Prepared in Cooperation with the Bureau of Reclamation 

Klamath River Water Quality and Acoustic Doppler Current 

Profiler Data from Link River Dam to Keno Dam, 2007 

Open-File Report 2008–1185 

U.S. Department of the Interior 

U.S. Geological Survey 
Front cover (clockwise, from left):

Link River, October 12, 2006; photograph by Scott Miller, Bureau of Reclamation, Klamath Falls, Oregon 

Aerial view of Lake Ewauna and the upstream end of the Keno reach of the Klamath River; photograph by Trisha 

Roninger, U.S. Fish and Wildlife Service 

Klamath River from Miller Island, August 28, 2007; photograph by Simon Poulson, University of Nevada, Reno 
Prepared in Cooperation with the Bureau of Reclamation 

Klamath River Water Quality and Acoustic Doppler Current 

Profiler Data from Link River Dam to Keno Dam, 2007 

By Annett B. Sullivan1, Michael L. Deas2, Jessica Asbill3, Julie D. Kirshtein4, Kenna Butler5, Marc A. Stewart6, 

Roy E. Wellman1, and Jennifer Vaughn2 

1U.S. Geological Survey, Portland, Oregon 

2Watercourse Engineering, Davis, California 

3Bureau of Reclamation, Klamath Falls, Oregon 

4U.S. Geological Survey, Reston, Virginia 

5U.S. Geological Survey, Boulder, Colorado 

6U.S. Geological Survey, Central Point, Oregon 

Open-File Report 2008-1185 

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 

For product and ordering information: 

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

Telephone: 1-888-ASK-USGS 

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its natural and living resources, natural hazards, and the environment: 

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

Telephone: 1-888-ASK-USGS 

Suggested citation: 

Sullivan, A.B., Deas, M.L., Asbill, J., Kirshtein, J.D., Butler, K., Wellman, R.W., Stewart, M.A., and Vaughn, J., 2008, Klamath 

River water quality and acoustic Doppler current profiler data from Link River Dam to Keno Dam, 2007: U.S. Geological 

Survey Open-File Report 2008-1185, 25 p.. 

Any use of trade, product, or firm 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. 

iv
Contents 

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

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

Acoustic Doppler Current Profiler Methods ....................................................................................................................3

Water Quality Sampling..................................................................................................................................................4

Site Locations and Frequency ....................................................................................................................................4

Sample Collection.......................................................................................................................................................5

Quality Control Samples .............................................................................................................................................6

Water Quality Analytical Methods...................................................................................................................................7

Nutrients, Particulate Carbon and Nitrogen, Iron, Silica, and Alkalinity.......................................................................7

Dissolved Organic Carbon and Specific UV Absorbance............................................................................................8

Bacterial Abundance and Morphology ........................................................................................................................9

Phytoplankton Enumeration and Species Identification ............................................................................................10

Zooplankton Enumeration and Species Identification ...............................................................................................10

Acoustic Doppler Current Profiler Data Summary ........................................................................................................12

May 30, 2007............................................................................................................................................................12

September 19, 2007 .................................................................................................................................................13

Cross-Sectional Velocity Direction and Magnitude ...................................................................................................14

Water Quality Data Summary.......................................................................................................................................14

Quality Control Results .............................................................................................................................................14

Nutrients, Iron, Silica, and Alkalinity..........................................................................................................................16

Particulate and Dissolved Organic Carbon ...............................................................................................................18

Bacterial Abundance and Morphology ......................................................................................................................18

Phytoplankton Enumeration and Species Identification ............................................................................................20

Zooplankton Enumeration and Species Identification ...............................................................................................20

Acknowledgements ......................................................................................................................................................21

References Cited..........................................................................................................................................................21

Appendix A—Acoustic Doppler Current Profiler Data...................................................................................................24

Appendix B—Water Quality Data (Excel files)..............................................................................................................24

Figures 

Figure 1. Map of the study area on the upper Klamath River, Oregon, and location of water quality and 

acoustic Doppler current profiler sites. ........................................................................................................................ 2

Figure 2. Acoustic Doppler current profiler flow measurements on the Klamath River between Link River 

Dam and Keno Dam on May 30, 2007, and September 19, 2007, and gaged flows at Link River and 

downstream of Keno Dam for the same dates...........................................................................................................13

Figure 3. Median concentrations of carbon, nitrogen, and phosphorus species; median zooplankton 

density; and median algal and bacterial biovolumes from all five mainstem Klamath River sites...................17

v 
Figure 4. Median concentrations of carbon, nitrogen, and phosphorus species; median zooplankton 

density; and algal and bacterial biovolumes at the five mainstem Klamath River sites using all data from 

April through November, 2007.......................................................................................................................................19

Tables 

Table 1. Klamath River mainstem and tributary sampling locations. ...................................................................... 5

Table 2. Analyzing laboratories and method references for water quality constituents.................................... 7

Table 3. Analyte reporting levels and blank results. ................................................................................................15

Table 4. Results of analyses of duplicate quality assurance samples .................................................................15

vi
Conversion Factors 

Inch/Pound to SI 

Multiply By To obtain 

foot (ft) 0.3048 meter (m) 

mile (mi) 1.609 kilometer (km) 

acre-foot (acre-ft) 1,233 cubic meter (m3

) 

mile per hour (mi/h) 1.609 kilometer per hour (km/h) 

cubic foot per second (ft3

/s) 0.02832 cubic meter per second (m3/s)

SI to Inch/Pound 

Multiply By To obtain 

centimeter (cm) 0.3937 inch (in.) 

micrometer (μm) 0.00003937 inch (in.) 

millimeter (mm) 0.03937 inch (in.) 

meter (m) 3.281 foot (ft) 

nanometer (nm) 0.00000003937 inch (in.) 

liter (L) 33.82 ounce, fluid (fl. oz) 

liter (L) 0.2642 gallon (gal) 

cubic meter (m3

) 264.2 gallon (gal) 

cubic centimeter (cm3

) 0.06102 cubic inch (in3) 

liter (L) 61.02 cubic inch (in3

) 

cubic meter (m3

) 35.31 cubic foot (ft3) 

gram (g) 0.03527 ounce, avoirdupois (oz) 

kilogram (kg) 2.205 pound avoirdupois (lb) 

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows: °F=(1.8×°C)+32 

Vertical coordinate information is referenced to the National Geodetic Vertical Datum of 1929 (NGVD 29). 

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

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

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

(μg/L). 

vii
Abbreviations and Acronyms 

ADCP, acoustic Doppler current profiler 

AFA, Aphanizomenon flos aquae 

AU, absorbance units 

DOC, dissolved organic carbon 

LT-MDL, long term method detection limit 

M, molarity or moles of solute per liter of solution 

μm, micrometer 

mg, milligram 

mL, milliliter 

N, normality, molarity multiplied by the number of protons exchanged in the reaction 

NWQL, National Water Quality Laboratory 

POC, particulate organic carbon 

RL, reporting level 

RM, river mile 

RPD, relative percent difference 

SUVA254, specific UV absorbance at 254 nm 

TSI, trophic state index 

USGS, U.S. Geological Survey 

UV, ultraviolet 

WWTP, wastewater treatment plant 

viii
Klamath River Water Quality and Acoustic Doppler Current 

Profiler Data from Link River Dam to Keno Dam, 2007 

By Annett B. Sullivan, Michael L. Deas, Jessica Asbill, Julie D. Kirshtein, Kenna Butler, Roy E. Wellman, Marc A. Stewart, 

and Jennifer Vaughn 

Abstract 

In 2007, the U.S. Geological Survey, Watercourse Engineering, and Bureau of Reclamation began a 

project to construct and calibrate a water quality and hydrodynamic model of the 21-mile reach of the 

Klamath River from Link River Dam to Keno Dam. To provide a basis for this work, data collection and 

experimental work were planned for 2007 and 2008. This report documents sampling and analytical 

methods and presents data from the first year of work. To determine water velocities and discharge, a 

series of cross-sectional acoustic Doppler current profiler (ADCP) measurements were made on the 

mainstem and four canals on May 30 and September 19, 2007. Water quality was sampled weekly at five 

mainstem sites and five tributaries from early April through early November, 2007. Constituents reported 

here include field parameters (water temperature, pH, dissolved oxygen concentration, specific 

conductance); total nitrogen and phosphorus; particulate carbon and nitrogen; filtered orthophosphate, 

nitrite, nitrite plus nitrate, ammonia, organic carbon, iron, silica, and alkalinity; specific UV absorbance at 

254 nm; phytoplankton and zooplankton enumeration and species identification; and bacterial abundance 

and morphological subgroups. 

