Procedures for Collecting and Processing Streambed 

Sediment and Pore Water for Analysis of Mercury as 

Part of the National Water-Quality Assessment Program

Open-File Report 2008–1279

National Water-Quality Assessment Program

U.S. Department of the Interior

U.S. Geological Survey
Cover: Sampling pore water, St Marys River, Florida (upper left); filtered pore water 

sample, Little Wekiva River, Florida (upper right); collecting surface streambed 

sediment, Oak Creek, Wisconsin (lower right); 2-cm surface streambed sediment 

sample, Beaverton Creek, Oregon (lower left); measuring in situ streambed sediment 

pH, Little Wekiva River, Florida (center). (All photographs by the authors.)
Procedures for Collecting and Processing 

Streambed Sediment and Pore Water for 

Analysis of Mercury as Part of the National 

Water-Quality Assessment Program

By Michelle A. Lutz, Mark E. Brigham, and Mark Marvin-DiPasquale

National Water-Quality Assessment Program

Open-File Report 2008–1279

U.S. Department of the Interior

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

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2008

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Suggested citation:

Lutz, M.A., Brigham, M.E., and Marvin-DiPasquale, M., 2008, Procedures for collecting and processing streambed 

sediment and pore water for analysis of mercury as part of the National Water-Quality Assessment Program: U.S. 

Geological Survey Open-File Report 2008–1279, 68 p.
iii

Foreword

The U.S. Geological Survey (USGS) is committed to providing the Nation with credible scientific 

information that helps to enhance and protect the overall quality of life and that facilitates 

effective management of water, biological, energy, and mineral resources (http://www.usgs.

gov/). Information on the Nation's water resources is critical to ensuring long-term availability 

of water that is safe for drinking and recreation and is suitable for industry, irrigation, and fish 

and wildlife. Population growth and increasing demands for water make the availability of that 

water, now measured in terms of quantity and quality, even more essential to the long-term 

sustainability of our communities and ecosystems.

The USGS implemented the National Water-Quality Assessment (NAWQA) Program in 1991 to 

support national, regional, State, and local information needs and decisions related to waterquality management and policy (http://water.usgs.gov/nawqa). The NAWQA Program is 

designed to answer: What is the condition of our Nation's streams and ground water? How are 

conditions changing over time? How do natural features and human activities affect the quality 

of streams and ground water, and where are those effects most pronounced? By combining 

information on water chemistry, physical characteristics, stream habitat, and aquatic life, the 

NAWQA Program aims to provide science-based insights for current and emerging water issues 

and priorities. From 1991-2001, the NAWQA Program completed interdisciplinary assessments 

and established a baseline understanding of water-quality conditions in 51 of the Nation’s river 

basins and aquifers, referred to as Study Units (http://water.usgs.gov/nawqa/studyu.html). 

Multiple national and regional assessments are ongoing in the second decade (2001—2012) 

of the NAWQA Program as 42 of the 51 Study Units are reassessed. These assessments 

extend the findings in the Study Units by determining status and trends at sites that have been 

consistently monitored for more than a decade, and filling critical gaps in characterizing the 

quality of surface water and ground water. For example, increased emphasis has been placed on 

assessing the quality of source water and finished water associated with many of the Nation's 

largest community water systems. In addition, national syntheses of information on pesticides, 

volatile organic compounds (VOCs), nutrients, selected trace elements, and aquatic ecology are 

continuing. 

The USGS aims to disseminate credible, timely, and relevant science information to address 

practical and effective water-resource management and strategies that protect and restore 

water quality. We hope this NAWQA publication will provide you with insights and information 

to meet your needs, and will foster increased citizen awareness and involvement in the 

protection and restoration of our Nation's waters. 

The USGS recognizes that a national assessment by a single program cannot address all 

water-resource issues of interest. External coordination at all levels is critical for cost-effective 

management, regulation, and conservation of our Nation's water resources. The NAWQA 

Program, therefore, depends on advice and information from other agencies–Federal, State, 

regional, interstate, Tribal, and local–as well as nongovernmental organizations, industry, 

academia, and other stakeholder groups. Your assistance and suggestions are greatly 

appreciated.

Matthew C. Larsen

Acting Associate Director for Water
iv

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v

Contents

Foreword ........................................................................................................................................................iii

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

Background.....................................................................................................................................................1

Studies of Hg in Stream Ecosystems.................................................................................................1

General Guidelines ..............................................................................................................................2

Reconnaissance Studies..............................................................................................................................6

Sampling Strategy.................................................................................................................................6

Sample Collection.................................................................................................................................6

Sample Processing...............................................................................................................................6

Detailed Studies.............................................................................................................................................6

Sampling Strategy.................................................................................................................................6

Reach Characterization ..............................................................................................................7

Establishing a Reach..........................................................................................................7

Transect Sampling..............................................................................................................7

Spatial Biogeochemical Sampling............................................................................................9

Temporal Biogeochemical Sampling......................................................................................11

Extrapolation of Data to the Reach Scale..............................................................................11

Sample Collection...............................................................................................................................12

Bed Sediment .............................................................................................................................12

Pore Water..................................................................................................................................12

Sample Processing.............................................................................................................................14

Bed Sediment .............................................................................................................................14

Reach Characterization ...................................................................................................14

Spatial and Temporal Biogeochemical Sampling........................................................14

Pore Water..................................................................................................................................14

Field Measurements....................................................................................................................................14

Stream Water ......................................................................................................................................15

Bed Sediment ......................................................................................................................................15

Oxidation-Reduction Potential.................................................................................................15

pH and Temperature..................................................................................................................16

Pore Water...........................................................................................................................................16

Sulfide..........................................................................................................................................16

ORP ..............................................................................................................................................16

pH.................................................................................................................................................17

Piezometric Head ...............................................................................................................................17

References Cited..........................................................................................................................................17
vi

Appendix 1. Method Summary Sheets ..................................................................................................19

Appendix 2. Primary and Ancillary Constituents Analyzed for in Bed Sediment

and Pore Water Collected for the National Water-Quality Assessment

(NAWQA) Program Detailed Mercury Studies...............................................................44

Appendix 3. Field Forms ...........................................................................................................................47

Appendix 4. Sample Labels .....................................................................................................................53

Appendix 5. Equipment Required for Bed-Sediment and Pore-Water Sampling in

Association with the National Water-Quality Assessment (NAWQA) Program

Reconnaissance and Detailed Mercury Studies...........................................................55

Appendix 6. Laboratory Contact Information for U.S. Geological Survey Laboratories

Performing Analyses for the National Water-Quality Assessment (NAWQA)

Program Reconnaissance and Detailed Mercury Studies ..........................................61

Appendix 7. Shipping Forms for Reconnaissance and Detailed Studies.........................................62

Contents—Continued

Figures

Figure 1. Map showing locations of sites sampled for National Water-Quality

Assessment (NAWQA) Program reconnaissance mercury studies .................. 3

Figure 2. Map showing locations of sites sampled for National Water-Quality

Assessment (NAWQA) Program detailed mercury studies ........................... 5

Figure 3. Diagram of simplified wadeable reach, with geomorphic channel units noted...... 8

Figure 4. Diagram of simplified reach and point-sampling locations for transect

sampling performed in association with reach characterization ..................... 10

Figure 5. Photograph showing surficial-sediment sample collected using a core 

(2 centimeters deep and 8 centimeters in diameter) and a stiff plastic sheet ...... 13

Figure 6. Photograph showing pore-water sampling equipment and compositing bottle ... 13

Figure 7. Photograph showing surficial-sediment core being deposited into the

methylmercury production- and degradation-potential-rates sampling 

apparatus .................................................................................... 15

Tables

Table 1. Overview of streambed-sediment and pore-water sampling efforts

associated with National Water-Quality Assessment (NAWQA) Program

reconnaissance and detailed mercury studies .......................................... 4

Table 2. Bed-substrate categories for classifying streambed sediment based on size

and organic content ........................................................................ 9
vii

Conversion Factors and Datum

Conversion Factors

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

centimeter (cm) 0.3937 inch (in.)

centimeter (cm) 0.01 meter (m)

millimeter (mm) 0.001 meter (m)

micrometer (μm) 10-6 meter (m)

meter (m) 3.281 foot (ft) 

Flow rate

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

Area

square meter (m2) 10.76 square foot (ft2) 

Volume

cubic centimeter (cm3) 0.06102 cubic inch (in3) 

milliliter (mL) 0.03382 ounce, fluid (fl. oz)

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

liter (L) 0.2642 gallon (gal)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

picogram (g) 10-12 gram (g)

nanogram 10-9 gram (g)

microgram (μg) 10-6 gram (g)

milligram (mg) 0.001 gram (g)

Density

gram per cubic centimeter (g/cm3) 62.4220 pound per cubic foot (lb/ft3) 

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

°F=(1.8×°C)+32

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

25°C).

Concentrations of chemical constituents in water are given in micrograms per liter (μg/L), 

micromoles per liter (μmol/L), milligrams per liter (mg/L), or nanograms per liter (ng/L).

Concentrations of chemical constituents in streambed sediment are given in micromoles per 

gram dry weight (μmol/g dry wt), milligrams per gram dry weight (mg/g dry wt), or nanograms 

per gram dry weight (ng/g dry wt).

Datum

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

Abbreviated Streambed-Sediment- and Water-Quality Units

Abbreviations Definition

°C degree Celsius

μg/L microgram per liter 

μm micrometer

μmol/g dry wt micromole per gram, dry weight

μmol/L micromole per liter

μS/cm at 25°C microsiemen per centimeter at 25 degrees Celsius

% percent

% dry wt percent, dry weight

% wet wt percent, wet weight

1/d per day 

cm centimeter

cm3 cubic centimeter

ft3/s cubic feet per second

g/cm3 wet sed gram per cubic centimeter, wet sediment

in. inch

L liter

L/(mg DOC*m) liter per (milligram of dissolved organic carbon * meter)

M molar

m meter

m2 square meter

mg/g dry wt milligram per gram, dry weight

mg/L milligram per liter

mL milliliter

mL PW/cm3 wet sed milliliter of pore water per cubic centimeter, wet sediment

mm millimeter

mV millivolt

N normal

ng nanogram

ng/g dry wt nanogram per gram, dry weight

ng/L nanogram per liter

nm nanometer

nmol/g dry wt/d nanomole per gram, dry weight, per day

pg/g dry wt/d picogram per gram, dry weight, per day

units/cm units per centimeter

V volt
ix

Abbreviations and Acronyms

Abbreviation and Acronym Definition

AVS Acid-volatile sulfide C Carbon

DO Dissolved oxygen

DOC Dissolved organic carbon

GCU Geomorphic channel unit

GLM Generalized linear model

GPS Global Positioning System

HCl Hydrochloric acid

Hg Mercury

Hg(II)R Reactive mercury

LEW Left edge of water

Log logarithm

LOI Loss on ignition

MCW Mean wetted channel width

MDP Methylmercury degradation potential

MeHg Methylmercury

MPP Methylmercury production potential N Nitrogen

NAD 83 North American Datum of 1983

NAWQA National Water-Quality Assessment Program

NWIS Nation Water Information System

ORP Oxidation-reduction potential

PVC Polyvinyl chloride ® Registered trademark

REW Right edge of water

SAOB Sulfide antioxidant buffer

STAID Station-identification number

SW Stream water T Temperature

THg Total mercury

USGS U.S. Geological Survey

WAAS Wide Area Augmentation System

WMRL Wisconsin Mercury Research Laboratory
x

Acknowledgments

Technical Reviewers

Brent R. Topping, Hydrologist, U.S. Geological Survey, Menlo Park, Calif.

Charles N. Alpers, Research Chemist, U.S. Geological Survey, Sacramento, Calif.

Technical Support

David P. Krabbenhoft, Research Hydrologist, U.S. Geological Survey, Middleton, Wis.

George R. Aiken, Hydrologist, U.S. Geological Survey, Boulder, Colo.

John F. DeWild, Hydrologic Technician, U.S. Geological Survey, Middleton, Wis.

Margo D. Corum, U.S. Geological Survey, Reston, Va.

Mark L. Olson, Biologist, U.S. Geological Survey, Middleton, Wis.

Shane D. Olund, Chemist, Interpoll Laboratories, Incorporated, Circle Pines, Minn.

William H. Orem, U.S. Geological Survey, Reston, Va.

Editorial and Graphics

Bonnie Stich Fink, Editor, U.S. Geological Survey, Louisville, Ky.

Jennifer L. Bruce, Geographer, U.S. Geological Survey, Middleton, Wis.

