U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigation Report 2004-5298

Prepared in cooperation with the U.S. Environmental Protection Agency and the Minnesota 

Department of Health

Development of a Benthic-Flux Chamber for Measurement 

of Ground-Water Seepage and Water Sampling for Mercury 

Analysis at the Sediment-Water Interface
Development of a Benthic-Flux Chamber 

for Measurement of Ground-Water 

Seepage and Water Sampling for Mercury 

Analysis at the Sediment-Water Interface

By M.A. Menheer

Prepared in cooperation with the U.S. Environmental Protection Agency and the Minnesota 

Department of Health

Scientific Investigation Report 2004-5298

U.S. Department of the Interior

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

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

U.S. Geological Survey, Reston, Virginia: 2004

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

Box 25286, Denver Federal Center

Denver, CO 80225

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

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

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

endorsement by the U.S. Government.

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

reproduce any copyrighted materials contained within this report. 

Suggested citation:

Menheer, M.A., 2004, Development of a bethic-flux chamber for measurement of ground-water seepage and water 

sampling for mercury analysis at the sediment-water interface: U.S. Geological Survey Scientific Investigation Report 

2004-5298, 14 p.
iii

Contents

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

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

Purpose and scope .............................................................................................................................. 2

Acknowledgments ............................................................................................................................... 2

Description of the flux chamber ................................................................................................................. 2

Methods ......................................................................................................................................................... 7

Seepage measurements ..................................................................................................................... 7

Water sampling .................................................................................................................................... 9

Measurement of ground-water seepage and water sampling ............................................................. 9

Seepage measurements ..................................................................................................................... 9

Water sampling .................................................................................................................................. 11

Potential improvements to the flux chamber ......................................................................................... 11

Summary ...................................................................................................................................................... 13

References ................................................................................................................................................... 13

Figures

Figure 1. Test site locations at Long Lake and Square Lake in Minnesota ......................................... 2

Figure 2. Schematic of the top and side views of the flux chamber. .................................................... 3

Figure 3. Schematic of the bottom view and photograph of bottom view of the flux chamber. ...... 4

Figure 4. Top view of flux chamber showing flow meter. ....................................................................... 5

Figure 5. Photograph of the data collection platform. ............................................................................ 6

Figure 6. Flux chamber and 55-gallon drum seepage meter deployed at Long Lake. ....................... 7

Figure 7. Schematic of the calibration tank. ............................................................................................. 8

Figure 8. Long Lake seepage from ground water. ................................................................................. 10

Figure 9. Square Lake seepage from ground water. ............................................................................. 10

Figure 10. Calibration tank seepage, January 23, 2004. ........................................................................ 11

Figure 11. Calibration tank seepage, January 27-28, 2004. .................................................................. 11

Tables

Table 1. Summary of flow data from calibration tests done in a calibration tank. ........................... 12
iv

Conversion Factors and Water-Quality Units

Multiply By To obtain

Centimeter (cm) 0.3939 inch (in.)

Meter (m) 3.281 feet (ft)

Kilometer 0.6214 mile (mi)

Gallon (gal) 3.785 liter (L)

Liter (L) 103 milliliter (mL)

Kilogram (kg) 2.205 pound, avoirdupois (lb)

Gallon per minute (gal/min) 0.06308 liter per second (L/sec)

Degrees Celsius (oC) 1.8(oC)+32 degrees Fahrenheit (oF)

Chemical concentrations: Chemical concentrations of substances in water are given in metric 

units of milligrams per liter, micrograms per liter, or nanograms per liter (ng/L). Micrograms per 

liter μg/L is a unit expressing the concentration of chemical constituents in solution as mass 

(nanograms) of solute per unit volume (liter) of water. One thousand nanograms per liter is 

equivalent to one microgram per liter.
Abstract

A benthic-flux chamber was constructed to collect data 

to determine the relation between ground- and surface-water 

interaction and mercury concentrations in water at the sediment-water interface. The benthic-flux chamber was successfully used to measure the rate of ground water seeping to 

surface water or surface water seeping to ground water, and to 

collect water samples for mercury analysis from the sedimentwater interface in a lake setting. The benthic-flux chamber 

was designed to be deployed in relatively calm fresh water 

lakes, in areas of water less than 2 meters deep. The groundwater seepage rate data were comparable to data from an 

in-line flow meter in a calibration tank and with data from two 

55-gallon drum seepage meters concurrently deployed in two 

different lakes. The benthic-flux chamber was used to collect 

possible water samples for analysis of total mercury and methylmercury concentrations. 

Introduction

Bioaccumulation of mercury in the aquatic food chain is 

related to microbial conversion of inorganic mercury to methylmercury near the sediment-water interface. Methylmercury 

(MeHg) is more toxic and bioaccumulative than inorganic 

mercury. Therefore, the concentration of methylmercury in 

water and sediments is a better indicator of mercury concentrations in fish than of total mercury (THg) (Bodaly and others, 1993). Bloom (1992) reports that as much as 95 percent 

of mercury in fish is MeHg.

Methylation of inorganic mercury and reduction of sulfate are related to microbial processes near the sediment-water 

interface where anoxic conditions exist (Branfireun and others, 

1999). Ground water with low dissolved-oxygen concentrations can create anoxic zones in the sediment-water interface 

where ground water discharges into the lake. Advection of 

ground water through the sediments can transport MeHg into 

the overlying water column. Although the sediment-water 

interface is known to be an active zone for mercury methylation (Kerry and others, 1991; Gilmour and others, 1992; 

Pak and Bartha, 1998), the influence of interactions between 

ground and surface water on the methylation process has not 

been thoroughly studied.