The ADCP measurements conducted in good weather conditions in May showed that four major 

canals accounted for most changes in discharge along the mainstem on that day. Direction of velocity at 

measured locations was fairly homogeneous across the channel, while velocities were generally lowest 

near the bottom, and highest near surface, ranging from 0.0 to 0.8 ft/s. Measurements in September, made 

in windy conditions, raised questions about the effect of wind on flow. 

Most nutrient and carbon concentrations were lowest in spring, increased and remained elevated in 

summer, and decreased in fall. Dissolved nitrite plus nitrate and nitrite had a different seasonal cycle and 

were below detection or at low concentration in summer. Many nutrient and carbon concentrations were 

similar at the top and bottom of the water column, though ammonia and particulate carbon showed more 

variability in summer. Averaged over the season, particulate carbon and particulate nitrogen decreased in 

the downstream direction, while ammonia and orthophosphate concentrations increased in the 

downstream direction. 

At most sites, bacteria, phytoplankton, and zooplankton populations reached their maximums in 

summer. Large bacterial cells made up most of the bacteria biovolume, though cocci were the most 

numerous bacteria type. The cocci were smaller than the filter pore sizes used to separate dissolved from 

particulate matter in this study. Phytoplankton biovolumes were dominated by the blue-green alga 

Aphanizomenon flos aquae most of the sampling season, though a spring diatom bloom occurred. 

Phytoplankton biovolumes were generally highest at the upstream Link River and Railroad Bridge sites 

and decreased in the downstream direction. Zooplankton populations were dominated by copepods in 

early spring, and by cladocerans and rotifers in summer, with rotifers more common farther downstream. 

1 
Introduction 

The Klamath River (fig. 1), which flows from Upper Klamath Lake about 255 mi through southern 

Oregon and northern California, is regulated for flows, irrigation, and hydropower generation. The first 

dam on the river is Link River Dam, a concrete structure owned by Bureau of Reclamation and operated 

by PacifiCorp to adjust levels in Upper Klamath Lake, regulate downstream flows, and divert water for 

irrigation or hydropower use (Pacificorp, 2002). Link River flows for 1 mile downstream of Link River 

Dam to the 20-mile-long Keno reach of the Klamath River; the first 2 wide and shallow miles of the

Klamath River downstream of Link River is named Lake Ewauna. Keno Dam, on the downstream end of 

the reach, is a concrete reregulating facility owned by PacifiCorp and operated by PacifiCorp in 

coordination with the Bureau of Reclamation. Keno Dam operations are designed to provide sufficient 

downstream flow and a steady reservoir elevation through the year. Normal full pool elevation of the 

Keno reach is 4,085 ft above NGVD 29, and total storage capacity is 18,500 acre ft. 

Figure 1. Map of the study area on the upper Klamath River, Oregon, and location of water quality and 

acoustic Doppler current profiler sites. 

2 
The State of Oregon classifies sites in this reach as having “very poor” water quality status, 

according to the Oregon Water Quality Index (Mrazik, 2007). In addition, the Keno reach has 

been designated as “water quality limited” on Oregon’s 303(d) list for ammonia and dissolved oxygen 

year-round, and pH and chlorophyll a in summer (Oregon Department of Environmental Quality, 2007). 

To address the 303(d) listing, a total maximum daily load (TMDL) process is under way. 

Water quality in this reach of the Klamath River is affected by a number of factors, including 

upstream conditions, tributary inflows and outflows, climate, and instream processes. For instance, 

Upper Klamath Lake, upstream of the reach, experiences large annual blooms of the blue-green alga 

Aphanizomenon flos aquae (AFA) (Wood and others, 2006). Inflows to the Keno reach also include two 

municipal wastewater treatment plants, the Lost River Diversion Channel, and Klamath Straits Drain, 

which itself is 303(d) listed for ammonia and oxygen year-round, and chlorophyll a (indicating excessive 

algal growth) in summer. To further understand the processes that contribute to water quality 

conditions in this reach of the Klamath River, a comprehensive suite of water quality constituents, 

including nutrients and phytoplankton, were measured at sampling intervals less than the travel time 

through the reach (weekly to biweekly). Acoustic Doppler current profiler (ADCP) work was conducted to 

increase understanding of flow and velocities in this reach. 

The purpose of this report is to present the methods and data from monitoring in Link River, the

Keno reach of the Klamath River, and tributaries from early April through early November 2007. Data 

reported here include ADCP flows and cross sections; water quality field parameters (temperature, pH, 

dissolved oxygen concentration, specific conductance); concentrations of total nitrogen and phosphorus; 

particulate carbon and nitrogen; filtered orthophosphate, nitrite, nitrite plus nitrate, ammonia, organic 

carbon, iron, silica, and alkalinity; specific UV absorbance at 254 nm; phytoplankton and zooplankton 

enumeration and species identification; and bacterial abundance and morphological subgroups. Results 

of this project that are more experimental in nature, including a series of 30-day biochemical oxygen 

demand experiments, will be presented elsewhere. Also, 12 continuous monitors were deployed in the 

reach measuring hourly water temperature, pH, dissolved oxygen concentration, and specific conductance; 

when processing is completed, those data will be online at http://or.water.usgs.gov/proj/keno_reach/

monitors.html. Together, these datasets will support interpretive analysis and model development and 

calibration in the reach by the U.S. Geological Survey (USGS), Watercourse Engineering, and Bureau 

of Reclamation, and provide data to others working in the Klamath Basin. 

Acoustic Doppler Current Profiler Methods 

To better characterize flow in the reach, a series of ADCP measurements were done on May 30, 

2007, and September 19, 2007, by USGS with assistance from the Bureau of Reclamation. ADCP 

technology allows three-dimensional velocity profiles and channel depth to be collected from a moving 

platform, usually a boat or tethered raft. The instrument’s movement, speed, and direction are measured 

by tracking the channel bottom. When a number of measurements are made in a river in a day, results can 

be used to check water balances and note occurrences of ungaged inflows or outflows. With 

measurements made bank-to-bank across a river channel, cross sectional data on velocity and velocity 

directions are collected. 

Measurements were made at locations on the mainstem and major flow inputs and outputs (fig. 1). 

The four major canal sites, the Lost River Diversion Channel, North Canal, ADY Canal, and Klamath 

Straits Drain, are monitored by acoustic index meters by the Bureau of Reclamation, and the USGS is 

currently developing ratings to verify the flows from these gages. Lost River Diversion Channel is located 

at RM 249.8, and water can be diverted from or returned to the Klamath River through this canal. North 

Canal removes water from Klamath River at RM 244.4. ADY Canal removes water from the river from 

3 
two locations on the river near RM 240.6 and 241.4. Klamath Straits Drain pumps water back into the 

river at RM 239.8 and 240.4. On the mainstem, Link River and Keno Dam flows have continuous flow 

gages operated by the USGS. 

Three crews made ADCP measurements on each of the days. One crew made measurements from a 

boat north of Miller Island on the mainstem Klamath River, a second crew made boat-based 

measurements south of Miller Island, and the third crew made land-based measurements of tributaries. 

The first crew used a 1,200 kHz Rio Grande ADCP (Teledyne RD Instruments) using Mode 5 or 11 

mounted inside an Ocean Science Riverboat; this configuration may have allowed the first crew to 

measure closer to shore than the second crew. The second crew used a 1,200 kHz Rio Grande ADCP on 

May 30, and a 600 kHz Rio Grande ADCP on Sept 19; this crew’s instrument was physically mounted to 

the side of the boat. The land-based crew used a StreamPro ADCP 2,000 kHz unit (Teledyne RD 

Instruments), and a bank-operated pulley system allowed a constant and slow speed across the channel. 

A portion of the edge of a cross section close the river banks cannot be measured because of 

minimum operational depth requirements for the instruments; in general, minimum measurement depth 

decreases with increasing transducer frequency. Aquatic vegetation on the banks affects the ability of an 

instrument to measure velocities, and, therefore, in places with thick aquatic vegetation near the shore, the 

amount of unmeasured flow on the side may have been greater. Edge discharges are estimated using an 

interpolation method based on the last recorded water velocities and the distance to the edge of water. 

Usually the estimated edge discharge is relatively small compared to the measured discharge. In addition 

to the unmeasured sections on the edges, an area near the surface and bottom of the water column is not 

measurable, due to the transducer depth and blanking distance at the surface and beam reflection issues at 

the bottom. 

On May 30, boat-based measurements were made at 11 locations on the mainstem Klamath River 

and on the Lost River Diversion Channel. Three canals were measured on land: North, ADY, and 

Klamath Straits Drain. One boat crew started near the Link River gage, upstream of Lake Ewauna, and 

headed south to Miller Island. Another boat crew made measurements south of Miller Island. Weather 

conditions were fairly stable throughout the day, with an increase in wind late in the day. 