Approving Official

Charles A. Peters, Wisconsin Water Science Center Director, U.S. Geological Survey, 

Middleton, Wis.
Procedures for Collecting and Processing Streambed 

Sediment and Pore Water for Analysis of Mercury as Part 

of the National Water-Quality Assessment Program

By Michelle A. Lutz, Mark E. Brigham, and Mark Marvin-DiPasquale

Abstract 

Mercury (Hg) contamination is an issue of national 

concern, affecting both wildlife and human health. The 

U.S. Geological Survey (USGS) National Water-Quality 

Assessment (NAWQA) Program, in association with the 

USGS Toxic Substances Hydrology Program and the USGS 

National Research Program, has initiated two levels of studies 

to investigate Hg contamination of the Nation’s streams: 

reconnaissance and detailed studies. Reconnaissance studies 

entailed one-time sampling events at 266 stream sites across 

the Nation. Detailed studies entailed intensive spatial and 

temporal sampling of a small number of streams across the 

Nation in an effort to develop a more complete, process-level 

understanding of benthic Hg geochemistry and the underlying 

factors controlling it. This report summarizes the sampling 

methods used for the collection and processing of streambed 

sediment and pore water in association with both of these 

study levels. Bed-sediment characteristics, such as organic 

content and grain size, strongly influence Hg geochemistry; 

detailed characterization of these constituents within a 

stream reach will allow for the extrapolation of related Hg 

biogeochemical constituents to the reach scale. 

Background

As of 2006, 48 States had issued fish-consumption 

warnings owing to mercury (Hg) contamination (U.S. 

Environmental Protection Agency, 2007). Hg toxicity 

in humans causes a variety of symptoms with primary 

damage affecting the central nervous system, brain, kidneys 

(Agency for Toxic Substances and Disease Registry, 1999), 

and cardiovascular system (Virtanen and others, 2005). 

Growth, reproductive, and behavioral effects have also been 

documented in wildlife (Hammerschmidt and others, 2002; 

Drevnick and Sandheinrich, 2003; Evers, 2005). 

Current (2008) Hg levels in the environment are caused 

by a combination of natural and anthropogenic sources 

(Nriagu, 1979; Swain and others, 1992). Hg enters most 

ecosystems predominantly through wet and dry atmospheric 

deposition of primarily inorganic forms from combustion 

sources (U.S. Environmental Protection Agency, 1997), 

although some ecosystems have substantial Hg sources related 

to mineral deposits, mining, or industrial uses. Entry of Hg 

into aquatic environments occurs by direct deposition to the 

water body, runoff from upland sources (attached to suspended 

soil or organic material or complexed with dissolved organic 

carbon (DOC)), or influx from shallow ground-water flow 

(U.S. Environmental Protection Agency, 1997; Grigal, 2002). 

Once in an aquatic system, Hg partitions strongly to bed and 

suspended sediment (U.S. Environmental Protection Agency, 

1997). Methylation of Hg in aquatic environments is largely 

mediated by sulfate-reducing bacteria (Gilmour and others, 

1992) and occurs primarily in bed sediment and wetlands, 

although recent evidence indicates that iron-reducing bacteria 

can also carry out inorganic Hg methylation (Fleming and 

others, 2006). The resulting methylmercury (MeHg) formed 

from these microbial reactions is highly toxic and readily 

biomagnifies in aquatic food webs (Weiner and others, 2003). 

Studies of Hg in Stream Ecosystems

The U.S. Geological Survey (USGS) National WaterQuality Assessment (NAWQA) Program is a national program 

comprised of study areas throughout the country representing 

major river-basins and aquifer systems (Gilliom and others, 

2001). The NAWQA Program, in association with the USGS 

Toxic Substances Hydrology Program and the USGS National 

Research Program, has initiated studies of Hg in streams to 

improve understanding of Hg cycling in stream systems. Two 

levels of studies have been conducted: reconnaissance studies 

and detailed studies (Brigham and others, 2003).
2 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Reconnaissance Hg studies provide a “snap-shot” of Hg 

concentrations in various media across a wide range of stream 

sites throughout the country. Hg and related constituents were 

measured in stream water, streambed sediment (table 1), and 

piscivorous fish. Reconnaissance sampling was done in 1998 

(Krabbenhoft and others, 1999; Brumbaugh and others, 2001), 

2002, and 2004–05 at 266 stream sites across the Nation 

(fig. 1). 

Detailed studies, designed to assess hydrologic, 

biogeochemical, and ecological controls on Hg transport, 

speciation, methylation, and bioaccumulation, focused on a 

smaller number of stream sites. Hg and related constituents 

were measured in precipitation, stream water, bed sediment 

and pore water (table 1), and aquatic biota. In 2002–06, 

eight sites were studied—two sites in Oregon, and three 

sites each in Wisconsin and Florida (fig. 2). Bed-sediment 

and pore-water samples were collected during 2003–04, 

and sampling was divided into three components (streamreach characterization, spatial geochemistry, and temporal 

geochemistry) distinguished by variations in strategy and 

purpose. 

This report represents an idealized version of the 

approach and field methods that were used to assess Hg and 

related constituents in bed sediment and pore waters as part 

of both the reconnaissance and detailed studies. It is intended 

for use as a protocol to guide future phases of these studies 

and other related studies in similar investigations of bed 

sediment and pore water. Explicit methodologies for sampling 

strategies as well as collection and processing procedures 

(appendix 1a–b) are intended for clarification and use during 

field activities.

General Guidelines 

Although this report covers two studies of different focus 

and scope, a number of general guidelines relating to sample 

collection, processing, and documentation are pertinent to 

both. 

Personnel should familiarize themselves with the 

clean-hands/dirty-hands sampling technique outlined by 

the U.S. Geological Survey (2006), as well as the cleaning 

and sampling methods of Shelton and Capel (1994) and 

Wilde (2004). Any equipment, or pieces thereof, contacting 

samples to be analyzed for Hg species should be made of 

glass, Teflon®, or other plastic. In shallow areas, sediment 

samples are collected directly from the streambed. However, 

in areas where the sediment is too deep to collect in this 

manner, a 9-in. square, stainless-steel Birge-Ekman grab 

sampler should be deployed to retrieve sediment. This grab 

sampler can collect fine-grained material from depth with 

minimal disturbance to the sediment/water interface. To 

minimize possible contamination, sediment samples should 

be collected from the center of the grab sampler, avoiding 

areas that are near or directly contacting metal surfaces. In 

addition to sediment-sampling activities, stream-water field 

measurements of pH, specific conductance, dissolved oxygen 

(DO), temperature, and streamflow also are collected at the 

time of sampling. 

Process samples at a clean, stable workspace immediately 

following collection. Ideal processing sites are grassy or 

well-vegetated parks with picnic tables or where a portable 

table can be set up. Avoid workspaces within 60 m of dusty 

areas such as roads; workspaces should be covered with clean 

plastic bags or sheeting. Dedicated water-quality laboratory 

vans with suitable workspaces are also acceptable as long 

as they have never transported Hg reagents or samples with 

suspected high-level Hg contamination. 

Proper documentation of field activities is a key 

component of sampling efforts. Personnel should be familiar 

with USGS water-quality sample coding (U.S. Geological 

Survey, 2006) and field forms (appendix 3); sample labels 

(appendix 4) and field forms should be filled out completely 

before leaving the stream. USGS station-identification 

number, mean sample time, date, and medium code together 

serve as the unique identifier for each sample in the National 

Water Information System (NWIS) database (U.S. Geological 

Survey, 2006). Where multiple samples of the same medium 

are collected from the same stream site on the same day, 

samples collected from different locations are distinguished 

from each other based on time; therefore, care should be 

taken when assigning times for samples, and the relationship 

between sample time and location should be documented 

on field sheets. Sketching a map of the stream reach is of 

particular importance. On the map, notations should include 

specific locations (with reference to bridge crossing/other 

permanent object), as well as the mean times and sediment 

characteristics of the areas sampled. Copies of digital 

orthophotos and topographic maps can be obtained on the 

World Wide Web (TerraServer-USA, 2008), and can aid in 

the drawing of stream shape and the location of sampling 

areas. Locational information should be supplemented with 

Global Positioning System (GPS) coordinates recorded at 

each sampling area; use of Wide Area Augmentation System 

(WAAS) and an external antenna provide reasonably accurate 

coordinates. Additional accuracy can be obtained by allowing 

GPS units to determine a time-averaged reading of a location. 
Background 

3

Figure 1. Locations of sites sampled for National Water-Quality Assessment (NAWQA) Program reconnaissance mercury studies.

EXPLANATION

StateSampling site

0 500 1,000 MILES

0 500 1,000 KILOMETERS

80°W 110°W

40°N 20°N

Base composited from Instituto Nacional de Estadística Geografía e Informática, Atlas of Canada, and U.S. Geological Survey, 1:10,000,000, 2004. Continental United States in Albers Conical Equal Area Projection, referenced to North American Datum of 1983. Alaska in Alaska Albers, referenced to North American Datum of 1983. Hawaii in Hawaii State Plane zone 1 FIPS zone 5101, referenced to North American Datum of 1983.

0 400 800 MILES

0 400 800 KILOMETERS

0 100 200 MILES

0 100 200 KILOMETERS

140°W 180°0'0"

50°N40°N

154°W 160°W

22°N18°N
4 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury Table 1. Overview of streambed-sediment and pore-water sampling efforts associated with National Water-Quality Assessment (NAWQA) Program reconnaissance and detailed mercury studies. [(For a detailed list of constituents refer to appendix 2.. cm, centimeter; THg, total mercury; MeHg, methylmercury; AVS, acid-volatile sulfide; DO, dissolved oxygen; T, temperature; LOI, loss on ignition; MPP, methylmercury production potential; MDP, methylmercury degradation potential; Hg(II)R, reactive mercury; DOC, dissolved organic carbon; ORP, oxidation-reduction potential] Sampling component Sediment sampling Pore-water sampling Field measurements Reconnaissance Sediment geochemistry Surface (0–2 cm, approximately) composite sample analyzed for THg, MeHg, AVS, and percent fines. None Stream water pH, specific conductance, DO, T, and streamflow. None associated with sediment sampling. Detailed Stream-reach characterization Surface (0–2 cm) grab sample analyzed for LOI and percent fines. None Stream water pH, specific conductance, DO, T, and streamflow. Visual and tactile assessment of grain size and organic content. Spatial and temporal geochemistry Surface (0–2 cm) composite sample for MPP and MDP rates, THg, MeHg, Hg(II)R, AVS, percent fines, and numerous other ancillary analyses 

(appendix 2).

2-cm depth (nominally) composite 

sample analyzed for THg, MeHg, DOC, nutrients, selected major anions, and numerous other ancillary analyses (appendix 2).

Stream water pH, specific conductance, DO, T, 

and streamflow.

Sediment ORP, pH, and T.Pore-water sulfide, ORP, and pH.Piezometric head. 
Background 

5

EXPLANATION

StateSampling site

0 500 1,000 MILES

0 500 1,000 KILOMETERS

80°W 110°W

40°N 20°N

Base composited from Instituto Nacional de Estadística Geografía e Informática, Atlas of Canada, and U.S. Geological Survey, 1:10,000,000, 2004. Albers Conical Equal Area Projection, referenced to North American Datum of 1983. 

OREGON

WISCONSIN

FLORIDA

Figure 2. Locations of sites sampled for National Water-Quality Assessment (NAWQA) Program detailed mercury studies.
6 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Reconnaissance Studies

NAWQA reconnaissance Hg studies examine Hg 

occurrence in stream water, bed sediment, and piscivorous 

fish as part of a one-time sample collection effort. The 

reconnaissance bed-sediment sample from each site is a 

composite of the sediment types present. Stream-water field 

measurements (table 1) are collected the same day as the 

sediment sample, in accordance with published methods 

(Wilde, variously dated; Rantz and others, 1982). 

Sampling Strategy

At each stream, identify 10 discrete depositional bedsediment zones and collect sediment from the top 2 cm 

(approximately) of each zone. Deposit collected sediment into 

a suitable container, and remove large objects such as sticks, 

rocks, and leafy debris. Ideal sediment volume is 120 mL, 

but, depending on the number of zones, considerably more 

sediment may be collected. Homogenize sediment to yield a 

single composite sample from each stream. Samples should be 

collected, homogenized, and processed (that is, subsampled 

and preserved) within 30 minutes to minimize the potential for 

re-oxidation of any sulfide present. Where this is not possible, 

reduce the number of sampled zones as needed, but use no 

fewer than five. Samples are analyzed for total Hg (THg), 

MeHg, acid-volatile sulfide (AVS), stable isotopes of carbon 

(C) and nitrogen (N), and percent fines (that is, percent of 

sediment less than 0.063 mm) (table 1). Collect quality-control 

samples, in the form of split replicates, at one out of every 

eight sites. 

