Use of Acoustic Backscatter and Vertical Velocity to Estimate

Concentration and Dynamics of Suspended Solids in Upper 

Klamath Lake, South-Central Oregon: Implications for 

Aphanizomenon flos-aquae

Scientific Investigations Report 2010–5203

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

U.S. Department of the Interior

U.S. Geological Survey
Cover: Acoustic Doppler current profiler (ADCP) with deployment platform prior 

to being deployed in the Upper Klamath Lake, Oregon, June 2005. (Photograph 

taken by Roy Wellman, U.S. Geological Survey.)
Use of Acoustic Backscatter and Vertical 

Velocity to Estimate Concentration and 

Dynamics of Suspended Solids in Upper 

Klamath Lake, South-Central Oregon: 

Implications for Aphanizomenon flos-aquae

By Tamara M. Wood and Jeffrey W. Gartner

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

Scientific Investigations Report 2010–5203

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: 2010

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Suggested citation:

Wood, T.M., and Gartner, J.W., 2010, Use of acoustic backscatter and vertical velocity to estimate concentration and 

dynamics of suspended solids in Upper Klamath Lake, south-central Oregon: Implications for Aphanizomenon flosaquae: U.S. Geological Survey Scientific Investigations Report 2010–5203, 20 p.
iii

Contents

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

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

Methods...........................................................................................................................................................3

Upper Klamath Lake Field Sites..........................................................................................................3

ADCP Measurements...........................................................................................................................3

Time Series Analyses...........................................................................................................................5

Converting ADCP Backscatter to Relative Backscatter and Suspended Solids 

Concentrations ........................................................................................................................5

Wind, Currents, and Water Temperature...................................................................................................6

Relative Backscatter Intensity ....................................................................................................................7

Vertical Velocities ........................................................................................................................................11

Suspended Solids Concentration..............................................................................................................12

Discussion and Conclusions......................................................................................................................16

Acknowledgments.......................................................................................................................................18

References Cited..........................................................................................................................................18

Figures

Figure 1. Map showing study area and locations of ADCP moorings, meteorological

stations, and water quality monitors, Upper Klamath Lake, south-central

Oregon, 2005–06 ........................................................................... 4

Figure 2. Graph showing diel patterns in the difference between water temperatures

measured near-surface and near-bottom at sites MDN, EPT, and MDT in Upper

Klamath Lake, south-central Oregon...................................................... 7

Figure 3. Contour plots showing daily variations in relative backscatter and water

current speed at the five ADCP deployment sites, Upper Klamath Lake,

south-central Oregon, 2005 ............................................................... 8

Figure 4. Bar graphs of profiles of correlation between water current speed and relative

backscatter at subseasonal time scales, at five sites where ADCPs were

deployed, Upper Klamath Lake, south-central Oregon, 2005........................... 9

Figure 5. Bar graphs of profiles of correlation between air temperature and relative

backscatter at subseasonal time scales, at five sites where ADCPs were

deployed, Upper Klamath Lake, south-central Oregon, 2005........................... 10

Figure 6. Graphs showing seasonally averaged diel patterns in near-surface vertical

velocity at five ADCP sites, Upper Klamath Lake, south-central Oregon, 2005 ...... 11

Figure 7. Graphs showing depth-averaged (computed) suspended solids concentration

(SSC) at five ADCP sites and dissolved oxygen at two water quality sites (MDT

and MDN), Upper Klamath Lake, Oregon, June 21– September 12, 2005 ............ 13

Figure 8. Graphs showing A: water temperature at site MDT, 1 m from surface, and 1 m

from bottom; B: Fraction of total water column mass contained in the upper

one-third of the water column, fraction of total water column mass contained

in the lower two-thirds of the water column at site ADCP1 ........................... 15

Figure 9. Graphs showing seasonally averaged diel pattern of depth-integrated

computed suspended solids concentration (SSC) in the entire water column

and in the upper and lower one-half (upper one-third and lower two-thirds at

ADCP1) of the water column ............................................................... 16
iv

Tables

Table 1. Correlation coefficients between vertical velocities and horizontal currents

and air temperature, Upper Klamath Lake, south-central Oregon..................... 12

Table 2. Correlations of computed suspended solids concentrations (SSC) at ADCP

sites with chlorophyll a and dissolved oxygen at water quality sites, Upper

Klamath Lake, south-central Oregon...................................................... 12

Table 3. Average mass and average daily range in mass of suspended solids at ADCP

sites, Upper Klamath Lake, south-central Oregon....................................... 14

Table 4. Correlation coefficients between the depth-integrated computed suspended

solids concentrations (SSC) at ADCP sites and depth-integrated horizontal

currents at the same site, or air temperature as measured at site WMR-MET,

Upper Klamath Lake, south-central Oregon ............................................. 14

Conversion Factors and Datums

Conversion Factors

Multiply By To obtain

centimeter (cm) 0.3937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

square meter (m2) 0.0002471 acre 

square meter (m2) 10.76 square foot (ft2) 

square kilometer (km2) 0.3861 square mile (mi2)

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

centimeter per second (cm/s) 0.328 foot per second (ft/s)

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

micrometer (μm) 3.937×10-5 inch (in)

cubic micrometer (μm3) 61.023 cubic inch (in3)

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

°F=(1.8×°C)+32.

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

or micrograms per liter (μg/L).

Datums

Vertical coordinate information is referenced to the Upper Klamath Lake Vertical Datum 

(UKLVD), which is used by the Bureau of Reclamation for reporting the elevation of Upper 

Klamath Lake. 

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

Elevation, as in this report, refers to distance above the vertical datum. 
Use of Acoustic Backscatter and Vertical Velocity to 

Estimate Concentration and Dynamics of Suspended 

Solids in Upper Klamath Lake, South-Central Oregon: 

Implications for Aphanizomenon flos-aquae

By Tamara M. Wood and Jeffrey W. Gartner

Abstract

Vertical velocity and acoustic backscatter measurements 

by acoustic Doppler current profilers were used to determine 

seasonal, subseasonal (days to weeks), and diel variation 

in suspended solids in a freshwater lake where massive 

cyanobacterial blooms occur annually. During the growing 

season, the suspended material in the lake is dominated by 

the buoyancy-regulating cyanobacteria, Aphanizomenon 

flos-aquae. Measured variables (water velocity, relative 

backscatter [RB], wind speed, and air and water temperatures) 

were averaged over the deployment season at each sample 

time of day to determine average diel cycles. Phase shifts 

between diel cycles in RB and diel cycles in wind speed, 

vertical water temperature differences (ΔT°), and horizontal 

current speeds were found by determining the lead or lag 

that maximized the linear correlation between the respective 

diel cycles. Diel cycles in RB were more in phase with ΔT° 

cycles, and, to a lesser extent, wind cycles, than to water 

current cycles but were out of phase with the cycle that 

would be expected if the vertical movement of buoyant 

cyanobacteria colonies was controlled primarily by light. 

Clear evidence of a diel cycle in vertical velocity was found 

only at the two deepest sites in the lake. Cycles of vertical 

velocity, where present, were out of phase with expected 

vertical motion of cyanobacterial colonies based on the 

theoretical cycle for light-driven vertical movement. This 

suggests that water column stability and turbulence were 

more important factors in controlling vertical distribution 

of colonies than light. Variations at subseasonal time scales 

were determined by filtering data to pass periods between 

1.2 and 15 days. At subseasonal time scales, correlations 

between RB and currents or air temperature were consistent 

with increased concentration of cyanobacterial colonies 

near the surface when water column stability increased 

(higher air temperatures or weaker currents) and dispersal 

of colonies throughout the water column when the water 

column mixed more easily. RB was used to estimate suspended 

solids concentrations (SSC). Correlations of depth-integrated 

SSC with currents or air temperatures suggest that depthintegrated water column mass decreased under conditions of 

greater water column stability and weaker currents. Results 

suggest that the use of measured vertical velocity and acoustic 

backscatter as a surrogate for suspended material has the 

potential to contribute significant additional insight into 

dynamics of Aphanizomenon flos-aquae colonies in Upper 

Klamath Lake, south-central Oregon.

Introduction

Upper Klamath Lake, the largest freshwater lake in the 

State, is located east of the Cascade Range in south-central 

Oregon. The lake has been historically eutrophic (Eilers and 

others, 2004) and has experienced annual occurrences of large 

cyanobacterial blooms (primarily Aphanizomenon flos‐aquae, 

or AFA) in recent decades. Growth and decomposition of 

dense AFA blooms frequently cause extreme water quality 

conditions characterized by high pH (9–10.2) and ammonia 

concentrations (> 0.5 mg/L unionized) and widely variable 

dissolved oxygen (anoxic to supersaturated) (Wood and 

others, 2006; Hoilman and others, 2008). These conditions 

are detrimental to the survival of two endangered fish species 

endemic to the lake, the Lost River and shortnose suckers. In 

order to complement water quality samples with better spatial 

and temporal resolution, it may be possible to use measured 

acoustic backscatter as a surrogate for suspended solids. In 

addition, if properly calibrated, acoustic Doppler current 

profilers (ADCPs) can provide non-intrusive measurements to 

compute time series of suspended solids concentration (SSC) 

profiles concurrent with measurements of three-dimensional 

velocity profiles (Gray and Gartner, 2009).
2 Acoustic Backscatter and Vertical Velocity, Upper Klamath Lake, Oregon: Implications for Amphanizomenon flos-aquae

Attempts to characterize suspended material from 

acoustic backscatter, a byproduct of ADCP velocity 

measurements, have increased as the use of ADCPs has 

become more widespread. Early studies used ADCP velocity 

and backscatter measurements to provide qualitative estimates 

of zooplankton biomass and diurnal patterns of vertical 

migration (Schott and Johns, 1987; Flagg and Smith, 1989; 

Heywood and others, 1991; Zhou and others, 1994), and 

even defined multiple diel migration layers (Plueddemann 

and Pinkel, 1989; Heywood, 1996; Pinot and Jansa, 2001; 

Ashjian and others, 2002; Sutor and others, 2005). Whereas 

most of these studies used relatively low frequency ADCPs 

(most often 150 kHz) in deep waters, Lorke and others 

(2004) applied acoustic backscatter from a 600 kHz ADCP to 

quantify distribution and movement of zooplankton, primarily 

Chaoborus flavicans, populations in lakes (< 50 m depth). 