On September 19, measurements from a boat were made at 10 locations on the mainstem. All four 

canals were measured on land. One boat crew began at Miller Island and traveled north. The other boat 

crew measured sites south of Miller Island and made one measurement at Miller Island. Weather 

conditions this day were not ideal, with weather severity increasing through the day; afternoon winds 

were near 10 mph with gusts over 20 mph. These deteriorating weather conditions made boat operation 

difficult and increased the error associated with ADCP measurements on this day. 

Final discharge values for a measurement are normally the average of four transects (two in each 

direction), and if any one transect exceeded 5 percent from the mean discharge for the measurement, four 

additional transects would usually be obtained. However, due to the time limitations, weather, and 

nonsteady flow conditions, it was not always practical to obtain more then four transects at each section 

during this study. Based on measuring conditions, a qualitative judgment of the overall measurement at a 

site is provided: Good, Fair, or Poor. A measurement rated “Good” is considered to be accurate to ±5 

percent, a “Fair” rating is accurate to ±8 percent, and a “Poor” rating is of lesser accuracy (Rantz and 

others, 1982; Oberg and others, 2005). All flows are reported to three significant digits. 

Water Quality Sampling 

Site Locations and Frequency 

Samples for water quality analysis were collected from five mainstem sites and five tributaries (fig. 

4 
1, table 1). Sampling began the first week of April and terminated the first week of November. In general, 

sampling was conducted weekly at the Link River, Miller Island, Keno, and Klamath Straits Drain sites, 

and every 2 weeks at the Railroad Bridge and KRS12a sites. The Lost River Diversion channel was 

sampled in spring and fall, periods when flow was to the Klamath River. The Keno Drain, Klamath Falls 

WWTP and a ditch near South Suburban WWTP were sampled in mid-August and mid-September. 

Table 1. Klamath River mainstem and tributary sampling locations. 

[Latitude and longitude format: dd mm ss; Abbreviations: RM, River Mile; WWTP, wastewater treatment plant; *, 

Klamath RM at confluence with tributary]

Site Name USGS Site Number Latitude Longitude Klamath RM

Mainstem Klamath River 

Link River 11507501 42 13 10 121 47 25 253.2

Railroad Bridge 421209121463000 42 12 09 121 46 30 251.7

Miller Island 420853121505500 42 08 53 121 50 55 245.9

KRS12a 420615121533600 42 06 15 121 53 36 238.3

Keno 11509370 42 07 41 121 55 44 234.9

Tributaries 

Klamath Falls WWTP 421257121463600 42 12 57 121 46 36 252.6*

Ditch near South Suburban WWTP 421148121461600 42 11 48 121 46 16 251.4*

Lost River Diversion Channel 421015121471800 42 10 15 121 47 18 249.7*

Klamath Straits Drain 420451121510000 42 04 51 121 51 00 240.5*

Keno Drain 420715121541000 42 07 15 121 54 10 236.6*

Samples for total nitrogen and phosphorus; particulate carbon and nitrogen; filtered orthophosphate, 

nitrite, nitrite plus nitrate, ammonia, and organic carbon were collected during most samplings. 

Phytoplankton species samples were collected during most mainstem samplings near the surface. Bacteria 

samples were taken at mainstem samplings, every 2 weeks. Zooplankton samples were taken at mainstem 

sites approximately every 2 weeks. Filtered iron and alkalinity were sampled monthly at Link River, 

Miller Island, and Keno. Filtered iron, along with filtered silica, was also sampled at Link River weekly 

from July through mid-October. 

Sample Collection 

During each sampling, field conditions were noted, and a vertical profile of pH, dissolved oxygen 

(DO), specific conductance, and water temperature was taken with a YSI 600XLM sonde. Grab water 

samples were taken with a van Dorn sampler and processed with a churn sample splitter. At most sites, 

samples were collected at 0.5 m depth. At four mainstem sites, a near-bottom sample was also collected 

for nutrients. Those samples were taken 1 m from the bottom, which was equivalent to 2.0 to 4.5 m from 

the surface depending on the site. All samples were kept on ice after collection. 

Unfiltered samples collected in the field included total nitrogen and phosphorus, carbon, bacteria, 

and phytoplankton. Samples for analysis of total nitrogen and total phosphorus were preserved by adding 

1 ml of 4.5 N sulfuric acid to each 125 mL sample bottle. Water for further processing of samples for 

particulate carbon and nitrogen and dissolved organic carbon was collected into 60 or 125 mL amber glass 

bottles that had been precombusted at 450 oC to remove any traces of carbon. Bacteria samples were 

5 
immediately preserved in 5 percent buffered formalin in 15 mL centrifuge tubes. Phytoplankton species 

samples were preserved with 1 percent Lugol’s solution in 250 mL amber bottles. 

Samples filtered in the field included nutrients, iron, silica, and, alkalinity. A Whatman capsule 

filter with a 0.45 μm pore size, rinsed with 500 mL of deionized water and 500 mL of sample, was used to 

collect these samples. Filtered samples taken near the bottom of the water column were pumped directly 

from the van Dorn sampler to the filter to minimize contact with the atmosphere. Filtered nutrients were 

collected into brown polyethylene bottles. Filtered iron was preserved with 2 mL of 7.7 N Ultrex grade 

nitric acid added to each 250 mL sample bottle. 

Zooplankton samples were taken by vertical tow with an 80 μm mesh Wildco Wisconsin net. The 

net assembly was rinsed with deionized water and specimens captured in a collector cup and transferred to 

a 250 mL sample bottle. At Link River, the current was too strong for a vertical tow, so known volumes 

were taken as grab samples at the surface and then passed through the zooplankton net assembly. 

Zooplankton samples were preserved in 23 percent isopropyl alcohol. 

Immediately upon return to the laboratory, all samples for organic carbon analysis were filtered 

using precombusted glass fiber filters and a Teflon filter apparatus, according to USGS procedures (Wilde 

and others, 2004). The filtrate was collected for dissolved organic carbon (DOC) analysis, and the glass 

fiber filters with retained particulate matter were submitted for analysis of particulate organic carbon 

(POC) and particulate nitrogen. Glass fiber filters had a nominal pore size of 0.7 μm. 

Samples were shipped on ice overnight to the laboratories. Through the season, a few coolers were 

delayed during shipping and arrived warm at the laboratories: two to the USGS National Water Quality 

Laboratory (NWQL) in Denver, Colorado, and two to the USGS microbiology lab in Reston, Virginia. 

Those samples were analyzed, but results are not reported here. 

Quality Control Samples 

Quality control samples collected as a regular part of the sampling program included blanks and 

replicates. Blanks were included to determine whether bias existed from contamination in any step of 

sampling and analysis. Replicate samples were taken to estimate variability from sampling and analysis. 

The number of quality control samples taken for each constituent was modified from guidelines from the 

USGS NAWQA program (Mueller and others, 1997), after considering Bureau of Reclamation guidelines 

(Bureau of Reclamation, 2005) and project needs. 

Field blanks collected at various sites through the season assessed the potential for contamination 

from the atmosphere, equipment, sample processing, transportation, and laboratory analysis. Lab blanks 

assessed the potential for contamination from transportation and laboratory analysis. Both field and lab 

blanks were collected using USGS-certified blank water. Blank results were evaluated in comparison to 

reporting levels determined by the laboratory for each constituent. For samples analyzed at the NWQL, 

the laboratory reporting level (RL) is usually equal to twice the long-term method detection level (LTMDL), which is determined statistically on an annual basis (Childress and others, 1999). 

Most field replicates, taken at various sites through the season, were subsamples from the same grab 

sample. Zooplankton duplicates, collected as sequential replicates, were the exception. Variability 

between duplicates was analyzed by calculating absolute differences and relative percent differences 

(RPD): 

100

2/)21(

)21( ×

+

− = Value ValueValue Value RPD

RPD was calculated for duplicates with concentrations more than 5 times the reporting limit, since 

percent differences for samples near the reporting limit can be high, even with small absolute differences. 

6 
Water Quality Analytical Methods 

Nutrients, Particulate Carbon and Nitrogen, Iron, Silica, and Alkalinity 

Nutrients, particulate carbon and nitrogen, iron, and silica were analyzed at the NWQL (table 2). 