Sample Collection

Sample collection focuses on the surface layer 

(approximately the upper 0–2 cm) of sediment. Several 

pieces of sampling equipment are suitable, depending 

upon availability of equipment and local conditions such 

as substrate type and depth of sampling zone (appendix 5). 

Typically, a short (approximately 10 cm) section of Teflon®

tube (1.5-in. diameter) is worked horizontally across the upper 

2 cm of sediment, using gloved hands, to collect sediment. 

The tube is then removed from the stream, excess water is 

decanted, and sediment is placed in a suitable container. Other 

acid-cleaned plastic sampling devices, such as plastic scoops, 

work well in certain stream environments. A similar procedure 

for NAWQA sediment sampling is outlined by Shelton and 

Capel (1994). 

Sample Processing

Process samples at a suitable workspace immediately 

after collection. To minimize the water-sediment partitioning 

of THg and MeHg, as well as the oxidation of reduced species, 

samples are not sieved. Stir collected sediment with a clean 

Teflon® policeman or plastic spoon for 30 to 60 seconds, 

taking care not to entrain air into the sample. Scoop (using 

plastic spoon) or pour sediment into jars to subsample for 

various analyses (THg and MeHg, AVS, stable C and N 

isotopes, and percent fines). Leave approximately 20 to 30% 

of the jar volume empty to allow room for expansion upon 

freezing. Preserve AVS samples with 0.3 mL of zinc acetate 

to minimize the oxidation of sulfide in the sample. Freeze 

THg and MeHg, AVS, and stable C and N isotope samples. 

Store samples to be analyzed for percent fines in a cool, 

dark location. Samples can be stored until all streams have 

been sampled, then submitted together to their respective 

laboratories (appendix 6) with the appropriate paperwork 

(appendix 7).

Detailed Studies

NAWQA detailed Hg studies examine Hg occurrence 

and cycling in precipitation, stream water, bed sediment, 

sediment pore water, and selected biota. Detailed bed 

sediment sampling is divided into three components: reach 

characterization, spatial biogeochemical sampling, and 

temporal biogeochemical sampling (table 1). The purpose 

and, therefore, strategy of each component differs; however, 

sample collection and processing methods remain the same 

throughout. Pore-water sampling is performed in conjunction 

with the spatial and temporal components of the detailed 

studies. Routine stream-water samples and field measurements 

are collected the same day as bed-sediment/pore-water 

sampling, in accordance with published methods (Rantz and 

others, 1982; U.S. Environmental Protection Agency, 1996; 

U.S. Geological Survey, 2006; Wilde, variously dated). 

Sampling Strategy

Hg partitioning in sediment is strongly influenced 

by organic content and grain size. Hg has a strong affinity 

for organic matter (Ravichandran, 2004; Lambertsson 

and Nilsson, 2006), and is therefore observed in higher 

concentrations in organic-rich sediments. There is an inverse 

relation between Hg and grain size, with Hg showing greater 

affinity for finer sediments (Förstner and Wittmann, 1981; 

Horowitz and Elrick, 1987). 
Detailed Studies 7

For the detailed Hg studies, loss on ignition (LOI) is used 

as a measure of sediment organic content and percent fines 

(that is, percent of sediment less than 0.063 mm) is used as 

a measure of grain size. Every sediment sample collected is 

analyzed for these constituents. Though not always explicitly 

stated, LOI is performed as an ancillary analysis on all 

sediment samples submitted to the USGS Wisconsin Mercury 

Research Laboratory (WMRL). 

Reach Characterization

Reach characterization yields a quantitative description 

of bed-substrate type abundance in streams, thereby allowing 

for the extrapolation of related constituents (measured during 

spatial sampling) to a scale more relevant to the stream. 

Establishing a Reach

The reach is considered a representative portion of the 

larger stream or segment that is amenable to sampling. It has 

relatively homogeneous physical, chemical and biological 

characteristics, and therefore, should not include substantial 

changes in streamflow, water-quality characteristics, basin 

characteristics, or any major hydrologic discontinuities (for 

example, waterfalls). Guidelines for establishing the reach are 

based on methods published by Fitzpatrick and others (1998). 

Reach location and length are determined by three factors: 

geomorphology (habitat type and distribution), local habitat 

disturbance, and wetted channel width. Wadeable reaches are 

preferable, if possible, for safety considerations and ease of 

sampling. 

Habitat types, or geomorphic channel units (GCUs), are 

different fluvial regimes resulting from the depositional and 

erosional patterns of the channel. GCU type and distribution 

are important considerations when determining reach location 

and length, as they categorize the stream at a scale relevant 

to the majority of biota in the stream (Frissell and others, 

1986). In wadeable streams, GCUs include riffles, runs, and 

pools (fig. 3). In unwadeable streams, GCUs include the 

insides and outsides of meander bends, crossovers, as well 

as forewater and backwater side habitats. Reach placement 

should aim to include two examples each of two GCUs 

that are representative of the overall GCU sequence in the 

stream (Fitzpatrick and others, 1998). If there are insufficient 

GCUs to fulfill this criterion, locate the reach in an area that 

accurately reflects the overall habitat characteristics for that 

stream. Areas occupying 50% or more of the stream width are 

considered distinct GCUs. 

Locate reaches in areas outside the hydraulic effects 

of bridges and other man-made objects. Placement of the 

first reach boundary is dependent upon the types of GCUs 

present and their distribution in the stream. If the stream has 

a sequence of distinct GCUs, place the boundary one-half the 

mean channel width upstream or downstream of the border 

between two GCUs. If, however, the GCUs are not as distinct 

or sequential, place the boundary approximately 10 times the 

mean channel width from the reference location (for example, 

bridge or gage). 

Reach length is determined by multiplying the average 

wetted-channel width by 20, as this typically contains 1 full 

meander wavelength (Leopold and others, 1964), and, 

therefore, should capture all GCUs present. In accordance with 

Fitzpatrick and others (1998), adopt minimum reach lengths 

of 150 m for wadeable streams and 500 m for unwadeable 

streams when calculated reach lengths are less than the 

minimum values. There is no maximum reach length. 

Once the reach location and length have been established, 

divide the reach into 15 equidistant transects. Transects 

are positioned perpendicular to the flow and flagged on 

both sides of the stream. Transect 1 corresponds with the 

downstream reach boundary, and Transect 15 corresponds 

with the upstream reach boundary. Collect 30-minute, timeaveraged GPS readings at the upstream and downstream 

reach boundaries, on the left and right edges of water. Include 

reach boundaries, transects, landmarks, distances, GCUs, 

and general shape of the stream on a field sketch. Record 

additional (instantaneous) GPS-coordinate readings at the left 

edge of water of each transect. 

Transect Sampling

Bed-substrate zones are classified into a minimum of 

four basic categories for the purpose of reach characterization: 

fine-grained organic-rich, mixed sand and fine-grained 

with intermediate organic content, sandy organic-poor, and 

other (table 2). Substrate zones described by the first three 

categories are assumed to be the most likely to contribute 

to sediment MeHg production and are the same categories 

as those used for spatial sampling. Substrates larger than 

sand (for example, gravel and cobble) are assumed to yield 

negligible contributions to sediment MeHg production and, 

in the most basic categorization scheme, are combined into a 

single category to expedite sampling. The expanded category 

list may be used to parse these substrates into multiple 

categories when a more detailed assessment of the substrate is 

desired (table 2).

The equidistant transects are used as arbitrary lines along 

which reach bed substrates are characterized. Measure and 

record the width of each bed-substrate zone encountered along 

each transect. Collect point samples of surficial sediment 

(0–2 cm) at the midpoint of each zone assumed to be an area 

of MeHg production (table 2, categories 2, 2.5, and 3; fig. 4). 

In areas where sediment cannot be retrieved for classification, 

tapping substrates with polyvinyl chloride (PVC) pipe 

can help to estimate substrate category. Upon contact with 

the substrate, the PVC pipe will show varying amounts of 

resistance, based on the substrate type—bouncing quickly 

back or changing course when encountering larger substrates, 
8 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Figure 3. Diagram of simplified wadeable reach, with geomorphic channel units noted.

Pool

Pool

Riffle

Riffle

Run

Run

Woody

debris

Point

bar

flow

flow

Submerged

boulder

Upstream

reach boundary

Downstream

reach boundary

Left edge of water

Right edge of water

Upstream

reach boundary

Downstream

reach boundary

Left edge of water

Right edge of water

EXPLANATION

Water

Unvegetated substrate

Riparian vegetation

Reach boundary

Basin
Detailed Studies 9

and slowing down or showing give when encountering finer 

substrates (sand and finer). Field personnel should familiarize 

themselves with the response of the PVC pipe to different 

sediment types in shallow areas where the sediment type has 

been classified. Where finer-scale classifications of sediment 

type are desired, the grab sampler can be used to obtain 

sediment for visual and tactile assessment. Transects are 

sampled in downstream to upstream order (that is, Transect 1 

to Transect 15) to minimize disturbance of unsampled 

transects. Samples are analyzed for LOI and percent fines. 

Quality-control replicate samples are collected at 

a minimum of 1 out of every 10 transects. Immediately 

following the completion of regular transect sampling, 

randomly choose transect numbers and resample. Characterize 

bed substrates and collect samples from the midpoints of 

zones with selected bed-sediment types, taking care to avoid 

disturbed sediment. Collected samples are analyzed for LOI 

and percent fines.

Spatial Biogeochemical Sampling

Spatial biogeochemical sampling yields a detailed 

characterization of sediment and pore water in different reach 

bed-sediment types. Select a minimum of three zone types 

per stream based on bed-sediment grain size and observable 

organic content. Potential sampling-zone types include 

fine-grained organic-rich zones, zones of mixed sand and 

fine-grained sediment with intermediate organic content, and 

sandy organic-poor zones (table 2). Collect an equal number 

of samples from each zone type present in the stream reach. 

Where this is not possible, give priority to more dominant 

zone types. If collecting multiple samples from the same type 

of zone, zones should be as spatially separated as possible 

within the reach. Once a zone has been selected, delineate an 

approximately 1 m2 sampling area within each zone. Collect 

samples from a variety of undisturbed locations within 

the delineated area. If this area does not provide enough 

material to collect both the bed-sediment and pore-water 

samples, expand sampling area within the bed-sediment zone. 

Sampling within and among sampling areas should be done 

in downstream to upstream order to minimize disturbance to 

unsampled areas.

Each sediment sample is a composite from a variety of 

locations within each sampling area and is analyzed for a 

variety of constituents. Use a core ring to collect sediment 

from a 0–2 cm depth. Divide collected sediment between 

sieved (1 mm) MeHg production- and degradation-potential 

(MPP and MDP, respectively) rates fraction and whole 

composite fraction; continue collecting sediment until the 

volume is sufficient to fill all jars submitted to laboratories for 

analysis. Primary sediment analyses include MPP and MDP 

rates, THg, MeHg, and reactive Hg (Hg(II)R), AVS, stable 

C and N isotopes, and percent fines. In addition to primary 

analyses, most laboratories perform additional analyses for 

related constituents (appendix 2). Take field measurements 

of oxidation-reduction potential (ORP), pH, and temperature 

at each sampling area after sample collection and processing 

is completed. After sediment field measurements have been 

taken, measure piezometric head at each sampling area 

(methods described in section, “Field Measurements”).

Table 2. Bed-substrate categories for classifying streambed sediment based on size and organic content.

