WMR

MDL

HDB

MDT

EPT

Sampling site

CHLOROPHYLL a CONCENTRATION, IN MICROGRAMS PER LITER

Figure 14. Relation of ammonia and orthophosphate concentrations to chlorophyll a

concentrations in water samples collected from Upper Klamath Lake, Oregon, 2005. 
22 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

Spatial Variability in Nutrient and Chlorophyll a

Concentrations

As with dissolved oxygen concentrations, the 

bathymetry of the lake appears to influence dissolved nutrient 

concentrations. Median concentrations of ammonia and 

orthophosphate were highest at the deep trench sites MDT and 

EPT (fig. 15), particularly during the period of bloom decline 

when dissolved nutrient concentrations were the highest of 

the season. Median concentrations of dissolved nutrients were 

Figure 15. Statistical distribution of ammonia, orthophosphate, total phosphorus, and chlorophyll a concentrations 

measured in water samples collected from Upper Klamath Lake, Oregon, 2005.

0

200

400

600

800

0

200

400

600

800

CONCENTRATION, IN MICROGRAMS PER LITER AMMONIA CONCENTRATION, IN MICROGRAMS PER LITER

ORTHOPHOSPHATE CONCENTRATION,

IN MICROGRAMS PER LITER

0

20

40

60

80

100

120

140

Ammonia

Orthophosphate

Chlorophyll a

Total Phosphorus

10th percentile

25th percentile

Median

75th percentile

90th percentile

Data value represents the 95th percentile

Concentrations, in micrograms per liter

Data value represents the 5th percentile

EXPLANATION

MDN WMR MDL HDB

SAMPLING SITE

MDT EPT

lowest at shallow sites MDN, WMR, MDL, and HDB, outside 

of the trench. This contrast indicates a greater degree of 

mineralization at the deep sites. The oxygen consumption rates 

obtained from dark bottles (discussed in section, “Dissolved 

Oxygen Production and Consumption Experiments”) do not 

indicate a large oxygen demand from the water column during 

the period of bloom decline. Therefore, oxygen consumption 

and mineralization processes likely occurred primarily at 

the sediment–water interface. This idea is supported by the 

downward vertical velocities measured near-bottom in the 
Dissolved Oxygen Production and Consumption Experiments 23

trench with ADCPs, in conjunction with sediments containing 

a large amount of organic matter (Gartner and others, 2007), 

which together indicate a great deal of settling of organic 

matter at the deep trench sites.

 Chlorophyll a and total phosphorus concentrations 

at sites HDB and MDT were higher than at the other sites 

(table 4). The high concentration of chlorophyll a and total 

phosphorus at site HDB may be explained by the fact that 

Howard Bay is largely isolated from the flow regime in the 

rest of the lake, and the bloom in this bay tends to develop 

and evolve somewhat independently of the bloom in the 

rest of the lake. The high chlorophyll a concentrations in 

samples collected at site MDT coincide with observations 

of the field crews of thick mats of AFA close to the water 

surface. Additionally, the primary location for companies 

collecting AFA for commercial production is near site MDT, 

indicating easy access to high concentrations of AFA near 

the surface at that site. These observations are consistent 

with the measurements made with the water quality monitors 

at MDT that show the water column there has a tendency 

to stratify more strongly than in the shallow parts of the 

lake (as discussed in the section on stratification and wind 

speed), particularly when air temperature is increasing, 

creating conditions that allow AFA colonies to make use of 

their buoyancy-regulating mechanism. On the basis of the 

circulation model, a counterclockwise flow cell forms east of 

Eagle Ridge and south of Bare Island that may capture large 

algal mats in a continuous loop (fig. 7). In addition, particletracking studies with the model have shown that water can 

be trapped in the cell for days, particularly when winds are 

weak (Cheng and others, 2005; Wood and Cheng, 2006). The 

combination of surface accumulation when conditions are 

stratified and relatively limited horizontal transport creates 

ideal conditions for AFA to form very dense blooms at this 

site.

Dissolved Oxygen Production and 

Consumption Experiments

Dissolved Oxygen Production and Consumption

The rate of change in dissolved oxygen concentration 

in light and dark incubation bottles at each level in the water 

column is shown as time series in figure 16. Rates obtained 

from the two light bottles were averaged for each rack depth. 

This was done for dark bottles when there were multiple dark 

bottles on a rack during an experiment, but only one dark 

bottle at each depth was used in most of the experiments. 

Typically, rates from light bottles represented net dissolved 

oxygen production (positive rates), and rates from dark bottles 

represented net dissolved oxygen consumption (negative 

rates). A maximum production rate of 1.47 (mg/L)/hr of 

oxygen was measured at site HDB on August 15 and a 

maximum consumption rate of –0.73 (mg/L)/hr of oxygen was 

measured at site MDN on August 10 (fig. 16). Because the 

bottles were filled with unaltered lake water, the experiments 

measured oxygen production and consumption of the entire 

planktonic community (phytoplankton, zooplankton, and 

bacteria). Because AFA typically constitutes more than 90 

percent of the phytoplankton by weight during the time of 

year when these experiments were conducted (Kann, 1997; 

Perkins and others, 2000), dissolved oxygen production was 

attributable mostly to photosynthesis by AFA. However, 

the abundance of oxygen consuming components of the 

planktonic community relative to AFA is less well known, 

particularly bacterial biomass. Large quantities of the 

zooplankter Daphnia plicaria, a cladoceran that dominates the 

zooplankton biomass in Upper Klamath Lake (Kann, 1997), 

were not observed in bottles during experiments. It is expected 

that AFA is a major contributor to oxygen consumption 

observed in the experiments, but without knowledge of 

the bacterial biomass relative to that of AFA it cannot be 

conclusively stated that AFA dominates dissolved oxygen 

consumption processes. 

The rate of change of dissolved oxygen concentration 

in dark bottles sometimes was positive (fig. 16), indicating 

the unlikely occurrence of oxygen production in absence of 

light. This problem was largely limited to the end of the field 

season in September and October. Measured positive changes 

in dark bottles in the raw data were small (median value of 

0.08 mg/L), suggesting that the changes were the result of 

the accuracy limits of the dissolved oxygen probe, which the 

manufacturer specifies as ±0.2 mg/L.

Excluding the positive rates of change of dissolved oxygen 

concentration in the dark bottles, consumption rates measured 

in dark bottles were comparable to the overnight consumption 

rates measured in Upper Klamath Lake in 2002 by Lieberman 

and others (2003). Consumption rates ranged from 0 to –0.73 

(mg/L)/hr of oxygen in this study, whereas consumption rates in 

the 2002 study ranged from –0.05 to –0.49 (mg/L)/hr of oxygen. 

The larger range of consumption rates determined in this 

study is attributable to annual variability and the fact that 

experiments in this study were conducted over a period of 

6 months, whereas the 2002 study was conducted during 2 

consecutive days in late July and 2 consecutive days in midSeptember. 

Greater consumption rates typically were measured in 

dark bottles on the upper incubation rack than in those on the 

lower incubation rack. Final bottle temperatures tended to be 

higher in the upper rack bottles than in the lower rack bottles, 

reflecting the difference in the ambient water temperatures. 

