Prepared in cooperation with the Bureau of Reclamation 

Water-Quality Data from Upper Klamath and Agency Lakes, 

Oregon, 2009–10

Open-File Report 2012–1142

U.S. Department of the Interior 

U.S. Geological Survey 
Cover: Meteorological and water quality monitoring site MDN on Upper Klamath Lake, Oregon, with Mt. McLoughlin 

in the background. (Photograph by D. Blake Eldridge, U.S. Geological Survey, July 12, 2011.) 
Water-Quality Data from Upper Klamath and Agency 

Lakes, Oregon, 2009–10

By D. Blake Eldridge, Sara L. Caldwell Eldridge, Liam N. Schenk, Dwight Q. Tanner, and Tamara M. Wood 

Prepared in cooperation with the Bureau of Reclamation 

Open-File Report 2012–1142

U.S. Department of the Interior 

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

 KEN SALAZAR, Secretary 

U.S. Geological Survey 

Marcia K. McNutt, Director 

U.S. Geological Survey, Reston, Virginia: 2012 

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Suggested citation: 

Eldridge. D.B., Caldwell Eldridge, S.L., Schenk, L.N., Tanner, D.Q., and Wood, T.M., 2012, Water-quality data from 

Upper Klamath and Agency Lakes, Oregon, 2009–10: U.S. Geological Survey Open-File Report 2012–1142, 32 p. 

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the 

U.S. Government 

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

reproduce any copyrighted material contained within this report.
iii

Contents

Significant Findings ........................................................................................................................................................ 1

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

Background ................................................................................................................................................................ 2

Description of Study Area .......................................................................................................................................... 5

Methods ......................................................................................................................................................................... 6

Continuous Water-Quality Monitors ........................................................................................................................... 6

Collection of Water-Quality Samples .......................................................................................................................... 8

Meteorological Sites ................................................................................................................................................... 9

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

Quality Control ............................................................................................................................................................. 10

Results ......................................................................................................................................................................... 13

Water-Quality Monitors ............................................................................................................................................ 13

Water-Quality Samples ............................................................................................................................................ 18

Meteorological Data ................................................................................................................................................. 24

Acknowledgments........................................................................................................................................................ 28

References Cited ......................................................................................................................................................... 28

Appendix A. Quality-Control Data for Water-Quality Samples ..................................................................................... 31

Appendix B. Data from Water-Quality Samples ........................................................................................................... 31

Appendix C. Concentrations of Un-Ionized Ammonia in Water-Quality Samples ........................................................ 31

Figures

Figure 1. Map showing location of meteorological (MET) sites, continuous water-quality monitoring sites, and 

continuous water-quality monitoring and sampling sites, Upper Klamath and Agency Lakes, Oregon, 2009–10.. .... 3

Figure 2. Graphs showing lakewide daily median dissolved oxygen concentration, dissolved oxygen percent 

saturation, pH, specific conductance, and water temperature in Upper Klamath Lake, Oregon, 2009–10.. ............ 14

Figure 3. Graphs showing dissolved oxygen concentration, dissolved oxygen percent saturation, pH, specific 

conductance, and temperature in Agency Lake, Oregon, 2009. .............................................................................. 16

Figure 4. Graphs showing dissolved oxygen concentration, dissolved oxygen percent saturation, pH, specific 

conductance, and temperature in Agency Lake, Oregon, 2010. .............................................................................. 17

Figure 5. Graphs showing concentrations of chlorophyll a, total phosphorus, total nitrogen, orthophosphate, 

ammonia, and nitrite plus nitrate, Upper Klamath Lake, Oregon, 2009.................................................................... 19

Figure 6. Graphs showing concentrations of chlorophyll a, total phosphorus, total nitrogen, orthophosphate, 

ammonia, and nitrite plus nitrate, Upper Klamath Lake, Oregon, 2010.................................................................... 20

Figure 7. Graphs showing concentrations of particulate nitrogen, particulate phosphorus, particulate carbon, and 

particulate inorganic phosphourus, Upper Klamath Lake, Oregon, 2009. ................................................................ 22

Figure 8. Box and whisker graph showing lakewide ratios for particulate carbon to particulate phosphorus (C:P), 

Upper Klamath Lake, Oregon, 2009. ....................................................................................................................... 23

Figure 9. Box and whisker graph showing lakewide ratios for particulate nitrogen to particulate phosphorus (N:P), 

Upper Klamath Lake, Oregon, 2009. ....................................................................................................................... 23

Figure 10A. Box and whisker graphs showing daily median wind speed and solar radiation at WRW meteorological 

site from June through September, Upper Klamath Lake, Oregon, 2009–10. ......................................................... 24
iv

Figure 10B. Box and whisker graphs showing daily median wind air temperature and relative humidity at WRW 

meteorological site from June through September, Upper Klamath Lake, Oregon, 2009–10. ................................. 25

Figure 11. Histograms showing wind speed and direction for meteorological (MET) sites near Upper Klamath Lake, 

Oregon, 2009. .......................................................................................................................................................... 26

Figure 12. Histograms showing wind speed and direction for meteorological (MET) sites near Upper Klamath Lake, 

Oregon, 2010. .......................................................................................................................................................... 27

Tables

Table 1. Summary of U.S. Geological Survey monitoring studies on Upper Klamath Lake, Oregon, since 2002. ..... 4

Table 2. Continuous water-quality monitoring and sampling sites, Upper Klamath and Agency Lakes, Oregon, 

2009–10. .................................................................................................................................................................... 6

Table 3. Meteorological sites and parameters measured, Upper Klamath Lake, Oregon, 2009–10.......................... 9

Table A1. Quality control data: blank samples from Upper Klamath Lake, Oregon, 2009 ....................................... 31

Table A2. Quality control data: routine split samples from Upper Klamath Lake, Oregon, 2009 ............................. 31

Table A3. Quality control data: replicate samples from Upper Klamath Lake, Oregon, 2009 .................................. 31

Table A4. Quality control data: interlaboratory measurements of split samples from Upper Klamath Lake, Oregon, 

2009 ......................................................................................................................................................................... 31

Table A5. Quality control data: nutrient spiked samples from Upper Klamath Lake, Oregon, 2009 ........................ 31

Table A6. Quality control data: blank samples from Upper Klamath Lake, Oregon, 2010 ....................................... 31

Table A7. Quality control data: routine split samples from Upper Klamath Lake, Oregon, 2010 ............................. 31

Table A8. Quality control data: replicate samples from Upper Klamath Lake, Oregon, 2010 .................................. 31

Table A9. Quality control data: interlaboratory measurements of split samples from Upper Klamath Lake, Oregon, 

2010 ......................................................................................................................................................................... 31

Table A10. Quality control data: nutrient spiked samples from Upper Klamath Lake, Oregon, 2010 ...................... 31

Table B1. Data from water-quality samples, Upper Klamath Lake, Oregon, 2009. ................................................. 31

Table B2. Data from water-quality samples, Upper Klamath Lake, Oregon, 2010. ................................................. 31

Table C1. Concentrations of un-ionized ammonia in water-quality samples, Upper Klamath Lake, Oregon, 2009. 31

Table C2. Concentrations of un-ionized ammonia in water-quality samples, Upper Klamath Lake, Oregon, 2010. 31
v 

Conversion Factors, Datums, and Abbreviations and Acronyms

Conversion Factors 

Multiply By To obtain

liter (L) 1.057 quart (qt)

meter (m) 3.281 foot (ft) 

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

microgram per liter (μg/L) 1.0 part per billion (ppb)

micrometer (μm) 3.937 × 10–5inch (in)

milligram per liter (mg/L) 1.0 part per million (ppm)

milliliter (mL) 0.03382 fluid ounce (oz)

millimeter (mm) 0.03937 inch (in)

square kilometer (km2) 0.3861 square mile (mi2)

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

°F=(1.8×°C)+32. 

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

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). 

Elevation, as used in this report, refers to the vertical distance above the Bureau of Reclamation datum. 
vi

Abbreviations and Acronyms 

Abbreviation or Acronym Definition

ACS American Chemical Society

ADAPS Automated Data Processing System

AFA Aphanizomenon flos-aquae

BRPNL Bureau of Reclamation Pacific-Northwest Regional Laboratory

CBL Chesapeake Biological Laboratory

DOC dissolved organic carbon

MRL minimum reporting level

NWIS National Water Information System

NWQL National Water Quality Laboratory

ORWSC Oregon Water Science Center

SRWQL Sprague River Water Quality Laboratory

USGS U.S. Geological Survey
1 

Water-Quality Data from Upper Klamath and Agency 

Lakes, Oregon, 2009–10

By D. Blake Eldridge, Sara L. Caldwell Eldridge, Liam N. Schenk, Dwight Q. Tanner, and Tamara M. Wood 

Significant Findings 

The U.S. Geological Survey Upper Klamath 

Lake water-quality monitoring program collected 

data from multiparameter continuous waterquality monitors, weekly water-quality samples, 

and meteorological stations during 2009 and 

2010 from May through November each year. 