Total phosphorus and total nitrogen concentrations were determined by alkaline persulfate digestion 

(Patton and Kryskalla, 2003). Orthophosphate was determined by colorimetry by reaction with 

ammonium molybdate in acidic solution to form phosphomolybdic acid, then reduction with ascorbic acid 

(Fishman, 1993). Nitrite was analyzed by colorimetry via reaction with sulfanilamide under acidic 

conditions to form a diazo compound that couples with N-1-naphthylethylenediamine dihydrochloride 

(Fishman, 1993). Nitrate plus nitrate was determined similarly, but nitrate was first reduced to nitrite with 

cadmium metal. Ammonia was measured by colorimetry through reaction with salicylate and 

hypochlorite in the presence of ferricyanide ions (Fishman, 1993). Iron was analyzed with inductively 

coupled plasma atomic emission spectrometry (Fishman, 1993), and silica with the molybdate blue 

method (Fishman and Friedman, 1989). 

Table 2. Analyzing laboratories and method references for water quality constituents. 

[Abbreviations: NWQL, National Water Quality Laboratory] 

Analyte Laboratory Method Reference 

Orthophosphate, as P USGS NWQL, Denver, Colorado Fishman, 1993 

Ammonia, as N USGS NWQL, Denver, Colorado Fishman, 1993 

Nitrate and nitrite, as N USGS NWQL, Denver, Colorado Fishman, 1993 

Nitrite, as N USGS NWQL, Denver, Colorado Fishman, 1993 

Total phosphorus USGS NWQL, Denver, Colorado Patton and Kryskalla, 2003 

Total nitrogen USGS NWQL, Denver, Colorado Patton and Kryskalla, 2003 

Particulate carbon USGS NWQL, Denver, Colorado Zimmerman and others, 1997 

Particulate nitrogen USGS NWQL, Denver, Colorado Zimmerman and others, 1997 

Iron USGS NWQL, Denver, Colorado Fishman, 1993 

Silica USGS NWQL, Denver, Colorado Fishman and Friedman, 1989 

Dissolved organic carbon USGS, Boulder, Colorado Aiken, 1992 

SUVA USGS, Boulder, Colorado Weishaar and others, 2003 

Total bacterial abundance USGS, Reston, Virginia Noble and Fuhrman, 1998; Weinbauer 

and others, 1998 

Alkalinity, as CaCO3 USGS, Klamath Falls, Oregon Rounds, 2006 

Phytoplankton, total density Aquatic Analysts, White Salmon, 

Washington 

American Public Health Association, 

2005; McNabb, 1960 

Zooplankton, total density ZP’s Taxonomic Services, Aberdeen, 

Washington 

American Public Health Assocation, 

2005 

7 
Particulate carbon and nitrogen concentrations were analyzed by combusting particulates retained 

on glass fiber filters in pure oxygen at 975 oC (Zimmerman and others, 1997). The combustion products 

were converted to CO2, H2O, and N2, and detected by thermal conductivity. In some analyses, a second 

sample filter was precombusted to remove organic carbon, allowing the measurement of particulate 

inorganic carbon. Particulate organic carbon (POC) is calculated as the difference between total 

particulate carbon (filter 1) and particulate inorganic carbon (filter 2). In many systems, particulate 

inorganic carbon is minimal, so measurement of total particulate carbon is equivalent to POC. In pilot 

work at Link River and Keno, particulate inorganic carbon was always below detection, so total 

particulate carbon was assumed equal to POC. 

NWQL has thorough internal quality assurance protocols, including standard reference samples, 

blanks, replicates, spikes, and calibration standards. These protocols are documented in Friedman and 

Erdmann (1982), Jones (1987), and Pritt and Raese (1995), and Maloney (2005). Samples analyzed at 

NWQL used USGS-certified field supplies during sampling including filters, bottles, and preservatives. 

Those supplies are subject to testing, inspection, and other quality assurance procedures (U.S. Geological 

Survey, no date). 

Alkalinity was analyzed within 24 hours of sample collection by titration following USGS methods 

(Rounds, 2006). Samples were run in duplicate, and results are averages of the duplicates. Two alkalinity 

standards from the USGS National Field Quality Assurance Program were analyzed, and both results 

were within 1 percent of the standard value. 

Dissolved Organic Carbon and Specific UV Absorbance

DOC concentrations were measured using the platinum catalyzed persulfate wet oxidation method 

on an O.I. Analytical Model 700 TOC AnalyzerTM (Aiken, 1992; Schuster, 2003), with the instrument 

warmed up at least 4 hours before analysis. Samples and standards were loaded onto an autosampler and 

introduced into the reaction vessel by means of a fixed-volume sample loop. The volume of the sample 

loop was kept small, usually 1 mL, to maintain linear instrument response (0–50 μg of carbon). The 

standard, automated analytical conditions called for 0.5 mL of 5 percent by volume phosphoric acid added 

to the sample. The sample was then purged for 2.0 minutes with nitrogen to remove inorganic carbon, 

after which 0.5 mL of 0.42 M sodium persulfate solution was added. The standard reaction time of 5 

minutes was used for the persulfate oxidation step. The instrument was calibrated with solutions of 

reagent-grade potassium hydrogen phthalate in distilled water. The standard curve, consisting of a 

minimum of five standards over the range of interest, was repeated for every 10–12 water samples 

analyzed in duplicate. All values are the averages of duplicate analyses. Standard deviation for the DOC 

measurement was ±0.2 mg/L. 

Ultraviolet-visible light absorbance analyses (UV-Vis) measurements were made on a HewlettPackard Model 8453TM photo-diode array spectrophotometer between λ=200 nm and λ=800 nm with 

distilled water as the blank using a 1 cm path-length quartz cell. Dissolved organic matter is a complex 

mixture of organic compounds, and absorbance measurements provide additional insight into its 

composition. The wavelength of λ=254 nm was chosen because it is the wavelength commonly associated 

with the aromatic moieties in a sample (Weishaar and others, 2003). Filtered samples at room temperature 

were analyzed using a quartz cell in the manual mode. The cell was rinsed with a small volume of sample 

before adding sample for analysis. The cell was then rinsed with distilled water before analyzing the next 

sample. Standard deviation for a UV absorbance measurement at 254 nm was ±0.002 AU. 

Specific UV Absorbance (SUVA), defined as the UV absorbance of a sample measured at a given 

wavelength divided by the DOC concentration, is an average molar absorbance for all the molecules that 

compose the DOC in a water sample. SUVA is a parameter that indicates the nature of DOC in a given 

8 
sample and has been used as a surrogate measurement of DOC aromaticity (Weishaar and others, 2003). 

SUVA values at 254 nm (SUVA254) are reported here because natural organic matter absorbs strongly at 

this wavelength, thereby giving increased sensitivity, and because of the strong correlation with the 

aromatic carbon content of natural organic matter at this wavelength. SUVA254 was determined by 

dividing the UV absorbance determined at λ=254 nm by the DOC concentration of the sample. Values are 

reported in units of L/(mg-m) and have a standard deviation of ±0.1 L/(mg-m). 

Bacterial Abundance and Morphology 

Processing of bacteria samples employed modifications of protocols from Noble and Fuhrman 

(1998), and Weinbauer and others (1998). Samples were stained for 15 minutes in the dark using Sybr 

Green I stain (Molecular Probes, Eugene, Oregon) at 1:5,000 dilution, and were filtered under gentle 

vacuum (<10kPa) onto a 0.2 μm aluminum oxide Anodisc 25 filter (Whatman International, Maidstone, 

England) backed by a 0.45 μm cellulose nitrate membrane filter (Fisher Scientific, Pittsburgh, 

Pennsylvania). The anodisc filter was mounted on a glass slide with a drop of antifade solution (50 

percent glycerol, 50 percent phosphate buffered saline, 0.5 percent ascorbic acid) and a 25 mm-square 

coverslip. Total cells were enumerated under blue excitation using a Zeiss epifluorescent microscope 

(Axio A1). At least 250 cells from at least 5 fields were counted per filter. Autofluorescent, bacteria-sized 

cells were also enumerated using a bandpass filter with emission from 575–640 nm. Attached cells were 

counted where possible, but early in the season the numbers were too low to get reliable counts. 

Three groups of bacteria were enumerated based on size and morphology: 

1. Large cells 

2. Vibrios 

3. Small cocci 

Group 1 bacteria were mostly stubby rods (over 90 percent), but also included narrower or longer 

rods and diplococci > 0.5 μm. Although it is not possible to determine bacterial identification and 

metabolic function based on morphology, this group could include Gram-negative, respiratory bacteria 

(aerobes, facultative anaerobes) phenotypically related to members of the genus Pseudomonas. Many 

bacteria in this physiological group are free-living in soil and water, and play an important role in 

decomposition, biodegradation, and carbon and nitrogen cycles. Some display bioluminesce, such as 

Photobacteria. Group 1 bacteria could also include gram-positive fermentative bacteria or enteric bacteria. 