The higher temperatures could explain the generally higher 

consumption rates in the bottles on the upper rack. 
24 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

OR19_0158_UKL_fig_16

1 JUNE 1 JULY 1 AUGUST 1 SEPTEMBER 1 OCTOBER

2005

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

RATE OF CHANGE IN DISSOLVED OXYGEN CONCENTRATION, IN MILLIGRAMS O2 PER LITER PER HOUR 

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

HDB

WMR

MDL

MDN

EPT

MDT

Upper rack—light bottle

Lower rack—light bottle

Upper rack—dark bottle

Lower rack—dark bottle

Figure 16. Rate of change in dissolved oxygen concentration measured from dissolved oxygen production and 

consumption experiments at sites in Upper Klamath Lake, Oregon, 2005.
Dissolved Oxygen Production and Consumption Experiments 25

Figure 17. Relation of the natural logarithm of chlorophyll 

a concentration to dissolved oxygen production in the 

upper and lower incubation racks during dissolved oxygen 

production and consumption experiments in Upper Klamath 

Lake, Oregon, 2005.

OR19_0158_UKL_fig_17

-0.4 -0.2 0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6

UPPER RACK

DISSOLVED OXYGEN PRODUCTION, IN MILLIGRAMS PER LITER PER HOUR

NATURAL LOGARITHM OF CHLOROPHYLL a CONCENTRATION [LN(MILLIGRAMS PER LITER)] 

1

2

3

4

5

6

7

8

1

2

3

4

5

6

7

8

LOWER RACK

Spearman Rank

Order Statistics:

r = 0.624

p < 0.0001

Spearman Rank

Order Statistics:

r = -0.0418

p = 0.767

With the exception of the first experiment at site WMR, 

upper incubation racks were positioned at 0.5 m below the 

water surface in the water column during all experiments 

at all sites (table 2). This placement provided a consistent 

framework with which to observe patterns in dissolved oxygen 

production in the upper 0.5 m of the water column. Dissolved 

oxygen production rates in the upper rack at site MDL were 

initially high in June, slowed through July, and recovered 

through August (fig. 16). A similar pattern was observed in 

the upper rack dissolved oxygen production at site MDN 

(fig. 16). Experiments were not conducted at sites EPT or 

MDT during June, but results of experiments done in July and 

August also show a decrease in upper rack production rates 

from the mid-July experiment to the late July–early August 

experiment at both sites, with a subsequent recovery of upper 

rack dissolved oxygen production rates through August. This 

pattern of decreasing oxygen production in upper portions of 

the water column through June and recovery through August 

is coincident with the patterns in chlorophyll a (fig. 10) and 

the decrease and recovery of dissolved oxygen concentration 

in the continuous water quality monitors, as discussed in the 

section, “Daily Median Water Quality Conditions.” When data 

from all experiments were combined, upper rack production 

rates also were positively correlated with the natural logarithm 

of chlorophyll a concentrations (fig. 17). The fact that no 

correlation was observed in data from the lower rack likely 

results from the effect of algal self-shading, as discussed in the 

section, “Depth of Photic Zone.” 

Because these experiments were not done at all 

sites during all weeks, a lakewide decrease in dissolved 

oxygen production rates in late July and early August 

cannot be confirmed, but the similarities of the production 

rate, chlorophyll a, and time series of dissolved oxygen 

concentration and percent saturation indicate that reduced 

AFA dissolved oxygen production contributed to the 

decreasing dissolved oxygen concentrations observed through 

July 2005. Because AFA at Agency Lake sites undergoes 

cycles of large blooms followed by substantial decline 

similar to the pattern seen in Upper Klamath Lake, decreased 

oxygen production by AFA also likely contributed to periods 

of decreasing dissolved oxygen concentrations observed at 

Agency Lake monitoring sites in July and August.

Depth of Photic Zone

When data from all experiments were combined, an 

inverse relation was observed between photic zone depth 

and the natural logarithm of chlorophyll a concentrations 

(fig. 18). This relation reflects the shading effect that 

blooms of AFA can have on the water column. During some 

experiments, rates from light bottles on the lower rack were 

negative. This happened most notably at site HDB during 

the August 15 experiment and at site MDL during the July 6 

experiment, when the average light bottle change in dissolved 

oxygen concentration on the lower rack was about –0.21 and 

0 1 2 3 4 5

NATURAL LOGARITHM OF CHLOROPHYLL a

CONCENTRATION [LN(MILLIGRAMS PER LITER)] 

1

2

3

4

5

6

7

8

Spearman Rank

Order Statistics:

r = -0.709

p < 0.0001

AVERAGE DEPTH OF PHOTIC ZONE, IN METERS

Figure 18. Relation of the natural logarithm of chlorophyll 

a concentration to the average depth of the photic zone 

for all dissolved oxygen production and consumption 

experiments in Upper Klamath Lake, Oregon, 2005.
26 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

–0.27 (mg/L)/hr of oxygen, respectively (fig. 16). Smaller 

negative rates were measured in light bottles on the lower 

incubator racks during several dates at sites MDN, EPT, and 

MDT. Comparison of the depth of the lower rack with the 

average depth of the photic zone during the experiments at 

each site (table 2) shows that these instances of net oxygen 

consumption in light bottles occurred when the bottles were 

near or below the photic zone. Furthermore, no correlation 

existed between oxygen production and chlorophyll a

concentration in lower incubation racks, whereas a positive 

correlation was observed in upper incubation racks (fig. 17). 

These findings indicate that self-shading by AFA during 

heavy blooms can cause metabolic respiration to exceed 

photosynthetic production during the daytime in parts of the 

water column that would otherwise be in the photic zone. 

Water Quality Conditions

Daily Median Water Quality Conditions

Time series of daily median water quality conditions 

at the two sites in Agency Lake are shown in figure 19. 

Temperature at both sites was similar throughout the field 

season. Daily median dissolved oxygen concentrations were at 

and slightly less than 4 mg/L (a high-stress dissolved oxygen 

concentration threshold for Upper Klamath Lake suckers 

[Loftus, 2001]) at site AGN during several days in July and 

for a few days in August. By contrast, comparable daily 

median dissolved oxygen concentrations occurred for only a 

short period in mid-August at site AGS. Through June, both 

sites recorded a steady increase in pH, with daily median pH 

reaching around 10 for both sites in late June and early July. 

In mid-July, however, pH varied considerably at site AGN 

as compared to site AGS. This variability continued until 

September, after which pH values were relatively stable at 

both sites. Early season similarity between sites AGN and 

AGS was evident in dissolved oxygen concentrations as well. 

Dissolved oxygen concentration varied more at site AGN 

than at site AGS beginning in late June. Coincident with pH, 

dissolved oxygen concentrations became more comparable 

between the two sites from September through the end of the 

field season. A similar relation between sites AGN and AGS 

also was observed in specific conductance values, with site 

AGN generally showing more variability as compared to site 

AGS from mid-July through the end of the field season. 