The results of these measurements and sample 

analyses, as well as quality-control data for the 

water-quality samples, are presented in this report 

for 14 sites on Upper Klamath Lake and 2 sites 

on Agency Lake. These 2 years of data 

demonstrate a contrast in the seasonal bloom of 

the dominant cyanobacterium, Aphanizomenon 

flos-aquae, that can be related to differences in 

the measured water quality and meteorological 

variables. Some of the significant findings from 

2009 and 2010 are listed below. 

Both 2009 and 2010 were characterized by 

two cyanobacteria blooms, but the blooms 

differed in timing and intensity. The first 

bloom in 2009 peaked in late June and at 

higher chlorophyll a concentrations at most 

sites than the first bloom in 2010, which 

peaked in mid-July. A major decline in the 

first 2009 bloom occurred in late July and 

was followed by a second bloom that peaked 

at most sites in mid-August and persisted 

through September. The decline of the weaker 

first bloom in 2010 occurred in early August 

and was followed by a more substantial 

second bloom that peaked between late 

August and early September at most sites. 

Dissolved oxygen minima associated with 

bloom declines occurred approximately 

2 weeks earlier in 2009 (mid-July) than in 

2010 (early August). pH maxima associated 

with rapid bloom growth occurred in late June 

and again in mid-August in 2009 and in midJuly and late August in 2010. 

In both years, the maxima for total 

phosphorus and total nitrogen concentrations 

coincided with the chlorophyll a maximum. 

The maxima for dissolved nutrient 

concentrations (orthophosphate, ammonia, 

and nitrite plus nitrate) coincided with the 

declines of the first blooms. 

Total particulate carbon, total particulate 

nitrogen, and total particulate phosphorus 

concentrations were measured in 2009 only. 

The ratios of carbon to phosphorus and 

nitrogen to phosphorus in particulates were 

the highest of the entire season during the 

rapid growth phase of the first bloom and 

were the lowest of the season during the 

decline of the first bloom. These ratios 

increased with the onset of the second bloom 

in that year, but to a lesser degree. 

Meteorological data show that 2009 was 

warmer (particularly in June and July), less 

windy, and more humid early in the season 

than 2010. The difference in water 

temperatures reflected the difference in air 

temperatures in that the lakes were warmer in 

2009 than in 2010 starting in early May, when 

the sensors were deployed, through most of 

June. Water temperature peaked at a higher 

value in 2009, and there were more clear days 

in June 2009 than in June 2010. 
2 

Introduction

Background 

Severe water-quality problems in Upper 

Klamath Lake (fig. 1) led to the listing of Lost 

River suckers (Deltistes luxatus) and shortnose 

suckers (Chasmistes brevirostris) as endangered 

in 1988 (Stubbs and White, 1993). In addition to 

several periods of high mortality, low rates of 

recruitment from the juvenile to the spawning 

adult stages in these fish populations have also 

been noted (Janney and others, 2008). This

change in the sucker age demographic may be 

linked to poor water quality associated with 

phytoplankton growth and fluctuations in water

chemistry. Since the construction of the Link 

River Dam (fig. 1) in 1921 and other

anthropogenic changes to the surrounding 

watershed, hypereutrophication of Upper 

Klamath Lake has caused the phytoplankton 

community in the lake to shift to a near 

monoculture of the cyanobacterium 

Aphanizomenon flos-aquae (AFA) during the 

summer (Kann, 1998; Perkins and others, 2000). 

Massive blooms and subsequent declines in 

abundance of the phytoplankton directly coincide 

with episodes of high pH (> 9), widely variable 

and often extreme dissolved oxygen

concentrations (anoxic to supersaturated), and 

high un-ionized ammonia concentrations (> 0.5 

mg/L as N; Hoilman and others, 2008; 

Lindenberg and others, 2009). Large AFA 

blooms and the accompanying degraded waterquality conditions also occur annually in Agency 

Lake, although the intensity and duration of such 

conditions usually differ from those in Upper 

Klamath Lake. 

The U.S. Geological Survey (USGS), in 

cooperation with the Bureau of Reclamation, 

began monitoring Upper Klamath Lake water 

quality in 2002 (table 1). From 2002 through 

2004, continuous monitoring was limited to the 

northern part of the lake in support of USGS 

telemetry tracking of endangered adult suckers 

(Wood and others, 2006). These 3 years of 

monitoring showed that the timing and severity of 

poor water-quality conditions in Upper Klamath 

Lake were highly variable from year to year. 

However, in each year, seasonal patterns of low 

dissolved-oxygen concentrations and high pH 

were well correlated with the dynamics of annual 

AFA blooms, and seasonally low dissolvedoxygen concentrations often occurred with the 

decline of the first AFA bloom. High fish 

mortality in 2003 was associated with a 

particularly severe low dissolved-oxygen event 

that coincided with a bloom decline at the end of 

July (Banish and others, 2009). 

In 2005, the USGS water-quality monitoring 

program expanded for Upper Klamath Lake and 

added monitoring sites in Agency Lake (table 1). 

Meteorological stations were established around 

the shoreline of Upper Klamath Lake, in addition 

to the two floating rafts used in previous years, to 

provide greater spatial resolution of wind data for

a hydrodynamic model (Wood and others, 2008; 

Hoilman and others, 2008). These stations also 

collected air temperature, relative humidity, and 

solar radiation data for use in a heat transport 

model (Wood and others, 2008). Monitoring in 

2005 included 15 continuous water-quality 

monitors at 13 sites in Upper Klamath Lake and 2 

monitors in Agency Lake that recorded hourly 

water temperature, pH, specific conductance, and 

dissolved oxygen concentration or percent 

saturation. At three sites in Upper Klamath Lake, 

where the depth was greater than 4 m, monitors 

were deployed at 1 m below the water surface 

and at 1 m above the lake bottom. At six sites, 

MDN, WMR, EPT, MDT, HDB, and MDL, lightand dark-bottle experiments were conducted to 

measure oxygen production and consumption 

(Hoilman and others, 2008). Samples to be 

analyzed for chlorophyll a and nutrients were 

also collected at these six sites. The results of the 

monitoring program in 2005 are summarized and 

interpretation of the data is provided in Hoilman 

and others (2008). 
3 

Figure 1. Map showing location of meteorological (MET) sites, continuous water-quality monitoring sites, and 

continuous water-quality monitoring and sampling sites, Upper Klamath and Agency Lakes, Oregon, 2009–10. 

Continuous monitoring and sampling site descriptions are shown in table 2, and meteorological station descriptions 

are shown in table 3.
4

Table 1. Summary of U.S. Geological Survey monitoring studies on Upper Klamath Lake, Oregon, since 2002. 

[Dissolved nutrients include ammonia plus ammonium, orthophosphate, and nitrite plus nitrate in all years. Although some years have the same number of 

continuous monitoring and/or water sampling sites, the locations of these sites may have changed. The number of continuous monitoring sites in Upper Klamath 

and Agency Lakes is shown. Phaeophytin a concentrations were also measured in all chlorophyll a samples but are not included in the table for simplicity. 

Floating meteorological stations were located at sites MDN and MDL between 2006 and 2010. DO, dissolved oxygen; SC, specific conductance; UKL, Upper 

Klamath Lake; Agency, Agency Lake; DOC, dissolved organic carbon; TSS, total suspended solids; RH, relative humidity] 

Study 

year

Number of 

continuous

monitoring 

sites

Continuously 

monitored 

parameters

Number, 

location of 

sampling 

sites

Parameters measured in 

water samples

Number of 

meteorological 

stations

Meteorological data 

(number of sites)

Additional 

data Reference(s)

2002 11

pH, DO, 

temperature, 

SC

4, Northern

UKL

chlorophyll a, total 

phosphorus, dissolved 

nutrients

2 Floating (profiling 

buoys)

Air temperature (1), Wind 

speed, direction (2), 

RH (1)

Profiling buoy 

at 2 sites

Wood and others, 

2006

2003 14

pH, DO, 

temperature, 

SC

3, Northern

UKL

chlorophyll a, total 

phosphorus, dissolved 

nutrients

2 Floating (profiling 

buoys)

Air temperature (1), Wind 

speed, direction (2), 

RH (1)

Profiling buoy 

at 2 sites

Wood and others, 

2006

2004 14

pH, DO, 

temperature, 

SC

4, Northern

UKL

chlorophyll a, total 

phosphorus, dissolved 

nutrients

2 Floating (profiling 

buoys)

Air temperature (1), Wind 

speed, direction (2), 

RH (1)

Profiling buoy 

at 2 sites

Wood and others, 

2006

2005 15

pH, DO, 

temperature, 

SC

6, UKL 

(lakewide); 

2, Agency

chlorophyll a, total 

phosphorus, dissolved 

nutrients

4 Land-based

2 Floating (profiling 

buoys)

Air temperature (3), Wind 

speed, direction (6), 

RH (3), Solar radiation (1)

DO production, 

consumption 

Hoilman and 

others, 2008

2006 19

pH, DO, 

temperature, 

SC

6, UKL 

(lakewide); 

2, Agency

chlorophyll a, total 

phosphorus, total nitrogen,

dissolved nutrients

4 Land-based

2 Floating (sites 

MDN, MDL)

Air temperature (5), Wind 

speed, direction (6), 

RH (5), Solar radiation (2)

DO production, 

consumption 

Lindenberg and 

others, 2009

2007 19

pH, DO, 

temperature, 

SC

6, UKL 

(lakewide); 