[Modified from Fitzpatrick and others (1998). mm, millimeter; N/A, not applicable; >, greater than; ≤, less than or equal to; bold text indicates bedsediment categories where samples will be collected]

Description Size

(mm)

Basic 

categories

Expanded 

categories

Smooth bedrock/concrete/hardpan N/A >3 1

Fine-grained; organic-rich N/A 2 2

Mixed sand and fine-grained; intermediate organic content ≤2 2.5 2.5

Sand; organic-poor > 0.063–2 3 3

Fine/medium gravel > 2–16 >3 4

Coarse gravel > 16–32 >3 5

Very coarse gravel > 32–64 >3 6

Small cobble > 64–128 >3 7

Large cobble > 128–256 >3 8

Small boulder > 265–512 >3 9

Large boulder/irregular bedrock/irregular hardpan/irregular artificial surface > 512 >3 10
10 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Point

bar

Woody

debris

flow

flow

Upstream

reach boundary

Downstream

reach boundary

Left edge of water

Right edge of water

Upstream

reach boundary

Downstream

reach boundary

Left edge of water

Right edge of water

Submerged

boulder

Transect 1

Transect 2

Transect 3

Transect 4

Transect 5

Transect 6

Transect 7

Transect 8

Transect 9

Transect 10

Transect 11

Transect 12

Transect 13

Transect 14

Transect 15

Transect 1

Transect 2

Transect 3

Transect 4

Transect 5

Transect 6

Transect 7

Transect 8

Transect 9

Transect 10

Transect 11

Transect 12

Transect 13

Transect 14

Transect 15

T9-3

T9-2

T9-1

EXPLANATION

Sand, organic-poor

Fine-grained, organic-rich

Bed Substrate Zones

Mixed sand and finegrained, intermediate 

organic content

Unsampled transect point

Transect line

Reach boundary

Gravel and cobble

Riparian vegetation

Wetted stream boundary

Sampled transect point

Basin

Figure 4. Diagram of simplified reach and point-sampling locations for transect sampling performed in association 

with reach characterization. Transect-point locations are at the cross-sectional midpoint of bed-substrate zones. Point 

numbering is indicated for transect 9 only; numbering strategy is identical for each transect. [T, transect number; leftmost point is always 1]
Detailed Studies 11

Each pore-water sample is a composite from a variety 

of locations within each sampling area and is analyzed for a 

variety of constituents. Use a sipper to collect pore water in 

roughly equal proportions from three or more undisturbed 

locations within the sampling area, each at a 2 cm depth, and 

composite in a 500-mL Teflon® bottle. Primary pore-water 

analyses include THg and MeHg, DOC, nutrients, and anions. 

In addition to primary analyses, most laboratories perform 

additional analyses for related constituents (appendix 2). 

Immediately following sample collection, preserve water for 

the measurement of sulfide and take ORP measurements. Set 

aside additional water for pH measurements, then subsample 

and preserve samples for laboratory analyses. Complete 

measurements for pH immediately after sample preservation.

Quality-control samples are collected for both sediment 

and pore water during spatial sampling. One of each type 

of quality-control sample should be collected for every 10 

regular samples collected. Sequential replicates are collected 

for both sediment and pore water, and are measured for all 

field measurements and laboratory constituents. Blanks are 

collected exclusively for pore water, and are measured for 

sulfide and all laboratory constituents. 

Temporal Biogeochemical Sampling

Temporal biogeochemical sampling is performed after 

data from spatial sampling has been interpreted, and yields a 

detailed characterization of seasonal variations in sediment 

and pore-water constituent levels at one sampling area per 

stream. Select the area showing the highest MPP rate during 

spatial sampling and perform quarterly assessments of 

constituent levels for 1 year (total of five samples from each 

sampling area). 

Use field notes from spatial sampling to locate the 

selected sediment-zone types, and delineate the sampling area. 

Note any changes that have occurred in or near the sampling 

area, paying particular attention to changes in sediment type. 

Methods for the collection of temporal sediment and porewater samples and field measurements are the same as those 

used for spatial sampling. 

Quality-control samples are collected for both sediment 

and pore water during temporal sampling. One of each type 

of quality-control sample should be collected for every 10 

regular samples collected. Sequential replicates are collected 

for both sediment and pore water and are measured for all 

field measurements and laboratory constituents. Blanks are 

collected exclusively for pore water, and are measured for 

sulfide and all laboratory constituents. Collect blank qualitycontrol samples during earlier sampling events, so that 

identified problems can be addressed. 

Extrapolation of Data to the Reach Scale

Spatial sampling characterizes the geochemistry of 

specific zone types present in the reach, but gives little 

indication as to the overall abundance of a given zone type. 

Using transect data, biogeochemical data from specific zone 

types can be extrapolated to the reach scale, thereby yielding 

values more representative of overall stream conditions. 

A variety of strategies exist for extrapolating spatial data 

to the reach scale; one such strategy is provided here in order 

to highlight details relevant to these types of calculations. To 

use this strategy, first develop site-specific linear regression 

relationships between dependent Hg variables and logtransformed LOI; for datasets containing LOI values of zero, 

a shift (for example, log[LOI + 1]) can be applied to allow all 

data to be log-transformed. For this example the Hg variables 

of interest will include THg and MeHg concentrations, and 

MPP rate. These variables can be expressed on a dry-mass 

basis or on a volumetric basis. Volumetric-basis Hg variables 

(Y,vol) are calculated for surface (0–2 cm) sediment samples 

using equation 1. 

Y Y dry mass

wet mass

bulk density

Y

vol = × × ,

where

is the measured Hgvariable in a given 

sample expressed on a dry-mass basis

for example, THg in ng Hg per gram, 

dry weight),

(

dry mass / is mass fraction of a whole wet

 sediment sampl

wet mass

e that is composed of dry sediment.

(1)

For parameters containing no censored (that is, values 

less than the minimum detection level) values, linear 

regression is performed using the generalized linear model 

(GLM) procedure in SAS® software (release 9.1.3, SAS 

Institute Inc., Cary, NC). For parameters containing censored 

values, maximum likelihood regression is performed using 

the LIFEREG procedure in SAS®. For maximum likelihood 

regressions, r 2 values are “likelihood r 2” (Helsel, 2005). Zerointercept regression models are used for each parameter. 

Spatially-weighted THg and MeHg concentrations and 

MPP rates are then determined for each stream reach by 

applying the regression relationships to the transect LOI data 

collected during reach characterization. For each transect 

segment at which LOI is measured (that is, where material was 

sand or finer, including organic-rich sediment), a regressionpredicted Hg variable (THg and MeHg concentration, MPP 

rate) is multiplied by the length of that segment. These values 

are then summed, and the sum is divided by the sum of all 
12 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

transect lengths (equation 2). The resulting value is a spatiallyweighted Hg variable, which accounts for the dependence of 

the Hg variable on LOI, and on the areal extent of organic 

matter (as measured by LOI). 

Y

Y L

L

Y

pred i i = ∑ , ,

where

is the spatially-weighted Hg variable,

Y is the Hg variable for the th transect segment,

L

pred ,i i

i

L

is length of the th transect segment, and

is the sum of

i

all transect lengths.

(2)

Although LOI samples are not collected from transect 

segments composed of material larger than sand, lengths from 

these segments are still included in the sum of all transect 

lengths; this, in effect, assigns a value of zero to Hg variables 

for these segments. 

Standard errors of prediction, as a percentage of the 

spatially-weighted Hg variable (percent SEY), are calculated 

according to equation 3. 

percent SE

L L SE

Y

SE

Y

i Y i

Y

= × ∑ ×100

2 2 ( / ) , ,

where

is the standard error of prediction of the

spatially-weighted Hg variable,

SEY i, , Ypred i is the standard error of prediction of ,

and the remaining parameters are defined

in equation 1.

(3)

Hg values also can be expressed on an areal basis. In 

order to do this, volumetric-basis Hg variables are used in the 

regression analysis, and the resulting, spatially-weighted value 

(Y) is multiplied by: 2 cm × 10,000 cm2/m2 × 0.001 μg/ng, 

where the interval of surface sediment sampled is 0–2 cm.

Sample Collection

Though the purpose and strategy of the components of 

the detailed Hg studies differ, the methodologies for sample 

collection are the same. 

Bed Sediment

Surface sediment (0–2 cm depth) is collected during all 

components of the detailed Hg studies using a polycarbonate 

core ring that is 2 cm deep and 8 cm in diameter (fig. 5). Press 

the core ring into the sediment until the top edge is flush with 

the sediment/water interface, and then gently scoop away 

sediment downstream of the core ring. Insert a stiff plastic 

sheet under the bottom of the core ring where the downstream 

sediment has been removed, and gently slide it under the core 

ring (keeping it flush with the core-ring bottom). Slowly lift 

the resulting patty and transfer the sediment to appropriate 

containers for compositing. In situations where streamflow 

velocity is sufficiently fast to disturb or erode fine sediment 

from the core during transport through the water column, place 

a second plastic sheet on the core ring before lifting. 

Pore Water

Pore water is sampled during both the spatial and 

temporal components of the detailed Hg studies. Pore water 

is collected by inserting a vented Teflon® probe into the 

sediment to the desired depth and pulling surrounding pore 

water through the vents (fig. 6). The attachment of an acrylic 

disc 2 cm from the vents minimizes the flow of stream water 

into the sampled area. Pore water is pulled through the probe 

and attached Teflon® tube using a peristaltic pump fitted 

with C-flex tube (Cole-Parmer). After flowing through the 

C-flex tube, pore water moves through a short section of 

Teflon® tube and into an in-line Teflon® filter cartridge with 

a pre-combusted quartz-fiber filter (47-mm diameter, 0.7-μm 

nominal pore size). The C-flex and Teflon® (short section) 

tube are secured together with a cable tie to prevent separation 

under pressure. All Teflon® and C-flex components are acid 

cleaned in the WMRL and double bagged in Ziploc® bags 

prior to use. 

When collecting a pore-water sample, place the acrylic 

disc flat on the surface of the sediment and insert the probe 

perpendicular to the sediment surface. Carefully hold the 

probe and acrylic disc in place. Movement of the probe can 

introduce channels for the influx of stream water, and should 

be prevented. 

With the probe deployed, but prior to connecting the 

in-line filter, pump pore water at a low flow rate; this allows 

an initial slug of sediment to evacuate the line. After the water 

runs fairly clear, attach the filter to the short section of Teflon®

tube. Hold the filter cartridge upright to purge the air from the 

filter, and then allow it to flush with a few milliliters of water; 

each composite sample collected may require multiple filters, 

and each time a new one is used it should be conditioned in 

this manner. Pumping depletes pore water in the desired depth 

increment, inducing infiltration of both deeper pore water and 

stream water to the sampling zone. To minimize this effect, 

pump pore water through the sampling apparatus at a slow 

rate. 

Filtered pore-water samples are collected into a clean 

500-mL Teflon® bottle. Inside each 500-mL bottle is a small 

volume of dilute hydrochloric acid (HCl). Pour acid off into 

a waste acid container, and rinse the bottle three times with 

small aliquots of filtered pore water from the sampling area 

before collecting the sample. Continue collecting sample water 

until the 500-mL Teflon® bottle is completely full. The probe 

should be deployed multiple times to collect a single sample, 

due to the depleting effect of pumping on pore water and the 

large volume of pore water required for these samples. Each 

time the probe is deployed, remove the filter and allow the 

sediment plug to evacuate the line before replacing it. 
Detailed Studies 13

Figure 5. Surficial-sediment sample collected using a core (2 centimeters deep and 8 centimeters in 

diameter) and a stiff plastic sheet. (Photograph by Dennis Wentz, U.S. Geological Survey, June 2003.)

Figure 6. Pore-water sampling equipment and compositing bottle. (Photograph by Michelle Lutz, U.S. Geological 

Survey, May 2006.)
14 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Most of the vials submitted for ancillary analyses are 

filled from this composite; the only exception is the anion vial. 

Fill anion samples directly from the sampling line to bypass 

the effects of the Teflon® bottle’s recent exposure to dilute 

HCl. 

Sample Processing

Immediately following sample collection, time-sensitive 

field measurements should be performed; then samples 

should be processed at a clean, stable workspace. Sample 

processing entails the subsampling and preserving of samples 

in preparation for laboratory analysis.

Bed Sediment

Although sample-collection methods are the same for 

all components, differences in purpose and strategy between 

components call for variations in processing methods. 

Reach Characterization

During reach characterization, point samples are collected 

along transects at the midpoints of each substrate zone that 

consists of sand or finer sediment. Sediment from each 

collected zone is divided between two jars: one for LOI and 

one for percent fines. Additional sediment is discarded into the 

stream. LOI samples are frozen immediately. Samples to be 

analyzed for percent fines are stored at ambient temperature in 

a cool, dark location. Both LOI and percent fines samples can 

be held until all streams have been sampled, and then shipped 

to the appropriate laboratories (appendix 6). 

Spatial and Temporal Biogeochemical Sampling

Bed-sediment samples collected for the spatial and 

temporal biogeochemical-sampling components are divided 

between sieved (1 mm) fractions for determination of MPP 

and MDP rates (approximately 7/8 of each patty) and whole 

composite fractions (approximately 1/8 of each patty). Bed 

sediment in both fractions are processed immediately after 

collection.