Lorke and others (2004) found very good correlation between 

backscatter estimates and measured concentrations and a 

strong correlation between up and down migration and times 

of sunset and sunrise.

Others have attempted to quantify the concentration of 

suspended solids that primarily are inorganic material through 

laboratory or field calibrations. Laboratory experiments 

designed to calibrate backscatter to SSC were conducted by 

Thorne and others (1991) and Lohrmann and Huhta (1994). 

Thevenot and others (1992) developed calibration parameters 

for reliable estimates of SSC as part of a study to monitor 

dredged material using Broadband-ADCPs (2.4 MHz and 

600 kHz). Thevenot and others (1992), Thevenot and Kraus 

(1993), and Holdaway and others (1999) found concentration 

estimates from calibrated backscatter were comparable 

or superior to estimates from transmissometers. Gartner 

(2004) computed SSC using 1.2- and 2.4-MHz ADCPs. 

Results compared favorably to those computed from optical 

backscatter sensors (OBS) (within about 10 percent of the 

range of OBS estimates and within about 40 percent of the 

mean of OBS estimates over a 7-day time series). Wall and 

others (2006) used ADCP backscatter to compute suspended 

sediment discharge. Regression of measured to computed SSC 

values resulted in an R2 of 0.86 and a standard deviation of 

7.9 mg/L over a range of about 5–75 mg/L. Finally, Topping 

and others (2007) applied a multi-instrument, multi-frequency 

approach; they related acoustic attenuation to concentration 

of suspended silt and clay and acoustic backscatter to 

concentration of suspended sand. Computed values were 

within 5 percent of those measured by conventional methods.

Examples of the application of ADCP backscatter 

measurements to the study of phytoplankton are scarce in 

the literature and typically provide descriptions of the spatial 

distribution of phytoplankton rather than predictions of 

phytoplankton biomass. The paucity of studies relating ADCP 

backscatter to phytoplankton may be a result of a limitation 

of the acoustic backscatter technique—the relation between 

particle size and acoustic frequency. Errors in estimates occur 

when the size of suspended material is too small or too large 

for the acoustic frequency being used.

Individual AFA cells typically are small (about 100–

130 μm3) (Konopka and others, 1987) and are often grouped 

in filaments ranging from 8 to 50 cells (Huisman and others, 

1999). Thus filament volumes might range from about 800 to 

6,500 μm3 (equivalent radii about 5–12 μm). However, the 

AFA is found in flakes consisting of thousands of filaments 

and the number of flakes may exceed thousands per liter at 

the height of the bloom (Geiger and others, 2004). Thus, 

AFA flakes have a range of equivalent radii from about 50 

to 250 μm. These particles far outnumber other scatterers in 

the lake and are well within the size range suitable for the 

frequency of ADCPs used in Upper Klamath Lake that are 

described here.

This paper describes a study to determine if 

relative backscatter, RB (acoustic backscatter corrected 

for transmission losses from acoustic beam spreading 

and attenuation in units of dB) and vertical velocity 

measurements by ADCPs can be used to better understand 

seasonal, subseasonal, and diel dynamics of cyanobacterial 

colonies (AFA) in a shallow freshwater lake. Here, the 

term seasonal refers to variations or trends that occur over 

time scales consistent with the ADCP deployment length 

(about 85–125 days). The term subseasonal is used to define 

variations or trends that have time scales greater than diel 

but less than seasonal, that is, time scales of days to weeks 

corresponding to weather patterns. The RB and vertical 

velocity data measured by ADCPs in Upper Klamath 

Lake were used to establish the typical diel cycles of mass 

distribution and movement through the water column, and 

how these cycles relate to the typical diel cycles in thermal 

stratification, mixing, and light availability. The theoretical 

model of light-driven vertical migration of buoyant 

cyanobacteria is based on the fact that density of cells 

changes during the day in response to availability of light and 

nutrients. When light is available in excess of growth capacity, 

cells become negatively buoyant by limiting the production 

of gas vesicles or by increasing carbohydrate production, 

thus gaining ballast. If nutrients are plentiful and cells are 

light-limited, cells become positively buoyant by consuming 

carbohydrate ballast or increasing the synthesis of gas 

vesicles. As a result, theoretically, if movement is light-driven 

then the cells of buoyant cyanobacteria generally rise in the 

water column during evening and early morning (during 

darkness) and sink in the water column during morning and 

afternoon (during daylight) (Konopka and others, 1987; 

Porat and others, 2001). Like the AFA dynamics, the external 

forcings that determine stratification and entrainment, that is, 

air temperature and wind speeds, also vary on subseasonal 

time scales. Therefore, the relation of RB and vertical velocity 

to wind-driven currents and air temperature on subseasonal 

time scales was investigated as well. Finally, SSC values 

(estimated from RB) were used to make inter-comparisons 

among sites, to investigate the relation to other water quality 

measurements (for example, chlorophyll a, dissolved oxygen, 

and water temperature), and to determine the movement of 

mass vertically through the water column. 
Methods 3

Methods

Upper Klamath Lake Field Sites

Upper Klamath Lake has a surface area of about 230 km2, 

but a mean depth of only about 2.4 m (fig. 1). The lake trends 

generally from northwest to southeast. The northern end of the 

lake is dominated by the marshes that surround Agency Straits, 

the lake’s connection to adjoining Agency Lake, and by the 

delta of the Williamson River, the largest tributary to the lake. 

At the southern end, the lake ends at the Link River Dam and 

the city of Klamath Falls, Oregon. Although most of the lake 

is relatively shallow, a 15-km-long trench with depths as great 

as about 15 m runs along the western side of the lake between 

Bare Island and Eagle Ridge to the north and Sesti Tgawaals 

Point to the south.

In response to water quality concerns, the U.S. 

Geological Survey (USGS) established a water-quality 

monitoring network in Upper Klamath Lake in 2002 (Wood 

and others, 2006). As part of ongoing research by the USGS, 

ADCP measurements of water velocity profiles were collected 

annually starting in 2003. Those ADCP measurements 

(Gartner and others, 2007) in conjunction with use of a 

numerical hydrodynamic model (Wood and others, 2008) 

provide understanding of horizontal water circulation in Upper 

Klamath Lake.

Locations of the (upward oriented) ADCP moorings 

in the lake were selected based on needs for calibration and 

validation of the numerical model used to describe wind 

driven circulation patterns present in the lake. During 2005 

and 2006, most of the ADCPs were deployed in generally 

shallow regions of the lake; however, one ADCP was moored 

in the channel on the western side of the lake at a depth of 

about 12–14 m during 2005 and 2006 (fig. 1). ADCP data 

from 2005 include measurements from five locations; this 

dataset constitutes the most complete simultaneous spatial 

coverage of velocity measurements in Upper Klamath Lake. 

The deployment periods for the ADCPs were June 21–

September 12, 2005, and May 24–September 25, 2006.

 The use of measurements of RB and vertical velocity 

was not an objective of the deployment of these instruments 

in 2005, nor was it anticipated. Therefore, water quality 

sample collection to support estimation of SSC from RB was 

not performed until the latter part of the 2006 field season at 

the two ADCP sites that were established in that year. Twenty 

water quality samples were collected in 2006 and analyzed 

for suspended solids using a gravimetric technique (SSC 

analytical method ASTM 3977-97) (American Society for 

Testing and Materials, 2000) and for percentage of organic 

material using a technique to determine the loss on ignition 

of volatile suspended solids (Fishman and Friedman, 1989). 

Results were used to convert backscatter measurements 

from the two ADCPs deployed that year to profiles of 

computed SSC. The water samples were taken at near-surface, 

mid‐depth, and near-bottom locations in the water column at a 

deep site (ADCP1) and a shallow site (ADCP9); ADCP9 was 

located about 1.5 km south and east of the location of ADCP3 

in 2005 (fig. 1). 