2, Agency

chlorophyll a, total 

phosphorus, total nitrogen,

dissolved nutrients, DOC

6 Land-based

2 Floating (sites 

MDN, MDL)

Air temperature (7), Wind 

speed, direction (8), 

RH (7), Solar radiation (4)

Microcystins, 

cylindrospermopsins

Kannarr and 

others, 2010; 

Eldridge and 

others, 2012

2008 19

pH, DO, 

temperature, 

SC

4, UKL 

(lakewide); 

2, Agency

chlorophyll a, total 

phosphorus, total nitrogen,

dissolved nutrients

6 Land-based

2 Floating (sites 

MDN, MDL)

Air temperature (7), Wind 

speed, direction (8), 

RH (7), Solar radiation (4)

Microcystins, 

cylindrospermopsins

Kannarr and 

others, 2010; 

Eldridge and 

others, 2012

2009 14

pH, DO, 

temperature, 

SC

5, UKL 

(lakewide); 

2, Agency

chlorophyll a, total 

phosphorus, total nitrogen,

dissolved nutrients, total 

particulate nutrients, TSS

4 Land-based

2 Floating (sites 

MDN, MDL)

Air temperature (6), Wind 

speed, direction (6), 

RH (6), Solar radiation (2)

Microcystins

Current study; 

Eldridge and 

others, 2012

2010 14

pH, DO, 

temperature, 

SC

4, UKL 

(lakewide); 

2, Agency

chlorophyll a, total 

phosphorus, total nitrogen,

dissolved nutrients

4 Land-based

2 Floating (sites 

MDN, MDL)

Air temperature (6), Wind 

speed, direction (6), 

RH (6), Solar radiation (2)

Microcystins

Current study; 

Eldridge and 

others, 2012
5 

In 2006, 23 continuous monitors were 

deployed at 19 sites in the open waters of Upper 

Klamath and Agency Lakes, but the locations of 

some sites were changed (table 1). Monitors were 

added at four new sites located 5–10 m from the 

shoreline of Upper Klamath Lake, and three sites 

were removed or consolidated. Light- and darkbottle experiments and weekly water samplings 

for the analyses of chlorophyll a and nutrients 

were continued at the same six sites as in 2005. 

The results of the monitoring program in 2006 

are summarized and interpretation of the data is 

provided in Lindenberg and others (2009). 

Continuous monitoring sites and 

meteorological stations in Agency Lake and in 

the open waters of Upper Klamath Lake were the 

same in 2007 and 2008 as in 2006 (two nearshore 

sites used in 2006 were moved in 2007). Water 

samples were collected at the continuous 

monitoring sites MDT, EPT, MDN, RPT (2007 

only), WMR, and HDB (2007 only). In 2007, the 

collection of samples for the determination of the 

concentration of dissolved organic carbon 

concentration was added to monitor conditions 

prior to and during the weeks following the 

breaching of levees at the Williamson River 

Delta. In addition, the 2007 sampling season was 

extended into November, and samples were 

collected until mid-October in 2008. The results 

of monitoring in 2007 and 2008 are summarized 

in Kannarr and others (2010). 

The long-term monitoring effort that began 

in 2005 continued in 2009–10 with some 

changes. This report presents the results of the 

2009–10 data-collection program, including data 

from continuous water-quality monitors, 

laboratory analyses of water samples, and data 

from meteorological stations. In both years, 16 

continuous water-quality monitors were operated 

at 14 sites in Upper Klamath Lake and Agency 

Lake, 5 fewer sites than in 2006–2008. The 

number of meteorological stations remained the 

same as in 2005 and 2006. In 2009, water 

samples were collected weekly for the analyses of 

chlorophyll a, total nutrients, dissolved nutrients, 

total particulate nutrients, total particulate carbon, 

and total suspended solids (TSS) from five 

continuous monitor sites, MDT, EPT, MDN, 

RPT, and WMR. Weekly water samples for the 

analyses of chlorophyll a, total nutrients, and 

dissolved nutrients were collected from four sites, 

MDT, EPT, MDN, and WMR in 2010 (water 

samples were not analyzed for total particulate 

carbon and nutrients in 2010). In 2009, the 

weekly collection of cyanotoxin (microcystins 

and cylindrospermopsins) data was added to the 

program (samples were collected less frequently 

for cyanotoxin analysis in 2007 and 2008). Those 

data are not discussed here, but are presented in 

Eldridge and others (2012). 

Description of Study Area

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

broad structural graben in south-central Oregon. 

Much of its 9,415-km2drainage basin is 

composed of volcanic deposits. The lake is large 

and shallow, with a surface area of 232 km2and 

an average depth of 2.8 m. The water depth 

throughout most of the lake (about 90 percent) is

less than 4 m; however, a narrow trench runs 

parallel to Eagle Ridge on the lake’s western 

shore, which has a full-pool depth of 

approximately 15 m at the deepest point. Agency 

Lake, just north of Upper Klamath Lake, adds 

about 38 km2of surface area to the Upper 

Klamath Lake–Agency Lake hydrologic system 

(Johnson, 1985). Agency Lake is also shallow, 

with a maximum depth of about 3 m and an 

average depth of 0.9 m. The largest single source 

of inflow to the lake is the mostly groundwaterfed Williamson River, which contributes nearly 

one-half, on an annual average, of incoming 

water (Hubbard, 1970) and enters Upper Klamath 

Lake near its northern end. Other tributaries to 

the system include the Wood River, Fourmile 

Canal, and Sevenmile Canal, which enter Agency 

Lake at its northern end (fig. 1). 

Upper Klamath Lake is a natural water body, 

but lake-surface elevation has been regulated 

since 1921, when the Link River dam (fig. 1) was 

completed at the southern outlet of the lake. The 

dam is operated by the Bureau of Reclamation. 
6 

The lake is now the primary water source for the 

Bureau of Reclamation’s Klamath Project, an 

irrigation system developed to supply water to 

farms and ranches in and around the Upper 

Klamath Basin (Bureau of Reclamation, 2000). 

Prior to autumn 2007, Agency Lake was 

connected to Upper Klamath Lake by a narrow 

channel (Agency Straits), but in October 2007 

levees surrounding the Tulana Farms portion of 

the Williamson River Delta (fig. 1) were 

breached as part of a major restoration project 

(Wong and others, 2010). In November 2008, 

levees around the Goose Bay portion of the delta 

were breached, and the current landscape 

configuration around the delta was created. Water 

can now move between Agency Lake and Upper 

Klamath Lake across the delta. The 2009 

monitoring season is the first in which the 

shoreline around the two lakes incorporated the

entire restored area of the delta. 

Methods

Continuous Water-Quality Monitors 

Two YSI model 600XLM continuous waterquality monitors (“sondes”) were deployed at 2 

sites in Agency Lake, and 14 sondes were 

deployed at 12 sites in Upper Klamath Lake (2 

sondes each were deployed at sites MDT and 

MDN; fig. 1, table 2). In Upper Klamath and 

Agency Lakes, 13 sondes were at 11 open-water 

sites (more than 10 m from shore), and 3 sondes 

were at 3 nearshore sites (5–10 m from shore or 

in reed beds adjacent to open water). All sondes 

recorded depth, dissolved oxygen concentration 

and percent saturation, pH, specific conductance, 

and water temperature at the beginning of every 

hour. Data were telemetered from a single site, 

MDN, in 2009 and 2010. 

Table 2. Continuous water-quality monitoring and sampling sites, Upper Klamath and Agency Lakes, 

Oregon, 2009–10.—continued

[Locations of sites are shown in figure 1. Sites are listed in order of decreasing depth. Vertical coordinate information 

is referenced to the Bureau of Reclamation datum, which is 1.78 feet above the National Geodetic Vertical Datum of 

1929 (NGVD 29). Horizontal coordinate information is referenced to the North American Datum of 1927 (NAD 27)]

Site name

Site name

abbreviation

USGS site

identification no.

Latitude

(north)

Longitude

(west)

Full-pool

measured 

depth

(meters)

Open-water sites

Middle of trench (lower) MDT-L 422305121553800 42°23'5.1'' 121°55'38.2'' 15.0

Middle of trench (upper) MDT-U 422305121553803 42°23'5.1'' 121°55'38.2'' 15.0

Eagle Point (lower) EPT-L 422559121574400 42°25'59.2'' 121°57'44.1'' 12.5

South end of trench (lower) SET-L 422128121530600 42°21'27.8" 121°53'05.9" 7.0

Midnorth (lower) MDN-L 422622122004000 42°26'21.5'' 122°00'40.0'' 4.2

Midnorth (upper) MDN-U 422622122004003 42°26'21.5'' 122°00'40.0'' 4.2

Modoc Rim MRM 422437121515200 42°24'37.3'' 121°51'52.4'' 3.7

Rattlesnake Point RPT 422042121513100 42°20'41.6'' 121°51'31.4'' 3.4

Agency North AGN 423335121564300 42°33'35.0'' 121°56'43.0'' 3.0

Fish Banks FBS 422808122024400 42°28'08.8'' 122°02'43.5'' 2.8
7 

Table 2. Continuous water-quality monitoring and sampling sites, Upper Klamath and Agency Lakes, 

Oregon, 2009–10.—continued

[Locations of sites are shown in figure 1. Sites are listed in order of decreasing depth. Vertical coordinate information 

is referenced to the Bureau of Reclamation datum, which is 1.78 feet above the National Geodetic Vertical Datum of 

1929 (NGVD 29). Horizontal coordinate information is referenced to the North American Datum of 1927 (NAD 27)]

Site name

Site name

abbreviation

USGS site

identification no.