Sieve samples for assays of MPP and MDP rates using a 

10×10 cm piece of 1-mm nylon mesh sieve. Attach the sieve 

to the top of a half-pint mason jar with the brass lid-ring; a 

250-mL plastic beaker with the bottom removed is secured 

upside-down to the top of the mason jar (fig. 7). Deposit a 

small amount of sediment in this enclosure, and tamp with a 

flat-bottomed acid-cleaned plastic bottle to sieve the sediment 

less than 1 mm into the mason jar. To minimize entrainment of 

air and unwanted changes in reduction-oxidation conditions, 

fill the half-pint jar to the top with sieved sediment and pore 

water. Remove brass lid-ring and mesh, and remove sediment 

from the threads of the jar using a Kimwipe®; then cap with 

the mason lid and secure with the cleaned brass lid-ring. Wrap 

Parafilm M® around the lid to seal it. Label the jar, place it 

into a foam sleeve, and seal it inside a Ziploc® bag. Samples 

for determination of MPP and MDP rates are stored on wet ice 

or in a refrigerator and should be shipped to the laboratory as 

soon as possible (optimally within 24 hours) after sampling.

Composite the unsieved portion of the sample into 

a 120-mL polypropylene jar and briefly stir with a clean 

Teflon®, plastic, or glass device, taking care not to entrain 

excessive air into the sample. Subsample sediment (using a 

clean plastic spoon, a 10 cm3 plastic syringe with the barrel 

end cut off, or by pouring) into four jars for (1) THg, MeHg, 

and Hg(II)R; (2) AVS; (3) stable C and N isotopes; and 

(4) percent fines analysis. Leave approximately 20 to 30% 

of total volume of the jars as headspace to allow room 

for expansion upon freezing. Both Hg and AVS samples 

are frozen immediately (preferably by placing in a cooler 

containing dry ice). Stable C and N isotope samples are stored 

on wet ice or in a refrigerator. Samples to be analyzed for 

percent fines are stored in a cool, dark location. All samples 

are considered preserved at this point, and are shipped to 

respective laboratories once all streams have been sampled 

(appendix 6). 

Pore Water

Pore-water samples are collected from a 2-cm depth and 

composited in a 500-mL Teflon® bottle. Once the Teflon®

bottle is completely full, rinse the anion vial and fill it with 

filtered pore water taken directly from the sampling line. 

Decant pore water from the Teflon® bottle into vials for all 

field measurements; preserve water for sulfide measurements 

and measure ORP immediately after sample collection. Set 

aside water for pH measurements. Decant pore water into vials 

for DOC and nutrient analyses; the DOC vial is filled without 

rinsing, and the nutrient vial is rinsed with small aliquots of 

composite water prior to filling. Preserve remaining composite 

water to a final volume of 1% HCl to preserve for THg and 

MeHg analysis. Store DOC and anion samples on wet ice, the 

nutrient sample on dry ice, and the preserved THg and MeHg 

sample in a cool, dark location. Complete measurements for 

pH immediately after sample preservation, and submit samples 

to respective laboratories once all streams have been sampled 

(appendix 6). 

Field Measurements

Field measurements taken at the time of sampling provide 

ancillary data that describe general media conditions (table 1). 

Prior to each day’s sampling, perform calibrations and checks 

for all instrumentation used, and record on field sheets. 

Techniques for calibration are outlined in the USGS National 

Field Manual (Wilde, variously dated), and manufacturer 

documentation. 
Field Measurements 15

Figure 7. Surficial-sediment core being deposited into the methylmercury production- and 

degradation-potential-rates sampling apparatus. (Photograph by Dennis Wentz, U.S. Geological Survey, 

June 2003.)

Stream Water

Stream-water field measurements are collected each day 

that samples are collected (table 1). Measure pH, specific 

conductance, dissolved oxygen, and temperature as outlined 

in the USGS National Field Manual (Wilde, variously dated). 

Obtain streamflow measurements from a nearby USGS gaging 

station, or determine manually, in accordance with Rantz and 

others (1982). 

Bed Sediment

Bed-sediment field measurements are taken for each 

composite sample collected for the spatial and temporal 

geochemistry components of the detailed studies (table 1). 

Measurements of interest are ORP, pH, and temperature; each 

measurement should be performed in replicate. 

Oxidation-Reduction Potential

The electrode used in the measurement of ORP is 

a refillable electrode (Orion® model 9180BN), and is 

therefore not amenable to submersion. Calibration of 

ORP instrumentation is performed in the laboratory, and 

is checked using the standard solution provided with the 

electrode, according to manufacturer instructions. If the ORP 

reading is outside of the allowable range (determined by the 

manufacturer) in the field, maintain the electrode according to 

manufacturer instructions or replace with a working electrode. 

Take measurements by retrieving a patty of sediment from the 

sampling area (using the same method as was used in sample 

collection) and inserting the electrode to the desired depth. 

Alternatively, to minimize exposure to oxygen, fill scintillation 

vial 2/3 of the way full with sediment from the patty, insert the 

electrode and wrap intersection with Parafilm M®. Readings 

likely will not completely stabilize; regardless of the method, 

record values quickly after insertion, as the ORP of the 

sediment changes quickly once exposed to air. 
16 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

pH and Temperature

The instrumentation used in the measurement of pH 

and temperature is a low-maintenance pH triode (Orion®

model 9107BN) with an automatic temperature compensator. 

Calibrate for pH according to manufacturer instructions. 

Temperature is calibrated by laboratory personnel and need 

not be verified in the field. The low-maintenance triode is 

sealed, which allows it to be submerged for the collection of 

in situ measurements. Alternatively, measurements may be 

taken by retrieving a patty of sediment from the sampling area 

(using the same method as was used in sample collection). 

If the temperature is measured in a sediment patty, rather 

than in situ, measure the temperature immediately while 

shielding the sample from direct sunlight to minimize heating. 

Regardless of the method used, insert the electrode to the 

desired depth and allow it to equilibrate until stable readings 

are obtained. 

Pore Water

Pore-water field measurements are collected for each 

pore-water sample collected (table 1). Measurements of 

interest are sulfide, ORP, and pH. 

Sulfide

Sulfide is measured using a refillable, silver/sulfide 

combination electrode (Orion® model 9616BN). It is 

shipped from the laboratory evacuated of filling solution. 

Approximately 12 hours before sampling, fill the electrode 

with the solution provided, then replace tape over the filling 

hole and cap the end for storage. Before each day’s sampling, 

pour the premeasured ascorbic acid into the premeasured 

sulfide antioxidant buffer (SAOB) (Brouwer and Murphy, 

1994), cap, and mix; then pour the mixture into the ascorbic 

acid vial, cap and mix. Finally, pour the mixture back into 

the SAOB container and let it sit for 10 minutes before using. 

The SAOB solution stabilizes sulfide in the samples for up 

to 24 hours, although measuring the samples as soon after 

collection as possible is recommended. Sulfide calibrations 

are done in the sulfur geochemistry laboratory, Reston, Va., 

before and after each field trip. Calibrations are conducted 

using serial dilutions of a sodium sulfide stock solution. The 

exact concentration of the sodium sulfide stock solution is 

determined by titration with a lead nitrate standard. Experience 

has demonstrated that the calibrations remain stable for at 

least several weeks, and changes in calibration curves for a 

given electrode vary only slightly over a year (W. Orem, U.S. 

Geological Survey, written commun., 2006).

Using the provided syringe, prepare scintillation vials 

(20-mL) containing 3 mL of the SAOB-ascorbic acid mixture. 

The number of scintillation vials prepared should equal the 

number of pore-water samples to be collected. Store the 

electrode in the remaining solution while not in use, including 

overnight. 

Sulfide is unstable until it is placed in the SAOB-ascorbic 

acid mixture. Therefore, immediately after sample collection, 

deposit 3 mL of pore water into a scintillation vial containing 

the premeasured SAOB-ascorbic acid mixture, cover, and 

shake briefly to mix. The preserved sulfide sample should be 

labeled, stored in a dark place, and measured within 24 hours 

of collection. 

To measure sulfide, remove the electrode from the 

SAOB-ascorbic acid mixture, rinse it with deionized (DI) 

water, dry, and uncover the filling hole. Stir the preserved 

sample gently using a Teflon®-coated magnetic stir bar 

(12.7-mm length). Lower the electrode into the sample. If the 

sample is below detection limit (-700 mV), the reading will 

not stabilize, and the electrode should be kept in the sample 

for 5 to 10 minutes. If the sample is above detection limit, 

the value will become stable much faster. Record the meter 

response in millivolts. Between samples, rinse the electrode 

with DI water and blot dry. 

Once all sampling has been completed, rinse the electrode 

inside and out with DI water, drain, cover the filling hole with 

tape, replace the cap, and ship back to the sulfur geochemistry 

laboratory in Reston, Va. 

ORP

Pore-water ORP is measured using a refillable glass 

microelectrode (Microelectrodes, Inc. model MI-800/710). 

The microelectrode is stored in a glass sheath containing 

a sponge moistened with DI water. Each day that field 

measurements are collected, move the sleeve away from 

the filling hole and check the calibration using the standard 

solution provided with the electrode, per manufacturer 

instructions. If the instrumentation reads outside of the 

allowable error (determined by the manufacturer), clean the 

metal tip of the electrode with a Kimwipe®. If it continues to 

read outside of the allowable error, a different electrode should 

be used. 

ORP is unstable and should be measured immediately 

after preserving the sulfide sample. To measure, pour a small 

amount of water from the composite sample into a clean 

scintillation vial. From the vial, draw water into a clean 

syringe that has been fitted with a short piece (approximately 

5 cm) of plastic tube, then expel air slowly from the syringe 

and tube, and place the electrode partially into the tube. Taking 

care not to get the filling hole wet, expel the water from the 

syringe past the electrode, noting mV readings. Readings will 

jump around as water pushes past the electrode; record the 

approximate median reading, paying particular attention to the 

readings from the last milliliter in the syringe. ORP readings 

should be taken in replicate.

Equipment used for ORP readings can be reused. 

Between samples, remove sample water; there is no need to 

rinse equipment or electrode. Blot the electrode dry, replace 

the stopper, and return to the glass sheath. 
References Cited 17

pH

The electrode used to measure pore-water pH is the same 

low-maintenance triode (Orion® model 9107BN) that is used 

in the collection of sediment field measurements. To collect 

the pH measurement, pour a small amount of pore water from 

the composite bottle into the same scintillation vial used for 

the ORP readings, and set aside; measurements should be 

taken immediately following sample processing. To measure, 

place the electrode in the water and record the value when 

stabilized. Readings should be taken in replicate.

Piezometric Head 

Piezometric-head measurements can be used to indicate 

whether the stream is potentially gaining or losing water to 

the hyporheic zone in the sampling area. Piezometric head is 

measured using a transparent (clear plastic) minipiezometer 

fitted to a stainless steel point; this apparatus is driven 

vertically into the sediment at a number of points in the 

sampling area. Insert the minipiezometer properly to the 

appropriate depth, then remove the metal sheath and apply 

a slight vacuum to the plastic tube. Leave open to the 

atmosphere. The water level in the tube equilibrates to a level 

corresponding to the pressure (head) in the hyporheic zone. 

Using a metric ruler, measure the difference (in millimeters) 

between the stream-water surface and the water surface in the 

tube and record value. If the water in the tube is above the 

stream-water surface, record the value as a positive number. If 

the water in the tube is below the stream-water surface, record 

the value as a negative number. 

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Toxicological profile for mercury (update): Atlanta, Ga., 

U.S. Department of Health and Human Services, Public 

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Mercury in stream ecosystems—New studies initiated by 

the U.S. Geological Survey: U.S. Geological Survey Fact 

Sheet 016–03, 4 p.

Brouwer, H., and Murphy T.P., 1994, Diffusion method 

for the determination of acid-volatile sulfides (AVS) in 

sediment: Environmental Toxicology and Chemistry, v. 13, 

p. 1273–1275. 

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J.G., and Echols, K.R., 2001, A national pilot study of 

mercury contamination of aquatic ecosystems along 

multiple gradients—bioaccumulation in fish: U.S. 

Geological Survey Biological Science Report 2001–0009, 

25 p.

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dietary methylmercury on reproductive endocrinology of 

fathead minnows: Environmental Science and Technology, 

v. 37, no. 19, p. 4390–4396.

Evers, D.C., 2005, Mercury connections—The extent and 

effects of mercury pollution in Northeastern North America: 

Biodiversity Research Institute, Gorham, Maine, 28 p.