Air temperature was recorded at a site located on the 

shoreline of the lake near the mouth of the Williamson River 

(WMR-MET). Wind speed and direction were measured 

from rafts at two sites on the lake [midnorth (MDN) and 

midlake (MDL)] and from one site on the shoreline of 

Howard Bay (HDB-MET). Water temperature and dissolved 

oxygen were measured using YSI 600XLM, 6920, or 6600 

continuous water quality monitors located at Eagle Point 

(EPT), midtrench (MDT), and in the northern part of the lake 

(MDN, fig. 1). Water depths at the start of the study period 

were 12.5 m at site EPT, 14.8 m at site MDT, and 4.5 m at site 

MDN. Two water temperature monitors were deployed at each 

of these sites, one at 1 m from the lake bottom, and one at 1 m 

from the lake surface. Chlorophyll a, as a surrogate for algal 

biomass, was determined from weekly water samples that 

were collected, preserved, and later analyzed by a commercial 

laboratory (Hoilman and others, 2008).

ADCP Measurements

The velocity profilers used in this study were 1,200 and 

600 kHz Broadband and Workhorse ADCPs manufactured by 

Teledyne RD Instruments. The location of the center of the 

lowest measurement (bin) for each ADCP profile depended on 

the mooring platform design and ADCP setup. The 600 kHz 

ADCP (deep station, ADCP1) was programmed with a 50 cm 

bin size, thus the center of the first bin was located at about 

125 cm above bottom and subsequent measurements in the 

profile were at 50 cm intervals. The center of the first bin 

in the 1,200 kHz datasets ranged from about 90 to155 cm 

above bottom depending on instrument and mooring design; 

subsequent measurements in the profile were at 25 cm 

intervals. The ADCPs recorded water velocity measurements 

every 30 minutes. Sufficient individual acoustic pulses 

(300 pings taking about 40–50 seconds) were averaged to 

decrease the theoretical standard deviation of the recorded 

horizontal velocities to be less than 0.7 cm/s for each 

measurement. Standard deviations for vertical velocities were 

approximately 0.3 cm/s.

ADCPs calculate water velocity from the Doppler 

frequency shift or phase difference of sound backscattered 

from particles in the water, under the assumption that the 

particles travel with the velocity of the water. However, 

vertical particle velocity and the vertical component of water 

velocity may differ greatly. Thus, the ADCP has the potential 

to quantitatively measure the vertical motion of inorganic 

particles or of biological populations that actively migrate 

within the water column. Although the theoretical standard 

deviation of vertical velocity measurements in Upper Klamath 

Lake were the same order of magnitude as the actual measured 

vertical velocities for each ensemble (of averaged single 

acoustic pings), additional averaging served to decrease the 
4 Acoustic Backscatter and Vertical Velocity, Upper Klamath Lake, Oregon: Implications for Amphanizomenon flos-aquae

Figure 1. Study area and locations of ADCP moorings, meteorological stations, and water quality 

monitors, Upper Klamath Lake, south-central Oregon, 2005–06.

tac11-0571_fig01

122°00’ 121°45'

Upper

Klamath

Lake

Aspen

Lake

River

Williamson

Howard

Bay

Ball

Bay

Ball

Point

Shoalwater

Bay

Wocus

Marsh

Pelican

Bay

Link

River

Lake

Ewauna

Agency

Lake

Moss Creek

Wood

River

Rock

Creek

Sprague

River

97

97

Buck

Island

Bare

Island

140

161

70

66

Modoc

Point

Klamath

Falls

Plum Valley

Eagle

Ridge

Modoc

Point

Link River 

Dam

ADCP7

ADCP6

ADCP5

ADCP3

ADCP1

HDB-MET

MDL

EPT

MDN

MDT

ADCP9

Sesti Tgawaals Point

Study

area

OREGON

0 5 Miles

0 5 Kilometers

42°

30’

42°

15’

0

50

ADCP6

MDL

HDB-MET

EPT

ADCP9

ADCP1

WMR-MET

EXPLANATION

Depth of Upper Klamath

 and Agency Lakes

Continuous water-quality

 monitoring station

Continuous water-quality

 monitoring station, and

 meteorological station

ADCP station

 2005

 2006

 2005–2006

Meteorological station 
Methods 5

standard deviation of the measurement. However, suspended 

material in an ADCP measurement bin may consist of a 

mixture of organic and inorganic material that may be actively 

rising, sinking, or passively moving with the water mass. 

It is only possible, therefore, to state that the average for 

the particles was rising, sinking, or stationary based on the 

computed vertical velocity.

A drawdown of just more than 1 cm/d throughout the 

summer meant that water depths at each ADCP site were 

approximately 1 m shallower at the end of the measurement 

period than they were at the start. Thus, there were 2-4 more 

good measurement bins at the start of the deployment than 

there were at the end of the deployment. Therefore, in order to 

identify near-surface characteristics, “near-surface” time series 

of measurements were created from appropriate bin data from 

sequentially lower bins as the deployment progressed and the 

water depth became gradually shallower. Lake water depths 

at the start of the 2005 deployments were as follows: ADCP1, 

14.2 m; ADCP3, 4.3 m; ADCP5, 5.6 m; ADCP6, 4.4 m; and 

ADCP7, 5.1 m. 

Time Series Analyses

Seasonally averaged diel cycles in wind speed, 

differences in water temperature between near-surface and 

near-bottom (ΔT°), RB, vertical velocity, horizontal current 

speed, and SSC were determined by averaging all valid 

measurements of the variable of interest collected during the 

(June–September) deployment at each sample time of day 

(for example, 00:00 h, 00:30 h, etc. for a 30-minute sampling 

interval). For variables measured by the ADCPs, seasonally 

averaged diel cycles were determined for each vertical 

measurement bin. Averaging over the deployment season 

exposed daily patterns that otherwise would be lost in large 

variability. The phase shift between diel cycles in RB and diel 

cycles in wind speed, ΔT°, and horizontal current speed were 

found by determining the lead or lag that maximized the linear 

correlation between the 24-hour time series.

Correlations between RB or vertical velocity and 

horizontal currents and water temperatures at subseasonal 

timescales were investigated by first filtering the time series 

in each bin with a series of Lanczos filters to remove high and 

low frequency variations to discern characteristics varying 

over time scales equivalent to weather patterns (Emery and 

Thompson, 2001). The first filter passed frequencies greater 

than 0.0667 cycles day-1 (15-day period), and then a second 

filter passed frequencies less than 0.833 cycles day-1 (1.2-day 

period). Pearson correlation coefficients were computed 

between the filtered RB or vertical velocity and horizontal 

current speed in each bin. 

Correlations between filtered RB in each vertical bin 

and air temperature were examined by processing the air 

temperature time series with the same set of Lanczos filters. 

The vertical velocity or SSC in the top one-half of the water 

column (top one-third in the case of ADCP1) was first 

averaged, then passed through the series of Lanczos filters, 

and then correlated with filtered horizontal currents, also 

averaged over the top one-half of the water column, and 

filtered air temperature. For the purposes of determining 

significance of the correlations, the degrees of freedom in the 

filtered time series was estimated to be N=63, which was the 

number of frequencies that still contained at least 1 percent of 

the total variance in the periodogram of the filtered time series. 

Using that number of degrees of freedom, rejection of the 

null hypothesis of no correlation would occur with 95 percent 

certainty at a correlation coefficient of 0.25.

Converting ADCP Backscatter to Relative 

Backscatter and Suspended Solids 

Concentrations

The theoretical technique presented here to convert 

acoustic backscatter to RB and ultimately to SSC is described 

in terms of the logarithmic form of the sonar equation, which 

is the typical method used for applications using ADCPs. It is 

well suited because commercially available ADCPs typically 

provide the conversion factor from raw backscatter counts 

to decibels, which facilitates accounting for transmission 

losses and empirical calibration of backscatter to SSC. The 

logarithmic form of the sonar equations can be inverted to 

obtain an expression for calculated SSC: SSCcomputed = 

10 (A + B × RB). The exponent contains the term for the RB, the 

sum of the echo level measured at the transducer plus the 

two‐way transmission losses (Thevenot and others, 1992), that 

is, RB = RL + 2TL, where RL is the reverberation level and 

2TL is the two-way transmission loss.

In its simplified form, the sonar equation (Urick, 1975) 

can be written as RL = SL – 2TL + TS, where SL is the source 

level, which is the intensity of emitted signal that is known or 

measurable, and TS is the target strength, which is dependent 

on the ratio of wavelength to particle diameter. All variables 

are measured in decibels. In terms of ADCP parameters, 

RL = Kc (E – Er ), where E is ADCP echo intensity recorded 

in counts, Er is ADCP received signal strength indicator 

(RSSI) reference level (the echo baseline when no signal is 

present), in counts, and Kc is the RSSI scale factor used to 

convert counts to decibels. Kc varies among instruments and 

transducers and has a value of 0.35–0.55 (Deines, 1999). The 

two-way transmission loss is defined as 2TL = 2(αw + αs)R + 

20log10 (R), where R is the range to the ensonified volume, 

in meters; αw is an absorption coefficient for water; αs is an 

attenuation coefficient accounting for viscous and scattering 

losses due to suspended particles, both in decibels per meter; 

2 (αw + αs) R is the combined transmission loss due to water 

absorption and sediment attenuation; and 20log10 (R) is the 

loss due to spreading. The absorption coefficient for water is 

a function of acoustic frequency, salinity, water temperature, 

and pressure (Schulkin and Marsh, 1962). Because of 

non‐spherical spreading in the transducer near field, the 

spreading loss is different in near and far transducer fields. 
6 Acoustic Backscatter and Vertical Velocity, Upper Klamath Lake, Oregon: Implications for Amphanizomenon flos-aquae

The transition between near and far transducer fields is called 

the critical range, Rcrit. Rcrit = π αt   λ where αt

 is the transducer 

radius, in centimeters, and λ is the acoustic wavelength. The 

near-field correction for spreading loss can be easily calculated 

as described in Downing and others (1995).