Sulfate reduction is a key process in the mercury cycle 

and has important implications at zones of ground-water/surface-water interaction. Gilmour and Henry (1991) suggest 

an ‘optimal’ relation between sulfate reducing bacteria and 

mercury methylation efficiency (percent of inorganic mercury 

that is methylated per unit time). At low concentrations in 

sediment pore water, sulfate (less than 19 mg/L) is the limiting 

factor on the growth and biotic activity of sulfate reducing 

bacteria. At high concentrations of sulfate (greater than 48 

mg/L) inhibition of methylation may occur. This may be due 

to the inhibition of sulfate-reducing bacteria by pore water 

sulfide (Gilmour and others, 1992), or the increased solubility 

and decreased availability of mercury to bacteria in sulfiderich pore-water (Paquette and Helz, 1997; Benoit and others, 

1999; Jay and others, 2000).

Transport rates of THg and MeHg from sediments in 

the past have been estimated using diffusive flux models, not 

direct measurement of the discharge of ground water to surface water. The models are based on concentration gradients 

between sediment pore water and overlying water between 

pore water concentrations at different sediment depths. Two 

difficulties exist with this approach: diffusive fluxes are subject to considerable uncertainty in model coefficients, and even 

modest ground-water-discharge rates yield advective fluxes 

that typically are much greater than diffusive fluxes.

There are two common problems in studying benthic 

processes with a benthic-flux chamber (hereinafter termed 

flux chamber). The first is the water contained within the flux 

chamber is isolated from the surrounding lake water. This 

creates a stagnant zone where the benthic currents that mix the 

water at and above the bottom sediments are eliminated, which 

in turn can induce marked changes in reduction oxidation 

chemistry. 

The second problem encountered by flux chambers is 

that biologic respiration and water-sediment processes may 

progressively reduce the dissolved-oxygen concentration of 

the water. Over time the water in the flux chamber no longer 

represents the chemistry of the ambient water at the sediment-water interface. Dissolved oxygen commonly is used 

Development of a Benthic-Flux Chamber for Measurement 

of Ground-Water Seepage and Water Sampling for 

Mercury Analysis at the Sediment-Water Interface

By M.A. Menheer
2 Development of a benthic-flux chamber for measurement of ground-water seepage and water sampling for mercury

as a surrogate measurement to determine when water samples 

collected from flux chambers may be compromised (Gill and 

others, 1999).

Purpose and Scope

To address these problems with flux chambers, the U.S. 

Geological Survey, in cooperation with the U.S. Environmental Protection Agency (USEPA) and Minnesota Department 

of Health (MDH), conducted a study to design a flux chamber 

that could be used to measure seepage rates and collect water 

samples from the sediment-water interface that minimizes the 

disturbance of ambient conditions. The data would be used to 

measure benthic fluxes of trace concentrations of water-quality parameters such as THg and MeHg. The purpose of this 

report is to describe (1) the design of the flux chamber, (2) 

ground-water seepage data collected using the flux chamber, 

and (3) mercury data from water samples collected using the 

flux chamber. Data were collected during November 2003 and 

January 2004. Flux chambers and 55-gallon drum seepage 

meters were deployed in Long Lake and Square Lake in Minnesota (fig. 1). Data from the two types of seepage measurements are compared.

Acknowledgments

The author extends thanks to Carl Herbandson, Minnesota Department of Health, Dr. Robert Ford, U.S. Environmental Protection Agency, Office of Research and Development, and Mark Brigham, U.S. Geological Survey, Minnesota 

District; for their technical assistance. Thanks also are given 

to Dave Krabbenhoft, U.S. Geological Survey, Wisconsin 

District; Don Rosenberry, U.S. Geological Survey, National 

Research Program; Dr. Gary Gill and Ron Lehman of the University of Texas, A&M, Galveston; and to Dave Shelander of 

Logix Engineering, Inc for the fabrication of the flux chamber. 

The author is grateful to a private landowner for generously 

allowing his property to be used to deploy and test the flux 

chamber.

Description of the Flux Chamber

A flux chamber (figs. 2 and 3) was designed to route 

ground water seeping from sediments through an ultrasonicflow meter. The flux chamber was made of a polycarbonate 

(vivac) plastic that was molded and welded into a 38.1-cm 

diameter by 20.3-cm high cylinder. Vivac was used because 

���������

����

����

����

����

���� ����

����

�����

����

�����

��

���

���

���

������� �

����

����

����

������

���������

������

��������� ������ ��������� ������

���� ��� ���� ��������

� ���� ��� ���� ������������

�

��������������

������������

����������������

�����������������

�����������

���

��������

����

����

����

�����

����

������

����

�������

�����

���� ������ �����

���������

����

�����

������

���������

������

������ ��������� ������ ���������

���� ��� ���� ��������

� ���� ��� ���� ������������

�

Figure 1. Test site locations at Long Lake and Square Lake in Minnesota
��������������������������

��������������������������

���������������������������

���������������������������

������������������� �����������������������

�����������������������

�����������������������

�������������

��������

����������

�������������

��������

����������

�������������������

�������������������

�����������������

�����������������

��������

���������

������������

������������

��������������

��������

Figure 2. Schematic of the top and side views of the flux chamber.