Data recorded at continuous water quality monitoring 

sites in Upper Klamath Lake were combined into a single 

dataset for each parameter to determine lakewide daily 

medians (fig. 20). Dissolved oxygen and pH values followed 

a similar trend of increasing and leveling off through June, 

then decreasing steadily through much of July. Dissolved 

oxygen concentration reached a minimum in the last half 

of July that lasted for nearly 2 weeks through the beginning 

of August, and pH reached a minimum in early August that 

lasted for only a few days. Both parameters simultaneously 

recovered relatively rapidly to predecline levels in August 

and maintained those levels with some fluctuation for the rest 

of the field season. Temperature gradually increased through 

mid-July, maintained a plateau from mid-July through midAugust (coinciding with the period of lowest dissolved oxygen 

and pH values), and gradually decreased for the remainder 

of the field season. Specific conductance had an early period 

of relative stability and then began a steady increase from 

mid-July, peaking coincidentally with the period of minimum 

dissolved oxygen and pH values. A sharp, short decrease to 

fairly steady specific conductance values for the remainder of 

the field season followed. 

Water temperatures in Agency and Upper Klamath Lakes 

(figs. 19 and 20) closely followed patterns in air temperature 

(fig. 6). Because these lakes are shallow, their small water 

columns contain a smaller thermal mass, relative to deep lakes, 

and therefore heat up and cool down more readily along with 

changes in air temperature. This process is aided by diurnal 

mixing known to occur in these lakes (Wood and others, 

2006).

Dissolved oxygen and pH values have a positive relation 

through photosynthetic activity and the carbonate buffering 

system of natural waters (Wetzel, 2001), which is evident 

in data from both lakes. Dissolved oxygen and pH values 

in Agency and Upper Klamath Lakes are related to bloom 

dynamics, but bloom dynamics in the two lakes are largely 

independent. The bloom patterns observed at sites AGN and 

AGS (fig. 11) are evident in the dissolved oxygen and pH 

data collected at those sites (fig. 19). The highly variable 

pH at site AGN through much of August corresponds to the 

variability observed in the AFA bloom at that site during this 

time. Because there was no late-season bloom in Agency 

Lake, dissolved oxygen concentrations remained largely 

undersaturated through the last half of August and September. 

Thus, pH values did not rebound to values seen earlier in the 

season, as they did during the late-season bloom in Upper 

Klamath Lake (fig. 20). 

In Upper Klamath Lake, the coincidence of the seasonal 

maximum in lakewide median specific conductance with the 

seasonal minimums in lakewide median dissolved oxygen 

and pH values (fig. 20) also is coincident with maximum 

concentrations of orthophosphate and total ammonia 

(fig. 10). An inverse correlation also was observed between 

chlorophyll a and both orthophosphate and total ammonia 

(fig. 14). These observations suggest that the ionic nutrients 

released by decaying algal cells influence the conductance of 

the water in Upper Klamath Lake. This situation may have 

occurred at site AGS in late July, when a sharp decrease in 

dissolved oxygen and pH values was coincident with a sharp 

increase in specific conductance (fig. 19). However, a similar 
Water Quality Conditions 27

Figure 19. Daily median temperature, dissolved oxygen concentration, dissolved oxygen percent saturation, pH, and 

specific conductance recorded by continuous monitors in Agency Lake, Oregon, 2005.

OR19_0158_UKL_fig_19

Sampling site

1 JUNE 1 JULY 1 AUGUST 1 SEPTEMBER 1 OCTOBER

2005

DISSOLVED OXYGEN CONCENTRATION

IN MILLIGRAMS PER LITER

0

2

4

6

8

10

12

14

16

18

20

SPECIFIC CONDUCTANCE, IN

MICROSIEMENS PER CENTIMETER

100

110

120

130

140

AGN

AGS

8

10

12

14

16

18

20

22

24

26

28

WATER TEMPERATURE

7.0

7.5

8.0

8.5

9.0

9.5

10.0

10.5

pH

DISSOLVED OXYGEN SATURATION,

IN PERCENT

TEMPERATURE, IN DEGREES CELSIUS

pH INCREASING ALKALINITY

0

50

100

150

200

250

SPECIFIC CONDUCTANCE

DISSOLVED OXYGEN CONCENTRATION

DISSOLVED OXYGEN PERCENT SATURATION

High stress threshold for Upper Klamath

Lake suckers (Loftus, 2001)

100% dissolved oxygen saturation.
28 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

OR19_0158_UKL_fig_20

DISSOLVED OXYGEN CONCENTRATION

DISSOLVED OXYGEN

CONCENTRATION, IN

MILLIGRAMS PER LITER

4

6

8

10

12

14

SPECIFIC CONDUCTANCE

SPECIFIC CONDUCTANCE,

IN MICROSIEMENS PER

CENTIMETER

108

110

112

114

116

118

120

122

124

WATER TEMPERATURE

TEMPERATURE,

IN DEGREES CELSIUS pH

10

12

14

16

18

20

22

24

26

pH

8.0

8.2

8.4

8.6

8.8

9.0

9.2

9.4

9.6

9.8

DISSOLVED OXYGEN

PERCENT SATURATION

1 JUNE 1 JULY 1 AUGUST 1 SEPTEMBER 1 OCTOBER

Period of seasonal bloom decline

0

30

60

90

120

150

180 DISSOLVED OXYGEN PERCENT SATURATION

Figure 20. Lakewide daily median dissolved oxygen concentration, dissolved oxygen percent saturation, temperature, 

pH, and specific conductance recorded by continuous monitors in Upper Klamath Lake, Oregon, 2005. 
Water Quality Conditions 29

increase in specific conductance was not recorded at site AGS 

when dissolved oxygen and pH values quickly decreased 

with the decline in bloom conditions there in mid-August. 

Nutrient release and uptake by the variable bloom at site AGN 

may have contributed to variability in specific conductance, 

particularly through July and early August. However, the 

inverse relation of specific conductance with dissolved oxygen 

and pH values was not as strong during this period at site AGN 

as in Upper Klamath Lake. The available data indicate that 

concentrations of other ions were more influential in patterns 

of specific conductance in Agency Lake. Higher variability in 

specific conductance at site AGN through the end of the field 

season could be the result of influent waters from the Wood 

River and Wood River wetland, to which site AGN is in close 

proximity relative to site AGS. The specific conductance in 

the Wood River wetland is dominated by chloride ions (K.D. 

Carpenter, U.S. Geological Survey, unpub. data, 2008). Similar 

variability in specific conductance was observed at sites WMR 

and FBS (sites in the proximity of the Williamson River and 

west-shore wetlands, respectively) relative to other sites in 

Upper Klamath Lake. 

Spatial Variability in Dissolved Oxygen 

Concentrations

Periods of very low dissolved oxygen concentrations in 

Upper Klamath Lake influence endangered sucker movements 

and have been implicated in die-off events of these species in 

Upper Klamath Lake (B.J. Adams and others, U.S. Geological 

Survey, unpub. data, 2005). To study the dynamics of 

dissolved oxygen in Upper Klamath Lake, time-series graphs 

of daily median dissolved oxygen percent saturation at each of 

the water quality monitoring locations (fig. 2) were examined 

(fig. 21). The graphs are ordered along the primarily clockwise 

current pattern in Upper Klamath Lake during the summer 

(fig. 7), beginning with the lower sonde at the middle of trench 

site (MDT-L). Periods of missing data at site MDT-L resulted 

from problems positioning the sonde at this site. Data for sites 

MDL and RPT are not shown but were similar to data from 

sites MPT and NBI. The graphs indicate that dissolved oxygen 

dynamics in the lake operated at two time scales in 2005: a 

long scale (months), and a short scale (days). 