Gartner (2004) describes a practical approach to compute 

a time series of SSC from a time series of ADCP acoustic 

backscatter. First, the RB is determined, and the log10 of the 

SSC measurements, SSCmeasured, are calculated. The needed 

calibration coefficients consisting of slope, B, and intercept, 

A, for a regression between log10(SSCmeasured ) and RB is 

determined such that log10(SSCmeasured ) = A + B × RB. The 

theoretical value for slope, B, is 0.1 and the intercept is a 

function of particle and instrument characteristics; values are 

appropriate for a concentration of uniform particles of the 

same mass and other properties (Thevenot and others, 1992). 

After values of A and B are determined for the distribution of 

particles in the field, new time series of profiles of SSC can 

be computed from ADCP RB profiles utilizing the exponential 

form of the equation, SSCcomputed = 10 (A+B×RB ). An alternative 

to using regression to determine A and B is to use the 

theoretical value of slope, B, equal to 0.1, and to calculate the 

intercept based on the log10 of the measured SSC and the RB

from A = log10(SSC) – 0.1 × RB. 

To determine appropriate calibration coefficients for 

data from Upper Klamath Lake, water quality samples were 

analyzed for mass concentration and percentage of organic 

material. Mass concentration of the 20 water quality samples 

collected in 2006 ranged from about 4 to 43 mg/L, but results 

from replicate pairs ranged from 0 to 100 percent (Gartner 

and others, 2007). SSC comprises both organic and inorganic 

fractions in Upper Klamath Lake. Because calibration 

coefficients depend on size and other characteristics of the 

suspended particles, temporal or spatial (including vertical) 

variations in the ratio of organic to inorganic material is of 

interest. The organic fraction dominates in Upper Klamath 

Lake; the average organic fraction for all 20 water samples 

was about 77 percent (standard deviation about 11 percent). 

Coefficients for use in converting RB measured in 2006 

to estimates of profiles of SSC were calculated several ways, 

including determining an average slope and average intercept, 

using a theoretical slope (0.1) and single average intercept, 

and using a theoretical slope (0.1) and intercepts calculated 

from near-surface, mid-depth, and near-bottom samples for 

the shallow and for the deep sites. Standard deviations of the 

differences between measured and estimated SSC for the three 

techniques were about 10.2, 22.8, and 9.9 mg/L, respectively. 

The organic fraction was generally somewhat lower 

near‐bottom than it was near-surface but still predominated. 

Although some spatial and temporal variations existed in SSC 

and the percentage of organic material, variations were small 

and the samples insufficient to calculate reliable trends. Thus, 

the theoretical slope (0.1) and different average intercepts 

for the deep and shallow sites were used but the intercepts 

were not varied with vertical position in the water column 

when estimating new profiles of SSC. For the four shallowest 

sites in 2005, SSC was computed from ADCP backscatter 

measured in 2005 using the theoretical slope (0.1) and the 

average intercept determined for the single shallow station in 

2006 (-7.08). For the deep site in 2005, the theoretical slope 

(0.1) and the average of the intercept determined for the deep 

station at the same location in 2006 was used (-6.92). (When 

this technique was applied to the 2006 datasets, the standard 

deviation was 19.1 mg/L.) 1,200 kHz ADCPs were used at all 

shallow stations and a 600 kHz ADCP was used at the deep 

station. 

No compensation was made for potential variations 

in ADCP transmit power (Deines, 1999; Wall and others, 

2006) from changes in internal battery voltage during the 

deployment. The average of the backscatter from all four 

ADCP acoustic beams was used in calculations as the beams 

have different source levels and sensitivities. Averaging also 

helps to overcome the impact of patchiness of the suspended 

material. In addition, transmission losses from particle 

attenuation were not accounted for in computing SSC.

Wind, Currents, and Water 

Temperature

Analyses of seasonally averaged wind graphs indicated 

that winds over Upper Klamath Lake displayed diel patterns 

(Gartner and others, 2007). During the 2005 field season, 

minimum wind speeds occurred during late morning (about 

1.75 m/s at 10:15 h at site MDN, about 3.0 m/s at 11:45 h 

at site HDB, and about 2.25 m/s at 12:15 h at site MDL); 

maximum wind speeds occurred during late evening (about 

6.0 m/s at 20:45 h at site MDN, about 5.5 m/s at 19:45 h at 

site HDB, and about 6.5 m/s at 21:30 h at site MDL). [All 

times shown are referenced to Pacific Daylight Standard Time 

(PDST).] Upper Klamath Lake is a wind-driven system with 

little river inflow, thus horizontal water currents are expected 

to be a function of wind patterns.

Velocity measurements by ADCPs showed that a 

generally clockwise circulation pattern was established in 

Upper Klamath Lake under prevailing (northwest to north) 

wind conditions (Gartner and others, 2007; Wood and others, 

2008). Although all ADCP records generally showed diel 

patterns in the water currents, the times of day of minimum 

and maximum current speeds were spatially variable in the 

lake because of the effects of bathymetry and geometry on 

water motion. The closest correspondence between times of 

maximum and minimum winds and maximum and minimum 

horizontal currents generally occurred at the southern end of 

the deep-water trench at site ADCP7. Maximum and minimum 

currents at site ADCP7 occurred within 1–2 hours of the 

corresponding wind events both near-surface and near-bottom. 

The largest offsets occurred in the middle of the lake at site 

ADCP6 (near MDL) where water currents led winds by 6–10 

hours near-surface and by 2–6 hours near-bottom. Thus, 

even though water currents in the lake are wind-driven, the 

response of the water currents to the wind varies in timing and 

magnitude around the lake. 
Relative Backscatter Intensity 7

Water temperature in the lake had a strong diel cycle, 

particularly near the surface. At times of maximum nearsurface water temperature, the difference in water temperature 

between the near-surface and near-bottom of the water column 

was enough to provide resistance to mixing, particularly 

at the deepest sites in the trench. On most days, the water 

temperature difference was eroded in late evening or early 

morning by a combination of high winds and cool air 

temperatures (Wood and others, 2006; Hoilman and others, 

2008). The ΔT° at sites MDT, MDN, and EPT were used to 

determine the seasonally averaged diel patterns (fig. 2). The 

maximum ΔT° was greatest at site MDT, the site closest to 

site ADCP1 and in the deepest water, and occurred there the 

latest in the day (19:00 h). The maximum ΔT° at site EPT, the 

closest to site ADCP5, was less than at site MDT and occurred 

at 18:00 h. The maximum ΔT° at site MDN, which was closest 

to site ADCP3 and in shallower water than sites EPT and 

MDT, was approximately the same magnitude as at site EPT 

but occurred earlier in the day at 16:00 h. Seasonally averaged 

diel patterns in ΔT° were not available near sites ADCP6 and 

ADCP7; values at site MDN were used when necessary for 

analyses because the water depths at sites ADCP6 and ADCP7 

were similar to that at site MDN.

Relative Backscatter Intensity

Seasonally averaged diel cycles of RB showed that there 

was a time in early- to mid-morning when vertical variation 

in RB was at a minimum and a time in mid- to late-afternoon 

when vertical variation in RB was at a maximum (fig. 3). 

Times of minimum (about 8:00–9:00 h) and maximum 

(about 15:00–19:00 h) RB near-surface occurred nearly 

simultaneously at the five ADCP sites (fig. 3), but varied 

widely near-bottom. At the deep site, ADCP1, the minimum 

RB near-bottom lagged the maximum near-surface by about 

2 hours. At the other four ADCP sites, located in shallower 

water than site ADCP1, the minimum RB in the lower part 

of the water column preceded the maximum at the surface 

by several hours. The maximum RB at the surface at sites 

ADCP3, ADCP6, and ADCP7 appears to spread downward 

during the evening and early morning hours and displace the 

near-bottom minimum, moving it closer to the bottom (fig. 3).

In addition, there was good correspondence between 

the timing of diel cycles of winds and RB at the surface. 

Comparisons of diel wind and RB cycles at the five ADCP 

sites showed that RB preceded corresponding wind by about 

2–4 hours. The average correlation coefficient, R, for the five 

sets of data was 0.92 (all p< 0.0001). Timing of patterns was 

far more variable near-bottom where RB lagged winds by 

2–10 hours (average R=0.88; all p< 0.0001). The shortest lag 

was at site ADCP6; the longest lags were at sites ADCP1 and 

ADCP7.

In contrast, there was no consistent relation between 

the diel cycles of the horizontal currents and RB. The 

timing between RB and water currents near-surface was 

between a 10-hour lead at site ADCP5 and a 9-hour lag at 

site ADCP3 (average R=0.78; all p< 0.0002). Similarly, the 

correspondence between water currents and RB also varied 

widely near-bottom, ranging from a 1-hour lead at site ADCP5 

to a 9-hour lag at site ADCP7 (average R=0.65; all p< 0.0005 

except site ADCP6 where R=0.21 and p=0.14). 

The best correspondence and smallest phase difference 

occurred between the diel cycles of ΔT° and RB near-surface. 