“Vibrios,” which make up Group 2 bacteria, are Gram-negative bacteria that have the cell shape of 

a curved rod or a comma. Members of the genus Vibrio are common in aquatic environments, and have 

structural and metabolic properties that overlap with both the enterics and the pseudomonads. In aquatic 

habitats they overlap with the pseudomonads in their ecology (decomposition, biodegradation, and the 

carbon and nitrogen cycles). 

Group 3 bacteria are cocci, spherical or oval bacteria. Their size in this system was mostly 0.1–0.2 

μm, with cells larger than or equal to 0.5 μm rare (<1 percent). 

Bacteria play a key role in recycling organic and inorganic matter, and constitute part of the pool of 

organic matter in aquatic ecosystems. Populations and dimensions of the three bacterial morphologies 

were used to estimate bacterial biovolume, and can be used to estimate bacterial biomass. Separation into 

morphological groups is important with these calculations because changes in the populations of larger 

cells may have a disproportional contribution to biovolume. 

9 
Phytoplankton Enumeration and Species Identification 

Analysis of phytoplankton included enumeration, identification, and estimations of biovolume. 

Permanent microscope slides were prepared by filtering an aliquot of each sample through a 0.45 μm 

membrane filter (American Public Health Association, 2005; McNabb, 1960). A section of filter was cut 

out and placed on a glass slide with immersion oil added to make the filter transparent. A cover slip was 

placed over the filter section, with nail polish applied to the periphery for permanency. The slides are 

archived indefinitely; water samples were placed in storage for at least one year. 

Enumeration of algal units (defined as discrete particles - cells, colonies, or filaments) was 

completed by counting along a measured transect of the microscope slide with a Zeiss standard 

microscope (1,000X, phase contrast). Only algae that were believed to be alive at the time of collection 

(intact chloroplast) were counted. At least 100 algal units were counted. Algae were identified using an 

extensive library of literature, including journal reprints, standard reference books, and internet reference 

sites. Most algae were identified by cross-referencing several taxonomic sources. Algal densities were 

calculated from the area observed (transect length times diameter of field of view), the effective filter 

area, and the volume of sample filtered. 

The microscope was calibrated using a standard concentration of latex spheres, 12,075 spheres/mL, 

provided by the U.S. Environmental Protection Agency (Cincinnati, Ohio). Duplicate preparations of the 

standard spheres were analyzed, with an average result of 11,700 spheres/mL. A computer program used 

to calculate algal densities compensated for this 3.1 percent error. The analyzing laboratory has 

participated in the analyses of split algae samples on several occasions, with general agreement between 

samples in terms of algae density and groups. Also on occasion, independent algae analysts have been 

contracted by the laboratory for second opinions on some difficult-to-identify algae species. 

Average biovolume estimates of each species were obtained from calculations of microscopic 

measurements of each algal unit, accurate to 0.1 mm with a stage micrometer. The number of cells per 

colony or the length of a filament was recorded during sample analysis to arrive at biovolume per unitalga. Average biovolumes and measurements were verified for each sample analyzed. 

Trophic State Index (TSI) based upon phytoplankton biovolume was developed from a data set of 

several hundred lakes located throughout the Pacific Northwest (Sweet, 1986). The index was derived in a 

similar fashion as Carlson (1977) derived indices for Secchi depth, chlorophyll a concentration, and total 

phosphorus concentration, and values agree well with Carlson’s indices. The unitless biovolume index 

ranges from one for ultraoligotrophic lakes to 100 for hypereutrophic lakes. The index is defined as: 

5*))1((log)( TSI biovolume = 2 B +

 where B is phytoplankton biovolume in μm/mL divided by 1,000 

Zooplankton Enumeration and Species Identification 

Analysis of zooplankton species included identification and enumeration (American Public Health 

Association, 2005). Samples were first split with a Folsom plankton splitter until an approximate 

subsample size of 400 total individual arthropods and 100 individuals of the most abundant species were 

reached. If the initial split did not achieve both of these criteria, then increasingly larger splits were 

enumerated until both criteria were met, or until the entire sample was counted. All rotifers and 

protozoans in the split were completely enumerated as well, unless their numbers significantly exceeded 

400 individuals, in which case a separate rotifer subsplit was made and counted for rotifers and 

protozoans. The statistical methodology for this approach was based upon Edmondson and Winberg 

(1971, p. 178) and assumed that the sampling methods (both in the field and during the splitting) followed 

10
a Poisson distribution. This assumption is violated for larger species such as those of Chaoborus and 

Leptodora; thus, all individuals of those taxa found in a sample were enumerated. The selected values of 

400 and 100 individuals provided a maximum statistical standard error of the mean of 5 and 10 percent, 

respectively (the formula used is: s = 1/√N, where N is the number of individuals found belonging to the 

taxon in question). Although the confidence limits for only total numbers and most abundant species were 

set by this procedure, the standard error of the mean for each species could be determined from the 

original tallies, using the previous formula for the Poisson distribution. Results are reported in 

numbers/m3

, and standard errors for each value are included in Appendix B. 

Standard zooplankton enumeration was done with a Wild M-3 microscope at 32X magnification. 

Samples were counted in an open counting chamber with six parallel channels following the procedures 

described in Edmondson and Winberg (1971, p. 131). Species identifications were made at higher levels 

of magnification under a compound microscope as needed. General taxonomic identifications followed 

Edmondson (1959), Pennak (1989), and Thorp and Covich (1991). Specific group references used include 

Berner (1994), Brooks (1957), Brandlova and others (1972), Deevey and Deevey (1971), DeMont and 

Hebert (1994), Dumont and Pensaert (1983), Hebert (2001), Korovchinsky (1992), Patterson (1996), 

Pontin (1978), Ruttner-Kolisko (1974), Stemberger (1979), and Taylor and others (2002). Identifications 

were to species for all adult and subadult crustaceans, excepting harpacticoid copepods and ostracods, and 

for most rotifers. Immature copepods through copepodite stage IV were identified as far as their 

developmental stage allowed. Confirmation of the identifications was made with results from previous 

investigations in the region of the study area. 

For length-frequency analysis, crustacean lengths were taken following the protocols described in 

Edmondson and Winberg (1971). Specifically, cladocerans were measured from the top of the head 

(helmet included) to the posterior edge of the carapace excluding any tail spine or mucro, and copepods 

were measured from the end of the cephalothorax to the end of the caudal rami, exclusive of the setae. 

An estimate of the intensity of planktivory based upon the density and relative abundance of the 

edible species present was made for each sample. Evaluation of the availability of the different 

zooplankton species as food items for particular species of fish was based upon an ongoing literature 

review starting with Brooks (1969) and continuing with Kerfoot (1980), Zaret (1980), and Carpenter and 

Kitchell (1993). This evaluation was kept up-to-date by regular reviews of recently published zooplankton 

predation studies in Limnology and Oceanography, and the Proceedings of the International Association 

of Theoretical and Applied Limnology (Verhein International Verein Limnologie), as well as the results 

of articles such as Eilers and others (2007). The earlier literature has been summarized in Canale and 

others (1975, 1976). 

Quality assurance included microscope calibration, replicate samples, independent analysis, and 

internal data verification. The basic quality control method used for enumerating zooplankton samples 

was the standard error value, an estimator of within-sample variability. Quality assurance and control for 

within-sample variability was maintained by routine re-analysis of 2 to 3 percent of all samples examined. 

The samples re-analyzed were selected at random, using a random number generator and the unique 

sequence number of each sample analyzed. Statistical analyses of past replicated counts indicated that the 

standard error values adequately estimate between 90 and 98 percent of all within-sample variability. 

Unlike the statistical parameter standard deviation, standard error does not provide a betweensample estimator of the population variance. Field replicate samples were collected to assess betweensample variability. Between-sample replicates taken at the same time and place have significantly higher 

variability due to plankton patchiness and species "swarms." 

11
Acoustic Doppler Current Profiler Data Summary 

Summary and raw transect data and plots of cross-sectional velocity direction and velocity are 

included as electronic files in the Appendix A. Local Agrimet weather data are included, as well as 

provisional Bureau of Reclamation continuous flow data from the canals from May 30 and September 19. 

A brief summary of the ADCP data is provided below. 