Variability on Monthly to Seasonal Time Scales

In the longer time scale, the dissolved oxygen patterns 

for sites in the north and west, principally sites MDT-L, 

MDT-U, EPT-L, EPT-U, SHB, BLB, MDN-L, MDN-U, 

and EHB, (fig. 21) follow a pattern similar to the lakewide 

median dissolved oxygen percent saturation (fig. 20). This 

pattern of gradual decline to substantially lower dissolved 

oxygen concentrations during the mid-season bloom decline 

and a recovery to predecline concentrations after the bloom 

recovered was not as strong at the other sites. This distinction 

was caused in large part by the bathymetry of the lake: 

sites MDT-L and EPT-L are in the trench portion of Upper 

Klamath Lake, where much of the water column lies below 

the photic zone. This characteristic provides more potential 

for oxygen consuming processes, such as sediment oxygen 

demand, algal respiration, and bacterial activity, to deplete 

dissolved oxygen, contributing to the gradual decline in 

dissolved oxygen concentration observed at these sites. The 

upper monitors at these deep sites also recorded this gradual 

seasonal decline in dissolved oxygen concentration because of 

frequent mixing within the water column, which is described 

later in this report. At most of the Upper Klamath Lake sites 

in the east and south, principally sites WMR, MPT, NBI, and 

HDB, the seasonal decline in dissolved oxygen was largely 

dampened (fig. 21), reflecting the smaller aphotic zone and 

lower potential for oxygen consumption in these shallower 

areas. Sites SHB, MDN-L, and BLB, although of similar depth 

to sites in the eastern portion of the lake (table 1), recorded a 

more pronounced seasonal decline in dissolved oxygen. This 

may be because sites SHB, MDN-L, and BLB receive water 

from the trench under the dominant flow pattern in the lake 

(fig. 7). The decline in dissolved oxygen at these sites is not as 

severe as that in the trench, however, because of the decreased 

potential for dissolved oxygen consumption in their shallower 

water columns. 
30 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

OR19_0158_UKL_fig_21

MDN-L

1 JUNE 1 JULY 1 AUGUST 1 SEPTEMBER 1 OCTOBER 0

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BLB

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LDOE described in text

Percent DO saturation corresponding 

to 4 mg/L during period of seasonal 

bloom decline

Period of seasonal bloom decline

EXPLANATION

Figure 21. Daily dissolved oxygen percent saturation at water quality monitoring sites in Upper Klamath Lake, 

Oregon, 2005. Graphs for each site are displayed in order along the predominantly clockwise flow path in Upper 

Klamath Lake.
Water Quality Conditions 31

OR19_0158_UKL_fig_21b

HDB

1 JUNE 1 JULY 1 AUGUST 1 SEPTEMBER 1 OCTOBER 0

30

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180

EHB

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MPT

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FBS

0

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Percent DO saturation corresponding 

to 4 mg/L during period of seasonal 

bloom decline

Period of seasonal bloom decline

EXPLANATION

Figure 21.—Continued
32 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

Variability on Short Time Scales

Variability occurring on the order of days can be seen in 

the daily median dissolved oxygen percent saturation graphs in 

figure 21. Events of extremely low dissolved oxygen percent 

saturation operating at these shorter time scales may indicate 

movement through the lake of masses of water that are low 

in dissolved oxygen, with the conditions observed first at one 

location and then at subsequent sites as water moves along 

dominant flow paths in the lake (fig. 7). The condition of the 

mass of water when it reaches the next station along the flow 

path provides information about the processes that occurred as 

the water traveled between monitoring locations.

The darkly shaded sections of the graphs in figure 21

highlight an LDOE that was first observed at site MDT-L. 

From August 19 through 22, daily median dissolved oxygen 

saturation declined to nearly 5 percent at site MDT-L. 

Conditions were not as severe near the top of the water column 

(at site MDT-U) during this time. From August 20 through 

August 24, a subsequent LDOE occurred at site EPT-L, 

with daily median percent saturation of dissolved oxygen 

reaching almost zero. Low dissolved oxygen concentrations 

were distributed throughout more of the water column at this 

site. A subsequent decline in dissolved oxygen concentration 

occurred at site SHB from August 21 through 25. Percent 

saturation of dissolved oxygen went from supersaturated 

before the event (about 140 percent) to just undersaturated 

(about 80 percent) during the event at site SHB. The LDOE 

was less severe at SHB, demonstrating mixing of the lowdissolved-oxygen water once it enters the northern part of 

the lake. A subsequent dip in dissolved oxygen saturation 

was observed at site BLB from August 23 through 27, but 

there was no evidence of the LDOE at site MDN around this 

time, indicating that the LDOE was transported by higher 

velocities across the mouth of Shoalwater and Ball Bays but 

largely bypassed MDN, and was probably eroded by mixing 

before reaching FBS, as there was no evidence of the LDOE 

at that site. The LDOE likely originated in the trench, because 

dissolved oxygen saturation at sites immediately south of the 

trench (sites NBI, EHB, and HDB; fig. 2) did not decrease 

significantly immediately preceding the August 19 event at 

site MDT-L (fig. 21).

Stratification and Wind Speed 

 Stratification of lake waters is caused by density 

differences between the upper and lower parts of the water 

column. These density differences are primarily the result of 

water temperature differences, allowing stratification to be 

identified by differences in temperature between near-surface 

waters and near-bottom waters. The three sites (MDN, EPT, 

and MDT) equipped with a continuous water quality monitor 

at both 1 m from the surface (the “upper sonde”) and 1 m from 

the bottom (the “lower sonde”) provided the means to examine 

the dynamics of water column stratification in Upper Klamath 

Lake. 

Vertical variability in water temperature, dissolved 

oxygen, and pH was calculated as the upper sonde value 

minus the lower sonde value for each hourly measurement at 

each site. Time series of these hourly vertical differences are 

compared with the hourly median wind speed at site MDN for 

a representative month of the 2005 field season (fig. 22). The 

diel (daily) pattern of vertical temperature variability observed 

in figure 22 is known to be typical of Upper Klamath Lake 

(Wood and others, 2006). This pattern appears to be driven, in 

part, by diel variations in wind speed. Typically, wind speeds 

are low enough to prevent water column mixing during the 

daylight hours and when skies are clear, maximizing solar 

heating of the water surface. Vertical temperature differences 

develop accordingly. During the evening, wind speeds 

increase, typically providing enough wind shear to induce 

water column mixing and erode stratification built up during 

the day. Even the deepest sites (EPT and MDT) undergo this 

diel buildup and breakdown of temperature vertical variability, 

although vertical temperature differences at site MDT (the 

deepest site) are consistently much greater than at site EPT. 