Description of the flux chamber 3
4 Development of a benthic-flux chamber for measurement of ground-water seepage and water sampling for mercury

��������������

��������

����������������������

�����������

������������

�����������

����������������

����������

���������������������������

�������������������

�������������������

�����������������

�������������

���������

�������������

���������

���������������

����������

������������

�����������

�������������������������������������������

Figure 3. Schematic of the bottom view and photograph of bottom view of the flux chamber (photograph by Michael Menheer).
it can be adequately cleaned to sample for trace levels of mercury. Teflon also was used for several of the ports and other 

parts of the flux chamber that came into contact with the water 

inside the flux chamber. 

The ultrasonic-flow meter (Controlotron 1010) has two 

main parts, a flow tube and a flow computer (figs. 4 and 5). 

The flow tube is a rigid 1.3-cm outside diameter Teflon tube, 

24.5 cm long. The flow tube was connected to the flow computer by electrical cables with barrel nut connectors on both 

ends of the flow tube. Densyl Tape, a water resistant fabric, 

was wrapped around the barrel nut connectors on the flow tube 

so it could be submerged in water. An ultrasonic-flow-meter 

port on the top of the flux chamber was used to route water 

through the flow tube. The flow tube contains two ultrasonic 

pulse transducers directed towards each other. Ultrasonic 

pulses are sent between the two transducers. The direction 

and rate of the water flowing through the tube varies the time 

delay of the signals. The signals sent in the same direction of 

the flow are received at a shorter time interval than the pulses 

sent in the opposite direction of flow; this time difference is 

proportional to the rate of flow. These data are measured and 

compiled as a flow rate in the flow computer (Paulsen and 

others, 2001).

An adjustable polyvinyl chloride (PVC) ring 1.3-cm thick 

by 3.2-cm wide was fitted around the outside of the flux chamber. The ring was used as a guide to indicate when the flux 

chamber was pushed far enough into the sediment and to seat 

the meter at a consistent depth in the sediment. This ring also 

served as a reference to calculate the volume of water that was 

in the flux chamber. Attaching flanges (10.2 cm widening to 

15.6 cm wide and 12.4 cm long) to the ring facilitated deployment in lakes with silty, soft sediments with minimal settling 

of the flux chamber over time.

A 5-cm circular hole was made in the top of the flux 

chamber to allow water to seep through the top of the flux 

chamber during deployment, thereby minimizing disturbance of the sediments. When the flux chamber is properly 

deployed, a pin is pulled and a spring-loaded port door made 

�����������������������

�����������

��������

����

��������

�������������������

����������

Figure 4. Top view of flux chamber showing flow meter (photgraph by Michael Menheer).

Description of the flux chamber 5
6 Development of a benthic-flux chamber for measurement of ground-water seepage and water sampling for mercury

from a piece of Teflon tightly closes this hole. This is done 

from the water surface.

The flux chamber was designed to slowly mix the water 

and to maintain ambient dissolved-oxygen concentrations to 

minimize the artificially induced changes in reduction-oxidation chemistry. A polycarbonate and Teflon magnetic stir 

assembly was designed to slowly circulate the water in the 

flux chamber to simulate benthic currents. A small motor 

was mounted outside the flux chamber and encased in polycarbonate plastic. The motor turned a magnet on the outside 

of the flux chamber that was partnered with another Tefloncoated magnet inside the flux chamber. The magnet inside the 

flux chamber was attached to the stirrer. This design avoids 

contamination from the motor, and prevents the motor from 

warming the water in the flux chamber.

A dissolved-oxygen meter with a Teflon probe was used 

to monitor the dissolved-oxygen concentrations inside the 

chamber. The data from the dissolved-oxygen meter were 

recorded by a datalogger. A small-volume, battery-powered 

air pump was connected to the datalogger and to an air bubbler on the flux chamber. The datalogger was programmed 

to monitor the dissolved-oxygen concentration. When the 

dissolved-oxygen concentration dropped to a user-defined percentage of the initial level, the air pump would turn on. The 

pump would run the air bubbler until the dissolved-oxygen 

concentration approached the initial concentration. The air 

could be pumped through a gold trap to remove any mercury 

that might contaminate the water in the flux chamber. The top 

of the flux chamber, above the air input, had an air bubbler 

outlet port that was kept closed with a buoyant disk. When air 

was pumped into the flux chamber, it would accumulate in this 

area and the disk would fall away from the opening, allowing 

air to leave the flux chamber.

An ultrasonic-flow-meter port on the top of the flux 

chamber was used to attach to Teflon tubing so water could 

be pumped from the flux chamber for collection of water 

samples. The ultrasonic-flow-meter port had a luer loc fitting 

threaded into it. When water samples were not collected, this 

port was closed with a luer plug.

A floating data collection platform, consisting of two 

pontoons and an aluminum frame, was used to hold the 

equipment needed to collect the seepage data (figs. 5 and 6). 

The equipment consisted of a datalogger, a dissolved-oxygen meter, an air pump, a battery for the datalogger, the flow 

�������������

�������������� ����������

����������������

�����������������

����������������

�����

�������

����������

��������� �������������

�������

������� ��������������

Figure 5. Photograph of the data collection platform (photograph by Michael Menheer).
computer, and a backup battery for the flow computer (fig. 

