U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2016–3051

July 2016

Figure 1. Location of the Brownlee, 

Oxbow, and Hells Canyon Dams study 

area along the Snake River at the Idaho 

and Oregon border. These three dams and 

associated reservoirs comprise the Hells 

Canyon Complex (HCC).

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Boise River

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Printed on recycled paper

Mercury Cycling in the Hells Canyon Complex of the 

Snake River, Idaho and Oregon

Introduction

The Hells Canyon Complex (HCC) is a hydroelectric 

project built and operated by the Idaho Power Company (IPC) 

that consists of three dams on the Snake River along the Oregon 

and Idaho border (fig. 1). The dams have resulted in the creation 

of Brownlee, Oxbow, and Hells Canyon Reservoirs, which 

have a combined storage capacity of more than 1.5 million 

acre-feet and span about 90 miles of the Snake River. The 

Snake River upstream of and through the HCC historically 

has been impaired by water-quality issues related to excessive 

contributions of nutrients, algae, sediment, and other pollutants. 

In addition, historical data collected since the 1960s from the 

Snake River and tributaries near the HCC have documented 

high concentrations of mercury in fish tissue and sediment 

(Harris and Beals, 2013). Data collected from more recent 

investigations within the HCC continue to indicate elevated 

concentrations of mercury and methylmercury in the water 

column, bottom sediments, and biota (Clark and Maret, 1998; 

Essig, 2010; Fosness and others, 2013). As a result, Brownlee 

and Hells Canyon Reservoirs are listed as impaired for mercury 

by the State of Idaho, and the Snake River from the Oregon and 

Idaho border through the HCC downstream to the Oregon and 

Washington border is listed as impaired for mercury by the 

State of Oregon.
Water samples are collected from discrete depths at many locations in Hells Canyon Complex reservoirs to 

evaluate spatial and temporal variability in concentrations of mercury, methylmercury, and other constituents.

Recently, the need to evaluate a range of reservoir operational scenarios has 

prompted interest in developing a better understanding of mercury dynamics within 

the HCC. Altering how water is released from Brownlee Reservoir has the potential to 

change the thermal regime of the Snake River downstream of the HCC. The presence 

of species listed under the Endangered Species Act, such as bull trout (Salvelinus 

confluentus) and fall Chinook salmon (Oncorhynchus tshawytscha), has made 

evaluating downstream thermal conditions a priority. Because the mercury dynamics 

in the HCC are not well understood, however, it is not clear how altering releases 

from Brownlee Reservoir would affect mercury cycling within the HCC, and whether 

changes in operations would increase methylmercury exposure to downstream species. 

To address this and other issues related to mercury in the HCC, the U.S. Geological 

Survey (USGS), in collaboration with IPC and the Idaho Department of Environmental 

Quality (IDEQ), started an investigation in 2014 to evaluate key processes controlling 

mercury transport, cycling, and bioaccumulation in the Hells Canyon reach of the Snake 

River. Specific project objectives include: 

• Determination of spatial variability and predominance of the specific forms of 

mercury in water, sediment, and biota; 

• Examination of the factors controlling the spatial and temporal variability 

of mercury; and 

• Determination of the mechanisms controlling mercury uptake, food-web 

transfer, and bioaccumulation.

This fact sheet describes current knowledge regarding mercury cycling in the 

HCC, and the interdisciplinary project investigating the processes that lead to increased 

mercury bioaccumulation in the HCC ecosystem.

Mercury Cycling in the Environment

Mercury (Hg) is a global pollutant that ultimately makes its way into every aquatic 

ecosystem through the hydrologic cycle. It has been well known as an environmental 

pollutant for several decades with the potential to have serious effects on human 

health (Wentz and others, 2014). Although mercury occurs naturally, industrialization 

has produced high levels of mercury in the environment and likely has resulted in 

high concentrations of mercury in fish on a global scale. Releases of mercury to the 

atmosphere from sources, such as 

burning of coal, artisanal mining, and 

incinerators, have resulted in long 

distance atmospheric transport and 

subsequent deposition and hydrologic 

transport through watersheds. Although 

atmospheric deposition of inorganic 

mercury probably contributes the 

majority of mercury to most aquatic 

systems, geologic and point-source 

discharges also may contribute mercury 

locally to streams, lakes, and other 

water bodies. 

Atmospheric deposition provides 

mercury to the aquatic environment 

primarily as inorganic mercury Hg(II). 

Once in a water body, mercury can 

follow various pathways and ultimately is 

removed by burial, loss to the atmosphere, 

or outflow (fig. 2). Inorganic mercury also 

can undergo rapid transformations, driven 

by bacteria, where it is converted to 

methylmercury (CH3Hg+ or MeHg). This 

step, referred to as inorganic mercury 

methylation, is ecologically important 

because: 

• Methylmercury is much more 

toxic than inorganic mercury; 

• Methylmercury easily moves into 

lower levels of the food web; and 

• Methylmercury efficiently 

biomagnifies to a high level 

through food webs. 