May 30, 2007 

With one boat crew working from upstream to downstream, a flow of 1,330 ft3/s was measured 

downstream of Lake Ewauna at river mile (RM) 251.6 (fig. 2). This measured flow is lower then the 

flows reported from the Link River gage upstream of Lake Ewauna, which ranged from 1,460 to 1,470 

ft3

/s at the time this measurement was made. The next two measurements were made at mile RM 250.6 

and upstream of the Lost River Diversion Channel at RM 250; the discharge for both of these was 1,350 

ft3

/s. A measurement in the mouth of the Lost River Diversion identified 292 ft3/s flowing out of Klamath 

River. This flow can be subtracted from the 1,350 ft3

/s, resulting in a predicted downstream flow of 1,060 

ft3

/s. A measurement of 1,110 ft3/s, made downstream of the Lost River Diversion Channel (RM 249.2), 

confirmed the predicted downstream flow. The flow measured at Miller Island (RM 245.7) was 1,200 

ft3/s. This flow agrees with the measurement of 1,190 ft3/s made downstream at RM 244.5 by the second 

crew. 

Starting at the downstream end of the reach, the second boat crew measured flow upstream of Keno 

Dam (RM 233.5) of 994 ft3/s, flow near Highway 66 (RM 234.8) of 914 ft3/s, and flow at RM 236.3 of 

978 ft3

/s. The next two measurements made upstream (RM 240.5) and downstream (RM 239.6) of 

Klamath Straits Drain, were 705 and 1,050 ft3/s respectively. This flow difference predicts an output from 

the Klamath Straits Drain of 345 ft3

/s, which was confirmed by the measurement of 340 ft3/s made in the 

drain by the third crew. The second crew finished by making a measurement of 1,190 ft3/s at RM 244.5, 

on the mainstem upstream of the ADY and North canals. This measurement subtracted from the 

measurement at RM 240.5 (705 ft3/s) results in a net reduction of 485 ft3/s, whereas the total flows for 

ADY and North canals as measured by the third crew result show a net withdrawal of 346 ft3/s. There is 

the possibility of marsh flow or storage between the measuring location on the North Canal and the 

mainstem Klamath River or withdrawals from other diversions not measured in this study. 

Most measurements on this day were rated fair (±8 percent) except for the two farthest downstream 

measurements, which were rated good (±5 percent), and the measurement at Miller Island (RM 245.7) 

which was rated poor (>±8 percent) due to afternoon wind affecting surface conditions there. 

12




















  



 



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September 19, 2007

Figure 2. Acoustic Doppler current profiler flow measurements on the Klamath River between Link River Dam and 

Keno Dam on May 30, 2007, and September 19, 2007, and gaged flows at Link River and downstream of Keno Dam 

for the same dates. 

September 19, 2007 

One crew began at Miller Island (RM 245.7), measuring 888 ft3/s (fig. 2), and then moved 

upstream. Klamath River flow downstream of the Lost River Diversion Channel (RM 249.2) was 

measured at 646 ft3

/s, and upstream of Lost River Diversion Channel (RM 250.0), measured flow was 406 

ft3/s. This pattern of higher Klamath River flows downstream of the Diversion Channel and lower flows 

upstream is inconsistent with measured discharge flowing out of Klamath River in the Diversion Channel 

measured by the land-based crew (442 ft3

/s flowing out of Klamath River). The boat crew measured 970 

ft3

/s upstream at RM 250.6. The main USGS measuring points at Link and Keno stayed relatively 

constant throughout the day, but a likely explanation for these changing flow patterns was the variable 

wind during these periods. 

The average measurement made downstream of Lake Ewauna at RM 251.6, between 14:41 and 

15:28, was 380 ft3

/s; however, the individuals transects ranged from 12.8 ft3/s (at 14:41) to 775 ft3/s (at 

15:28). During this time the Link River gage, essentially all flow upstream of Lake Ewauna, ranged from 

only 532 to 564 ft3/s. 

13
The second boat crew made measurements at Miller Island and sites south of Miller Island, starting 

at Keno and working upstream. Measured flow above Keno Dam (RM 233.5) was 468 ft3/s, 482 ft3/s near 

HWY 66 (RM 235), and 464 ft3

/s at RM 236.2. 

The subsequent measurements, from RM 239.6 downstream of Klamath Straits Drain and RM 

240.5 upstream of the drain indicated highly variable flow conditions. Three sets of measurements were 

completed at RM 239.6 between 14:04 and 14:46, with average flows of 122, –66.4, and 45.8 ft3/s. An 

average measurement of 468 ft3/s was made upstream of the Klamath Straits Drain (RM 240.5), though 

the individual transects ranged from 64.6 ft3

/s (at 15:01) to 1,000 ft3/s at (15:26). Measurements at this 

location by the second crew were made at the same time as the first crew was measuring at RM 251.6, 

where individual transects also ranged low to high within that same time period. Wind speeds at the 

Klamath Falls KFLO Agrimet station between 14:00 and 15:30 averaged 8.1 mph with 15-minute peak 

wind gusts between 12.9 and 22.1 mph (Appendix A). Deployment of several continuously measuring 

bottom-mounted ADCPs is planned for 2008 to further investigate the effect of weather and wind 

conditions on flow and circulation in this reach of the Klamath River. 

The second boat crew finished by making a second measurement at Miller Island (RM 245.7) of 

1,060 ft3/s. The Miller Island measurement made between 16:16 and 16:39 was higher then the 888 ft3/s 

measured by the first crew earlier in the day (11:00–11:30). The land-based crew measured 129 ft3

/s to the 

Klamath River from the Klamath Straits Drain and 177 and 46.7 ft3/s leaving the river from the ADY and 

North Canals, respectively. 

Most mainstem boat-based measurements were rated poor (>± 8 percent) due to slow water 

velocities, relatively fast boat speeds, and the wavy and choppy surface conditions; the exceptions were 

the two most downstream sites, which were rated fair (±8 percent). All land-based canal measurements 

were rated fair. 

Cross-Sectional Velocity Direction and Magnitude 

The direction of velocities across the channel was more homogeneous than the magnitude, which 

was usually lowest near the channel bottom and sides, and highest near-surface (Appendix A). Many 

sections showed fairly symmetrical velocities bank-to-bank, with some exceptions, RM 249.2 for 

example. Measured cross-sectional velocities there on May 30 were between 0 and 0.8 ft/s. 

More variability was observed in cross-sectional velocity direction and velocity on September 19. 

Increased variability due to nonideal measuring conditions and effects of strong wind on circulation was 

not quantified. Measured cross-sectional velocities had a similar range to those measured on May 30. 

Water Quality Data Summary 

Water quality data summarized here are provided in appendix tables (PDF and Excel files) that can 

be accessed through links at the end of the text. A brief data summary is presented below to highlight 

quality control results, seasonal trends, concentration ranges, differences between concentrations at the 

top and bottom of the water column, major species, and notable trends between sites. 

Quality Control Results 

Program-level quality assurance for blanks assumes that when field blank concentrations are less 

than the reporting level, regular samples are free of contamination. It is further assumed that systematic 

blank results higher than the RL are notable, whereas a rare random blank higher than the RL is of less 

concern. For analytes with reporting levels, concentrations in 129 of 130 blanks (>99%) analyzed 

throughout the sampling season were below the RL (table 3): the only blank above the RL was one 

14
particulate carbon blank of 0.15 mg/L, 0.03 mg/L above the RL of 0.12 mg/L. A reporting level was not 

designated for UV absorbance, but blank values were near at or near zero, and much lower than all 

measured values. Blank results show no evidence of systematic contamination. 

Table 3. Analyte reporting levels and blank results. 

[Abbreviations: RL, reporting level; mg/L, milligrams per liter; P, phosphorus; N, nitrogen; >, greater than; NA, no 

blanks were above RL; *, RL not determined, median and range of all blanks given] 

Analyte Units RL Number of 

blanks 

Number of 

blanks > RL Value of blanks > RL 

Orthophosphate, as P mg/L 0.006 16 0 NA 

Ammonia, as N mg/L 0.02 16 0 NA 

Nitrate and nitrite, as N mg/L 0.06 16 0 NA 

Nitrite, as N mg/L 0.002 16 0 NA 

Total phosphorus mg/L 0.02 16 0 NA 

Total nitrogen mg/L 0.06 16 0 NA 

Particulate carbon mg/L 0.12 9 1 0.15 

Particulate nitrogen mg/L 0.022 9 0 NA 

Iron mg/L 0.006 6 0 NA 

Dissolved organic carbon mg/L 0.7 10 0 NA 

UV absorbance 1/m * 10 * median: 0.001 

range: 0.000 – 0.007 

Analysis of duplicate filtered samples showed low variability (table 4). All duplicates (≥5x RL) for 

filtered orthophosphate, ammonia, nitrite, DOC, UV absorbance, iron, and alkalinity were below 8 

percent RPD, with medians of all duplicates for those analytes 4 percent or less. There was more 

variability for duplicates of unfiltered samples, that is, those that included particulate matter. The 

macroscopic size and tendency of AFA to form clumps likely contributed to this variability. There is 

greater uncertainty with these data due to the inherent difficulties of sampling particulate matter. Several 

samples for total nitrogen and phosphorus, and particulate carbon and nitrogen that had higher RPD were 

submitted for reanalysis at NWQL, and all original analyses were confirmed. 