Fitzpatrick, F.A., Waite, I.R., D’Arconte, P.J., Meador, M.R., 

Maupin, M.A., and Gurtz, M.E., 1998, Revised methods for 

characterizing stream habitat in the National Water-Quality 

Assessment Program: U.S. Geological Survey Water 

Resources Investigations Report 98–4052, 67 p.

Fleming, E.J., Mack, E.E., Green, P.G., and Nelson, 

D.C., 2006, Mercury methylation from unexpected 

sources—Molybdate-inhibited freshwater sediments and 

iron-reducing bacterium: Applied and Environmental 

Microbiology, v. 72, no. 1, p. 457–464.

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the aquatic environment: New York, Springer-Verlag, 486 p.

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1986, A hierarchical framework for stream habitat 

classification—Viewing streams in a watershed context: 

Environmental Management, v. 10, p. 199–214.

Gilliom, R.J., Hamilton, P.A., and Miller, T.L., 2001, The 

National Water-Quality Assessment Program—Entering a 

new decade of investigations: U.S. Geological Survey Fact 

Sheet 071–01, 6 p.

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Sulfate stimulation of mercury methylation in freshwater 

sediments: Environmental Science and Technology, v. 26, 

p. 2281–2287.

Grigal, D.F., 2002, Inputs and outputs of mercury from 

terrestrial watersheds—A review: Environmental Reviews, 

v. 10, no. 1, p. 1–39.

Hammerschmidt, C.R., Sandheinrich, M.B., Wiener, J.G., 

and Rada, R.G., 2002, Effects of dietary methylmercury on 

reproduction of fathead minnows: Environmental Science 

and Technology, v. 36, no. 5, p. 877–883.
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Helsel, D.R., 2005, Nondetects and data analysis—Statistics 

for censored environmental data: New York, John Wiley & 

Sons, 266 p.

Horowitz, A.J., and Elrick, K.A., 1987, The relation of stream 

sediment surface area, grain size, and composition to trace 

element chemistry: Applied Geochemistry, v. 2, p. 437–451.

Krabbenhoft, D.P., Weiner, J.G., Brumbaugh, W.G., Olson, 

M.L., DeWild, J.F., and Sabin, T.J., 1999, A national pilot 

study of mercury contamination of aquatic ecosystems 

along multiple gradients, in Morganwalp, D.W., and 

Buxton, H.T., eds., U.S. Geological Survey Toxic 

Substances Hydrology Program—proceedings of the 

technical meeting, Charleston, S.C., March 8–12, 1999: 

U.S. Geological Survey Water-Resources Investigations 

Report 99–4018B, p. 147–159.

Lambertsson, L., and Nilsson, M., 2006, Organic 

material—the primary control on mercury methylation 

and ambient methyl mercury concentrations in estuarine 

sediments: Environmental Science and Technology, v. 40, 

p. 1822–1829.

Leopold, L.B., Wolman, M.G, and Miller, J.P., 1964, Fluvial 

processes in geomorphology: San Francisco, W.H. Freeman 

and Company, 522 p. 

Nriagu, J.O., 1979, The biogeochemistry of mercury in the 

environment: Elsevier/North Holland, Biomedical Press, 

696 p.

Rantz, S.E., and others, 1982, Measurement and computation 

of streamflow—Volume 1—Measurement of stage and 

discharge: U.S. Geological Survey Water-Supply Paper 

2175, 284 p. 

Ravichandran, M., 2004, Interactions between mercury and 

dissolved organic matter—A review: Chemosphere, v. 55, 

p. 319–331.

Shelton, L.R., and Capel, P.D., 1994, Guidelines for collecting 

and processing samples of stream bed sediment for analysis 

of trace elements and organic contaminants for the National 

Water-Quality Assessment Program: U.S. Geological 

Survey Open-File Report 94–458, 20 p.

Swain, E.B., Engstrom, D.R., Brigham, M.E., Henning, T.A., 

and Brezonik, P.L., 1992, Increasing rates of atmospheric 

mercury deposition in midcontinental North America: 

Science, v. 257, p. 784–787. 

Terraserver-USA, 2008, Orthophotos: accessed August 1, 

2008, at http://www.terraserver-usa.com/

U.S. Environmental Protection Agency, 1996, Method 

1669—Sampling ambient water for trace metals at EPA 

water quality criteria levels: EPA–821/R–96–008, 36 p.

U.S. Environmental Protection Agency, 1997, Mercury 

study report to Congress volume III—fate and transport of 

mercury in the environment: EPA–452/R–97–005, [359] p. 

U.S. Environmental Protection Agency, 2002, Method 1631, 

Revision E—Mercury in water by oxidation, purge and trap, 

and cold vapor atomic fluorescence spectrometry: 

EPA–821–R–02–019, 38 p.

U.S. Environmental Protection Agency, 2007, 2005/2006 

National listing of fish advisories: U.S. Environmental 

Protection Agency Fact Sheet EPA–823–F–07–003, 7 p.

U.S. Geological Survey, 2006, User’s manual for the National 

Water Information System of the U.S. Geological Survey 

Water-Quality System (ver. 4.4): U.S. Geological Survey 

Open-File Report 2006–1145, 372 p.

Virtanen, J.K., Voutilainen, S., Rissanen, T.H., Mursu, 

J., Tuomainen, T.-P., Korhonen, M.J., Valkonen, V.-P., 

Seppänen, K., Laukkanen, J.A., and Salonen, J.T., 2005, 

Mercury, fish oils, and risk of acute coronary events and 

cardiovascular disease, coronary heart disease, and allcause mortality in men in eastern Finland: Arteriosclerosis, 

Thrombosis, and Vascular Biology, v. 25, p. 228–233.

Weiner, J.G., Krabbenhoft, D.P., Heinz, G.H., and 

Scheuhammer, A.M., 2003, Ecotoxicology of mercury, in

Hoffman, D.J., and others, eds., Handbook of ecotoxicology 

(2d ed.): Boca Raton, Fla., CRC Press, p. 407–461.

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sampling (version 2.0): U.S. Geological Survey Techniques 

of Water-Resources Investigations, book 9, chap. A3, 

accessed August 1, 2008, at http://pubs.water.usgs.gov/

twri9A3

U.S. Geological Survey, September 2006, Collection of water 

samples (version 2.0): U.S. Geological Survey Techniques 

of Water-Resources Investigations, book 9, chap. A4, 

accessed August 1, 2008, at http://pubs.water.usgs.gov/

twri9A4
Appendix 1 19

Appendix 1. Method Summary Sheets

Appendix 1a. Method summary sheets: reconnaissance studies.

Sampling strategy 

1. Advanced preparation for sampling

a. Personnel familiarize themselves with sampling techniques presented by Shelton and Capel (1994)

b. Procure proper sampling equipment

•	 Acceptable streambed-sediment collection devices

° Guillotine sampler (Shelton and Capel, 1994)

° An approximately 10-cm section of 1.5-in.-diameter Teflon® tube (modified piece of the guillotine 

sampler) (Shelton and Capel, 1994)

° Teflon® spoon, scoop, or spatula sampler (Shelton and Capel, 1994)

° Other plastic spoons/scoops are suitable

	Plastic scoops can be formed by cutting a plastic sample bottle

•	 Additional equipment required for unwadeable streams

° Birge-Ekman grab sampler (9-in. square)

•	 Acceptable bed sediment compositing containers include glass, Teflon®, or other plastic bowl, tub, or pail

c. Clean glass, Teflon® and plastic equipment according to trace-element cleaning methods (Shelton and Capel, 1994; 

Wilde, 2004)

2. Prepare for field measurements

a. Before each day’s sampling prepare equipment for field measurements

•	 Record all calibrations on field sheets

•	 SW field measurements

° pH, specific conductance, dissolved oxygen (DO), and temperature

	Calibrate multiparameter meter according to manufacturer instructions

° Streamflow

	Either

– Verify rated gage is working properly

– Verify proper operation of equipment used for direct measurement, according to Rantz 

and others (1982) and manufacturer instructions

b. Collect SW field measurements the same day as bed-sediment sample collection

3. Sampling overview

a. Target time

•	 30 minutes for collection and processing (that is, subsampling and preserving) of bed-sediment samples

b. Collect and process each sample as quickly as possible to minimize oxidation of sulfide in sediment samples

4. Bed-sediment sampling

a. Regular samples

•	 Depth: top 2 cm (approximately)

•	 Sample type: composite

•	 Analyses:

° Total mercury (THg) and methylmercury (MeHg)

° Acid-volatile sulfide (AVS)

° Percent fines

•	 Collection strategy

° Identify depositional zones for sampling

	Number of zones should be between 5 (minimum) and 10 (optimal)

– Collect sediment from as many zones as possible, keeping target time in mind

	Spatially separated throughout the stretch of stream sampled
20 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Sampling strategy (continued)

° Sampling location

	Undisturbed sediment

	Collect sediment from several locations within each zone

° Collect sediment (top 2 cm depth, approximately)

	Directly from streambed

	Where stream is too deep to collect sediment directly from streambed, use a 9-in. Birge-Ekman 

grab sampler

– Retrieve sediment

– Collect sediment for sample from the surface (top 2 cm, approximately) of the retrieved 

sediment

– Avoid areas near/in contact with metal surfaces

° Deposit collected sediment into composite container

	Target volume: 120 mL

	Remove woody debris, rocks, and other large items from the sample

	Process sample immediately after collection to minimize oxidation of sulfide

b. Quality-control samples

•	 Replicates

° Type: split

° Frequency: 1 replicate for every 8 sites sampled

° Analyses: all laboratory analyses performed for regular samples

Sample collection 

1. Bed-sediment-sample collection

a. Variety of equipment (and therefore techniques) are acceptable

•	 Work an approximately 10-cm section of Teflon® tube (1.5-in.-diameter) horizontally across the upper 2 cm 

of sediment

•	 Scoop up the top 2 cm of sediment using a spatula or scoop

b. Decant water

c. Deposit into container (bowl, tub, or pail) for compositing

Sample processing

1. Bed-sediment-sample processing

a. Mix sediment by stirring the sample

•	 30 to 60 seconds

•	 Try not to entrain air into sample

Appendix 1. Method summary sheets—Continued

Appendix 1a. Method summary sheets: reconnaissance studies—Continued.
Appendix 1 21

Appendix 1. Method summary sheets—Continued.

Appendix 1a. Method summary sheets: reconnaissance studies—Continued.

Sample processing (continued) 

b. Place sediment in jars using a plastic spoon or Teflon® policeman

•	 Leave headspace of approximately 20 to 30 percent of container volume (for expansion upon freezing)

•	 Fill jars for analyses:

° Total mercury (THg) and methylmercury (MeHg)

	30-mL polypropylene jar (acid-rinsed)

	Store on dry ice/in freezer

	Ship

–	 Timing: once all streams have been sampled

–	 To: Wisconsin Mercury Research Laboratory (WMRL)

–	 Conditions: dry ice

° Acid-volatile sulfide (AVS)

	30-mL polypropylene jar (not acid-rinsed)

	Preserve immediately 

– Add 0.3 mL of zinc-acetate solution to the sediment using a disposable pipet

 Pipets are graduated at 0.1-mL increments

– Stir sample well with disposable pipet

	Store on dry ice/in freezer

	Ship

–	 Timing: once all streams have been sampled

–	 To: Sulfur geochemistry laboratory

–	 Conditions: dry ice

° Percent fines

	30-mL polypropylene jar (not acid-rinsed)

	Store at ambient temperature in a cool, dark location (don’t freeze)

	Ship

–	 Timing: once all streams have been sampled

–	 To: Sediment laboratory

–	 Conditions: ambient temperature (cool, dark location)
22 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies.