Latitude

(north)

Longitude

(west)

Full-pool

measured 

depth

(meters)

Open-water sites

North Buck Island NBI 421838121513900 42°18'38.0'' 121°51'39.0'' 2.8

Williamson River outlet WMR 422719121571400 42°27'19.4'' 121°57'13.6'' 2.5

Agency South AGS 423124121583400 42°31'24.9'' 121°59'03.4'' 2.5

Nearshore sites

South Shore SSR 421410121492000 42°14'10.0" 121°49'20.0" 2.5

Goose Bay East GBE 422739121540800 42°27'38.8" 121°54' 7.5" 2.4

Williamson Delta West WDW 422842121584300 42°28'41.9" 121°58'43.4" 2.2

Sondes at most sites were placed horizontally 

in the water column 1 m from the lake bottom. 

Placing the sondes horizontally avoids sensor 

contact with the lake bottom in windy conditions 

and ensures that the depth sensor is located near 

the same depth as the other sensors, which are 

approximately 0.15 m below it on the sonde. At 

sites with a water depth of less than 2 m, sondes

were placed at the midpoint of the water column. 

The sonde depth of 1 m from the lake bottom was 

selected to provide data relevant to the bottomdwelling suckers. At MDN only, one sonde was 

installed vertically at 1 m between the sensors 

(pH, dissolved oxygen, and specific conductance) 

and the lake bottom, and another sonde was 

placed at 1 m between the sensors and the water 

surface to avoid damage to attached 

communication cables that were used for data 

telemetry. In addition, two sondes were placed 

horizontally on the same mooring at fixed depths 

of 1 m from the lake surface and at 1 m from the 

sediment at MDT to monitor water-quality 

conditions near the water surface and to provide 

comparisons to conditions near the lake bottom. 

Quality control of the data was determined 

by field information collected during weekly site 

visits and by processing the time series according 

to the procedures described in Wagner and others 

(2006). During site visits, sondes were cleaned 

and the depths at which they were located in the 

water column were confirmed. Prior to each 

cleaning, field measurements of dissolved oxygen 

concentration, pH, specific conductance, and 

temperature at the depth of the site sonde were 

recorded with a newly calibrated reference sonde 

to assess the site sonde’s performance. Site 

sondes were deployed for approximately 3 weeks 

before being replaced. After retrieval, the 

calibration of each site sonde was evaluated to 

measure calibration drift during deployment. The 

raw continuous data from site sondes were 

uploaded to the USGS automated data-processing 

system (ADAPS). Corrections to data due to 

biological fouling and calibration drift were 

calculated and applied in ADAPS according to 

Wagner and others (2006). 
8 

Collection of Water-Quality Samples 

Water samples were collected weekly 

between May 20, 2009, and September 28, 2009, 

and between May 12, 2010, and September 27, 

2010, according to established sampling 

protocols (U.S. Geological Survey, variously 

dated). Samples were analyzed for concentrations 

of total phosphorus, total nitrogen, chlorophyll a,

phaeophytin a, and dissolved nutrients: ammonia 

plus ammonium (hereafter referred to as 

ammonia), orthophosphate, and nitrite plus 

nitrate. Additionally, 2009 samples were 

analyzed for total suspended solids, total 

particulate carbon, total particulate nitrogen, total 

particulate phosphorus, particulate inorganic 

carbon, and particulate inorganic phosphorous. 

Sampling was conducted at the continuous waterquality monitoring sites MDT, EPT, MDN, and 

WMR in 2009 and 2010 and also at RPT in 2009 

only (fig. 1; RPT was not sampled in 2010). 

Water samples to be analyzed for total 

phosphorus, total nitrogen, chlorophyll a, and 

phaeophytin a were collected by integrating equal 

amounts of water over the depth of the water 

column (depth integration). Depth-integrated 

samples were collected in two 2-L polyethylene 

bottles held in a weighted cage. Bottle caps with 

two small ports, one for the inflow of water and 

another for the escape of displaced air, were used. 

The cage and sample bottles were lowered at a 

constant rate through the water column to within 

0.5 m from the bottom at sites less than 10.5 m 

(“shallow” sites: MDN, WMR, and RPT). At 

sites greater than 10.5 m (“deep” sites: EPT and 

MDT), samples were collected to a depth of 10 m 

in order to assure the integrity of the depth 

integration (sample collection bottles may fill 

completely before reaching the surface when 

sampling at depths greater than 10 m, which 

would prevent the sample from being collected 

evenly over the entire sampled depth). The 

contents of sample bottles from multiple 

collections at each site were composited and 

mixed in a churn splitter prior to filling analysis 

bottles. 

Water samples analyzed for dissolved 

nutrients (ammonia, orthophosphate, and nitrite 

plus nitrate), total suspended solids (TSS), total 

particulate carbon (TPC), particulate inorganic 

carbon (PIC), total particulate nitrogen (TPN), 

total particulate phosphorous (TPP), and 

particulate inorganic phosphorous (PIP) were 

collected from a point mid-depth in the water 

column at shallow sites. At deep sites, water was 

collected at two points in the water column (at 

one-quarter and three-quarters of the total depth). 

Samples were collected by lowering one end of 

the sample tubing fixed to a sonde to the 

appropriate depth in the water column, and lake 

water was pumped to the surface with a 

peristaltic pump. After purging the tubing for 2 

minutes with lake water, unfiltered samples for 

TSS, TPC, PIC, TPN, TPP, and PIP analyses 

were collected. Samples for dissolved nutrient 

analyses were filtered through a 0.45-μm capsule 

filter connected to the outflow end of the tubing. 

All water samples were chilled on site and 

during transport. Total phosphorus and total 

nitrogen samples were preserved immediately 

after collection with the addition of 1 mL of 4.5 

normal (4.5 N) sulfuric acid. Dissolved nutrient, 

total phosphorus, and total nitrogen samples were 

analyzed at the Sprague River Water Quality 

Laboratory (SRWQL) in Chiloquin, Oregon. 

Dissolved nutrient samples were analyzed using 

USGS methods I-2525-89 and I-2522-90 for 

ammonia, I-2545-90 for nitrite plus nitrate, and I2606-89 and I-2601-90 for orthophosphate 

(Fishman, 1993). Concentrations of ammonia in 

the un-ionized form (NH3) were determined from 

tabulated percentages of un-ionized ammonia as a 

function of pH and temperature (U.S. 

Environmental Protection Agency, 1979a) and 

the measured concentrations of ammonia plus 

ammonium in water samples. Total phosphorous 

and total nitrogen samples were analyzed using 

USGS method I-4650-03 (Patton and Kryskalla, 

2003). Water samples collected for chlorophyll a

and phaeophytin a analyses were passed through 

47-mm-diameter, 1.2-μm pore size, glass-fiber 

(GF/F) filters (Whatman, Inc., Piscataway, New 
9 

Jersey) at the USGS Klamath Falls Field Station 

and immediately frozen. These samples were 

stored and analyzed according to Standard 

Method 10200H (American Public Health 

Association, 2005) at the Bureau of Reclamation 

Pacific-Northwest Regional Laboratory (BRPNL) 

in Boise, Idaho. 

Water samples for TSS, TPC, TPP, TPN, 

PIP, and PIC analyses were collected in 2009 

only. Samples for TPC, TPN, and PIC analyses 

were filtered at the Klamath Falls Field Station 

using pre-combusted 25-mm-diameter, 0.7-μm

pore size, glass fiber filters (GF/F). Lake water 

collected for TSS, TPP, and PIP analyses was 

filtered using 47-mm-diameter, 0.7-μm pore size,

GF/F (filters used for TSS analysis were preweighed). All filtered samples were immediately 

frozen and shipped to the University of Maryland 

Chesapeake Biological Laboratory (CBL) in 

Solomons, Maryland, for analysis. TPC, TPN, 

and PIC samples were analyzed according to U.S. 

Environmental Protection Agency method 440.0 

(Zimmerman and others, 1997). TPP and PIP 

samples were analyzed according to Aspila and 

others (1976). TSS is the retained material on a 

tared glass filter pad after filtration of a wellmixed sample of water (U.S. Environmental 

Protection Agency, 1979b; American Public 

Health Association, 2005). Data from all 

laboratories were archived in the USGS National 

Water Information System (NWIS). 

Meteorological Sites 

The locations of meteorological sites are 

shown in figure 1 and listed in table 3. Windspeed and direction data were collected by R.M. 