5). The combined weight of the equipment was 35 kilograms. 

The data-collection platform was anchored in place, near the 

deployed flux chamber, using two aluminum rods on either 

side of the data-collection platform, and was chained to an 

earth anchor for added security. The aluminum rods allowed 

the data-collection platform to move up and down in response 

to wave activity.

Methods

Seepage-rates and mercury concentration data were collected to evaluate the performance of the flux chamber. The 

flux chamber was tested in a calibration tank to determine 

the accuracy of the ultrasonic-flow meter. The flux chamber 

was then deployed in two lakes. Seepage data were collected 

during fall 2003 concurrently using the flux chamber and 

two traditional 55-gallon drum seepage meters at two lakes 

(Lee, 1977). Water samples were collected from one of the 

two lakes, during fall 2003. The flux chamber was tested and 

recalibrated in a calibration tank during January 2004 after the 

field deployment.

Seepage Measurements

The seepage meter was attached to the flux chamber 

and was tested in a sand-bed calibration tank (fig. 7). The 

tank was designed so the seepage of water moving through 

the sand could be accurately measured and varied. A George 

Fischer (GF) Signet micro-flow (0.113 - 2.65 L/min.) in-line 

flow meter was used to measure the seepage rate of the water 

moving through the sand and across the sand-water interface. 

Raising or lowering the head of the water source provided 

control of the seepage rate to test the flow meter over a range 

of seepage rates. The water overflowed from the tank through 

a spigot into a basin. The seepage rate could be verified by 

measuring the water coming from the spigot using a graduated 

cylinder. A peristaltic pump was used to pump the water from 

the basin back into the water source. The pump and the trans-

����������������������������

������������

������������������������

Figure 6. Flux chamber and 55-gallon drum seepage meter deployed at Long Lake (photograph by Michael Menheer).

Methods 7
8 Development of a benthic-flux chamber for measurement of ground-water seepage and water sampling for mercury

ducer were connected to a datalogger that was programmed to 

turn the pump on and off to maintain a constant water level in 

the water source. This allowed calibration tests to be conducted for extended periods of time at a constant seepage rate.

The flux chamber was field tested by deploying it in two 

lakes in east-central Minnesota known to have measurable 

ground-water discharge, Long Lake in Ramsey County and 

Square Lake in Washington County (Alexander and others, 

2001; J. Lundy, hydrologist, Minnesota Pollution Control 

Agency, oral commun., 2003). Seepage measurements were 

made in both lakes. 

The in-lake test deployments were made in firm, sandy 

bottom sediments at locations free of vegetation to avoid loss 

of ground-water seepage from obstructions or poor contact 

with the sediment. The flux chamber and two 55-gallon drum 

seepage meters were inverted under water to ensure all the air 

was removed, then pressed into the lake sediments approximately 5 cm. The flux chamber and the 55-gallon drum 

seepage meters were deployed 2-3 m from shore in water 

approximately 1 m deep. The ultrasonic-flow meter tube was 

submerged next to the chamber, and a piece of vinyl tubing 

38-41 cm in length was used to connect the chamber to the 

ultrasonic-flow meter. The 55-gallon drums were fitted with a 

garden hose threaded fitting. Plastic (polyethylene) bags were 

secured to a threaded ball valve using electrical tape. The 

bags were prefilled with 500 to 600 mL of lake water and the 

air was removed before they were attached to the drums. The 

fittings on the bags were then threaded onto the drums. Once 

they were securely attached, the starting time was noted when 

the valves were opened. The volume of water in the bags was 

measured using an electronic scale before and after deployment. It was assumed that 1 mL of water equaled 1 gram. 

The end time of the test was noted when the valve was closed, 

and the bag was removed from the drum and weighed. 

The 55-gallon drum seepage rate was calculated with the 

following formula:

Seepage = dV/dt (1)

where dV = V2 - V1, (2)

V2 = ending bag volume, in milliliters,

V1 = starting bag volume, in milliliters, and

dV = difference in volume in milliliters.

dt = t2 - t1 (3)

t

2

 = test ending time, in minutes,

t

1

 = test start time, in minutes, and

dt = length of test, time in minutes.

The seepage rates were converted from milliliters per 

minute (mL/min) to centimeters per day (cm/day). This 

was done to normalize the seepage to area. It made the data 

directly comparable between the two types of seepage meters 

used which had different diameters. The following formula 

was used:

(mL/min)*(1,440 min/day)/(3.14159*r2) = (cm/day) (4)

����������

������������������

��������������������

����

�����

�������

����������

�������������������

��������������������� �������

����� ������������

����������������

��������

�����������

�������������

������������

��������

����������

�������������������

����������������

���������������

���������������

����������������������������������������������������������

�����������

���������

��������������

�������� ������������

Figure 7. Schematic of the calibration tank.
where r is the radius, in centimeters, of the drum or flux 

chamber being used.

The flux chamber and the seepage meters were given 

time to equilibrate before initial measurements were made 

(Rosenberry and Morin, 2004). The time period required 

before stable flow was established varied based on seepage 

rate and the size of the flux chamber. The flux chamber was 

deployed for a minimum of 30 minutes before tests began. 