Comparisons of diel cycles of RB and ΔT° showed little or no 

phase difference near-surface (RB lagged ΔT° by 0–1 hour; 

average R=0.93; all p<0.0001). Near-bottom, RB lagged ΔT° 

by 8–14 hours (average R=0.87; all p<0.0001).

The RB was most uniform through the water column 

in the morning, coincident with minimum temperature 

stratification, and most surface-intensified in the afternoon, 

coincident with the maximum temperature stratification. 

0 4 8 12 16 20 24

HOUR IN DAY

0.0

0.5

1.0

1.5

2.0

2.5

TEMPERATURE DIFFERENCE,

IN DEGREES CELSIUS

EPT

MDT

MDN

Figure 2. Diel patterns in the difference between water 

temperatures measured near-surface and near-bottom at sites 

MDN (4.5 m depth), EPT (12.5 m depth), and MDT (14.8 m depth)

in Upper Klamath Lake, south-central Oregon. Diel patterns 

are derived from an average of hourly monitor measurements 

between June 2, 2005, and October 9, 2005. Minimum temperature 

differences occur between 07:00 h (sites MDN and EPT) and 

08:00 h (site MDT); maximum temperature differences occur 

between 16:00 h (site MDN) and 19:00 h (site MDT). The maximum 

standard error of the estimate of the average temperature 

difference is 0.07 oC at sites EPT and MDN, and 0.14 °C at site MDT.
8 Acoustic Backscatter and Vertical Velocity, Upper Klamath Lake, Oregon: Implications for Amphanizomenon flos-aquae

Figure 3. Daily variations in relative backscatter and water current speed at the five ADCP deployment 

sites, Upper Klamath Lake, south-central Oregon, 2005. Diel patterns are derived from an average of 

30-minute ADCP measurements between June 21, 2005, and September 12, 2005. The maximum standard 

error of the estimate of mean relative backscatter as a function of hour in the day and depth in the 

water column is 0.9 dB, 6.3 dB, 1.2 dB, 1.4 dB, and 0.8 dB for ADCP1, ADCP3, ADCP5, ADCP6, and ADCP7, 

respectively. The maximum standard error of the estimate of mean horizontal current speed as a function 

of hour in the day and depth in the water column is 1.7, 5.2, 2.0, 1.5, and 1.7 cm/s for sites ADCP1, ADCP3, 

ADCP5, ADCP6, and ADCP7, respectively.

tac11-0571_fig03

ADCP1

ADCP3

ADCP5

ADCP6

ADCP7

HEIGHT ABOVE BOTTOM, IN METERS 

0 4 8 12 16 20 24 0 4 8 12 16 20 24

TIME OF DAY, IN HOURS

RELATIVE BACKSCATTER,

IN DECIBELS

CURRENT SPEED,

IN CENTIMETERS PER SECOND

15

12

10

8

6

4

2

3

2

1

4

2

3.5

3

2.5

2

1.5

4

3

2

110

105

100

95

100

95

90

95

90

85

100

95

90

100

95

90

85

12

10

8

6

4

2

1

2

3

4

2

3.5

3

2.5

2

1.5

4

3

2

10

5

10

5

10

5

6

4

10

5
Relative Backscatter Intensity 9

The diel cycle in RB was more closely aligned to the timing 

of ΔT° and, to a lesser extent, to diel wind cycles than to 

the timing of the maximum and minimum in currents. 

Daily surface intensification of RB was consistent with the 

accumulation of buoyant particles, but the diel cycle was 

about 12 hours out of phase with the theoretical light-driven 

movement of a buoyant cyanobacteria, in which colonies 

increasingly rise as darkness progresses and increasingly 

sink as light progresses. (Times of minimum and maximum 

RB near-surface were about 8:00–9:00 h and 15:00–19:00 h, 

respectively.)

At subseasonal time scales, correlations between filtered 

RB and water currents were positive through most of the 

water column at all but site ADCP3, the shallowest ADCP site 

(fig. 4). At sites ADCP1, ADCP3, ADCP5, and ADCP7, the 

correlations decreased away from the bottom and (except at 

ADCP5) became negative within the upper bins, indicating a 

dispersal of mass away from the surface to deeper in the water 

column and, possibly, increased resuspension of bed material 

with increased water current speeds. The negative correlations 

near-surface were consistent with a near-surface mixed layer 

of approximately 1 m at sites ADCP1 and ADCP7, and closer 

to 1.75 m at site ADCP3, in which mass decreased as water 

current speeds increased. The lack of negative correlations in 

upper bins at site ADCP5 may indicate a thin surface mixed 

layer within the zone that was unmeasured by the ADCP 

(< 0.5 m). The correlations at site ADCP6 were weak with 

little vertical variation, suggesting that the relation between 

RB and currents may be a function of advection rather than 

entrainment.

0

2

4

6

8

10

12

-0.5 0.0 0.5 -0.5 0.0 0.5 -0.5 0.0 0.5

0

1

2

3

4

5

HEIGHT ABOVE BOTTOM, IN METERS 

CORRELATION COEFFICIENT

0

1

2

3

4

ADCP5 ADCP7 ADCP1

ADCP3 ADCP6

Figure 4. Profiles of correlation between water current speed and relative backscatter at 

subseasonal time scales, at five sites where ADCPs were deployed, Upper Klamath Lake, southcentral Oregon, 2005. Correlation coefficients > 0.25 are significant (p < 0.05). 
10 Acoustic Backscatter and Vertical Velocity, Upper Klamath Lake, Oregon: Implications for Amphanizomenon flos-aquae

Correlations between filtered RB and air temperature at 

subseasonal time scales (fig. 5) were largely a reverse of the 

correlations with currents (fig. 4). To some extent, this results 

from negative correlations between water current speeds and 

air temperature (weather systems that are accompanied by 

lower than average air temperatures tend to be associated 

with stronger than average winds and resulting wind-driven 

currents). The correlations displayed in figure 5 also are 

consistent with the effect that air temperature has on water 

column mixing. Increased water temperature in the upper 

water column (from warmer air temperature) increases 

the resistance to mixing; colder air has the opposite effect. 

Negatively buoyant particles settle out of the water column 

and positively buoyant particles rise to the surface when 

mixing is suppressed. Correlations between RB and air 

temperature were negative through most of the water column 

at all sites except ADCP7, where the correlation was positive 

in the upper one-half of the water column (fig. 5). The 

negative correlation decreased moving away from the bottom 

and became positive nearer the surface at sites ADCP1, 

ADCP3, ADCP6, and ADCP7, suggesting the accumulation of 

mass in the upper water column as air temperature increased. 

This is consistent with the near-surface correlations between 

RB and water current speeds (fig. 4) at sites ADCP1, ADCP3, 

and ADCP7. 

0

2

4

6

8

10

12

-0.5 0.0 0.5 -0.5 0.0 0.5 -0.5 0.0 0.5

0

1

2

3

4

5

HEIGHT ABOVE BOTTOM, IN METERS 

CORRELATION COEFFICIENT

0

1

2

3

4

ADCP5 ADCP7 ADCP1

ADCP3 ADCP6

Figure 5. Profiles of correlation between air temperature and relative backscatter at 

subseasonal time scales, at five sites where ADCPs were deployed, Upper Klamath Lake, 

south-central Oregon, 2005. Correlation coefficients > 0.25 are significant (p < 0.05). 
Vertical Velocities 11

Vertical Velocities

The analysis of the vertical velocities was limited to the 

top one-half of the water column (top one-third at site ADCP1) 

in order to avoid any influence of local bottom topography. 

This was done by vertically averaging the velocities over 

appropriate upper bins. 

Seasonally averaged vertical velocities were negative 

(indicating sinking) throughout the day at sites ADCP5, 

ADCP6, and ADCP7. Only site ADCP1 included a sustained 

period of positive (rising) velocity from about 12:00 to 

24:00 h. Site ADCP3 displayed no clear trend (fig. 6). The 

diel cycles were most pronounced at sites ADCP1 and ADCP5 

where the daily minimum vertical velocity was negative and 

occurred nearly simultaneously with the maximum surface 

current speed (site ADCP5), or 2–3 hours later (site ADCP1). 

Daily minimum vertical velocities occurred several hours prior 

to minimum ΔT°. At site ADCP5, the daily maximum vertical 

velocity was still negative, indicating sinking, and occurred 

just prior to minimum surface current speed and the maximum 

ΔT°. At site ADCP1, the daily maximum vertical velocity was 

positive, indicating rising, and followed minimum surface 

current speed and was coincident with the maximum ΔT°. At 

both sites, the maximum upward (site ADCP1) or minimum 

downward (site ADCP5) vertical velocity was coincident 

with the near-surface maximum in RB (fig. 3). Similar to 

diel patterns of RB, the diel patterns of vertical velocity also 

were out of phase with the theoretical model for light-driven 

vertical movement of buoyant cyanobacteria colonies.

Pearson correlation coefficients between filtered vertical 

velocities and horizontal current speeds (at subseasonal time 

scales) in the top one-half of the water column were significant 

and negative at sites ADCP1 and ADCP5 (table 1). These 

negative correlations were consistent with weaker currents 

resulting in disentrainment of positively buoyant particles, and 

with the correlation between RB and horizontal current speeds 

at site ADCP1 that showed more accumulation of mass near 

the surface with weaker currents. The correlation between 

near-surface vertical velocity and horizontal current speeds 

also was significant at site ADCP7, but the correlation was 

positive, suggesting that sinking particles were disentrained as 

horizontal current speeds decreased. 