Table 4. Results of analyses of duplicate quality assurance samples—continued

[Abbreviations: mg/L, milligrams per liter; RPD, relative percent difference; ≥, greater than or equal to; RL, reporting 

level; pctl, percentile; NA, no duplicate results were ≥5x RL; *, RL was not determined, so RPD was calculated for all 

duplicates]

Difference between duplicates 

Analyte Duplicates Units 

Absolute difference RPD, % 

 (for duplicates ≥ 5x RL) 

Median 10th pctl | 90th pctl Median 10th pctl | 90th pctl 

Orthophosphate, as P 15 mg/L 0.001 0.000 | 0.003 1.0 0.0 | 2.1 

Ammonia, as N 15 mg/L 0.003 0.001 | 0.007 0.9 0.7 | 2.5 

Nitrate and nitrite, as N 15 mg/L 0.001 0.000 | 0.008 NA NA 

Nitrite, as N 15 mg/L 0.000 0.000 | 0.000 0.0 0.0 | 2.0 

Total phosphorus 15 mg/L 0.01 0.00 | 0.04 3.5 2.2 | 15.4 

15
Table 4. Results of analyses of duplicate quality assurance samples—continued

[Abbreviations: mg/L, milligrams per liter; RPD, relative percent difference; ≥, greater than or equal to; RL, reporting 

level; pctl, percentile; NA, no duplicate results were ≥5x RL; *, RL was not determined, so RPD was calculated for all 

duplicates]

Difference between duplicates 

Analyte Duplicates Units 

Absolute difference RPD, % 

 (for duplicates ≥ 5x RL) 

 Median 10th pctl | 90th pctl Media

n 10th pctl | 90th pctl 

Total nitrogen 15 mg/L 0.06 0.03 | 0.34 4.4 1.3 | 17.0 

Particulate carbon 14 mg/L 0.27 0.07 | 1.02 11.5 2.9 | 25.9 

Particulate nitrogen 14 mg/L 0.06 0.00 | 0.18 7.2 0.6 | 38.3 

Iron 3 mg/L 0.002 0.000 | 0.004 4.0 0.8 | 5.8 

Dissolved organic carbon 16 mg/L 0.2 0.0 | 0.5 1.3 0.0 | 3.9 

UV absorbance 16 1/m 0.002 0.000 | 0.005 0.5* 0.0 | 2.2* 

Bacterial abundance 6 106

 cells/mL 19.8 7.8 | 45.6 44.0* 14.1 | 62.3* 

Alkalinity, as CaCO3 3 mg/L 0.8 0.3 | 1.0 1.7 0.6 | 1.9 

Phytoplankton, density 8 number/mL 324 71 | 1,332 9.9* 6.8 | 34.4* 

Zooplankton, density 5 number/m3 8,667 1,444 | 13,555 30.0* 23.5 | 58.6* 

Nutrients, Iron, Silica, and Alkalinity 

Total nitrogen concentration at mainstem sites was lowest in spring and highest in summer, with a 

gradual decrease late in the sampling season (fig. 3); concentrations at mainstem sites ranged between 

0.70 and 5.85 mg/L. Concentrations at the top and bottom of the water column were generally similar; 

any notable differences occurred in summer. Tributary total nitrogen concentration (Appendix B) ranged 

from 0.98 to 26.9 mg/L, with highest values near the wastewater treatment plant outflows. 

Particulate nitrogen had seasonal patterns similar to total nitrogen, with mainstem concentrations 

between 0.08 and 3.93 mg/L. Averaged over the sampling season, the percent of total nitrogen that was 

particulate decreased in the downstream direction at mainstem sites; this was especially true later in the 

season. Tributary particulate nitrogen concentrations ranged from 0.08 to 2.49 mg/L. 

Ammonia concentrations at Link River were below 0.100 mg/L and fairly constant until after midOctober, when concentrations increased, up to 0.530 mg/L. The seasonal pattern at that upstream site was 

different from that at other mainstem sites, which experienced increases in ammonia concentrations by 

early July, with maximums in midsummer. At some of the farther downstream sites, on some dates in 

summer, ammonia also exhibited large variation (over 100 percent difference) between the top and 

bottom of the water column. Averaged over the entire sampling season, ammonia concentrations 

increased in the downstream direction: 0.089 mg/L at Link River, 0.238 mg/L at Railroad Bridge, 0.413 

mg/L at Miller Island, 0.501 mg/L at KRS12a, and 0.560 mg/L at Keno. Tributary ammonia concentration 

ranged from 0.039 to 1.090 mg/L. 

Concentrations of nitrite plus nitrate at all mainstem sites were below the reporting level (0.060 

mg/L) from June 26 to August 14, with some site’s concentration below the reporting level as early as 

16
May 8 (Link River), or as late as September 25 (Railroad Bridge). Concentrations at the top and bottom of 

the water column were similar. In the Klamath Straits Drain, nitrite plus nitrate concentrations were 

mostly above detection, ranging between 0.072 and 0.439 mg/L. Other tributary concentrations ranged 

between below detection and 21.9 mg/L, with highest values from the site near the Klamath Falls 

wastewater treatment plant. 

0

10,000

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Apr May Jun Jul Aug Sep Oct Nov

copepods

cladocerans

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Concentration, in mg/L as N

2007

Concentration, in mg/L as P Concentration, in mg/L

Zooplankton density, number/m

Phytoplankton biovolume (106

μm3/mL) Bacterial biovolume (106 μm3/mL)

2007

0

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3

Figure 3. Median concentrations of carbon, nitrogen, and phosphorus species; median zooplankton density; and 

median algal and bacterial biovolumes from all five mainstem Klamath River sites. 

Filtered nitrite, which has a lower reporting level than nitrite plus nitrate, remained above detection 

at most mainstem sites, though at low concentrations. At mainstem sites concentrations ranged between 

17
0.002 and 0.025 mg/L. The Klamath Straits Drain had nitrite concentrations between 0.003 and 0.112 

mg/L. Other tributary concentrations ranged from below detection to 0.085 mg/L. 

Total phosphorus concentrations at mainstem sites ranged between 0.05 to 0.50 mg/L, and filtered 

orthophosphate concentrations ranged between 0.010 and 0.272 mg/L. Both total phosphorus and filtered 

orthophosphate concentrations at mainstem sites increased into summer and decreased into fall (fig. 3). 

Overall, orthophosphate increased in the downstream direction (fig. 4). Tributary concentrations ranged 

between 0.16 and 7.34 mg/L total phosphorus, and 0.013 and 6.07 mg/L orthophosphate, with the higher 

concentrations from samplings near the wastewater treatment plant outflows. 

Filtered iron concentrations at Link River decreased from June through mid-October, from 106 to 

22 μg/L. At Miller Island and Keno, concentrations of filtered iron sampled monthly from June through 

October, were between 93 to 39 μg/L. Concentrations at the top and bottom of the water column at those 

sites were similar, except for the Miller Island sample on June 19, where the top of the water column had 

filtered iron concentration of 45 μg/L and the bottom had concentrations of 92 μg/L. 

At Link River, filtered silica concentrations ranged from 32.3 to 52.5 mg/L, increasing from July 

through mid-September. 

Alkalinity generally increased in the downstream direction, higher at Miller Island and Keno than at 

Link River on any sampling date. Alkalinity ranged from 44.6 to 76.6 mg/L as CaCO3. The only tributary 

sampled for alkalinity was Klamath Straits Drain, with an alkalinity of 136.0 mg/L as CaCO3. 

Particulate and Dissolved Organic Carbon 

Concentrations of particulate organic carbon (POC) ranged from 0.49 to 17.89 mg/L at mainstem 

sites; concentrations were generally lowest in spring, increased in June, remained elevated through the 

summer, and decreased in fall (fig. 3). Concentrations at the top and bottom of the water column were 

similar in spring and fall, with more variation in summer; when different, POC concentrations were 

generally higher near the surface, but depending on the site or date, concentrations were sometimes higher 

at the bottom of the water column. Klamath Straits Drain POC concentrations ranged between 0.75 and 

7.15 mg/L through the season, with highest concentrations in April. Other tributary POC concentrations 

ranged between 0.51 to 15.8 mg/L. 