The flux chamber was left deployed overnight and seepage 

rates were measured the following day. Several tests of different lengths of time were done before the flux chamber and the 

55-gallon drums were moved to determine an average seepage 

rate. Field tests of flux chamber operation were made during 

November 2003. The weather conditions were windy with 

rough, cold water (4–7 degrees Celsius). Fifty-five-gallon 

drum seepage meters were concurrently deployed within 1-2 

m of the flux chamber to obtain comparable measurements. 

The water was clear in both lakes so it was possible to visually 

inspect the 55-gallon drum seepage meters and the flux chamber (fig. 6) to ensure they were pressed deeply enough into the 

lake sediments.

Water Sampling

Water samples were collected in Square Lake. A water 

sample was collected outside of the flux chamber to establish 

an ambient background concentration. A replicate sample 

was collected from the flux chamber. An equipment blank 

was collected in the office following the sample collections. 

Blank water was obtained from the USGS, Wisconsin District 

Mercury Laboratory, Middleton, Wisconsin.

Water samples were collected from the flux chamber 

using a peristaltic pump and following a “dirty hands” and 

“clean hands” protocol (Olson and DeWild, 1999). This 

involved two individuals who collected the samples. The 

equipment had been cleaned prior to sampling. This cleaning was in accordance with the USGS National Field Manual 

(U.S. Geological Survey, 1998) cleaning procedures and 

included a 10 percent hydrochloric acid (HCl) rinse by the 

personnel who were to collect the samples. Each sampler 

wore shoulder-length polyethylene gloves and wrist-length 

nitrile gloves. The two samplers waded upwind to the flux 

chamber, a section of acid cleaned Teflon tubing was connected to the top of the flux chamber and to an acid cleaned 

section of C-Flex pump head tubing. Water was pumped from 

the flux chamber using a peristaltic pump. Laboratory-cleaned 

Teflon sample bottles were double-bagged in resealable plastic 

bags. The “dirty hands” sampler opened the outside bag. The 

“clean hands” sampler touched only the inside bag and the 

sample bottle. A lake sample was collected by submerging the 

bottles to a depth of 0.2 m. A multiparameter meter was used 

to measure the water temperature, specific conductance, dissolved oxygen, and pH of the lake water surrounding the flux 

chamber. The THg and MeHg samples were preserved with 

10 mL and 5 mL of 6N HCl, respectively. Preservation was 

done within several hours of sample collection. Samples were 

then stored in a laboratory refrigerator until shipped, on ice, to 

the USGS, Wisconsin District Mercury Laboratory (DeWild 

and others, 2001). 

Measurement of Ground-Water 

Seepage and Water Sampling

Seepage Measurements

The trial deployment of the flux chamber was done in 

Long Lake in Ramsey County, Minnesota (fig. 6). The water 

temperature varied from 3 to 5 degrees Celsius during the trial 

period. The specific conductivity of the water was 568 microSiemens per centimeter (μS/cm) at 25 degrees Celsius. There 

were moderate sized waves. A seepage rate was recorded 

every 5 seconds by the ultrasonic-flow meter. These were 

averaged and one value per minute was recorded. The data are 

presented in figure 8. It was noticed during this deployment 

that the ultrasonic-flow meter drifted over time. The initial 

flow rates reported by the ultrasonic-flow meter fell within 

the range that was concurrently measured using two 55-gallon drums. The downward trend in seepage shown in figure 8 

continued and later measurements drifted to zero and negative 

flows. It did not appear that the drift in the meter was due to 

wave effects as is discussed in several papers (Shum, 1992; 

Libelo and MacIntyre, 1994; Taniguchi and Fukuo, 1996). 

The drift in the ultrasonic-flow meter was linear over the entire 

period of deployment. It did not vary cyclically as one would 

expect if it were wave induced. Also, the drift continued even 

after the wind calmed and the waves lessened. The minimum, 

maximum, and average flow rates for the ultrasonic-flow 

meter were 1.55, 39.47, and 18.06 cm/day, respectively. The 

minimum, maximum, and average seepage rates for the two 

55-gallon drum seepage meters were 1.84, 26.0, and 11.20 cm/

day, respectively. The ultrasonic-flow meter would occasionally report a noticeably anomalous value, either considerably 

higher or lower than the average flow reading.

The second test deployment of the flux chamber was 

along the west shore of Square Lake in Washington County, 

Minnesota the following week. The water was calm. The 

temperature of the water was 4 to 6 degrees Celsius. The 

specific conductivity of the water was 282 μS/cm at 25 degrees 

Celsius. A flow rate was recorded every 5 seconds by the 

ultrasonic-flow meter. These were averaged and one value per 

minute was calculated. The ultrasonic-flow meter rates again 

slowly drifted linearly, slowly decreasing over time. The data 

are presented in figure 9. The seepage rates were closely comparable between the ultrasonic-flow meter and the 55-gallon 

drum seepage meter. The minimum, maximum, and the average values for the ultrasonic-flow meter were 5.90, 18.29, and 

13.06 cm/day, respectively. The minimum, maximum, and 

Measurement of ground-water seepage and water sampling 9
10 Development of a benthic-flux chamber for measurement of ground-water seepage and water sampling for mercury

��

��

��

��

��

��

��

��

�

�

�������������������������������

�����

�����

�����

�����

�����

�����

�����

�����

�����

�����

�����

�����

�����

����

�����

�����

�����

�����

����

�����

�����

�����

�����

�����

�����

�����

�����

�����

����� �����

�����

����� �����

�����

������������� ��������

����

��������

����

�����������������������������

������������������������������������

����������������������������������������

Figure 8. Long Lake seepage from ground water.