Sampling strategy 

Reach characterization: establishing a reach

1. Prepare for field measurements

a. Before each day’s sampling prepare equipment for field measurements

•	 Record all calibrations on field sheets

•	 Stream-water (SW) field measurements

° pH, specific conductance, dissolved oxygen (DO), and temperature

	Calibrate multiparameter meter according to manufacturer instructions

° Streamflow

	Either

– Verify rated gage is working properly

– Verify proper operation of equipment used for direct measurement, according to Rantz 

and others (1982) and manufacturer instructions

2. Collect SW sample and field measurements

a. Collect routine SW sample and field measurements the same day as streambed-sediment sample collection

•	 SW samples are collected before any other personnel have entered the stream to minimize sample bias

caused by disturbance/suspension of sediment

3. Determine reach length

a. Use measuring tape or rangefinder to determine wetted-channel width in three representative locations

b. Calculate mean wetted-channel width (MCW)

c. Multiply MCW by 20 to determine reach length

•	 Wadeable reaches must be ≥ 150 m in length

•	 Unwadeable reaches must be ≥ 500 m in length

4. Determine reach boundary locations

a. Reaches are relatively homogenous lengths of stream and should not contain

•	 Substantial changes in

° Streamflow

° Water quality characteristics

° Basin characteristics

•	 Major hydrologic discontinuities (for example, waterfalls)

b. Determine reach location

•	 Locate reach in an area that includes two examples each of two geomorphic channel units (GCUs) that are

representative of the overall GCU sequence in the stream (distinct GCUs occupy 50% or more of the stream 

width)

° Where abundance of GCUs is insufficient, locate reach in area where GCU sequence reflects overall 

stream characteristics

•	 Locate reach upstream or adequately downstream of hydraulic effects resulting from man-made disturbances

c.	 Place first reach boundary:

•	 If stream has distinct, sequential GCUs

° 0.5 × (MCW) from border between two GCUs

•	 If stream has no distinct, sequential GCUs

° 10 × (MCW) from reference location (for example, bridge or gage)

5. Determine, flag, and georeference transect locations

a. Measure distance from reference location (for example, bridge or gage) to closest reach boundary and mark with 

appropriate flag (that is, Transect 1 for downstream boundary, Transect 15 for upstream boundary)
Appendix 1 23

b.	 Determine distance between transects:

Reach length/14 = distance between each of the 15 transects

c. Flag transects on both sides of stream with numbered stake flags

•	 Orient transects perpendicular to the flow

•	 When flagging, try to avoid being in the water/disturbing the sediment

•	 Flag from upstream to downstream (Transect 15 to Transect 1)

° This positions personnel to begin sampling from downstream to upstream

d. Georeference reach boundary transects using Global Positioning System (GPS) unit

•	 Locations to reference (directionality is assigned while facing downstream)

° Upstream reach boundary transect (Transect 15)

	Left edge of water (LEW)

	Right edge of water (REW)

° Downstream reach boundary transect (Transect 1)

	LEW

	REW

•	 Engage features

° Wide Area Augmentation System (WAAS)

° Time-averaging

° External antenna

•	 Allow unit to average for 30 minutes in each location

•	 Record

° Location in degrees/minutes/seconds

° Datum (North American Datum of 1983 (NAD 83) preferred)

° Accuracy (with units)

e. Georeference remaining transects using GPS unit

•	 Location to reference at each transect

° LEW

•	 Engage features

° WAAS

° External antenna

•	 Take instantaneous reading

•	 Record

° Location in degrees/minutes/ seconds

° Datum (NAD 83 preferred)

° Accuracy (with units)

Reach characterization: transect sampling strategy

1. Mapping and sampling overview

a. Target time

•	 No specific time limit

b. Map bed-substrate zones and collect samples from downstream to upstream, by transect

c. Samples are processed (that is, subsampled and stored at appropriate temperatures) as they are collected; no 

additional processing is required

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
24 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

2. Map bed-substrate zones

a. Decide whether to use basic or expanded substrate categories (table 2)

•	 Basic is recommended

b. Extend measuring tape across stream at transect location

•	 Distance along tape should increase from LEW to REW

•	 Anchor each end of the measuring tape with a stake

c. Classify substrate zones into defined categories

•	 Start at the LEW and proceed across stream

•	 Basic categories for classification (table 2)

° Fine-grained, organic-rich (category 2)

° Mixed sand and fine-grained, intermediate organic content (category 2.5)

° Sand, organic-poor (category 3)

° Other (category >3)

•	 Categorize substrates

° Obtain sediment directly from streambed for assessment

	Visual assessment

	Tactile assessment

	Partitioning through 0.063-mm sieve

	(For expanded categories, use meterstick for additional size assessments)

° Alternatives for where stream is too deep to collect sediment directly from streambed for assessment

	Tap a polyvinyl chloride (PVC) pipe against the substrate to estimate substrate category

– To prepare

 In shallow areas where substrates are easily classified, note characteristic responses 

of the pipe to different bed substrates

– Pipe responds differently to different substrates

 Larger substrates (table 2, category >3)

 Bounce back quickly

 Change course

 Finer substrates (table 2, categories 2, 2.5, and 3)

 Pipe will stop slowly/show resistance

	Retrieve sediment using a 9-in. Birge-Ekman grab sampler

– Visual assessment

– Tactile assessment

– Partitioning through 0.063-mm sieve

d. Record boundaries of bed substrate zones

•	 Record position of the LEW on measuring tape

•	 Proceed along transect toward the REW

° For each bed substrate zone

	Record position of right edge of zone on measuring tape

	Determine width of zone

	Collect bed-sediment samples, where appropriate

•	 Record position of the REW on measuring tape

•	 Determine wetted width of stream (that is, the distance between the LEW and the REW)

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
Appendix 1 25

3. Collect transect samples

a. Regular samples

•	 Sample type

° Surface sediment 

	Depth: 0–2 cm

	Sample type: grab

	Analyses: loss on ignition (LOI) and percent fines

•	 Sampling location

° Bed-substrate zones in categories 2, 2.5, and 3 (table 2)

° Position at the midpoint of that zone

° Undisturbed sediment

° Record position of sampling location on measuring tape

•	 Sampling strategy

° Collect sediment sample (0–2 cm depth), as patty

	Directly from streambed

	Where stream is too deep to collect sediment directly from streambed, use a 9-in. Birge-Ekman 

grab sampler

– Retrieve sediment

– Take a 0–2 cm patty from the surface of the retrieved sediment

– Avoid areas near/in contact with metal surfaces

° Divide each patty between jars for analysis

	LOI

	Percent fines

° Store jars at appropriate temperatures immediately

° Discard remaining sediment into stream

b. Quality-control samples

•	 Replicates

° Type: sequential

° Frequency: 1 replicate transect for every 10 transects sampled

° Analyses: LOI and percent fines

° Details:

	After completion of transect sampling, randomly select transects for replicate sampling (for 

example, by selecting numbers out of a hat)

	Note widths of bed-substrate zones, as was done during collection of regular sampling

	Collect sediment at the midpoints of bed-substrate zones in categories 2, 2.5, and 3

– Undisturbed sediment

– If sediment is disturbed (likely), shift sampling location slightly within zone

4. Document sample information

a. Key sample identification information

•	 Station-identification number (STAID)

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
26 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

•	 Date

•	 Mean sample time

° Samples of the same medium collected from the same stream site on the same day are distinguished 

from each other on the basis of mean sample time in the National Water Information System (NWIS) 

database

•	 Medium code

° “H” for regular samples

° “W” for replicate samples

b. Fill out all sample labels

c. Fill out forms

•	 Field forms

° Fill out all field forms completely in the field

° Draw map of stream reach

	Use orthophotos and topographic maps to assist in drawing stream

– http://www.terraserver-usa.com/

	Draw and label each transect

	Record stream and riparian features

	Indicate position of reference location (for example, bridge/gage)

– Record distance from nearest reach boundary to reference location

	Indicate flow direction

	Draw any other distinguishing features that will assist in reestablishing that same reach again

•	 Shipping forms

° Shipping forms may be filled out in the office, prior to shipping samples

d. Verify that all labels and forms are in agreement regarding key sample-identification information

Spatial biogeochemical sampling: preparation and sampling area selection

1. Prepare for field measurements

a. Approximately 12 hours before sample collection 

•	 Fill sulfide electrode with filling solution provided

•	 Replace tape over filling hole

•	 Cap the end

b. Before each day’s sampling prepare equipment for field measurements

•	 Record all calibrations and calibration checks on field sheets

•	 SW field measurements

° pH, specific conductance, dissolved oxygen (DO), and temperature

	Calibrate multiparameter meter according to manufacturer instructions

° Streamflow

	Either

– Verify rated gage is working properly

– Verify proper operation of equipment used for direct measurement, according to Rantz 

and others (1982) and manufacturer instructions

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
Appendix 1 27

•	 Sulfide

° Sulfide is calibrated by laboratory personnel and need not be verified in the field

° Prepare sulfide antioxidant buffer (SAOB)-ascorbic acid mixture

	Pour premeasured ascorbic acid into the premeasured SAOB, cap, and mix

	Pour mixture into the ascorbic acid vial, cap, and mix

	Pour mixture back into the SAOB container

	Let mixture sit 10 minutes

	Use syringe to distribute 3 mL of the mixture to each of a number of 20-mL scintillation vials

– Number of scintillation vials should equal the number of pore-water samples to be 

collected

	Store electrode in mixture when not in use

•	 Oxidation-reduction potential (ORP) calibration checks

° Sediment

	Remove plug from filling hole

– Verify levels of filling solution in electrode, and if low, replenish with provided filling 

solution

	Check calibration against standard solution provided by the manufacturer

– If reading is outside the error allowed by the manufacturer, maintain according to 

manufacturer instructions

– If electrode continues to read outside of allowable error, do not use electrode

– Check calibration of secondary electrode

° Pore water

	Remove microelectrode from glass sheath

	Move sleeve away from filling hole

– Verify levels of filling solution in electrode, and if low, replenish with provided filling 

solution

	Check calibration against standard solution provided by the manufacturer

– If reading is outside the error allowed by the manufacturer, clean metal tip with 

Kimwipe®

– If electrode continues to read outside of allowable error, do not use electrode

– Check calibration of secondary electrode

•	 pH calibration

° Calibrate according to manufacturer instructions

° Sediment and pore-water pH measurements are collected using the same electrode

•	 Temperature

° Temperature is calibrated by laboratory personnel and need not be verified in the field

2. Collect SW sample and field measurements

a. Collect routine SW sample and field measurements the same day as sediment- and pore-water-sample collection

•	 SW samples are collected before any other personnel have entered the stream to minimize sample bias

caused by disturbance/suspension of sediment

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
28 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

3. Locate and characterize substrate zones

a. Locate zones in reach having bed substrates of sand or fine-grained sediment

•	 Take care not to disturb zones until sample has been collected

° Walk along shore

° Walk on coarse substrates in-stream

b. Classify substrate zones of sand or fine-grained sediment into defined categories

•	 Categories for classification (table 2)

° Fine-grained, organic-rich

° Mixed sand and fine-grained, with intermediate organic content

° Sand, organic-poor

•	 Categorize substrates

° Obtain sediment directly from streambed for assessment

	Visual assessment

	Tactile assessment

	Partitioning through 0.063-mm sieve

° Where stream is too deep to collect sediment directly from streambed, use a 9-in. Birge-Ekman grab 

sampler

	Visual assessment

	Tactile assessment

	Partitioning through 0.063-mm sieve

c. Note relative abundance of substrate zones in each category

4. Select bed-sediment zones for sampling

a. Sampling-area selection criteria (in order of priority)

•	 Undisturbed sediment

•	 Grain size and organic content

° Obtain at least one sample from each of the three zone types of interest (table 2) present in the reach

° Where this is not possible, obtain a minimum of 3 samples from different zones in as many categories 

as possible

•	 Representativeness of zones

° Collect an equal number of samples from each of the represented categories

° Where this is not possible, give priority to categories that are more dominant in the stream reach

•	 Spatial separation between zones

° Zones of similar classification that are being sampled should be as spatially separated as possible

b. Delineate sampling area within each zone

•	 1 m2

•	 Mark edges with stake flags

Spatial biogeochemical sampling: sample collection strategy

1. Sampling overview

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
Appendix 1 29

a. Target time

•	 No specific time limit

b. Collect samples from downstream zones first, then work upstream

c. Collect and process each sample as quickly as possible to minimize oxidation of sulfide in sediment and porewater samples

2. Bed-sediment sampling

a. Regular samples

•	 Depth: 0–2 cm

•	 Sample type: composite

•	 Analyses:

° MeHg production- and degradation-potential (MPP and MDP, respectively) rates

° THg, MeHg, and reactive mercury (Hg(II)R)