Diel cycles in the vertical variability of dissolved oxygen 

and pH also were observed, but vertical differences in these 

constituents were more likely to persist longer than 24 hours, 

especially at sites MDT and EPT. This likely results because 

AFA colonies, having the ability to regulate buoyancy, may 

congregate near the surface, maintaining vertical variability 

in dissolved oxygen and pH while temperature becomes more 

evenly distributed.
Water Quality Conditions 33

OR19_0158_UKL_fig_22

HOURLY DIFFERENCE IN TEMPERATURE BETWEEN UPPER AND LOWER SONDES

DIFFERENCE IN TEMPERATURE,

IN DEGREES CELSIUS

0

2

-1

4

6

8

MDN

Sampling site

MDT

EPT

HOURLY MEDIAN WIND SPEED AT MDN

WIND SPEED, IN METERS PER SECOND

0

2

-2

4

6

8

10

HOURLY DIFFERENCE IN DISSOLVED OXYGEN BETWEEN UPPER AND LOWER SONDES

DIFFERENCE IN DISSOLVED

OXYGEN, IN MILLIGRAMS PER LITER 0

-5

10

20

30

HOURLY DIFFERENCE IN pH BETWEEN UPPER AND LOWER SONDES

DIFFERENCE IN pH

0

1

-0.5

2

3

3 10 15 20 25 30 1

AUGUST

2005

SEPTEMBER

2005

Figure 22. Representative hourly vertical variability in pH, dissolved oxygen, and temperature at sites MDN, MDT, and 

EPT, and hourly median wind speed at site MDN, Upper Klamath Lake, Oregon, 2005.
34 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

Periods of lighter wind result in less wind shear at the 

lake surface and less energy for mixing, allowing stratification 

to persist longer than one diel cycle. Stratification persisted, 

for example, at both trench sites from August 27 to August 

29. During this period, the minimum vertical variability 

in temperature was about 1°C at both sites EPT and MDT. 

Winds rarely were greater than 5 m/s immediately preceding 

and during this time period. This period of lighter winds still 

provided enough energy to induce diel mixing at the shallower 

MDN site.

Water column stratification affects the dissolved oxygen 

dynamics. During periods of stratification, the upper water 

column can become decoupled from the lower water column, 

allowing oxygen consuming processes such as sediment 

and water column oxygen demand and algal respiration to 

deplete the lower part of the water column of oxygen, creating 

potentially unsuitable conditions for fish. Deeper waters in 

the trench, although typically undergoing a diel mixing of 

water, have more resistance to mixing than shallower waters 

because less of the water column is subject to solar heating, 

allowing for development of a greater temperature (density) 

gradient. Accordingly, deeper sites have a smaller proportion 

of water in the photic zone, which allows oxygen consumption 

processes to have a greater role in dissolved oxygen dynamics. 

Therefore, the lowest near-bottom dissolved oxygen 

concentrations during periods of stratification are likely to 

occur in the trench. This was observed in 2005 as well as in 

previous years (Wood and others, 2006). Extended periods of 

stratification may be an important source of chronic stress to 

fish, but they have not been identified as the most important 

cause of the extreme LDOEs that lead directly to fish die-offs 

(Wood and others, 2006).

Timing of Daily Extremes in Water 

Quality Conditions

The timing of daily minimum dissolved oxygen 

concentrations, daily maximum pH, and daily maximum water 

temperature were related to the total water column depth 

at the site. To aid in describing these patterns, histograms 

displaying the timing of the daily extreme parameter value 

from representative shallow (HDB), mid-depth (BLB), and 

deep (EPT) sites are shown in figure 23 for each of these water 

quality parameters. These histograms display the normalized 

frequency of occurrence of the daily extreme water quality 

reading as a function of the hour of day. Shallow sites (HDB, 

AGS, WMR, NBI, and FBS) had an approximate full pool 

depth of 2.5 to 2.8 m (table 1). Middepth sites (AGN, SHB, 

RPT, BLB, and MPT) had an approximate full pool depth 

of 3.0 m to 3.7 m. Deep sites (MDN, MDL, EHB, EPT, and 

MDT) had an approximate full pool depth of greater than 4.2 

m. Patterns in the timing of daily extreme parameter values 

appeared over a continuum of water column depth, so the 

categories of shallow, middepth, and deep are not necessarily 

delineated by fixed depth. 

The daily minimum dissolved oxygen concentration 

at shallow sites tended to occur around 7:00 a.m. The daily 

maximum in pH and temperature occurred most frequently 

in the afternoon to early evening between 3:00 and 8:00 p.m. 

This pattern reflects the strong influence of the diel cycle of 

photosynthesis and respiration where the sonde is positioned, 

which is typically within the photic zone at these sites, and is 

consistent with findings from data collected in previous years 

(Wood and others, 2006).

At middepth sites, however, the period of day when 

daily minimum dissolved oxygen concentration occurred 

became less well defined. At deep sites, there was no distinct 

period of the day when daily minimum dissolved oxygen 

concentrations tended to occur. The time of day when daily 

maximum pH values were likely to occur broadened at 

middepth sites to include more of the early morning hours 

and some late morning hours. At the deep sites, no strong 

tendency for the timing of daily maximum pH to occur in a 

specific time window was observed. A similar progression 

from shallow to deep sites was observed for the timing of 

daily maximum temperature: a strong likelihood for daily 

maximum temperature to occur in the early evening at shallow 

sites, a broadening of this time window into the late evening 

at middepth sites, and the weakest tendency for the daily 

maximum temperature to occur during a distinct time window 

at the deep sites.

The tendency of daily extreme parameter values to 

occur throughout the day at deep sites is caused by the 

increased tendency for these sites to develop thermal (density) 

stratification and the position of the sonde in aphotic waters at 

deeper sites. Below the photic zone, the rate of consumption of 

dissolved oxygen by metabolic respiration and other oxygendemanding processes within the water column is greater than 

the rate of oxygen production by photosynthesis. Near the 

bottom, sediment oxygen demand also consumes dissolved 

oxygen from the water. If the water column develops even a 

small amount of stratification, dissolved oxygen can reach 

minimum daily concentrations in the lower part of the water 

column at any time of day, even during daylight hours. This 

is because dissolved oxygen concentration below the photic 

zone will decrease until a mixing event erodes the thermal 

stratification and mixes the lower layer, which is relatively 
Water Quality Conditions 35

OR19_0158_UKL_fig_23

HDB—DISSOLVED OXYGEN

BLB—DISSOLVED OXYGEN

EPT—DISSOLVED OXYGEN

HOUR OF DAY

NORMALIZED FREQUENCY OF

DAILY MINIMUM DISOLVED OXYGEN (n/nT)

HDB—TEMPERATURE

BLB—TEMPERATURE

EPT—TEMPERATURE

NORMALIZED FREQUENCY OF

DAILY MAXIMUM TEMPERATURE (n/nT)

HDB—pH

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

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

BLB—pH

EPT—pH

NORMALIZED FREQUENCY OF

DAILY MAXIMUM pH (n/nT)

0

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Figure 23. Daily extreme of dissolved oxygen concentration, pH, and water temperature from a representative 

shallow (HDB), middepth (BLB), and deep site (EPT) in Upper Klamath Lake, Oregon, 2005.
36 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

depleted of dissolved oxygen, with the upper layer, which 

contains a relatively higher concentration after being in 

the photic zone over the course of the day. At deeper sites, 

therefore, the minimum dissolved oxygen concentration does 

not always occur in the early morning just before dawn, but 

has more potential to occur throughout the day, depending on 

when the wind picks up and mixes the water column. Water 

column stratification and sonde position in the water column 

affects the timing of daily maximum pH and temperature in a 

similar manner.