��

��

��

��

��

��

�

�

�

�

�

�������������������������������

�����

���������������

�����

�����

�����

�����

�����

�����

�����

�����

�����

�����

�����

����������������� �����������������

�����

�����

�����

�����

�����

�����

����� �����

�����������������������������

������������������������������������

����������������������������������������

Figure 9. Square Lake seepage from ground water.

the average values for the two 55-gallon drum seepage meters 

were 10.99, 16.80, and 11.16 cm/day, respectively.

The ultrasonic-flow meter was tested and recalibrated in 

the calibration tank after it had been field tested. A flow rate 

was recorded every minute by both the ultrasonic- and the 

in-line- flow meter. Several times during calibration the flow 

was stopped and the ultrasonic-flow meter was manually reset 

to zero flow. The range of in-line flow rates on the January 
23, 2004 test varied between 10 and 35 cm/day (fig. 10). The 

duration of the test was 338 minutes. When compared, 88 

percent of the ultrasonic-flow rates and the in-line flow meter 

rates were within 20 percent (table 1). The rates varied on 

the January 27, 2004 calibration test between 5 and 39 cm/day 

(fig. 11). The duration of the test was 1,407 minutes. When 

compared 55 percent of the readings were within 20 percent, 

69 percent were within 30 percent (table 1). The data from 

these two tests are presented in figures 10 and 11, and table 

1. The zero values when the flow was turned off were not 

included in this summary.

Water Sampling

A sequential replicate water sample was collected to test 

the design of the flux chamber. A dip sample was collected 

directly from the lake to establish background concentrations. 

The water samples were collected at Square Lake, November 

20, 2003. The replicate sample was collected from the flux 

chamber immediately following the collection of the lake 

sample. The flux-chamber samples yielded THg concentrations of 0.47 and 0.53 nanograms per liter (ng/L). The lake 

sample was 0.27 ng/L. The MeHg concentrations for all three 

of the samples were below the detection limit of 0.04 ng/L.

The flux chamber was cleaned by rinsing it with 10 

percent HCl acid. The sample tubing was cleaned by pumping similar acid through it. The flux chamber was not cleaned 

by soaking it in an acid bath because of the size of the 

chamber and the amount of acid that would be required. An 

office equipment blank was collected several weeks after the 

environmental samples. The flux chamber and tubing were 

cleaned prior to collection of the equipment blank. The blank 

was collected in the office laboratory by inverting the flux 

chamber, pouring blank water into the flux chamber, rinsing the water around in the flux chamber, and then using the 

sample tubing to pump it into the sample bottles. The office 

equipment blank concentration for THg was 0.79 ng/L, and for 

MeHg was below the detection limit of 0.04 ng/L. 

The data indicates that the flux chamber is suited for 

sampling water with mercury concentrations greater than 

0.1 ng/L. At sites where concentrations are low (<1.0 ng/L), 

greater attention needs to be given to cleaning protocols and 

collecting quality-control and quality-assurance data to verify 

the accuracy of the data.

Potential Improvements to the Flux 

Chamber

The following is a discussion of design changes that 

would improve the flux chamber. These changes were beyond 

the scope of this study.

The physical dimensions of the flux chamber could be 

larger. This would have integrated data and seepage from 

a larger area. The material used for the flux chamber could 

be thicker making it more durable. This would also make it 

��

��

��

��

��

�

���

�������������������������������

�����

��������������������

����������

����������

�����

����������

����������

����������

�����

����������

����������

����������

�����

����������������

���������������������

������������������

�����������������������������

Figure 10. Calibration tank seepage, January 23, 2004.

Potential improvements to the flux chamber 11
12 Development of a benthic-flux chamber for measurement of ground-water seepage and water sampling for mercury

January 23, 2004 Calibration Test

Start: 1/23/2004 11:13:00 AM

End: 1/23/2004 4:51:00 PM

Test duration: 338 minutes (5 hours 38 minutes)

January 27, 2004 Calibration Test

Start: 1/27/2004 9:12:00 AM

End: 1/28/2004 8:39:00 AM

Test duration: 1,407 minutes (23 hours 27 minutes)

Percent difference between Inline and ultrasonic-flow metersNumber of 

recorded flow 

rates

Percent of total 

measurements made 

during test

Percent difference 

between Inline and 

ultrasonic-flow meters

Number of 

recorded flow 

rates

Percent of total 

measurements made 

during test

0 - 10 202 67 0 - 10 493 35

11 - 20 64 21 11 - 20 278 20

21 - 30 22 7 21 - 30 202 14

31 - 40 1 0 31 - 40 133 10

41 - 50 2 1 41 - 50 95 7

51 - 60 0 0 51 - 60 99 7

61 - 70 1 0 61 - 70 76 5

71 - 80 2 1 71 - 80 5 0

81 - 90 2 1 81 - 90 5 0

>90 4 1 >90 13 1

total: 300 100 total: 1399 100

Table 1. Summary of flow data from calibration tests done in a calibration tank.