YoungTM model 05103-5 wind monitors at a 

height of 3 m at the land-based sites and at a 

height of 2 m at the floating sites. Campbell 

Scientific® CS215 or HMP35C relative humidity 

and air-temperature sensors collected air 

temperature and relative humidity data at a height 

of 2 m at the land-based sites and at a height of 

1.5 m at the floating sites. Additionally, solarradiation data were collected at WRW-MET 

using a Li-Cor LI200SZ pyranometer and at 

SSHR-MET using an Eppley Laboratory 

Precision Spectral Pyranometer (PSP) and a 

Precision Infrared Radiometer (PIR). The PSP 

measures solar irradiance (shortwave radiation), 

whereas the PIR measures incoming atmospheric 

irradiance (longwave radiation). Data collected 

from all sensors at a site were collected and 

stored every 10 minutes by a Campbell Scientific 

CR510, CR10, or CR10X data logger. A 12-volt 

battery charged by a solar-power array provided 

power to each site. Data were retrieved from the 

data loggers during site visits approximately 

every 2 weeks during the field season. During 

these visits, sensors were cleaned and checked for 

catastrophic problems by comparison with handheld sensors. Raw meteorological data were 

loaded into ADAPS and processed in a similar 

manner as the water-quality monitor data. 

Table 3. Meteorological sites and parameters measured, Upper Klamath Lake, Oregon, 2009–10.—continued

[Site locations are shown in figure 1.]

Meteorological 

site name

Site name 

abbreviation

USGS site 

identification no. Latitude (north)

Longitude 

(west) Parameters measured

Midnorth1 MDN-MET 422622122004000 42°26'21.5'' 122°00'40.0'' Wind speed and direction, air 

temperature, relative humidity

Williamson 

River West 

WRW-MET 422807121572500 42°28'7.1" 121°57'25.0" Wind speed and direction, air 

temperature, relative humidity, 

solar radiation

Ball Bay BLB-MET 422341122003800 42°23'40.9'' 122°00'38.4'' Wind speed and direction, air 

temperature, relative humidity
10

Table 3. Meteorological sites and parameters measured, Upper Klamath Lake, Oregon, 2009–10.—continued

[Site locations are shown in figure 1.]

Meteorological 

site name

Site name 

abbreviation

USGS site 

identification no. Latitude (north)

Longitude 

(west) Parameters measured

Midlake1 MDL-MET 422312121515900 42°23'12.0'' 121°51'59.1'' Wind speed and direction, air 

temperature, relative humidity

Howard Bay HDB-MET 421846121542800 42°18'46.2'' 121°54'28.0'' Wind speed and direction, air 

temperature, relative humidity

South Shore SSHR-MET 421402121491400 42°14'02.76'' 121°49'14.38'' Wind speed and direction, air 

temperature, relative humidity, 

solar radiation

1

Floating site 

Data Processing 

Lakewide daily median values were 

calculated from data received from continuous 

water-quality monitors. The values were 

calculated from 24 hourly measurements made at 

all eligible open-water Upper Klamath Lake sites 

combined. Prior to calculating daily median 

values, data from water-quality monitors were 

screened using temporal and spatial criteria. At 

least 19 of 24 hourly measurements from a site on 

a given day had to be present for the site to be 

included in the lakewide calculation for that day. 

In addition, to apply the spatial criterion, at least 

9 of the 11 continuous monitor sites had to have 

enough data to be included in the calculation of 

each daily median. At sites in Agency Lake, the 

data were not combined, but at least 20 of 24 

hourly measurements had to be present in order 

to calculate the daily median. 

For statistics at individual meteorological 

sites, the temporal criterion required that at least 

20 of 24 hourly measurements made in one day 

were present in order to calculate the daily 

median. Air-temperature, relative humidity, wind 

speed, and wind direction data were collected at 

six sites, and those data were combined to 

calculate a lakewide daily median. Data from at 

least five of the six sites had to be included in 

order to compute a lakewide daily median. Solarradiation data were collected at only two sites 

(SSHR and WRW), and those data were not 

combined before calculating a daily median. 

Quality Control

Quality-control samples were collected at 

site MDN for all sample types in 2009 and 2010. 

These samples included a field equipment blank 

(the first sample collected every week) for total 

phosphorus, total nitrogen, dissolved nutrients, 

total particulate nutrients (2009 only), and total 

particulate carbon (2009 only); a laboratory blank 

for particulate nutrient (2009 only), particulate 

carbon (2009 only), and chlorophyll a samples;

and either a sequential replicate sample (hereafter 

referred to as a “replicate” sample) or a split 

replicate sample (hereafter referred to as a “split” 

sample). Blank spike and sample matrix spike 

samples were also collected twice each year for 

total and dissolved nutrient analyses to measure 

bias in the analytical procedures used by 

SRWQL. Blank spike samples were used as 

standard reference samples in that they provided 

a point of comparison for the sample matrix 

spikes, which were used to measure site- and 

situation-dependent bias in analyzing the 

environmental samples. 

Field equipment blanks consisted of 

American Chemical Society (ACS) reagent-grade 

inorganic blank water processed onsite through 

clean sampling equipment prior to processing 

environmental samples. Laboratory blanks for 

chlorophyll a, phaeophytin a, and total particulate 

nutrients were collected using ACS reagent-grade 

inorganic blank water processed in the laboratory 
11

through a clean filter and filtering apparatus prior 

to processing environmental samples. Total 

particulate carbon laboratory blanks were 

collected from pesticide-grade (organic) blank 

water. The filter membranes were frozen and sent 

for analysis with environmental samples. 

Analysis of blank samples determines if 

equipment cleaning, sample collection and 

handling, sample storage and processing, sample 

analysis, sample transport, and collection 

equipment cause measurable contamination to 

environmental samples. 

Replicate and split samples were collected on 

alternating weeks throughout the sampling period 

and submitted to SRWQL, BRPNL, and CBL.

Spike samples were collected twice during the 

sample season and submitted blindly to SRWQL. 

SRWQL participates in the USGS Standard 

Reference Sample Project, which compares 

laboratories nationwide for quality control. In 

addition, samples for quality control analyses 

submitted to SRWQL and BRPNL were 

evaluated according to the USGS Branch of 

Quality Systems Laboratory Evaluation Project 

(BQS LEP) to validate the use of these 

laboratories in the Upper Klamath Lake longterm water-quality monitoring project. The 

SRWQL (BQS laboratory 697) evaluation began 

May 2007, and the Bureau of Reclamation (BQS 

laboratory 746) evaluation began November 

2008. CBL is currently being evaluated. Results 

of both BQS LEP projects indicate that the 

laboratory methods, performance data, and 

concentration ranges of submitted samples are 

appropriate and applicable to the ongoing Upper 

Klamath Lake monitoring study. Replicate 

environmental samples were collected twice in 

rapid succession from the same location (the 

entire sample collection procedure was completed 

twice) and analyzed to determine variability of 

the system, variability of collection, and 

variability in the analytical methods. Split 

samples are environmental samples collected 

once and divided into two or more samples 

(analysis bottles were filled sequentially from the 

same churn) to determine the variability in 

sample splitting and in the analytical methods. 

Although replicate samples measure all 

variability in field and laboratory procedures, 

split samples were collected in addition to 

replicates to isolate sources of analytical 

variability. This allows the determination of how 

much variability is due to sampling versus 

analysis. Spike samples were prepared at the 

USGS Klamath Falls Field Station by adding 

target compounds (a field-matrix spike mixture) 

to ACS reagent-grade inorganic blank water and 

to environmental samples collected concurrently 

with non-spiked samples. In addition, 

interlaboratory split samples were collected twice 

each year and submitted to SRWQL, BRPNL, 

CBL, the USGS National Water Quality 

Laboratory (NWQL), Aquatic Research, Inc., 

Seattle, Washington, and the USGS Oregon 

Water Science Center, Portland, Oregon 

(ORWSC; for chlorophyll a only) to determine 

variability in the analytical methods used by these 

laboratories. 

In 2009, the percentage of blank samples 

with concentrations larger than the minimum 

reporting level (MRL) was 10 percent or less for 

most analytes. The two exceptions were total 

particulate carbon, with 31 percent of field blank 

samples exceeding the MRL, and ammonia, with 

55 percent of field blank samples exceeding the 

MRL (appendix A, table A1). Concentrations of 

particulate carbon in environmental samples were 

typically larger than the concentrations detected 

in the blanks, as the 10th percentile of 

environmental samples was 0.67 mg/L and the 

median was 3.37 mg/L. In contrast to the 

environmental sample concentrations, the median 

concentration in particulate carbon blank field 

samples above the minimum reporting limit was 

0.12 mg/L, and the concentrations of 90 percent 

of these samples were below 0.19 mg/L. 

Therefore, low-level contamination indicated by 

the blanks did not limit the use of these data. 

Most concentrations of ammonia in the 

environmental samples were larger than the 

concentrations detected in the blanks. The median 

value of the ammonia field blank samples with
12

concentrations greater than the minimum 

reporting limit was 0.013 mg/L, and 90 percent of 

these samples had concentrations below 0.021 

mg/L (the 90th percentile). However, these 

concentrations were minimal when compared 

with concentrations in the environmental 

samples, in that the 10th percentile of the 

environmental samples was 0.016 mg/L and the 

median was 0.11 mg/L. Therefore, contamination 

did not substantially limit the use of the data. 