These patterns are similar to those seen in previous 

years (Wood and others, 2006). However, a continuum of 

characteristics from shallow to deep sites was more apparent 

in 2005 because of the wider distribution of sites around the 

lake and the greater range of site depths.

Occurrence and Duration of Water 

Quality Conditions Potentially 

Harmful to Fish

Dissolved Oxygen Concentration, 

pH, and Temperature

In order to identify periods when conditions of dissolved 

oxygen concentration, pH, and temperature potentially 

harmful to fish were present in Upper Klamath Lake and 

the spatial extent of these conditions, hourly data were 

collected at each site of conditions when dissolved oxygen 

concentration was less than 4 mg/L, pH was greater than 

9.7, or temperature was greater than 28oC. These values are 

based on high stress thresholds for Upper Klamath Lake 

suckers (Loftus, 2001). The percentage of sites at which a 

potentially harmful condition was recorded at least once in 

a day was calculated, providing the “one-reading” statistic. 

Additionally, 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. 

The counts per day were divided by the total possible sitehours in the day (24 hours multiplied by the number of sites 

in Upper Klamath Lake), providing a percentage of site-hours 

in the day during which potentially harmful conditions were 

recorded, referred to as the “percent of site-hours” statistic. 

The “one-reading” statistic provides a measure of the physical 

presence of that condition in the lake. It also represents the 

maximum percentage of the lakewide site-hours that would 

meet the criterion if, at each site where at least one reading 

met the condition, the condition persisted for an entire 24 

hours. The “percent of site-hours” statistic coupled with 

the “one-reading” statistic, then, provides a measure of the 

persistence of the condition throughout the day at sites where 

that condition was recorded. These statistics were graphed as a 

time series of daily values for dissolved oxygen concentration, 

pH, and temperature. Graphs of these statistics for dissolved 

oxygen concentration and pH are shown in figure 24. Only one 

observation of temperature above 28 oC was made during the 

2005 field season, at the upper sonde at site MDT on August 

7 at 7:00 p.m. Because temperature exceeding the criterion 

was observed only once, a graph of potentially harmful 

temperature is not shown.

Figure 24 reflects the primary LDOE of 2005, which 

occurred in late July and early August (fig. 20), and shows 

that when this event occurred, it was not severe. Most of the 

16 Upper Klamath Lake sondes (50–60 percent) recorded a 

dissolved oxygen concentration of less than 4 mg/L at least 

once during each day in mid-July through early August, but 

only 25–35 percent of the site hours recorded these conditions 

during this period. This pairing of the “one reading” and 

“site hours” statistics indicates two possible scenarios: either 

the condition was widespread but marginally persistent 

throughout the day at all sites recording this condition, or the 

condition was widespread but persistent at only a few of the 

sites that logged the condition. Time series of daily median 

dissolved oxygen percent saturation for each Upper Klamath 

Lake sonde (fig. 21) indicated that the latter explanation is 

most likely. (Note that water temperatures were around 21°C 

throughout Upper Klamath Lake at this time, corresponding to 

52 percent dissolved oxygen saturation when dissolved oxygen 

concentration is 4 mg/L, denoted by the red line on the plots 

in (figure 21). Sites in and northwest of the trench were the 

only sites having notably low daily median dissolved oxygen 

concentration at this time, and only sites in the trench had 

daily median dissolved oxygen concentration near zero percent 

saturation. At sites where potentially harmful dissolved 

oxygen concentrations did not persist throughout the day (sites 

out of and away from the trench), the previously discussed 

timing histograms (fig. 23) indicate that when these conditions 

occurred, they occurred during the early morning hours. 
Occurrence and Duration of Water Quality Conditions Potentially Harmful to Fish 37

Figure 24. Lakewide measures of conditions potentially harmful to fish in Upper Klamath Lake, Oregon, 2005: dissolved 

oxygen concentration less than 4 milligrams per liter, and pH greater than 9.7. 

OR19_0158_UKL_fig_24

DISSOLVED OXYGEN CONCENTRATION LESS THAN 4 MILLIGRAMS PER LITER

PERCENT

1 JUNE 1 JULY 1 AUGUST 1 SEPTEMBER 1 OCTOBER

Period of seasonal bloom decline

0

20

40

60

80

100

0

20

40

60

80

100

pH GREATER THAN 9.7

Percentage of daily site-hours 

meeting condition

Percentage of sites with at least 

one reading meeting condition

Potentially harmful pH values were measured within a 

large portion of the lake twice during the 2005 field season, 

from late June through mid-July and again from mid-August 

through early September. As with the LDOE previously 

described, conditions resulting from potentially harmful 

pH values occurred during these times and may have been 

persistent throughout the day at few sites when this condition 

was present. Because of the positive relation between 

dissolved oxygen concentration and pH, and the decreased 

dissolved oxygen concentrations at sites in and northwest of 

the trench, sites with persistently high pH were mostly east 

and south of the trench.

Ammonia

When high ammonia concentrations occur concurrently 

with high pH and temperature, a significant fraction of the 

total concentration is present in the un-ionized ammonia 

form (fig. 25), which is particularly toxic to aquatic life. 

The dependence on pH is stronger than the dependence on 

temperature; at 22oC and a pH of 9, for example, 31 percent 

of the ammonia will be in un-ionized form, but at 22oC 

and a pH of 9.5, the fraction increases to 59 percent (U.S. 

Environmental Protection Agency, 1998). Because ammonia 

concentration tended to peak when the bloom declined (with 

an associated decrease in pH), the maximum concentrations 

of un-ionized ammonia, which occurred simultaneously 

with high pH values, often were mismatched in time from 

maximum concentrations of total ammonia. Mean lethal 

un-ionized ammonia concentration to larval and juvenile 

suckers, as determined by Saiki and others (1999), ranged 

between 480 and 1,290 μg/L. Concentrations of un-ionized 

ammonia measured in Upper Klamath Lake did not reach the 

concentrations determined to be lethal to endangered larval 

and juvenile suckers. Because ammonia was released into 

the water column concurrently with AFA bloom decline and 

decreasing pH, the maximum concentrations of un-ionized 

ammonia, which occurred simultaneously with high pH values 

at the peak of the bloom, were offset in time from maximum 

concentrations of total ammonia. 

Although un-ionized ammonia concentrations did not 

reach lethal values, the combination of low dissolved oxygen 

and high un-ionized ammonia concentrations was stressful 

to fish, probably making them more susceptible to disease. 