Dissolved organic carbon (DOC) concentrations at mainstem sites ranged between 5.2 and 13.4 

mg/L. Like POC, concentrations of DOC were lowest in spring, increased into summer, and decreased in 

fall (fig. 3). DOC concentrations at the top and bottom of the water column were similar. The Klamath 

Straits Drain had higher DOC concentrations than the mainstem, ranging from 13.2 to 45 mg/L, with 

highest concentrations in May and June. Other tributaries had DOC concentrations between 6.0 and 21.5 

mg/L. 

SUVA254, a measure of the aromaticity of DOC, ranged from 2.1 to 3.7 L/(mg-m), was highest in 

spring and decreased into summer at mainstem sites. SUVA254 in the Klamath Straits Drain ranged from 

2.5 to 3.2 L/(mg-m), and SUVA254 in other tributaries ranged between 1.1 to 2.8 L/(mg-m). 

Together, POC and DOC make up total organic carbon (TOC). Averaged over the sampling period, 

particulate carbon constituted 32 percent of TOC at the Link River and Railroad Bridge sites, 21 percent 

at Miller Island, 18 percent at KRS12a, and 16 percent at Keno, decreasing in the downstream direction. 

Depending on the date or site, POC could make up from 6 to 68 percent of TOC. 

Bacterial Abundance and Morphology 

Total bacterial populations ranged from 1.4 x 106 to 170 x 106 cells/mL, and generally increased 

18
into summer. Group 3 (cocci) was the most abundant bacteria morphotype, averaging 93 percent of total 

cell counts (at all sites through the season), with a range from 41 to 98 percent of total bacterial 

abundance. They were the smallest bacteria, with diameters of 0.1 to 0.2 μm. Their diameters were 

smaller than the filter pore size used for nutrient filtration (0.45 μm) and the pore size used to separate 

particulate carbon and nitrogen from dissolved organic carbon (0.7 μm). 

River Mile

Concentration, in mg/L as N Concentration, in mg/L as P Concentration, in mg/L

Zooplankton density, number/m3

Phytoplankton biovolume (106 μm3/mL) Bacterial biovolume (106 μm3/mL)

River Mile

0

2

4

6

8

10

12

14

16

18

bluegreen

diatom

cryptophyte

green

0

10,000

20,000

30,000

40,000

50,000

60,000

234 238 242 246 250 254

rotifers

copepods

cladocerans

0.0

0.2

0.4

0.6

0.8

1.0

1.2

234 238 242 246 250 254

large cells

vibrios

cocci

0

2

4

6

8

10

12

DOC

POC

0.0

0.5

1.0

1.5

2.0

2.5

3.0

total N

ammonia

nitrate+nitrite

0.00

0.04

0.08

0.12

0.16

0.20

0.24

234 238 242 246 250 254

total P

ortho P

Figure 4. Median concentrations of carbon, nitrogen, and phosphorus species; median zooplankton density; and 

algal and bacterial biovolumes at the five mainstem Klamath River sites using all data from April through November, 

2007 

Although cocci were the most numerous bacteria, group 1 bacteria (large cells) made up most of the 

bacterial biovolume (figs. 3 and 4). The total bacterial biovolume maximum occurred between late June 

and September, depending on the site. Biovolumes ranged from 127,000 to 10,500,000 μm3

/ml, with an 

19
average for all sites and dates of 1,350,000 μm3

/ml. 

There is no simple way to functionally divide the bacteria based on morphology. For instance, no 

consistent relationship between morphology and autofluorescence was observed. Bacteria cells were 

observed to attach to living algae and algal debris, and in one instance dense attachment to the nitrogenfixing nodules on AFA was observed. Cells attached to algae were counted; however, slide preparations 

had little particulate material. To have a count greater than zero, a particle with attached cells had to 

appear in one of the counting fields. In some cases, such particles were observed outside the counting 

fields; these samples are designated as <0.03 x 106

 attached cells. 

Phytoplankton Enumeration and Species Identification 

Through the season, 108 species of phytoplankton were identified; most were classified as bluegreens, cryptophytes, diatoms, or greens. AFA, a blue-green alga, was the most frequently identified 

species and also had the highest overall average density (51 percent), followed by Cryptomonas erosa

(11.9 percent) and Rhodomonas minuta (5.4 percent), both cryptophytes, and Ankistrodesmus falcatus

(3.1 percent) a green alga. 

Phytoplankton biovolumes ranged from 106,000 to 264,000,000 μm3/mL. Diatoms were the 

predominant group in spring. By early June, blue-green algae, AFA in particular, became dominant, with 

biovolumes increasing dramatically (fig. 3), especially at the upstream sites. At Link River and Railroad 

Bridge, blue green algae made up almost 100 percent of all algae species through late October. With 

increasing distance downstream, blue-green algae were less dominant after early July. At Miller Island 

and KRS12a, blue-greens were still common, but periods with notable diatom and cryptophyte 

populations occurred. At Keno, farthest downstream, there was a mix of blue-greens and crytophytes after 

early July, as well as populations of diatoms and green algae. Considering the whole sampling season, 

phytoplankton biovolumes were highest at Link River and Railroad Bridge, and lowest at Keno (fig. 4). 

The trophic state index (TSI) for mainstem sites ranged between 33.7 and 90.1. Of the 

phytoplankton samples collected in this study, 1 sample had a TSI considered “oligotrophic,” 34 as 

“mesotrophic,” 53 as “eutrophic,” and 44 as “hypereutrophic”, according to the classification system in 

Atlas of Oregon Lakes (Johnson and others, 1985). 

Phytoplankton data in the appendix comprise sample identification, total density, total biovolume, 

TSI, and top five most common algae species and their relative densities. Combined species lists of all 

species within related groups of samples are provided to allow greater sensitivity in comparing different 

sites or dates. Algae species are compiled according to their relative densities. 

Zooplankton Enumeration and Species Identification 

Over the sampling season, 64 taxa of zooplankton were identified; most were cladocerans, 

copepods, or rotifers. The most frequently identified cladocerans were Daphnia pulicaria and Chydorus 

sphaericus, the most frequently identified copepods were copepod nauplii (early stage copepods of 

undetermined species) and cyclopoid copepodites (intermediate-late stage cyclopoid copepods of 

undetermined species), and the most frequently identified rotifers were Keratella hiemalis and Euchlanis 

dilatata. 

Total zooplankton density ranged from 500 to 190,000/m3. At Link River density was highest in 

April. At the other mainstem sites, farther downstream, total zooplankton densities were highest in 

summer. Copepods were dominant at most sites in April (fig. 3). In late spring and summer, at Link River, 

cladocerans became the most common group, while farther downstream at Railroad Bridge both 

cladocerans and rotifers were seen in summer. With increasing distance downstream, rotifers became 

20
more common (fig. 4). 

Zooplankton data in Appendix B comprise a zooplankton species list, as well as zooplankton 

densities per species per sample. Total density of the major zooplankton groups present in the samples 

and the standard error for each species density are also presented. 

Acknowledgements 

This study was made possible with primary funding from the Bureau of Reclamation, with 

additional support from the USGS Hirsch Fund. Damion Ciotti, Matthew Kritzer, Scott Miller, Gunter 

Schanzenbacher, and April Tower (Bureau of Reclamation) conducted weekly water quality field work. 

Dean Snyder (USGS) assisted with fieldwork and analyzed alkalinity samples. Jim Sweet (Aquatic 

Analysts) analyzed algae species samples. Allan Vogel (ZP’s Taxonomic Services) analyzed the 

zooplankton samples. Elizabeth Jones (USGS) conducted bacteria counts. Mary Voytek and George 

Aiken of the USGS National Research Program provided guidance to bacteria and DOC work, 

respectively. Tim Dalrymple, Jon House, and Mark Schuster (USGS) participated in ADCP work, with 

boat support from the Bureau of Reclamation. Assistance from Jason Cameron (Bureau of Reclamation), 

Stewart Rounds, Joseph Rinella, Dennis Lynch, and Matthew Johnston (USGS) were important to the 

success of the project. Jacqueline Olson (USGS) prepared the map, and reviews by Valerie Kelly and 

Dwight Tanner (USGS) improved the manuscript. 

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 Appendix A—Acoustic Doppler Current Profiler Data 

Click on the links to retrieve data. 

Cross-sections, Link River to Keno Dam (PDF files) 

5/30/07 

9/19/07 

Streamflow, Link River to Keno Dam (Excel files) 

5/30/07

9/19/07

Appendix B—Water Quality Data (Excel files)

Constituent analyses

Quality-assurance data

Bacteria summary

Phytoplankton/zooplankton summary 

Phytoplankton raw data files

Zooplankton raw data files

24