The split and replicate samples for 2009 

(appendix A, tables A2 and A3) showed mean 

relative percent differences less than 20 percent, 

with the exception of the total particulate split 

samples for carbon, nitrogen, and phosphorus and 

the replicate samples for total particulate carbon, 

particulate inorganic phosphorus, and total 

suspended solids. This difference in the majority 

of split and replicate samples generally agrees 

with results of previous quality-control sampling 

in this long-term monitoring program (total 

particulate nutrient and carbon samples were 

collected only in 2009; Hoilman and others, 

2008; Lindenberg and others, 2009; Kannarr and 

others, 2010). Between 2005 and 2008, the 

median difference between most split or replicate 

samples did not exceed 15 percent (chlorophyll a 

and phaeophytin a samples collected in 2007 

were determined to be of poor quality and, 

therefore, not reported). However, in 2008, the 

median differences between split phaeophytin a 

samples, split chlorophyll a samples, and 

replicate chlorophyll a samples were between 20 

and 25 percent, while replicate phaeophytin a 

varied by 39 percent. The particulate analyses, 

conducted in 2009, were of solid samples, so 

more variability is expected in the subsampling 

procedure compared to liquid samples. The 

coefficients of variation for most interlaboratory 

split samples were less than 30 percent, which is 

similar to results from between 2006 and 2008 

(the interlaboratory split analysis was not 

performed in 2005, and the analysis was 

performed only once in 2007). In 2009, three sets 

of interlaboratory split samples, for ammonia, 

total particulate carbon, and total particulate 

nitrogen concentrations, had coefficients of 

variation above 30 percent (appendix A, table 

A4). The ammonia split on September 14, 2009, 

had a 48-percent coefficient of variation when the 

mean of the sample concentrations was 19.7 

μg/L. However, on July 21, 2009, the split among 

the same laboratories showed a coefficient of 

variation of 5 percent when the mean of the 

sample concentrations was 933 μg/L, indicating 

more analytical variability at the lower 

concentration. The interlaboratory splits of total 

particulate carbon and nitrogen on July 21, 2009, 

had coefficients of variation of 57 and 63 percent, 

respectively, when the mean concentrations in the 

samples were 538 μg/L for total particulate 

carbon and 95.4 μg/L for total particulate 

nitrogen. On September 14, 2009, the coefficients 

of variation were 4 percent for total particulate 

carbon and nitrogen when the mean concentration 

of the samples was approximately an order of 

magnitude higher, also indicating more analytical 

variability at lower concentrations. 

Bias measured by analysis of spike samples 

is known as “recovery,” which is a measure of 

analyte in a sample expressed as the percentage 

of the spiked amount (U.S. Geological Survey, 

2006). The recovery in a sample without loss or 

gain of the measured analyte (due to degradation 

or matrix character) should be 100 percent. In 

2009, mean nutrient spike recoveries ranged 

between 72 and 122 percent (appendix A, table 

A5) with two exceptions from ammonia spikes. 

The low recovery on July 27 in 2009 (37 percent) 

in a spiked environmental sample matrix 

occurred when the spiked contribution (0.027 

mg/L) was small in comparison to the sample 

concentration of 1.26 mg/L. The high recovery on 

July 27 in 2009 (mean of 140 percent) was in 

low-level spiked blank water. However, the 

recoveries of ammonia from mid-level and highlevel spiked blank water on that date were 105 

and 99 percent, respectively. 

Results of quality-control sampling and 

analyses show improvement in the quality of data 

collected in 2010. Only one blank sample (5 

percent of all blanks) for total nitrogen and one 
13

blank sample for ammonia, in 2010, contained a 

concentration larger than the MRL. The 

concentrations of these samples were 0.076 mg/L 

for total nitrogen and 0.017 mg/L for ammonia 

(the MRL for total nitrogen was 0.060 mg/L and 

the MRL for ammonia was 0.012 mg/L; appendix 

A, table A6). Concentrations in split and replicate 

samples for analytes common to both years were 

generally more variable in 2010 than in 2009, but 

the maximum mean difference in 2010 split

samples was 15 percent (total phosphorus 

samples), and replicate samples in 2010 showed 

mean differences of 19 percent (for total 

phosphorus samples) or less, indicating that the 

data were of good quality (appendix A, tables A7 

and A8). The sole exception to this was the 

phaeophytin a replicate samples, which had a 

mean relative difference of 27 percent. 

Phaeophtyin a is analyzed in the same samples 

collected and analyzed for chlorophyll a, and the 

mean relative difference in chlorophyll a samples 

was 16 percent, which is similar to the variation 

measured in most years. The coefficient of 

variation for interlaboratory split samples in 2010 

was 30 percent (for nitrite plus nitrate and 

phaeophytin a on September 20, 2010) or less 

(appendix A, table A9), and there was little 

difference in the results of interlaboratory split 

events that year. In contrast to 2009 samples, 

ammonia interlaboratory split samples collected 

in 2010 and sent to the same laboratories as in 

2009 showed a maximum coefficient of variation 

at 10 percent. Mean nutrient spike recoveries in 

2010 ranged between 78 and 135 percent 

(appendix A, table A10) with two exceptions 

from total nitrogen spikes. The low-level spiked 

blank water on August 17 in 2010 had a recovery 

of 156 percent, but the recoveries of total 

nitrogen from mid-level and high-level spiked 

blank water on that date were 98 and 100 percent, 

respectively. The spiked environmental sample 

matrix on September 27 in 2010 had a high mean 

recovery of 157 percent (appendix A, table A10). 

Results

Field crews collected data from a network of 

multiparameter continuous water-quality 

monitors, water-quality samples, and 

meteorological sites in Upper Klamath and 

Agency Lakes in 2009–10 to assess water-quality 

conditions and processes. The network provided 

data at high temporal resolutions that can be 

related to bloom conditions, weather, bathymetry, 

and currents and that are central to future waterquality modeling efforts. Continued operation of 

the monitoring sites and meteorological sites will 

provide a long-term dataset that will enable the 

identification of water-quality dynamics and 

trends in Upper Klamath Lake. 

Water-Quality Monitors 

In 2009, the lakewide daily median values 

calculated from Upper Klamath Lake continuous 

monitor data showed periods of extreme 

dissolved oxygen conditions (both super- and 

undersaturated) and pH (> 9) indicative of 

respiration (oxygenic photosynthesis) and 

subsequent decomposition during the AFAdominated bloom cycle (fig. 2). Lakewide 

median dissolved oxygen concentrations (8–10 

mg/L) and percent saturation (100–120 percent) 

were high at the beginning of the 2009 field 

season (early May) and declined in late June. The 

decline in dissolved oxygen conditions reached a 

minimum (3.3 mg/L, 44 percent) in late July 

coincident with a minimum in lakewide median 

pH (7.4) and elevated specific conductance (123 

μS/cm; the seasonal maximum in specific 

conductance occurred several days later). These 

conditions were associated with the first rapid 

decline in the AFA-dominated bloom and are 

consistent with observations made in 2005, 2006, 

and 2008 (Hoilman and others, 2008; Lindenberg 

and others, 2009; Kannarr and others, 2010). A 

second period of elevated lakewide median pH (> 

9) occurred between early August and late 

September, indicating a second period of elevated 

phytoplankton growth (fig. 2). Dissolved oxygen 
14

Figure 2. Graphs showing lakewide daily median dissolved oxygen concentration, dissolved oxygen percent 

saturation, pH, specific conductance, and water temperature in Upper Klamath Lake, Oregon, 2009–10. Data from 

nine open-water sites where continuous monitors were deployed were combined to calculate daily median values. 
15 

concentrations and pH values increased rapidly 

after the minima in late July, peaking in midAugust with values of 11.5 mg/L and 9.7 pH 

units respectively, and gradually declined to 8.6 

mg/L and 8.3 pH units, respectively, on October 

4 in 2009, the last day of data for the season. 

Dissolved oxygen saturation also followed these 

trends, decreasing to values below 100 percent 

after the first week in September, a pattern that 

continued into late September. These data are 

characteristic of two distinct AFA-dominated 

growth and decline events in the 2009 field 

season. 

Two periods of elevated pH values (> 9.0) 

and dissolved oxygen conditions, representing 

AFA-dominated bloom growth, were also 

observed in 2010 (fig. 2). The first period 

occurred from early July to the beginning of 

August, and the second occurred from midAugust to late September. The pH maximum 

during the first period of elevation in 2010 

occurred later in the season than during the first 

period of 2009. In 2010, the minimum lakewide 

daily median dissolved oxygen concentration and 

percent saturation, indicating a decline in the 

bloom, was less extreme (5.0 mg/L, 74 percent 

saturation) and occurred later in the season (on 

July 30, 2010) than in 2009. This minimum was 

nearly coincident with a pH minimum (8.5 pH 

units on August 7, 2010) and a peak in specific 

conductance (121 μS/cm on August 9, 2010). 

Following the pH and dissolved oxygen minima 

in late July–early August 2010, values gradually 

increased and remained steady for the rest of the 

season with pH values between 8.5 and 9.5 and 

dissolved oxygen concentrations between 5.5 and 

10.5 mg/L (between 75 and 128 percent 

saturation). These data, along with the trends in 

chlorophyll a concentration (discussed below), 

show that the first and largest AFA-dominated 

growth and decline event of 2010 occurred later 

in the season than in 2009. 