��

��

��

��

��

�

���

�������������������������������

�����

��������������������

����������

����������

�����

����������

����������

����������

�����

�����

����

����������

����������

�����

���������������� ����������������

�����������������������������

���������������������

������������������

Figure 11. Calibration tank seepage, January 27-28, 2004.

easier to make the ports in the flux chamber, some of which 

were threaded. 

The ultrasonic-flow meter drifts over time. A closeable 

valve on the flux chamber or inline with the tubing from the 

flux chamber to the flow tube would be useful to set the seepage to zero. A valve could be attached to the datalogger so it 

would automatically be closed at regular intervals. This would 

allow the drift to be quantified over time. An alternative would 

be to install a valve that could be manually closed and the 

meter could be reset to zero at regular intervals.
The ultrasonic-flow meter was powered by an internal 

12-volt battery. An external battery extended the length of 

continuous operation to about 48 hours. A solar panel could 

be mounted on the floating platform to further extend the battery life of the meter.

The stirrer moved in jerky movements and was stopped if 

it encountered an obstruction. Stronger magnets could be used 

to produce a dependable, smoother operation.

The dissolved-oxygen probe was labor intensive to 

maintain and became an ongoing effort of time and supplies 

and was not used when field testing the flux chamber. There 

was concern about damaging the fragile probe. Because the 

dissolved-oxygen probe was not used, air was not pumped into 

the flux chamber. To monitor the dissolved-oxygen concentration in the flux chamber, either small volumes of water could 

be withdrawn periodically and tested with a dissolved-oxygen 

meter, or the water coming from the flow tube could be routed 

into a standard multiparameter meter to continuously monitor 

the dissolved-oxygen concentration of the water coming from 

the flux chamber. This would avoid the contamination issues 

from the dissolved-oxygen probe and allow pH, specific conductivity, and water temperature data to be collected.

The springs on the spring loaded port door snapped the 

cover in place, closing the opening forcefully. This could agitate the sediments, which the port door was designed to avoid. 

This could have been lessened, if not completely alleviated, by 

a change in design that would not have lifted the Teflon cover 

as high. Over time the springs had a tendency to rust. This 

could have been resolved by using stronger springs and replacing them on a routine basis.

The buoyant disk to close the outlet for the air that was 

pumped into the chamber worked, but the seal was not tight. 

Water was able to leak from this port. The issue with water 

leaking from various ports was noticed when the chamber was 

inverted and filled with water. When deployed in the field, the 

water pressure against the ports would only be a fraction of 

what this experiment showed. A Teflon coated O-ring around 

the buoyant disk would have given it a tighter seal.

Prior to water sampling, careful cleaning of the flux 

chamber and the sampling tubing is needed. This includes 

soaking them in a 10 percent HCl acid bath or rinsing them 

with acid. Collection of numerous quality-control and qualityassurance samples, especially equipment blanks, is needed to 

monitor the flux chamber performance, specifically to monitor 

any contamination that might result from inadequate cleaning 

procedures. 

Summary

The U.S. Geological Survey in cooperation with the U.S. 

Environmental Protection Agency and the Minnesota Department of Health conducted a study during November 2003 and 

January 2004 at Long Lake and Square Lake in Minnesota to 

measure ground-water seepage rates. A benthic-flux chamber 

was constructed and used to measure ground-water seepage 

rates and to collect water samples. The ground-water seepage rate data was verified by testing the flux chamber in a 

calibration tank and by deploying it in two fresh water lakes 

alongside other 55-gallon drum seepage meters. The flux 

chamber seepage rate data were comparable to rates measured 

concurrently in the calibration tank by an in-line flow meter. 

The seepage rate in the calibration tank also was verified by 

measuring the seepage over time using a graduated cylinder. 

The seepage rate data from two lakes also were comparable 

between the flux chamber and two concurrently deployed 

55-gallon drum seepage meters. The minimum, maximum, 

and average flow rates for the ultrasonic-flow meter at Long 

Lake were 1.55, 39.47 and 18.06 cm/day compared to 1.24, 

26.0, and 11.20 cm/day for the 55-gallon drum seepage meter. 

The minimum, maximum, and average flow rates for the 

ultrasonic-flow meter at Square Lake were 5.90, 18.29, and 

13.06 cm/day compared to 10.94, 16.80, and 11.16 cm/day for 

the 55-gallon drum seepage meter. The flux-chamber samples 

yielded THg concentrations of 0.47 and 0.53 nanograms per 

liter (ng/L). The lake sample was 0.27 ng/L.

The flux chamber was successfully used to (1) measure 

ground-water seepage rates and (2) collect water samples for 

analysis of mercury concentrations at the nanogram per liter 

level. Several modifications could improve the general performance and the accuracy of the flux chamber, most notably: 

increasing the size of the flux chamber; manually setting the 

seepage to zero and resetting the ultrasonic-flow meter to 

evaluate meter drift; routing the outflow from the ultrasonicflow meter through a multiparameter (dissolved oxygen, 

pH, specific conductivity, and water temperature) meter; and 

soaking or copiously rinsing the flux chamber and the sample 

tubing in a 10 percent hydrochloric acid solution in the cleaning procedure. 

References

Alexander, S., Setterholm, D., Tipping, R., and Meyer, G., 

2001, The influence of ground water on the quality of lakes 

in the Carnelian-Marine watershed district: Minnesota Geological Survey, CD ROM, 33 p.