0.3

0.2

0.1

0.0

-0.1

-0.2

-0.3

-0.4

0.0

-0.1

-0.2

-0.3

-0.4

-0.5

0.2

0.1

0.0

0.1

0.2

0.3

0.4

0.5

Top one-half (ADCP3/5/6/7)

 or one-third (ADCP1) of

 water column

Time of minimum

 surface current speed

Time of maximum

 surface current speed

Time of minimum

 surface-to-bottom

 temperature difference

Time of maximum

 surface-to-bottom

 temperature difference

AVERAGE VERTICAL VELOCITY, IN CENTIMETERS PER SECOND

0 4 8 12 16 20 24

0 4 8 12 16 20 24

HOUR OF DAY

ADCP1 ADCP3

ADCP5 ADCP6

ADCP7

EXPLANATION

Figure 6. Seasonally averaged diel patterns in near-surface vertical velocity at five ADCP sites, Upper Klamath Lake, 

south-central Oregon, 2005. The time of maximum and minimum near-surface current speeds and maximum and minimum 

water temperature top-to-bottom differences are shown for reference. Diel patterns are derived from an average of 

30-minute ADCP measurements between June 21 and September 12, 2005. The maximum standard error of the estimate of 

average vertical velocity is 0.03 cm/s for sites ADCP1, ADCP3, and ADCP7, and 0.05 cm/s for sites ADCP5 and ADCP6.
12 Acoustic Backscatter and Vertical Velocity, Upper Klamath Lake, Oregon: Implications for Amphanizomenon flos-aquae

The correlations between near-surface vertical velocities 

and air temperature generally were small with the exception 

of those at site ADCP1, where the correlation was positive 

(table 1). The sign of the correlation indicates that, when 

mixing was suppressed by high surface temperature, 

positively buoyant particles were preferentially disentrained. 

This is consistent with the results of the correlation of RB

with air temperature (fig. 5), which indicated the potential 

for accumulation of mass near the surface at high air 

temperatures. Thus, at least at the deepest site (ADCP1), a 

tendency for mass to accumulate near surface with both weak 

horizontal currents and high temperatures was supported by 

the behavior of both RB and vertical velocities.

Suspended Solids Concentration

Although using RB to discern seasonal, subseasonal, 

and diel variations of suspended material is enlightening, RB

does not allow direct comparisons among measurements by 

different instruments or locations. However, use of measured 

or computed SSC (in units of mass/volume rather than dB) 

does allow quantitative comparisons between datasets, 

meaningful comparisons to other water quality variables, and 

investigation of the movement of mass through the water 

column. For this reason, profiles of SSC were computed using 

acoustic backscatter measurements at the five ADCP sites in 

2005.

The time series of SSC calculated from RB show distinct 

differences between the sites (fig. 7). Overall through the 

season, the depth-averaged concentrations were highest 

at the deepest site, ADCP1. Concentrations were second 

highest at the northernmost site, ADCP3, but were lowest at 

ADCP5, another site in the northern part of the lake. These 

relative concentrations were consistent with the chlorophyll a

samples collected at four sites during the 2005 season. The 

median chlorophyll a concentrations of 12 samples collected 

between June and September at site MDT (near site ADCP1), 

site MDN (near site ADCP3), site EPT (near site ADCP5), 

and site MDL (near site ADCP6) were 122.5, 99.0, 36.5, and 

59.7 μg/L, respectively. The correspondence between the two 

variables was further tested with linear regression between 

the depth-averaged chlorophyll a and the median value of the 

computed depth-averaged SSC during the 2 hours surrounding 

the time of sample collection and at the most closely situated 

ADCP site (table 2). At the two sites that were coincident with 

a water quality site, sites ADCP1 and ADCP6, the correlation 

coefficients were 0.46 and 0.63, respectively. At the other two 

sites, which were each located about 1.5 km from the nearest 

water quality site, the correlation coefficients were 0.47 and 

0.43 at sites ADCP3 and ADCP5, respectively. All correlation 

coefficients were at least weakly significant (p< 0.16).

The computed SSC also shows some correspondence 

with continuous measurements of dissolved oxygen (DO) 

from monitors located at the water quality sites, two of which 

are shown in figure 7. The seasonal minimum in DO at site 

MDN was an indicator of a severe decline in the AFA bloom 

between the last week in July and the first week in August 

(Hoilman and others, 2008). The lowest DO values during 

this time coincided with low SSC at sites ADCP1, ADCP3, 

and ADCP5. A common characteristic of a major bloom 

decline in the lake is that it is most severe in the deep trench 

and in the northern part of the lake (Wood and others, 2006; 

Hoilman and others, 2008; Lindenberg and others, 2008), 

which is consistent with the fact that the late July/early August 

minimum in SSC was most prominent at the sites in the 

northern part of the lake (sites ADCP3 and ADCP5) and in the 

trench (site ADCP1), and was least prominent at site ADCP6 

(fig. 7). In order to quantify the correspondence between SSC 

and DO, the correlation coefficient between the daily median 

value of depth-averaged SSC and the daily median value of 

DO, measured 1 m from the bottom of the lake at the closest 

water quality site, was calculated (table 2). At all sites, the 

correlations with DO were significant with p< 0.02. 

ADCP site

Correlation of vertical velocities with

Horizontal 

current speeds Air temperature

ADCP1 -0.52 0.47

ADCP3 .15 .01

ADCP5 -.43 .17

ADCP6 -.09 .19

ADCP7 .44 -.10

Table 1. Correlation coefficients between vertical velocities 

and horizontal currents and air temperature, Upper Klamath Lake, 

south-central Oregon.

[Locations of ADCP sites are shown in figure 1. Vertical velocities and 

horizontal current speeds were averaged over the top one-half (top one-third 

at ADCP1) of the water column. Air temperature was measured at site WMRMET. Time series were filtered to pass periods between 1.2 and 15 days. 

Correlation coefficients greater than 0.25 are significant and indicated by 

boldface type (p< 0.05)]

ADCP 

site

Water 

quality 

site

Correlation of SSC with

Depth-averaged 

chlorophyll a

(N≥12)

Daily median 

dissolved oxygen

(N≥78)

ADCP1 MDT 0.46 0.30

ADCP3 MDN .47 .45

ADCP5 EPT .43 .34

ADCP6 MDL .63 .27

Table 2. Correlations of computed suspended solids 

concentrations (SSC) at ADCP sites with chlorophyll a and 

dissolved oxygen at water quality sites, Upper Klamath Lake, 

south-central Oregon.

[Locations of sites are shown in figure 1. All correlations of SSC with 

chlorophyll a are at least weakly significant (p<0.16) and all correlations of 

SSC with dissolved oxygen are significant (p<0.02). ADCP, acoustic Doppler 

current profiler; N, number; ≥, equal to or greater than]
Suspended Solids Concentration 13

tac11-0571_fig07

1 m from bottom

1 m from surface

0

50

100

150

0

10

20

0

50

0

50

JULY 1 JULY 15 AUG 1 AUG 15 SEPT 1 SEPT 15

DAY IN 2005

0

50

0

50

100

0

10

20

ADCP1

ADCP3

ADCP5

ADCP6

ADCP7

MDT

MDN

DEPTH-AVERAGED SSC,

IN MILLIGRAMS

PER LITER

DEPTH-AVERAGED SSC,

IN MILLIGRAMS

PER LITER

DISSOLVED OXYGEN,

IN MILLIGRAMS

PER LITER

DEPTH-AVERAGED SSC,

IN MILLIGRAMS

PER LITER

DISSOLVED OXYGEN,

IN MILLIGRAMS

PER LITER

JUNE 15

Figure 7. Depth-averaged (computed) suspended solids concentration (SSC) at five ADCP sites and dissolved 

oxygen at two water quality sites (MDT and MDN), Upper Klamath Lake, Oregon, June 21– September 12, 2005.
14 Acoustic Backscatter and Vertical Velocity, Upper Klamath Lake, Oregon: Implications for Amphanizomenon flos-aquae

Computed SSC can provide insight into how mass moves 

vertically through the water column at diel time scales. The 

computed SSC at each bin in the vertical water column was 

used to calculate the fraction of total water column mass 

in the upper and lower one-half of the water column as a 

function of time (upper one-third and lower two-thirds of 

the water column at site ADCP1). Surface intensification 

is indicated when the fraction of water column mass in the 

upper one‐half of the water column (upper one-third at site 

ADCP1) is greater than 50 percent (33 percent at site ADCP1); 

bottom intensification is indicated when the fraction of water 

column mass in the lower portion of the water column is 

greater than 50 percent (67 percent at site ADCP1). A typical 

10-day period of record shows that mass was concentrated 

in the upper portion of the water column during those 

hours of the day when there was some thermal stability in 

the water column. As the surface started to cool and winds 

increased, the water column became well-mixed (fig. 8) from 

decreased stratification and increased turbulence. This short 

period of record is typical of the longer record, in which 

surface intensification as a daily phenomenon was common 

and bottom intensification was uncommon, but occurred 

occasionally at site ADCP1. 