Lakewide daily median water temperatures 

in 2009 were greater in May and early June than 

in 2010 (fig. 2). The largest difference in water 

temperature between the two years occurred on 

May 29, when water temperature was 7.8°C 

warmer in 2009 than in 2010. In general, daily 

median water temperatures continued to be lower 

throughout the 2010 field season than in 2009. 

Daily median water temperatures peaked on 

August 1 in 2009 at 24.3°C and on July 30 in 

2010 at 22.6°C. Water temperatures declined 

following these peaks in both years, although the 

initial decline after the peak was rapid over the 

first week in August 2009 and more gradual over 

the rest of the season in 2010. 

In 2009 and 2010, water-quality conditions 

were also monitored at the Agency Lake northern 

and southern sites (AGN and AGS, respectively). 

Water-quality trends and the timing of minima in 

pH and dissolved oxygen concentrations at AGS 

in 2009 were similar to those in Upper Klamath 

Lake, whereas trends and timing between Upper 

Klamath Lake and AGN were different. For 

example, the AGN data do not show the late July 

minimum in pH that was observed at AGS (fig. 

3) and in the Upper Klamath Lake lakewide pH 

median. A maximum in specific conductance 

occurred at AGS in late July, 2009, coincident 

with the maximum in Upper Klamath Lake, but 

unlike Upper Klamath Lake, a second maximum 

occurred in mid-August, nearly one month later. 

As in Upper Klamath Lake, the 2010 

dissolved oxygen conditions in Agency Lake 

were low to moderate compared to those in 2009. 

At AGS, for example, dissolved oxygen in 2010 

varied little through the first half of June and 

ranged from a high of 210 percent saturation 

(15.9 mg/L) to a low of 47 percent (4.16 mg/L; 

fig. 4). pH values at AGS, after reaching a peak 

of 10 in mid-July 2010, remained at 9.6 or above 

through August, whereas in 2009, pH ranged 

between 10 and 7.3 over the same time period. 

Therefore, as in Upper Klamath Lake, there was 

evidence in Agency Lake that the AFAdominated bloom cycle of growth and decline 

was weaker in 2010 than in 2009.
16

Figure 3. Graphs showing dissolved oxygen concentration, dissolved oxygen percent saturation, pH, specific 

conductance, and temperature in Agency Lake, Oregon, 2009. 
17

Figure 4. Graphs showing dissolved oxygen concentration, dissolved oxygen percent saturation, pH, specific 

conductance, and temperature in Agency Lake, Oregon, 2010. 
18

Water-Quality Samples 

In 2009, peak concentrations of chlorophyll 

a occurred at several sites in late June, and again 

in late August through early September (fig. 5), 

indicating two distinct growth periods of the 

AFA-dominated bloom that year. The early 

season peak values of chlorophyll a occurred on 

June 30 in 2009 at RPT, MDT, EPT, and MDN 

and at concentrations of 419, 281, 149, and 162 

μg/L, respectively. Concentrations peaked again 

at these sites between August 17 and September 

14 in 2009, with concentrations of 157, 314, 143, 

and 317 μg/L, respectively. Two distinct highs 

were also observed in samples from WMR, 

although concentrations were generally lower at 

this site. Chlorophyll a concentrations decreased 

over 3 to 5 weeks after both peaks in 2009, 

coincident with decreases in dissolved oxygen 

concentration and pH, indicating a period of 

bloom decline and associated phytoplankton 

degradation. Total phosphorus and total nitrogen 

concentrations also peaked at several sites in late 

June to early July and again in mid-August to 

early September, following the trends in 

chlorophyll a at each site and reflecting the 

incorporation of nitrogen and phosphorus into 

biomass (fig. 5). In general, total phosphorus and 

total nitrogen concentrations increased 

throughout the sample season without decreasing 

during the major bloom decline periods. This 

indicates that much of the phosphorus and 

nitrogen measured as total concentrations during 

periods of bloom decline were in the form of 

dissolved nutrients, which are released as cells 

lyse and decompose. Concentrations of dissolved 

nutrients (orthophosphate, ammonia, and nitrite

plus nitrate) remained low through June and most 

of July and increased at all sites during the first 

decline in chlorophyll a concentrations. 

Maximum concentrations of un-ionized ammonia 

occurred in late August–early September 2009, 

after the maxima in total ammonia concentrations 

and during the second period of elevated pH 

following the major bloom decline (appendix C, 

table C1). Concentrations remained below 260 

μg/L, well below the level determined by Saiki 

and others (1999) to be lethal for endangered 

larval and juvenile suckers. Nitrite plus nitrate 

concentrations were less than 100 μg/L at all sites 

for most of the 2009 field season, although there 

was a noticeable increase in late September at 

WMR and RPT, the two shallow sites. 

In 2010, chlorophyll a concentrations 

remained at or near the detection limit until early 

July. Concentrations at all sites increased in July, 

and there was evidence of a weak decline 

between mid-July and the beginning of August at 

all sites except MDT. After that, chlorophyll a

concentrations at all sites increased to seasonal 

maximum values in late August or in September. 

The early season peak values were generally 

lower and occurred nearly three weeks later than 

in 2009. Chlorophyll a concentrations measured 

on July 19 were 59, 59, 89, and < 292 μg/L at 

MDN, WMR, EPT, and MDT, respectively. 

Overall, the decline of the bloom between July 19 

and August 2 in 2010 started from lower peak 

values and was weaker than the bloom decline 

between June 30 and July 21 in 2009. The 2010 

decline was not apparent at all of the sites visited. 

At MDT, chlorophyll a concentrations were 252 

μg/L on August 2, while concentrations at the 

other three sites visited were between 4.6 and 

26.2 μg/L. In 2010, total phosphorus and total 

nitrogen concentrations largely followed the 

trends in chlorophyll a at each site and, compared 

to 2009, remained at lower values well into July 

(fig. 6). However, the seasonal maximum values 

were higher for total phosphorus at MDN, WMR, 

EPT, and MDT, respectively, in 2010 (260, 340, 

310, and 800 μg/L) than in 2009 (290, 250, 240 

and 390 μg/L). 

Peak concentrations of orthophosphate, 

ammonia, and nitrite plus nitrate occurred 

between late July and early August in 2010 with 

the first minor bloom decline. These peaks were 

followed by decreasing concentrations through 

the first half of September and increasing 

concentrations to smaller maxima in late 

September. Dissolved nutrient concentrations 

were also lower in 2010 than in 2009. 
19

Figure 5. Graphs showing concentrations of chlorophyll a, total phosphorus, total nitrogen, orthophosphate, 

ammonia, and nitrite plus nitrate, Upper Klamath Lake, Oregon, 2009. Site descriptions are shown in table 2. 
20

Figure 6. Graphs showing concentrations of chlorophyll a, total phosphorus, total nitrogen, orthophosphate, 

ammonia, and nitrite plus nitrate, Upper Klamath Lake, Oregon, 2010. Site descriptions are shown in table 2. 
21

Peak values of 110 μg/L orthophosphate, 779 

μg/L ammonia, and 94 μg/L nitrite plus nitrate 

were measured at MDN in 2010, while peak 

values of 152 μg/L orthophosphate, 1,250 μg/L 

ammonia, and 170 μg/L nitrite plus nitrate were 

recorded at MDN in 2009. Overall, changes in 

2010 dissolved nutrient concentrations were 

similar to those observed in 2009, but the range 

of values was less pronounced. This pattern was 

also delayed by several weeks in 2010 compared 

to 2009. Maximum concentrations of un-ionized 

ammonia were observed at most sites in mid-July 

to early August in 2010, temporally overlapping 

more than in 2009 with the seasonal ammonia 

concentration maxima (appendix C, table C2). 

Differences in nutrient dynamics observed 

between 2009 and 2010 show that, although 

seasonal water-quality conditions on Upper 

Klamath Lake are highly variable, some patterns 

are consistently observed from year to year. 

Total particulate nitrogen, phosphorus, and 

carbon concentrations were measured in water 

samples collected in 2009 only (fig. 7). Peak

concentrations were observed at most sites in late 

June, corresponding with peaks in chlorophyll a

(figs. 5 and 7). Maximum concentrations of 

particulate carbon and nutrients occurred at RPT 

on June 30, 2009, with concentrations of 4.76 

mg/L particulate nitrogen, 0.26 mg/L particulate 

phosphorus, and 23.8 mg/L particulate carbon. 

Particulate carbon and nutrient concentrations at 

all sites decreased after the first peak in late June 

to minimum values in mid-July that coincided 

with the bloom decline (as determined by 

chlorophyll a concentrations and maxima in 

dissolved nutrient concentrations). From mid-July 

to the end of August, concentrations of 

particulate nutrients generally followed the same 

trends as chlorophyll a and total nitrogen and 

phosphorus concentrations.

Particulate carbon to particulate phosphorus 

ratios (C:P) and particulate nitrogen to particulate 

phosphorus ratios (N:P) were calculated using 

particulate nutrient data from 2009 (figs. 8 and 

9). Median values of both C:P and N:P ratios 

were highest (exceeding 100 and 20, 

respectively) from June 16 to June 23. This was 

the period of most rapid growth in the bloom.