The exact mechanism(s) by which 

mercury is methylated, and subsequently 

enters the food chain, are still not 

completely understood, and probably 

vary among ecosystems. It is understood 

that the reaction can be carried out by 

microbes that thrive where oxygen 

levels are depleted, including sulfate 

(SO4

-2) and iron-reducing bacteria. In 

the aquatic environment, this reaction 

often occurs at the sediment-water 

interface, in low-oxygen zones of the 

water column, and in areas where organic 

matter is decomposed. Demethylation, 

the process by which methylmercury is 

converted back to inorganic mercury or 

to elemental mercury (HGo

), occurs in 

the water column and in sediment. In the 

water column, demethylation is driven 

primarily by sunlight, and the resulting 

inorganic or elemental mercury can be 

volatilized from a water body back to the 

atmosphere. Various bacteria in sediment 

also can degrade methylmercury. 
Figure 2. Mercury cycling pathways in aquatic environments are very complex. The various 

forms of mercury can be converted from one to the next; most important is the conversion of 

inorganic mercury to methylmercury (MeHg), the most toxic form. Ultimately, mercury ends up in 

the sediments, fish, and wildlife, or returns back to the atmosphere by volatilization.

Mercury Cycling in Aquatic Systems

Inflow/Runoff

Outflow

Settling/Resusp

Diffusion

Wet and dry 

Deposition

MeHg

Hg(0)

Hg(II)

Volatilization

Hg(II) MeHg

Bioaccumulation

Burial

Burial

Settling/Resusp 

Diffusion

How methylmercury enters the base of the food chain likely involves the direct 

adsorption of methylmercury from the water column by phytoplankton, and (or) 

consumption of methylmercury containing particles (including bacteria, decomposing 

organic matter, and living phytoplankton) by the next higher level in the food chain 

(likely zooplankton). Once in the food chain, methylmercury bioaccumulates in 

organisms (including humans) because it is taken up more rapidly than it can be 

eliminated. Methylmercury concentrations also increase two- to five-fold across trophic 

levels—a process called biomagnification. The combined effects of bioaccumulation 

and biomagnification are generally compounded the longer an organism lives. In aquatic 

systems, large, long-lived, predatory game fish and wildlife typically have the highest 

mercury levels. Although fish consumption has well-established health benefits, it is also 

the primary exposure pathway for methylmercury; health concerns arise when elevated 

concentrations of mercury are detected in fish targeted for commercial, subsistence, or 

recreational consumption.

Mercury in the Hells Canyon Complex

The water-quality conditions in the Snake River, together with the presence of the 

HCC dams, may be creating an environment that is efficient at converting inorganic 

mercury to methylmercury. Based on recent data collected from Hells Canyon Reservoirs 

(Fosness and others, 2013), methylmercury concentrations and the percentage of mercury 

in the form of methylmercury in the bottom sediments and deep parts of the water column 

are substantially elevated compared to other natural waters and reservoirs in Idaho, 

Oregon, and Washington. In addition to water and sediment, fish-tissue data indicate that 

methylmercury is elevated in the HCC food web. Samples of similar-sized smallmouth bass 

collected by the IPC during 2013 (fig. 3) 

indicate that starting in the Snake River 

near the inflow of Brownlee Reservoir 

(river mile [RM] 348), methylmercury 

concentrations in fish tissue generally 

increase downstream through the HCC, 

followed by a decrease downstream 

of Hells Canyon Dam toward the 

confluence of the Snake and Salmon 

Rivers (RM 188). Of 198 similar-sized 

smallmouth bass collected between the 

inflow to Brownlee Reservoir and the 

Salmon River confluence, 31 percent 

exceeded the State of Idaho human 

health fish-tissue criterion for mercury 

of 0.3 milligram per kilogram (mg/kg; 

wet weight), and 96 percent exceeded the 

more stringent State of Oregon criterion 

of 

0.04 mg/kg (wet weight).

 Although much of the mercury 

in the environment originates from 

anthropogenic sources, the accumulation 

in freshwater aquatic ecosystems is not 

a simple function of local or regional 

mercury inputs. Studies show that 

even sites with similar mercury inputs 

can produce fish with methylmercury 

concentrations ranging more than 

an order of magnitude (Scudder and 

others, 2009; Wentz and others, 2013). 

However, based on previous mercury 

research, there are characteristics 

within the HCC that are consistent with 

increased susceptibility to methylmercury 

accumulation. The Snake River changes 

from a riverine to a lacustrine, or laketype environment in the upstream 

reach of the HCC. As it transitions 

to a lacustrine system, it delivers 

abundant nutrients, organic material, 

and sediments, much of which settles 

to the bottom in the upstream transition 

zone. As with many large water bodies, 

the reservoirs in the HCC undergo 

summertime thermal stratification. As air 

temperatures rise each spring, heat from 

the sun warms the inflowing river water 

and the surface layer in the reservoirs. 