Lethal concentrations of un-ionized ammonia might occur for 

short periods of time or in localized areas more susceptible to 

extremes in temperature and pH, such as shallow water.
38 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

OR19_0158_UKL_fig_25

0

200

400

600

800

MDN

EXPLANATION

WMR

MDL 

HDB 

MDT (GRAPH A ONLY) 

EPT (GRAPH A ONLY) 

MDT Upper

GRAPHS B, C AND D ONLY

EPT Upper

MDT Lower

EPT Lower

10 JUNE 1 JULY 1 AUGUST

2005

1 SEPTEMBER 1 OCTOBER

A

B

C

D

CHLOROPHYLL a CONCENTRATION,

IN MICROGRAMS PER LITER

TOTAL AMMONIA 

CONCENTRATION, IN MICROGRAMS 

PER LITER

UN-IONIZED AMMONIA

CONCENTRATION, IN

MICROGRAMS PER LITER

BLOOM

DECLINE

0

200

400

600

800

1,000

1,200

0

50

100

150

200

7

8

9

10

pH

MDT on Sept. 20; 2,055 Mg/L

MDT on Sept. 13; 1,121 Mg/L

HDB on Sept. 19; 1,354 Mg/L

Figure 25. (A) chlorophyll a concentration, (B) total ammonia concentration, (C) un-ionized ammonia concentration, 

and (D) pH in water samples collected at all sites, Upper Klamath Lake, Oregon, 2005. 
Summary and Conclusions 39

Summary and Conclusions

Water quality degradation in Upper Klamath Lake has 

led to critical fishery concerns for the region, including the 

listing of Lost River and shortnose suckers as endangered 

in 1988. The algal community of the lake has shifted to a 

near monoculture of the cyanobacterium (blue-green alga) 

Aphanizomenon flos-aquae (AFA) during summer, massive 

blooms of which have been directly related to episodes of 

poor water quality in Upper Klamath Lake. The growth and 

decomposition of AFA blooms in the lake frequently cause 

extreme water quality conditions characterized by high pH 

values (9‐10), widely variable dissolved oxygen conditions 

(anoxic to supersaturated), and high un-ionized ammonia 

concentrations (greater than 0.5 mg/L). Large blooms of 

AFA and the associated water quality concerns also occur in 

Agency Lake.

The U.S. Geological Survey (USGS) began monitoring 

water quality in Upper Klamath Lake in 2002 in cooperation 

with the Bureau of Reclamation to supplement data collected 

previously by the Klamath Tribes since 1990. During 2002-04, 

the USGS water quality monitoring program study area was 

limited mostly to the northern one-third of Upper Klamath 

Lake. In 2005, the existing water quality monitoring program 

expanded to become lakewide in Upper Klamath Lake and to 

include Agency Lake.

Data from multiparameter continuous water quality 

monitors, physical water samples, and meteorological 

sites were collected from Upper Klamath and Agency 

Lakes, Oregon, in 2005 to assess water quality conditions 

and processes. The data show that the significant factors 

controlling water quality processes included AFA dynamics, 

lake bathymetry, and wind speed.

Diel photosynthesis–respiration processes and the 

seasonal pattern of changes in AFA biomass (inferred from 

chlorophyll a concentrations) lead to variation in dissolved 

oxygen, orthophosphate, and ammonia concentrations; 

pH; and specific conductance values. In previous years, 

AFA biomass increased markedly, then sharply declined, 

resulting in low dissolved oxygen concentrations and release 

of nutrients to the water column. In 2005, chlorophyll a

concentrations increased in early July and then sharply 

declined during late July–early August. Daily medians 

calculated for all sites in Upper Klamath Lake show 

seasonally increased dissolved oxygen concentrations 

coinciding with an increase in pH in early July, followed 

by a decrease in dissolved oxygen concentrations and pH 

values and an increase in specific conductance values in late 

July–early August. In addition, orthophosphate and ammonia 

concentrations increased during the bloom decline in late 

July–early August. These water quality changes coincide with 

the AFA bloom in early July and decline in late July–early 

August. The inverse relation of specific conductance with 

dissolved oxygen concentration and pH observed from 

mid-July through early August in Upper Klamath Lake was 

attributable to the release of ionic nutrients from decaying 

AFA cells during the bloom decline.

Qualitative observations of the AFA bloom, verified by 

chlorophyll a concentration data provided by the Klamath 

Tribes, were directly related to patterns observed in dissolved 

oxygen concentration and pH in Agency Lake. Differences 

in water quality patterns observed between Upper Klamath 

Lake and Agency Lake were attributable to differences in 

bloom dynamics between the two lakes. Variability in specific 

conductance at sites near rivers and wetlands in Agency Lake 

and Upper Klamath Lake suggests that these influent waters 

may locally influence specific conductance.

In dissolved oxygen production and consumption 

experiments, the maximum observed dissolved oxygen 

production was 1.47 milligrams per liter per hour of oxygen, 

and the maximum observed dissolved oxygen consumption 

was –0.73 milligrams per liter per hour of oxygen. Dissolved 

oxygen production in the upper water column declined 

through July and recovered through August. The observed 

pattern was similar to that of dissolved oxygen concentrations 

measured by continuous water quality monitors in the 

lake during this time. In addition to seasonal changes, 

photosynthesis and respiration processes affect the timing of 

the daily extreme water quality parameters. At shallow sites, 

the daily extreme water quality parameter readings occurred 

during relatively well-defined time intervals linked to diel 

patterns of sunlight and solar heating. These time intervals 

became broader and less well defined at deeper sites as a result 

of the increased potential for water column stratification. 

Coupled with AFA dynamics, wind speed and 

temperature variations also effect diel changes in dissolved 

oxygen concentrations in Upper Klamath Lake. In response 

to episodes of low wind speed or to a deep-water-column 

configuration, the lower portion of the water column can be 

independent from the upper column and more susceptible to 

oxygen consuming biological processes that lower dissolved 

oxygen concentrations.

Bathymetry was the primary factor influencing the 

magnitude of the seasonal pattern of dissolved oxygen 

concentration at the deepest and shallowest monitoring 

locations around Upper Klamath Lake. Wind-driven 

circulation patterns determined the degree to which the 

seasonal extremes occurred at sites of similar depth that 

were either northwest or south and east of the trench under 

the prevailing clockwise circulation pattern. Because the 

northern part of the lake (preferred habitat for adult suckers) 

receives waters from the trench under the dominant circulation 

pattern, the monitoring sites there tended to record lower 

seasonal minimums of dissolved oxygen concentration than 

did the sites in the lake that are south and east of the trench. 
40 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

These factors also influenced shorter timescale dynamics of 

dissolved oxygen concentration, as evidenced by a mass of 

water with a low dissolved oxygen concentration that was first 

observed in the trench and migrated to subsequent sites along 

the dominant flow path during a period of 1–2 days. This event 

illustrates how oxygen-depleted water emerging from the 

trench is re-oxygenated as it travels through shallower areas in 

the northern part of the lake. 

Monitoring water quality parameters (temperature, 

dissolved oxygen concentration and saturation, pH, and 

un-ionized ammonia concentration) allowed identification 

of the extent and duration of conditions potentially harmful 

to fish. Although high temperatures may have caused stress 

to fish and other aquatic species during the 2005 study, 

water temperatures never exceeded the critical value of 

28oC in Upper Klamath Lake. Periods of dissolved oxygen 

concentrations potentially harmful to fish were largely 

confined to the trench and a few sites in the northern part of 

the lake and were not persistent. On two occasions pH values 

potentially harmful to fish occurred within a significant 

portion of Upper Klamath Lake, but the data showed that these 

values were not persistent. Un-ionized ammonia did not reach 

concentrations potentially harmful to fish.