When computed SSC was averaged over the season to 

produce the seasonally averaged diel cycle, a clear pattern 

of afternoon surface intensification emerged at each site 

(fig. 9). The mass in the top one-half of the water column (top 

one-third at site ADCP1) reached a maximum near the time 

corresponding to the maximum ΔT°. The mass in the bottom 

ADCP 

site

Mean depth 

during 

deployment 

(m)

Average mass 

(mg/m2

)

Average range 

in mass

(mg/m2

)

ADCP1 13.7 549 107

ADCP3 3.9 186 132

ADCP5 5.1 22 13

ADCP6 4.0 75 69

ADCP7 4.5 32 13

Table 3. Average mass and average daily range in mass of 

suspended solids at ADCP sites, Upper Klamath Lake, southcentral Oregon. 

[Locations of sites are shown in figure 1. ADCP, acoustic Doppler current 

profiler; m, meter; mg/m2, milligram per square meter]

one-half (two-thirds at site ADCP1) reached a minimum a few 

hours ahead of the maximum in mass in the top one-half of the 

water column at all sites except site ADCP1, where it instead 

reached a minimum a few hours later than the maximum 

in mass in the top one-half. The depth-integrated mass was 

greatest at site ADCP1; however, the average daily change 

in mass was the smallest percentage of the total mass (about 

19 percent, table 3), whereas the average daily change in mass 

was the largest percentage of the total mass at site ADCP6 

(about 92 percent) and site ADCP3 (about 71 percent), the two 

most shallow sites. 

Pearson correlation coefficients between depth-integrated 

computed SSC and horizontal current speeds at subseasonal 

time scales were positive and significant at sites ADCP1, 

ADCP5, and ADCP6 (table 4). The Pearson correlation 

coefficients between depth-integrated computed SSC and 

air temperature at subseasonal time scales were negative at 

the two deepest sites, ADCP1 and ADCP5, and were not 

significant at the other sites. These correlation results indicate 

that there was more total suspended mass in the water column 

at the deepest sites when the air temperature was cooler and 

more total mass in the water column at three of the five sites 

when the current speeds were stronger. These relations are 

consistent with both increased resuspension as current speeds 

increase and increased sedimentation as air temperatures 

increase and are consistent with the correlations between 

vertical profiles of RB and current speeds, and between 

vertical profiles of RB and air temperatures. 

ADCP site

Correlation of SSC with

Currents 

at ADCP site

Air temperature at 

site WMR-MET

ADCP1 0.45 -0.33

ADCP3 -.17 -.09

ADCP5 .52 -.41

ADCP6 .34 -.02

ADCP7 -.04 .21

Table 4. Correlation coefficients between the depth-integrated 

computed suspended solids concentrations (SSC) at ADCP sites 

and depth-integrated horizontal currents at the same site, or air 

temperature as measured at site WMR-MET, Upper Klamath Lake, 

south-central Oregon. 

[Locations of sites are shown in figure 1. Time series were filtered to pass 

periods between 1.2 and 15 days. Correlation coefficients greater than 0.25 are 

significant and indicated by boldface type (p<0.05). ADCP, acoustic Doppler 

current profiler]
Suspended Solids Concentration 15

tac11-0571_fig08

24

28

WATER 

TEMPERATURE,

IN DEGREES

CELSIUS

21

22

23

24

25

26

27

28

0

20

40

60

80

PERCENT PERCENT PERCENT PERCENT PERCENT

0

20

40

60

80

100

0

5

10

15

0

20

40

60

80

100

0

1

0.5

1.5

0

20

40

60

80

100

0

0.05

0.1

0

20

40

60

80

100

0

0.1

0.2

0.3

0.4

0.5

0

20

40

60

80

100

July 17 July 19 July 21 July 23 July 25 July 27

DATE IN 2005

0

SSC

mg/m2 × 10 5 

SSC

mg/m 2 × 105

SSC

mg/m 2 × 10 5

SSC

mg/m 2 × 10 5

SSC

mg/m 2 × 10 5

0

0.1

0.2

0.3

0.4

A

B

C

D

E

F

G

H

I

J

K

1 m from bottom

1 m from surface

Top one-half (ADCP3/5/6/7) or 

one-third (ADCP1) of water column

Bottom one-half (ADCP3/5/6/7) or 

two-thirds (ADCP1) of water column

Figure 8. A: water temperature at site 

MDT, 1 m from surface, and 1 m from bottom; 

B: Fraction of total water column mass 

contained in the upper one-third of the water 

column, fraction of total water column mass 

contained in the lower two-thirds of the water 

column at site ADCP1. D, F, H, J: Fraction of 

total water column mass contained in the upper 

one-half of the water column, fraction of total 

water column mass contained in the lower 

one-half of the water column, at sites ADCP3, 

ADCP5, ADCP6, and ADCP7, respectively. C, 

E, G, I, K: Depth-integrated suspended solids 

at sites ADCP1, ADCP3, ADCP5, ADCP6, and 

ADCP7, respectively.
16 Acoustic Backscatter and Vertical Velocity, Upper Klamath Lake, Oregon: Implications for Amphanizomenon flos-aquae

Discussion and Conclusions

In order to draw conclusions regarding the behavior of 

cyanobacterial colonies in Upper Klamath Lake based on 

RB and vertical velocities measured by ADCPs, one must be 

confident that the scatterers reflecting the acoustic signal back 

to the instruments are primarily cyanobacterial colonies. There 

is no way to differentiate among actively growing AFA, other 

organisms, and resuspended organic and inorganic material in 

RB data. However, most of the suspended material collected 

from the ADCP sites in September 2006 was organic material: 

62–95 percent at the shallow site and 48–85 percent at the 

deep site; the organic fractions near-surface generally were 

somewhat higher than organic fractions near-bottom (Gartner 

and others, 2007). The organic fraction comprises both 

phytoplankton and zooplankton. AFA completely dominates 

the phytoplankton species from June to October, reaching as 

much as 50 mg/L (wet weight) (Kann, 1998). The dominant 

zooplankton in the lake is Daphnia pulicaria; typical 

maximum seasonal concentrations are about 100 individuals 

per liter, and dry weights seldom exceed a few milligrams 

per liter (Kann, 1998). The D. pulicaria have the potential 

to affect the measured backscatter (and vertical velocity), 

especially because of their large size—the average length of 

the largest size class of D. pulicaria was 1.74 mm in 2005, and 

the average dry weight per individual was 20.75 μg/animal 

(A. St. Amand, Phycotech, unpub. data, 2005). The number 

of cyanobacterial colonies in the water column, however, 

typically is at least an order of magnitude higher than the 

number of D. pulicaria, suggesting that D. pulicari and other 

zooplankton contribute a minor component to the measured 

backscatter and vertical velocity.

Figure 9. Seasonally averaged diel pattern of depth-integrated computed suspended solids concentration (SSC) in 

the entire water column and in the upper and lower one-half (upper one-third and lower two-thirds at ADCP1) of the 

water column. Time of maximum and minimum near-surface and near-bottom current speed and maximum and minimum 

surface-to-bottom temperature difference are shown for reference. Computed SSC are derived from an average of 

30-minute values between June 21 and September 12, 2005. Shading indicates ± 1 standard error around the estimate of 

mean SSC concentration.

tac11-0571_fig09

0

0.1

0.2

0

0.1

0.2

0

1

2

3

Entire water column

Top one-half (ADCP3/5/6/7) or

 one-third (ADCP1) of water column

Bottom one-half (ADCP3/5/6/7) or

 two-thirds (ADCP1) of water column

Time of minimum

 bottom current speed

Time of maximum

 bottom current speed

Time of minimum

 surface-to-bottom

 temperature difference

Time of maximum

 surface-to-bottom

 temperature difference

Time of minimum surface

 current speed

Time of maximum surface

 current speed 

ADCP1 ADCP3

ADCP5 ADCP6

ADCP7

DEPTH-INTEGRATED SUSPENDED SOLIDS (mg/m2×10 5

)

0 4 8 12 16 20 24

0 4 8 12 16 20 24

HOUR OF DAY

EXPLANATION
Discussion and Conclusions 17

With regard to the inorganic fraction, resuspension of the 

bed material would be consistent with the observed positive 

and increasing correlation of RB with horizontal currents 

with distance beneath the water surface at all measurement 

sites except site ADCP6. However, resuspended bed material 

in Upper Klamath Lake would be expected to be at least 

partially organic silt (Laenen and LeTourneau, 1996; Wood, 

2001). Northwest winds greater than 4.5 m/s are sufficient 

to resuspend bed sediment (Laenen and LeTourneau, 1996). 

Typical SSC values were calculated to be about 200 mg/L at 

low lake elevations of 4,137 ft (1,260.96 m, corresponding 

to a mean lake depth of 1.5 m) but only about 5 mg/L at a 

lake elevation of 4,140 ft (1,261.87 m corresponding to a 

mean lake depth of 2.4 m) (Laenen and LeTourneau, 1996). 

Lake elevations ranged from 4,143.1 to 4,139.5 ft (1,262.82 

to 1,261.72 m) during the 2005 ADCP deployments. (Lake 

elevations are from USGS water level gage 11507001.) 