The warm water, direct sunlight, and 

abundant nutrients, in the upstream 

riverine environment and the reservoirs, 

provide an ideal environment for 

phytoplankton production. 
TAC16-1072_fig 03

Weiser River

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Mercury concentration in fish tissue, in milligrams per killogram wet weight

River mile (RM) from mouth of the Snake River

Oregon criterion for mercury in tissue

Idaho criterion for

mercury in tissue

Brownlee

Reservoir

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Brownlee

Dam

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RM 188

RM 215

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Figure 3. Longitudinal distribution of mercury concentrations in tissue samples 

from individual smallmouth bass (Micropterus dolomieu), ranging between 250 and 

300 millimeters in length, collected along the Snake River from the inflow of Brownlee 

Reservoir (RM 348) to upstream of the confluence with Salmon River (RM 188). Data 

provided by Jim Chandler, Idaho Power Company (2013).

Zooplankton (far left) and fishtissue (left) samples are collected 

to evaluate mercury uptake and 

food web transfer in the 

Hells Canyon Complex.

Because warm water near the surface is less dense than the colder 

underlying water, thermal stratification results in a warmer layer of water 

(epilimnion) that floats over a colder, denser underlying layer of water 

(hypolimnion). As algae and organic material delivered by the inflowing 

water and produced in the epilimnion sink through the water column, 

they are decomposed by aerobic bacteria, which accelerate the depletion 

of dissolved oxygen in the water column (fig. 4). 
Riverine inputs oforganic 

material, nutrients, and sulfate

Organic 

carbon

Elevated 

MeHg

Hg(II)

Water 

column 

mixing

Increased 

methylation

Increased primary production

Mn

Decomposition

and settling

Brownlee Dam

Fe S

Reflux from 

sediments

Decomposition

and burial

2

2 .5

2 .5

3

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5

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10

1 1

River mile 290

1,800

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2,050

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Dissolved oxygen (mg /L ): 0. 511 .522 .533 .544 .555 .566 .577 .588 .599 .5 10 11 1211.5 10.5

April 2015

Elevation, in feet above mean sea level

22 .5 3 .54 .5 5 5 .5

6

6

6 .5

7

8 .5

8 .5

290 295 300 305 310 315 320 325 330

 (mg/L): 0.511. 522.533.544.555.566.577.588.599.5 10

September 2015

Dissolved oxygen 10.5 11 1211.5

River mile

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Elevation, in feet above mean sea level

A.

B.

Figure 4. Conceptual model of organic enrichment, decomposition, and mercury cycling in 

Brownlee Reservoir. 

Surficial and core sediment samples are collected 

from the bottom of Hells Canyon Complex reservoirs to 

evaluate potential contributions of methylmercury and 

other constituents from sediment to the hypolimnion.

As oxygen is consumed, conditions in the hypolimnion and in the deeper layers 

of the upstream riverine and transition zones can become anoxic (without oxygen) 

and anaerobic bacteria, which include those that convert inorganic mercury to 

methylmercury, begin to decompose organic material. Seasonal water column sampling 

in the HCC indicates that methylmercury concentrations increase in the hypolimnion 

during the summer and autumn each year as Brownlee and Hells Canyon Reservoirs 

thermally stratify and oxygen is consumed at depth. In Brownlee Reservoir, oxygen 

consumption and anoxic conditions in the hypolimnion begin to occur in the spring near 

river mile 310 where the river transitions to a lacustrine environment (fig. 5A). By late 

summer Brownlee Reservoir is typically anoxic throughout the hypolimnion (fig. 5B). During 

late autumn and early winter, thermal stratification of the water column in the reservoirs 

breaks down, causing methylmercury in the hypolimnion to mix with water from the 

rest of the water column where the methylmercury can be exported downstream. The 

annual cycle begins again in the spring as Brownlee and Hells Canyon Reservoirs begin 

to restratify.

Figure 5. Oxygen consumption and anoxic conditions in Brownlee Reservoir typically start in the spring near river mile 310 where the Snake River 

delivers abundant nutrients and organic matter to the reservoir (A). By late summer, the reservoir is typically completely stratified and devoid of 

oxygen throughout the hypolimnion (B).
ISSN 2327-6932 (online)

http://dx.doi.org/10.3133/fs20163051

Authors: 

Gregory M. Clark1, Jesse Naymik2, David P. Krabbenhoft1, 

Collin A. Eagles-Smith1, George R. Aiken1, Mark C. MarvinDiPasquale1

, Reed C. Harris3, and Ralph Myers2

1

U.S. Geological Survey.