The expanded network of continuous water quality 

monitoring sites, physical water samples, and meteorological 

sites provided information critical to understanding lakewide 

water quality dynamics in Upper Klamath Lake. The network 

provides a greater awareness of water quality conditions 

in relation to circulation and water column stratification 

patterns and is central to future water quality modeling 

efforts. Continued operation of the monitoring sites to collect 

a long-term data set also would enable the identification of 

water quality status and trends in Upper Klamath Lake. Future 

monitoring would be enhanced by the addition of two sites to 

better quantify conditions surrounding the trench. One of the 

new sites would best be located between sites MDL and MDT, 

and the other between sites EPT and MDN, to better quantify 

the differences in algal dynamics between these sites. 

Atmospheric conditions were monitored at 

meteorological sites over and around Upper Klamath Lake. 

Patterns of air temperature and relative humidity were 

consistent with the hot, dry summers typical of the Upper 

Klamath Lake basin. Wind speed and direction measurements 

showed significant differences in wind patterns around the 

lake, particularly between the northern part of the lake and 

areas to the south. The finer resolution of meteorological 

conditions in and around Upper Klamath Lake provided by 

these meteorological sites will improve water quality modeling 

results and enhance understanding of water quality dynamics 

in Upper Klamath Lake.

Acknowledgments

The commitment of Rip Shively and Scott Vanderkooi 

of the USGS Klamath Falls Field Station is gratefully 

acknowledged for facilitating the water quality field program 

with the use of boats, trucks, field equipment, and office 

and laboratory facilities. 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 of this study, and their efforts are gratefully 

acknowledged: Jason Cameron from the Bureau of 

Reclamation in Klamath Falls; Christine Adelsberger, Melissa 

Berhardt, Pamela Burns, Anna Glass, and Jim Harris from 

the USGS in Klamath Falls; Amy Brooks, Micelis Doyle, 

and Matt Johnston from the USGS Oregon Water Science 

Center. Reviews by John Williams and Annett Sullivan from 

the USGS Oregon Water Science Center; and Jennifer Graham 

and Andrew Ziegler from the USGS in Lawrence, Kansas, 

significantly improved this manuscript.

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Appendix A 43

AMMONIA

0

50

100

N=10 N=12

N=10

N=10

N=9

CHLOROPHYLL a 0

10

20

30

40

50

60

70

80

NITRITE-PLUSNITRATEORTHOPHOSPHATE TOTAL

PHOSPHORUS

MICROGRAMS PER LITER

MICROGRAMS PER LITER

0

10

20

30

40

10th percentile

25th percentile

Median

75th percentile

90th percentile

Data value represents the 95th percentile

Concentrations, in micrograms per liter N= Number of points

Data value represents the 5th percentile

EXPLANATION

800

780

Figure A1. Distribution of differences from the median 

concentrations among split sample interlaboratory 

measurements of samples from the water quality data 

collection program in Upper Klamath and Agency Lakes, 

Oregon, 2005.

Appendix A. Quality Control and Quality Assurance of Water Samples

Thirty percent of the samples to be analyzed for dissolved 

nutrient concentration and 35 percent of the samples to be 

analyzed for total phosphorus concentration were for quality 

assurance purposes, which included field blanks (the first 

sample collected every week) and either a split sample 

or a method replicate (each type every other week). Field 

blanks are samples of reagent grade inorganic blank water 

processed onsite through clean sampling equipment, before an 

environmental sample is collected. Analysis of blank samples 

determines if the processes of collection, handling, transport, 

and analysis cause measurable contamination. Split samples 

are environmental water samples collected once and divided 

into two samples that are used to determine the variability in 

the analytical methods. Replicate samples are environmental 

samples collected twice in rapid succession from the same 

location and analyzed to determine both the variability of the 

system and the variability in the analytical methods. 

The results of the quality assurance sampling indicated 

that precision and accuracy were acceptable and the variability 

in sampling and processing was lower than seasonal variability 

(table A1). The field blank concentrations of total phosphorus 

and orthophosphate were less than the laboratory minimum 

reporting level. The same was true for the field blank 

concentration of nitrite-plus-nitrate, except that one outlier 

sample held some contamination. The field blank samples 

of ammonia revealed some contamination, although it was 

minimal compared to the concentrations of the environmental 

samples. Ammonia concentration in the field blanks was 

considerably reduced, compared to that in previous years, 

by the use of capsule filters. Contamination of ammonia 

blanks in 2003 and 2004 was attributable to atmospheric 

deposition (Wood and others, 2006). Twice during the season, 

split samples were sent to two other laboratories in addition 

to NWQL and Aquatic Analysts. The interlaboratory split 

samples were analyzed to determine variability in analytical 

methods between the laboratories. In addition, some of the 

split samples were collected to examine variability that might 

be expected as a result of differences in the protocols used by 

USGS and those used by the Klamath Tribes in the collection 

of their long-term biweekly dataset. Box plots showing the 

statistical distribution of the difference between individual 

split sample concentrations and the median concentration 

of all of the split samples taken from the same churn splitter 

indicate that the variance in laboratory processing and analysis 

is generally low, except in the case of ammonia (fig. A1). 

The outliers in the distribution of the ammonia splits can all 

be attributed to the use of a non-USGS protocol and a single 

non-USGS laboratory. The reason for the high ammonia 

concentrations in these samples has yet to be determined, but 

the results do not indicate that the rest of the ammonia samples 

collected as part of this monitoring program are biased high. 
44 Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

Table A1. Quality-assurance results for water quality data collection program, Upper Klamath and Agency Lakes, Oregon, 

2005.

[mg/L, milligram per liter; MRL, minimum reporting level. >, greater than; ≤, less than or equal to]

Blank samples

Analyte

Number of samples Percentage of 

blank samples

MRL 

(mg/L)

Number of 

blank samples 

≤MRL

Value of blank samples 

>MRL (mg/L)

Blank Total Maximum Median

Orthophosphate-P 41 198 21 0.006 41 – –

Ammonia-N 41 198 21 .010 24 0.043 0.015

Nitrite-plus-nitrate-N 41 198 21 .016 40 .022 –

Total phosphorus 41 170 24 .004 41 – –

Chlorophyll a 3 130 2 – – – –

Split samples

Analyte

Number of samples

Percentage of 

split samples

Difference between split samples

Split Total Median 

(mg/L)

Median

(percent)

Orthophosphate-P 6 198 3 0.001 3

Ammonia-N 6 198 3 .002 11

Nitrite-plus-nitrate-N 6 198 3 .000 0

Total phosphorus 5 170 3 .010 8

Chlorophyll a 5 130 4 0.035 14

Replicate samples

Analyte Number of samples Percentage of 

replicate 

samples

Difference between replicate samples

Replicate Total Median

(mg/L)

Median 

(percent)

Orthophosphate-P 10 198 5 0.001 2

Ammonia-N 10 198 5 .003 13

Nitrite-plus-nitrate-N 10 198 5 .000 0

Total phosphorus 12 170 7 .024 13

Chlorophyll a 9 130 7 0.019 9
Manuscript approved for publication, February 20, 2008

Prepared by the USGS Publishing Network, 

Bob Crist

Bill Gibbs

Ellen Hardy

Jackie Olson

Bobbie Jo Richey 

Sharon Wahlstrom

Cheri Yoesting

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

Director, Oregon Water Science Center

U.S. Geological Survey 

2130 SW 5th Avenue

Portland, Oregon 97201

http://oregon.usgs.gov/
Hoilman and others— Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005—Scientific Investigations Report 2008–5026