Thus, with deeper lake levels, even with average diel winds 

exceeding 4.5 m/s for several hours during late evening and 

early morning, typical values of resuspended material were 

expected to be low in 2005. In addition to predictions for 

relatively low levels of mobilized bed material, the measured 

RB was usually less near-bottom than it was near-surface on 

both daily and seasonal time scales at each of the five ADCP 

sites. Although wind speeds were periodically high enough 

to resuspend bed materials and distribute mass throughout 

the water column, evidence of resuspended material should 

be evident with increased RB measurements near-bottom. 

Correlations of RB with current speeds were weaker than for 

RB with wind or RB with ΔT°; correlations were particularly 

poor at sites ADCP3 and ADCP6. In addition, the timing 

between RB and wind and RB and current speeds varied 

greatly among the five ADCP sites. If resuspended bed 

material were a substantial portion of the suspended material 

in the water column, it would be expected that the extrema of 

diel cycles of RB generally would coincide with the extrema 

of diel cycles of near-bottom currents, which was not the 

case except at sites ADCP3 and ADCP5 where the extrema 

in RB and near-bottom currents occurred within about an 

hour of each other. Mass was infrequently concentrated in 

the lower part of the water column, although it did happen 

occasionally, particularly at site ADCP1 where the current 

speeds were highest (fig. 9). Thus, the observations tended to 

support the hypothesis that the correlation of RB with currents 

near- bottom was related more to mixing of suspended 

material downward from the surface than to resuspension 

of bed materials. Finally, the computed SSC was correlated 

with dissolved oxygen and chlorophyll a, other water 

quality indicators of bloom dynamics. It seems reasonable 

to conclude, therefore, that RB is a useful surrogate for 

cyanobacterial mass (dominated by AFA) in Upper Klamath 

Lake although the presence of unknown, but generally small 

amounts of inorganic and organic sediments, detrital AFA 

particles, and zooplankton may decrease accuracy of results. 

The theoretical model of light-driven vertical migration 

does not take into account the entrainment into turbulent 

eddies that occurs in wind-driven surface mixed layers 

(Reynolds, 2006). In Upper Klamath Lake, this mixed layer 

can extend to the bottom when winds are strong or to less 

than a meter from the surface when winds are light and the 

top-to-bottom temperature difference in the water column 

provides resistance to mixing. Because Upper Klamath Lake 

is shallow and mixes on an almost daily basis, it is likely that 

the vertical migration pattern of the colonies is controlled 

by the concurrent physical turbulence and thermal (density) 

characteristics of the water column as well as light availability. 

The seasonally averaged diel cycles in measured RB, 

surface vertical velocity, and computed SSC provided insight 

into the behavior of AFA colonies on diel time scales. The diel 

pattern in RB showed a maximum near the surface of the water 

column on a daily basis at all sites as the thermal stability of 

the water column increased in the afternoon, the result of a 

combination of rising colonies accumulating there and growth. 

The afternoon setup of thermal stability also resulted in a 

minimum in the measured RB near the bottom at each site 

as floating colonies rose to the surface and sinking colonies 

settled out of the water column. A minimum in colonies near 

the surface and the most uniform distribution of colonies 

through the water column coincided with the period from 

late night to mid-morning associated with the minimum in 

temperature stratification (figs. 3 and 9).

Interpretation of the seasonally averaged diel cycle 

in vertical velocities was complicated by the fact that the 

measured velocity is an average of the motion of all suspended 

particles sampled by the ADCP acoustic beams, which may be 

a mix of positively, negatively, and neutrally buoyant particles. 

At the three shallowest sites, there was little evidence of any 

diel cycle in the surface vertical velocities, which generally 

were negative, and between -0.1 and -0.2 cm/s, except at 

site ADCP3 where positive velocities as much as 0.1 cm/s 

dominated the diel pattern. There were small diel fluctuations 

that were not consistent from site to site, but there was no 

indication of a daily switch between positively and negatively 

buoyant colonies consistent with light-driven migration. Only 

at the two deepest sites, ADCP1 and ADCP5, was there clear 

evidence of a diel cycle. At site ADCP5, that pattern was 

manifested as smaller sinking velocities in the afternoon; 

near-surface vertical velocity ranged from about -0.4 cm/s in 

the early morning to about -0.15 cm/s in the mid-afternoon. 

The diel cycle was strongest at site ADCP1, where the 

measured vertical velocity ranged from -0.15 cm/s in the early 

morning to +0.15 cm/s in the late afternoon. Both the floating 

and sinking velocities were large, implying that mass could 

be depleted or could accumulate at the surface in a matter of 

a few hours, which is supported by the highly dynamic diel 

cycles in surface RB. This is consistent with observations by 

Moreno-Ostos and others (2009), who concluded that diatom 

and AFA mass at the surface responded to changes in the wind 

stress within about 30 and 80 minutes, respectively. 
18 Acoustic Backscatter and Vertical Velocity, Upper Klamath Lake, Oregon: Implications for Amphanizomenon flos-aquae

When RB was converted to SSC, it was possible to 

calculate the movement of mass vertically through the water 

column. At all sites, based on the seasonally averaged diel 

cycle, mass was concentrated in the upper water column 

through the afternoon and evenly distributed between the 

upper and lower water column in the early morning hours, 

consistent with growth in the upper water column in the 

afternoon, and mixing of the water column in the early 

morning. As was the case with the RB data, there was limited 

occurrence of mass concentration in the lower water column 

that would indicate potential resuspension of sediments. The 

depth-integrated mass at each site peaked in the late afternoon 

to early evening, usually a few hours later than the maximum 

in the upper water column. The difference between the daily 

minimum and maximum in depth-integrated mass at each 

site was large, ranging from 19 percent of the average at site 

ADCP1 to 92 percent of the average at site ADCP6. The 

highly dynamic nature of the diel cycle required large loss 

rates due to sedimentation and mortality within the water 

column, and large growth rates. 

On subseasonal time scales, negative correlations of RB

and air temperature decreased from near-bottom upward and 

became positive at near-surface in the water column at most of 

the ADCP sites. Positive correlations of RB and current speeds 

decreased from near-bottom upward and became negative 

near-surface at three ADCP sites. Because resuspended bed 

sediments were a minor component of suspended material, 

this correlation probably resulted primarily from a dispersal of 

colonies throughout the water column when the water column 

mixed more easily. The negative correlation near-surface 

at three ADCP sites indicated that colonies accumulated 

near‐surface under conditions of increased water column 

stability. Moreno-Ostos and others (2009) observed the same 

relation between the vertical distribution of buoyant AFA and 

wind-induced mixing, and demonstrated that this behavior 

of positively buoyant colonies was easily distinguished from 

the behavior of negatively buoyant diatoms, which became 

depleted at the surface and accumulated in the lower water 

column when mixing was suppressed. At the two deepest 

sites, the surface vertical velocities were positively correlated 

with air temperature, consistent with decreased entrainment 

of floating colonies when air temperature increased. These 

correlations were consistent with increased concentration of 

AFA colonies near the surface when water column stability 

increased and dispersal of colonies throughout the water 

column when the water column mixed more easily. The 

depth-integrated mass at the two deepest sites was negatively 

correlated with air temperature and positively correlated 

with horizontal current speed. Thus, although the total water 

column SSC peaked with the highest air temperatures of the 

day on a daily basis, higher air temperatures were associated 

with lower total water column SSC on a subseasonal time 

scale. At site ADCP7, located at the mouth of Howard Bay, the 

correlations were inconsistent, but the maximum horizontal 

current speeds occurred near-bottom rather than near-surface 

or at mid-depth as they did at the other sites (Gartner and 

others, 2007; fig. 3). The near-surface currents and advection 

of suspended material were complicated by the movement of 

water across the entrance to Howard Bay at this site.

Successful application of a surrogate technology such as 

analysis of time series of measurements of RB in conjunction 

with analysis of water samples has the potential to provide 

a less costly and labor intensive means of determining 

continuous and high resolution characteristics of the variable 

under study that is not otherwise possible. Analyses of both 

RB and computed SSC, in conjunction with profiles of vertical 

velocity and an understanding of horizontal water current 

speeds measured by ADCPs in Upper Klamath Lake during 

2005 contribute significant additional insights into seasonal, 

subseasonal, and diel patterns of AFA population dynamics in 

the lake. 

Acknowledgments

The authors gratefully acknowledge the assistance of 

personnel from the USGS California Water Science Center, 

the USGS Oregon Water Science Center, and the USGS 

Klamath Falls Field Station who participated in various 

aspects of the fieldwork. Discussions with J. Rueter (Portland 

State University), J. Kann (Aquatic Ecosystem Sciences), and 

A. St. Amand (Phycotech) were very helpful. This work was 

partially funded by the U.S. Fish and Wildlife Service Hatfield 

Restoration Program (Interagency Agreement 814506H520) 

and the USGS National Research Program. Finally, the 

authors would like to thank several anonymous reviewers 

whose comments significantly aided in the preparation of this 

manuscript.

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2147afe590018767d3.
Publishing support provided by the U.S. Geological Survey

Publishing Network, Tacoma Publishing Service Center

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

 Director, Oregon Water Science Center

U.S. Geological Survey

2130 SW 5th Avenue

Portland, Oregon 97201

http://or.water.usgs.gov
Wood and Gartner— Acoustic Backscatter and Vertical Velocity, Upper Klamath Lake, Oregon: Implications for Aphanizomenon flos-aquae —SIR 2010–5203