2

Idaho Power Company.

3

 Reed Harris Environmental Ltd.

All photographs provided by U.S. Geological Survey.

For more information:

Director, Idaho Water Science Center, 

U.S. Geological Survey

230 Collins Road, Boise, Idaho 83702

http://id.water.usgs.gov/

Publishing support provided by the U.S. Geological Survey, 

Science Publishing Network, Tacoma Publishing Service Center

Much of the foundational work on mercury in freshwater 

aquatic environments has focused on natural lakes, and 

accordingly, mercury contamination in streams and reservoirs 

is an important area of research. The Snake River in the HCC 

provides an ideal opportunity to evaluate potential important 

drivers of mercury accumulation in rivers and established 

reservoir ecosystems, 

for instance: 

• How does the water quality of the inflowing Snake River 

affect the mercury dynamics in the HCC? 

• How does the seasonal cycle of reservoir stratification 

and destratification influence the mass transport of 

mercury into and out of the HCC? 

• Are reservoir bottom sediments a source of stored 

inorganic mercury that can be methylated and transported 

to the water column? 

• Where in the water column, and during what time of the 

year, is methylmercury entering the food web? 

• Do differences in food web complexity result in greater 

mercury bioaccumulation in the reservoirs of the HCC 

compared to upstream and downstream of the HCC? 

The USGS, in collaboration with IPC and IDEQ, initiated 

its investigation of mercury in the HCC in the spring of 2014. 

The study plan uses both routine and intensive assessments 

to evaluate temporal and spatial patterns in the production, 

transport, and bioaccumulation of mercury and methylmercury 

throughout the HCC. The routine assessments include:

• Regular water-column profiles of physical characteristics 

related to stratification; 

• Chemical sampling from discrete parts of the water 

column in Brownlee and Hells Canyon Reservoirs; 

• Reservoir inflow and outflow sampling to evaluate the 

mercury mass balance; and 

• Zooplankton and fish sampling to evaluate temporal 

patterns in mercury uptake and food web transfer. 

Results from the routine assessments will provide a 

basic understanding of the spatial and temporal occurrence 

of the forms of mercury, and will explain how those forms 

are transported into and through the HCC. Biannual intensive 

assessments are designed to provide more complete spatial 

coverage and in-depth understanding of factors related to 

methylation rates in sediment and the water column; photodegradation of methylmercury and volatilization from the 

water column; the role of organic matter and water chemistry 

in mercury methylation; and biomagnification through different 

compartments of the food web. Although the study will likely 

take between 5 and 8 years to complete, the exact timeline 

may vary because the study will use an adaptive science 

strategy providing opportunities to modify the approach 

based on the results. The results from this study will provide 

resource managers an improved scientific understanding of the 

hydrologic, geochemical, and ecological processes controlling 

mercury cycling in the HCC. In addition, a long-term goal is 

to develop a predictive model for methylmercury, which can 

be used to evaluate the effects of potential future operational 

and water-quality changes in the Snake River that could affect 

the aquatic resources within the HCC and downstream. The 

study results also should be transferrable to other large existing 

reservoirs and aquatic ecosystems where mercury problems may 

exist, or may occur in the future. 

References Cited

Clark, G.M., and Maret, T.R., 1998, Organochlorine compounds 

and trace elements in fish tissue and bed sediments in the 

Lower Snake River Basin, Idaho and Oregon: U.S. Geological 

Survey Water-Resources Investigations Report 98-4103, 35 p.

Essig, D.A., 2010, Arsenic, mercury, and selenium in fish tissue 

and water from Idaho’s major rivers—A statewide assessment: 

Boise, Idaho Department of Environmental Quality, 64 p. 

Fosness, R.L, Naymik, Jesse, Hopkins, C.B., and DeWild, J.F., 

2013, Water column and bed-sediment core samples collected 

from Brownlee Reservoir near Oxbow, Oregon, 2012: U.S. 

Geological Survey Data Series 809, 44 p.

Harris, R.C., and Beals, C., 2013, Hells Canyon Complex 

mercury data assessment: Draft Technical Memorandum 

prepared for Idaho Power Company by Reed Harris 

Environmental Ltd., 38 p.

Scudder, B.C., Chasar, L.C., Wentz, D.A., Bauch, N.J., Brigham, 

M.E., Moran, P.W., and Krabbenhoft, D.P., 2009, Mercury 

in fish, bed sediment, and water from streams across the 

United States, 1998–2005: U.S. Geological Survey Scientific 

Investigations Report 2009–5109, 74 p.

Wentz, D.A., Brigham, M.E., Chasar, L.C., Lutz, M.A., and 

Krabbenhoft, D.P., 2014, Mercury in the nation’s streams—

Levels, trends, and implications: U.S. Geological Survey 

Circular 1395, 90 p.