After June 23, both ratios decreased, and 

biweekly medians remained below 100 and 20, 

respectively, through August 31, although both 

ratios exhibited significant variability between 

sites on any given sampling day. Lowest median 

values occurred on July 27 in 2009 at 60.3 for 

C:P and on July 21 in 2009 at 8.00 for N:P 

(shown within the range of values between July 

14 and July 21, 2009, when the median N:P ratio 

was 12), coinciding with low chlorophyll a

concentrations and elevated dissolved nutrient 

concentrations (fig. 5) at most sites. 

Particulate inorganic carbon and phosphorus 

samples were collected at MDN and MDT (two 

samples were collected at MDT, at one-quarter 

and three-quarters of total water depth) during the 

2009 field season. At MDN, nine samples were 

collected for particulate inorganic phosphorus 

from June 16, 2009, through August 31, 2009, 

and four samples were collected for particulate 

inorganic carbon from June 16, 2009, through 

July 7, 2009. Particulate inorganic carbon was not 

detected in any samples above the method 

detection limit of 0.076 mg/L and, as a fraction of 

the total particulate carbon, never exceeded 0.026 

mg/L in all samples. Particulate inorganic 

phosphorus was measured in nine samples from 

MDN (concentrations between 0.007 and 0.069 

mg/L) and in five samples each from MDT at 

one-quarter and three-quarters water column 

depths (concentrations between 0.012 and 0.068 

at one-quarter depth and between 0.013 and 0.090 

mg/L at three-quarters depth; fig. 7). As a 

fraction of the total particulate phosphorus, 

particulate inorganic phosphorus ranged from 

0.25 on June 16, 2011, to 0.79 on August 17, 

2009. 
22

Figure 7. Graphs showing concentrations of particulate nitrogen, particulate phosphorus, particulate carbon, and 

particulate inorganic phosphourus, Upper Klamath Lake, Oregon, 2009. Site descriptions are shown in table 2. 
23

Figure 8. Box and whisker graph showing lakewide ratios for particulate carbon to particulate phosphorus (C:P), 

Upper Klamath Lake, Oregon, 2009. Data from two consecutive sample weeks are grouped in each box and 

whisker plot (N=14). 

Figure 9. Box and whisker graph showing lakewide ratios for particulate nitrogen to particulate phosphorus (N:P), 

Upper Klamath Lake, Oregon, 2009. Data from two consecutive sample weeks are grouped in each box and 

whisker plot (N=14). See figure 8 for explanation of plot components. 
24

Meteorological Data 

Box and whisker graphs were constructed 

using the daily median values from WRW-MET 

(fig. 1, table 2) in 2009 and 2010 (fig. 10). 

Between June and September, 2009 and 2010, 

daily median wind speeds were widely variable 

but typically between 1 and 6 m/s (fig. 10A). 

Wind speeds were higher and more variable in 

June and July 2010 than during the same period 

in 2009. The maximum daily median wind speed 

was 5.5 m/s in 2009 and 6.2 m/s in 2010. The 

June 2009 interquartile range for daily median 

wind speed was 2.3–3.1 m/s, whereas the June 

2010 interquartile range was 2.0–4.2 m/s. Wind 

direction data collected between October 1 in 

2008 and September 30 in 2010 show that the 

highest winds were predominantly from the west 

at sites MDN and WRW (figs. 11 and 12), which 

are at the northern end of Upper Klamath Lake. 

The meteorological sites located on the southern 

end of the lake and shoreline, HDB, MDL, and 

SSHR, recorded highest winds predominantly 

from the north-northwest. Winds recorded at 

BLB were predominantly from the north to 

northwest, and a second prevailing wind occurred 

from the south. 

The daytime solar radiation median values 

(fig. 10A) reflect patterns of clear sunny days 

typical in the Klamath Basin during the summer 

season. Higher median values of solar radiation 

occurred in June 2009 than in the same month in 

2010, indicating more partly cloudy days in June 

2010. Median values for August and September 

were similar for both years. Following the peak 

of each year, maximum solar radiation values 

gradually began to decline with the shorter days 

of the fall and winter. 

Figure 10A. Box and whisker graphs showing daily median wind speed and solar radiation at WRW 

meteorological site from June through September, Upper Klamath Lake, Oregon, 2009–10. See figure 8 

for explanation of plot components. 
25

Air temperature was higher in June 2009 

(median value 14.7°C) than in June 2010 (median 

value 13.5°C) (fig. 10B). Air temperatures 

peaked in July of both years, but were higher in 

2009 (median value 22.1°C) than in 2010 

(median value 21.1°C). Overall, air temperatures 

in June, July, and September were higher in 2009 

than in 2010, and in August they were similar 

(median values of 18.8°C and 19.1°C in 2009 and 

2010, respectively). 

Relative humidity was higher in June 2009 

(median 71 percent) than in June 2010 (median 

64 percent)(fig. 10B). However, in September, 

the median relative humidity was 72 percent in 

2010, compared to 58 percent in 2009. Median 

relative humidity values were nearly equal and 

the lowest of the season during July and August 

of both years. Minimum values of relative 

humidity typically correlated with peak values in 

air temperature, illustrating the Klamath Basin’s 

semiarid climate. 

Figure 10B. Box and whisker graphs showing daily median wind air temperature and relative humidity at

WRW meteorological site from June through September, Upper Klamath Lake, Oregon, 2009–10. See 

figure 8 for explanation of plot components. 
26

Figure 11. Histograms showing wind speed and direction for meteorological (MET) sites near Upper Klamath Lake, 

Oregon, 2009. Site descriptions are shown in table 3. 
27

Figure 12. Histograms showing wind speed and direction for meteorological (MET) sites near Upper Klamath Lake, 

Oregon, 2010. Site descriptions are shown in table 3. 
28

The meteorological data generally show that 

2009 was less windy and more humid early in the 

season, had more clear days in June, and was 

warmer throughout the summer and early fall 

than during the same time periods in 2010. These 

differences in weather may help to account for 

the larger early bloom and more severe bloom 

decline observed in 2009, which has been 

previously cited (Perkins and others, 2000; Kann 

and Welch, 2005). In years when a severe 

midseason bloom decline has been observed on 

Upper Klamath Lake, the decline has often 

occurred during periods of sustained high 

temperature and low wind (Wood and others, 

2006; Hoilman and others, 2008; Lindenberg and 

others, 2009; Kannarr and others, 2010), which 

increases water column stability (Kann and 

Welch, 2005) and permits the development of 

dense phytoplankton blooms (Eldridge and 

others, 2012). 

Acknowledgments

We thank the reviewers who provided 

comments on this document. We also gratefully 

acknowledge the assistance of Scott Vanderkooi 

and many personnel of the USGS Klamath Falls 

Field Station for facilitating the water-quality 

field program with the use of boats, trucks, field 

equipment, and office and laboratory facilities. 

Many people contributed to the field work of this 

study: Mary Lindenberg (2009), Kristofor 

Kannarr (2009 and 2010), Cynthia King (2009), 

Kristin Harbin (2009 and 2010), and Matthew 

Wilson (2009). The efforts of Amy Brooks and 

Matt Johnston from the USGS Oregon Water 

Science Center in processing and checking the 

continuous datasets were critical to the success of 

the monitoring program. 

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31

The appendix tables are in separate Excel 

files that can be accessed at 

http://pubs.usgs.gov/of/2012/1142.

Appendix A. Quality-Control Data for 

Water-Quality Samples

Table A1. Quality-control data from water-quality 

samples, Upper Klamath Lake, Oregon, 2009: Blank 

samples. 

Table A2. Quality-control data from water-quality 

samples, Upper Klamath Lake, Oregon, 2009: Routine 

split samples. 

Table A3. Quality-control data from water-quality 

samples, Upper Klamath Lake, Oregon, 2009: 

Replicate samples. 

Table A4. Quality-control data from water-quality 

samples, Upper Klamath Lake, Oregon, 2009: Split 

sample interlaboratory measurements. 

Table A5. Quality-control data from water-quality 

samples, Upper Klamath Lake, Oregon, 2009: Nutrient 

spiked samples. 

Table A6. Quality-control data from water-quality 

samples, Upper Klamath Lake, Oregon, 2010: Blank 

samples. 

Table A7. Quality-control data from water-quality 

samples, Upper Klamath Lake, Oregon, 2010: Routine 

split samples. 

Table A8. Quality-control data from water-quality 

samples, Upper Klamath Lake, Oregon, 2010: 

Replicate samples. 

Table A9. Quality-control data from water-quality 

samples, Upper Klamath Lake, Oregon, 2010: Split 

sample interlaboratory measurements. 

Table A10. Quality-control data from water-quality 

samples, Upper Klamath Lake, Oregon, 2010: Nutrient 

spiked samples.

Appendix B. Data from Water-Quality 

Samples

Table B1. Data from water-quality samples, Upper 

Klamath Lake, Oregon, 2009.

Table B2. Data from water-quality samples, Upper 

Klamath Lake, Oregon, 2010.

Appendix C. Concentrations of UnIonized Ammonia in Water-Quality 

Samples

Table C1. Concentrations of un-ionized ammonia in 

water-quality samples, Upper Klamath Lake, Oregon, 

2009.

Table C2. Concentrations of un-ionized ammonia in 

water-quality samples, Upper Klamath Lake, Oregon, 

2010.
32

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