Benoit, J.M., Gilmour, C.C., Mason, R.P., and Heyes, A., 

1999, Sulfide controls on mercury speciation and bioavailability to methylating bacteria in sediment pore waters: 

Environmental Science and Technology, v. 33, p. 951-957.

Bloom, N.S., 1992, On the chemical form of mercury in edible 

fish and marine invertebrate tissue: Canadian Journal of 

Fisheries and Aquatic Science, v. 49, p. 1010-1017.

Bodaly, R.A., Rudd, J.W.M., Fudge, R.J.P., and Kelly, C.A., 

1993, Mercury concentrations in fish related to size of 

remote Canadian Shield lakes: Canadian Journal of Fisheries and Aquatic Sciences, v. 50, p. 980-987.

References 13
14 Development of a benthic-flux chamber for measurement of ground-water seepage and water sampling for mercury

Branfireun, B.A., Roulet, N.T., Kelly, C.A., and Rudd, J.W.M., 

1999, In situ sulphate stimulation of mercury methylation 

in a boreal peatland: Toward a link between acid rain and 

methylmercury contamination in remote environments: 

Global Biogeochemical Cycles, v. 13, no. 3, p. 743-750.

DeWild, J.F., Olson, M.L., and Olund, S.D., 2001, Determination of methylmercury by aqueous phase ethylation, followed by gas chromatographic separation with cold vapor 

atomic fluorescence detection: U.S. Geological Survey 

Open-File Report 01-445, 14 p. 

Gill, G.A., Bloom, N.S., Cappellino, S., Driscoll, C.T., Dobbs, 

C., McShea, L., Mason, R., and Rudd, J.W.M., 1999, Sediment-water fluxes of mercury in Lavaca Bay, Texas: Environmental Science and Technology, v. 33, no. 5, p. 663-669.

Gilmour, C.C., and Henry, E.A., 1991, Mercury methylation in 

aquatic systems affected by acid deposition: Environmental 

Pollution, v. 71, p. 131-169.

Gilmour, C.C., Henry, E.A., and Mitchell, R., 1992, Sulfate 

stimulation of mercury methylation in freshwater sediments: 

Environmental Science and Technology, v. 26, no. 11, p. 

2281-2287.

Jay, J.A., Morel, F.M.M., and Hemond, H.F., 2000, Mercury 

speciation in the presence of polysulfides: Environmental 

Science and Technology, v. 34, no. 11, p. 2196-2200.

Kerry, A., Welbourn, P.M., Prucha, B., and Mierle, G., 1991, 

Mercury methylation by sulphate-reducing bacteria from 

sediments of an acid stressed lake: Water, Air, and Soil Pollution, v. 56, p. 565-575.

Lee, D.R., 1977. A device for measuring seepage flux in lakes 

and estuaries: Limnology and Oceanography, v. 22, no. 1, 

p. 140-147.

Libelo, E.L., and MacIntyre, W.G., 1994, Effects of surfacewater movement on seepage-meter measurements of flow 

through the sediment-water interface: Applied Hydrogeology, v. 2, no. 4, p. 49-54.

Olson, M.L., and DeWild, J.F., 1999, Techniques for the 

collection and species-specific analysis of low levels of 

mercury in water, sediments, and biota, in Morganwalp, 

D.W., and Buxton, H.T., eds., U.S. Geological Survey 

Toxic Substances Hydrology Program—Proceedings of the 

technical meeting, Charleston, North Carolina, March 8–12, 

1999, volume 2 of 3—Contamination of hydrologic systems 

and related ecosystems: U.S. Geological Survey WaterResources Investigations Report 99-4018B, p. 191–200.

Pak, K.R., and Bartha, R., 1998, Mercury methylation and 

demethylation in anoxic lake sediments and by strictly 

anaerobic bacteria: Applied and Environmental Microbiology, v. 64, no. 3, p. 1013-1017.

Paquette, K.E., and Helz, G.R., 1997, Inorganic speciation of 

mercury in sulfidic waters—The importance of zero-valent 

sulfur: Environmental Science and Technology, v. 31, no. 7, 

p. 2148-2153.

Paulsen, R.J., Smith, C.F., O’Rourke, D., and Wong, T., 2001, 

Development and evaluation of an ultrasonic ground water 

seepage meter: Ground Water, v. 39, no. 6, p. 904-911.

Rosenberry, D.O., and Morin, R.H., 2004, Use of an electromagnetic seepage meter to investigate temporal variability 

in lake seepage: Ground Water, v. 42, no. 1, p. 68-77.

Shum, K.T., 1992, Wave-induced advective transport below 

a rippled water-sediment interface: Journal of Geophysical 

Research, v. 97, no. C1, p. 789-808.

Taniguchi, M., and Fukuo, Y., 1996, An effect of seiche on 

groundwater seepage rate into Lake Biwa, Japan: Water 

Resources Research, v. 32, no. 2, p. 333-338.

U.S. Geological Survey, 1998, National field manual for the 

collection of water-quality data: U.S. Geological Survey 

Techniques of Water-Resources Investigations, book 9, 

chapters A1-A9, variously paged, http://water.usgs.gov/

owq/FieldManual.
Menheer—Development of a Benthic-Flux Chamber for Measurement of Ground-Water Seepage and Water Sampling for Mercury Analysis at the SedimentWater Interface—Scientific Investigation Report 2004-5298

Printed on recycled paper