° AVS

° Percent fines

•	 Take care not to disturb any additional sediment in the sampling area

•	 Collection strategy

° Sampling location

	Undisturbed sediment

	In (or adjacent to) the delineated sampling area

	Spatially separated throughout the sampling area

	Downstream to upstream

° Collect sediment sample (0–2 cm depth), as patty

	Directly from streambed

	Where stream is too deep to collect sediment directly from streambed, use a 9-in. Birge-Ekman 

grab sampler

– Retrieve sediment

– Take a 0–2 cm patty from the surface of the retrieved sediment

– Avoid areas near/in contact with metal surfaces

° Divide each patty between fractions

	Sieved MPP- and MDP-rates fraction

– 7/8 of each patty

	Whole composite fraction

– 1/8 of each patty

° Collect sufficient patties to fill all jars for analysis

° Process sample immediately

° Perform field measurements in replicate

	ORP

– Collect patty of sediment (0–2 cm depth) and use one of the following methods

 Insert electrode into patty

 Fill scintillation vial 2/3 full, insert electrode, wrap top with Parafilm M®

– Readings likely will not completely stabilize

– Record values quickly, as ORP of sediment changes rapidly with exposure to air

– Repeat

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
30 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

	pH and temperature

– Use one of the following methods

 Insert electrode directly into sediment to a depth of 2 cm

 Allow electrode to remain in sediment until readings stabilize

 Collect patty of sediment (0–2 cm depth)

 Minimize changes in sediment being measured

 Work quickly 

 Shield patty from sunlight to minimize heating

 Insert electrode into sediment patty

– Allow electrode to remain in sediment until readings stabilize

– Record readings for pH and temperature

– Repeat

b. Quality-control samples

•	 Replicates

° Type: sequential

° Frequency: 1 replicate for every 10 regular samples

° Analyses: all field measurements and laboratory analyses performed for regular samples

3. Pore-water sampling

a. Regular samples

•	 Depth: 2 cm

•	 Sample type: composite

•	 Analyses:

° THg and MeHg

° Dissolved organic carbon (DOC)

° Nutrients

° Anions

•	 Take care not to disturb any additional sediment in the sampling area

•	 Collection strategy

° Deploy probe to 2 cm depth in at least three locations

° Sampling location

	Undisturbed sediment

	In (or adjacent to) the delineated sampling area

	Spatially separated throughout the sampling area

	Downstream to upstream

° Collect pore water into 500-mL Teflon® bottle

° Collect roughly equal volumes from each location

° Fill anion vial directly from sampling line (not part of composite)

° Reserve water for field measurements

	Sulfide – preserve water

– Decant water from 500-mL Teflon® bottle into an empty 20-mL scintillation vial

– Use syringe to transfer 3 mL to scintillation vial containing 3 mL of SAOB-ascorbic acid 

mixture

– Cap and shake briefly to mix

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
Appendix 1 31

– Label vial

– Store at ambient temperature in a cool, dark location

– Measure within 24 hours

	ORP – measure

– Decant water from 500-mL Teflon® bottle into an empty 20-mL scintillation vial

– Place short piece (approximately 5 cm) of plastic tube on syringe

– Draw water from scintillation vial into syringe

– Move sleeve away from filling hole in the electrode

– Place electrode partially into tube

– Expel water past electrode

 Take care not to get the filling hole wet

– Note mV readings, and record approximate median

 Pay particular attention to the last 1 mL of water

– Repeat

	pH – set aside water

– Decant water from 500-mL Teflon® bottle into an empty 20-mL scintillation vial

– Set aside and measure immediately after sample processing

° Process sample immediately

° Perform remaining field measurements

	pH

–	 Timing: immediately after sample processing

– Measure pH

 Lower electrode into sample

 Allow reading to stabilize

 Record value

 Repeat

	Sulfide 

–	 Timing: within 24 hours of sample collection

– Prepare electrode

 Remove from SAOB-ascorbic acid mixture

 Rinse with deionized water

 Blot dry with Kimwipe®

 Uncover filling hole

– Measure sulfide

 Stir preserved sample with 12.7-mm Teflon®-coated, magnetic stir bar

 Lower electrode into sample

 Allow readings to stabilize

 Record value in mV

 If sample is below detection limit (-700 mV), readings will not stabilize

 Keep electrode in sample for 5 to 10 minutes, then record value in mV

 Repeat

– Between samples, rinse electrode with deionized water, and blot dry with Kimwipe®

– Store electrode in SAOB-ascorbic acid mixture (prepared fresh daily) when not in use

– After sampling is completed, 

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
32 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

 Prepare electrode for shipment back to laboratory 

 Remove filling solution

 Rinse inside and outside with deionized water

 Convert mV readings to concentrations

b. Quality-control samples

•	 Blanks

° Frequency: 1 blank for every 10 regular samples

° Analyses: sulfide field measurement and all laboratory analyses performed for regular samples

° Blank waters to be used

	Sulfide

– Inorganic blank water

	THg and MeHg 

– Milli-Q® water obtained from the WMRL

	DOC

– Certified organic-free water

	Nutrients and anions

– Inorganic blank water

•	 Replicates

° Type: sequential

° Frequency: 1 replicate for every 10 regular samples

° Analyses: all field measurements and laboratory analyses performed for regular samples

4. Piezometric-head measurements

a. Measure after sediment- and pore-water sample collection

b. Making measurements

•	 Collect at multiple depths

° 10 cm

° 20 cm

° 30 cm

•	 Collect in each area sampled for sediment and pore water

5. Georeference each sampling area using a GPS unit

a. Engage features

•	 WAAS

•	 External antenna

b. Record

•	 Location in degrees/minutes/seconds

•	 Datum (NAD 83 preferred)

•	 Accuracy (with units)

6. Document sample information

a. Key sample identification information

•	 Station-identification number (STAID)

•	 Date

•	 Mean sample time

° Samples of the same medium collected from the same stream site on the same day are distinguished 

from each other on the basis of mean sample time in the NWIS database

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
Appendix 1 33

•	 Medium code

° Sediment

	“H” for regular samples

	“W” for replicate samples

° Pore water

	“F” for regular samples

	“Z” for replicate samples

	“Q” for blank samples

b. Fill out all sample labels

c. Fill out forms

•	 Field forms

° Fill out all field forms completely in the field

° Draw map of stream reach

	Use orthophotos and topographic maps to assist in drawing stream

– http://www.terraserver-usa.com/

	Record stream and riparian features

	Draw, label, and classify each zone and sampling area

– Assign a letter-number combination name to each sampling area

 The letter should be based on sediment grain size and observable organic content 

(table 2)

 F = Fine-grained, organic-rich

 M = Mixed sand and fine-grained, intermediate organic content

 S = Sand, organic-poor

 The number should be based on the sample order by sediment type

 For example, F2 was collected from a fine-grained, organic-rich sediment 

zone, and that zone was the second zone of this type sampled at that stream

– Briefly describe additional sediment characteristics

– Indicate distance to reference location (for example, bridge/gage)

– Indicate flow direction

– Draw any other distinguishing features that will assist in finding sampling area locations 

again

° Record relationship between sampling-area name and key sample-identification information for NWIS 

on MPP- and MDP-rates field form

•	 Shipping forms

° Fill out Wisconsin Mercury Research Laboratory (WMRL) analytical services request form

	Use a new sheet for each sample collected

° Remaining shipping forms may be filled out in the office, prior to shipping samples 

d. Verify that all labels and forms are in agreement regarding sampling-area names and key sample-identification 

information

Temporal biogeochemical sampling: preparation and sampling area selection

1. Prepare for field measurements

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
34 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

a. Approximately 12 hours before sample collection 

•	 Fill sulfide electrode with filling solution provided

•	 Replace tape over filling hole

•	 Cap the end

b. Before each day’s sampling prepare equipment for field measurements

•	 Record all calibrations and calibration checks on field sheets

•	 SW field measurements

° pH, specific conductance, dissolved oxygen (DO), and temperature

	Calibrate multiparameter meter according to manufacturer instructions

° Streamflow

	Either

– Verify rated gage is working properly

– Verify proper operation of equipment used for direct measurement, according to Rantz 

and others (1982) and manufacturer instructions

•	 Sulfide

° Sulfide is calibrated by laboratory personnel and need not be verified in the field

° SAOB-ascorbic acid mixture

	Pour premeasured ascorbic acid into the premeasured SAOB, cap, and mix

	Pour mixture into the ascorbic acid vial, cap, and mix

	Pour mixture back into the SAOB container

	Let mixture sit 10 minutes

	Use syringe to distribute 3 mL of the mixture to each of a number of 20-mL scintillation vials

– Number of scintillation vials should equal the number of pore-water samples to be 

collected

	Store electrode in mixture when not in use 

•	 ORP calibration checks

° Sediment

	Remove plug from filling hole

– Verify levels of filling solution in electrode, and if low, replenish with provided filling 

solution

	Check calibration against standard solution provided by the manufacturer

– If reading is outside the error allowed by the manufacturer, maintain according to 

manufacturer instructions

– If electrode continues to read outside of allowable error, do not use electrode

– Check calibration of secondary electrode

° Pore water

	Remove microelectrode from glass sheath

	Move sleeve away from filling hole

– Verify levels of filling solution in electrode, and if low, replenish with provided filling 

solution

	Check calibration against standard solution provided by the manufacturer

– If reading is outside the error allowed by the manufacturer, clean metal tip with 

Kimwipe®

– If electrode continues to read outside of allowable error, do not use electrode

– Check calibration of secondary electrode

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
Appendix 1 35

•	 pH calibration

° Calibrate according to manufacturer instructions

° Sediment and pore-water pH measurements are collected using the same electrode

•	 Temperature

° Temperature is calibrated by laboratory personnel and need not be verified in the field

2. Collect SW sample and field measurements

a. Collect routine SW sample and field measurements the same day as sediment- and pore-water-sample collection

•	 SW samples are collected before any other personnel have entered the stream to minimize sample bias

caused by disturbance/suspension of sediment

3. Locate temporal sampling area (spatial sampling area with highest measured MPP rate)

a. Consult field notes

•	 GPS coordinates

•	 Maps

•	 Field descriptions

b. Do not disturb bed-sediment-sampling zone

c. Delineate sampling area within each zone

•	 1 m2

•	 Mark edges with stake flags

Temporal biogeochemical sampling: sample collection strategy

1. Sampling overview

a. Target time

•	 No specific time limit

b. Collect and process samples as quickly as possible to minimize oxidation of sulfide in sediment and pore-water 

samples

2. Bed-sediment sampling

a. Regular samples

•	 Depth: 0–2 cm

•	 Sample type: composite

•	 Analyses:

° MPP and MDP rates

° THg, MeHg, and Hg(II)R

° AVS

° Percent fines

•	 Take care not to disturb any additional sediment in the sampling area

•	 Collection strategy

° Sampling location

	Undisturbed sediment

	In (or adjacent to) the delineated sampling area

	Downstream to upstream

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
36 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

° Collect sediment sample (0–2 cm depth), as patty

	Directly from streambed

	Where stream is too deep to collect sediment directly from streambed, use a 9-in. Birge-Ekman 

grab sampler

– Retrieve sediment

– Take a 0–2 cm patty from the surface of the retrieved sediment

– Avoid areas near/in contact with metal surfaces

° Divide each patty between fractions

	Sieved MPP- and MDP-rates fraction

– 7/8 of each patty

	Whole composite fraction

– 1/8 of each patty

° Collect sufficient patties to fill all jars for analysis

° Process sample immediately

° Perform field measurements in replicate

	ORP

– Collect patty of sediment (0–2 cm depth) and use one of the following methods

 Insert electrode into patty

 Fill scintillation vial 2/3 full, insert electrode, wrap top with Parafilm M®

– Readings likely will not completely stabilize

– Record values quickly, as ORP of sediment changes rapidly with exposure to air

– Repeat

	pH and temperature

– Use one of the following methods

 Insert electrode directly into sediment to a depth of 2 cm

 Allow electrode to remain in sediment until readings stabilize

 Collect patty of sediment (0–2 cm depth)

 Minimize changes in sediment being measured

 Work quickly 

 Shield patty from sunlight to minimize heating

 Insert electrode into sediment patty

– Allow electrode to remain in sediment until readings stabilize

– Record readings for pH and temperature

– Repeat

b. Quality-control samples

•	 Replicates

° Type: sequential

° Frequency: 1 replicate for every 10 regular samples

° Analyses: all field measurements and laboratory analyses performed for regular samples

3. Pore-water sampling

a. Regular samples

•	 Depth: 2 cm

•	 Sample type: composite

•	 Analyses:

° THg and MeHg

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
Appendix 1 37

Sampling strategy (continued)

° DOC

° Nutrients

° Anions

•	 Take care not to disturb any additional sediment in the sampling area

•	 Collection strategy

° Deploy probe to 2-cm depth in at least three locations

° Sampling location

	Undisturbed sediment

	In (or adjacent to) the delineated sampling area

	Spatially separated throughout the sampling area

	Downstream to upstream

° Collect pore water into 500-mL Teflon® bottle

° Collect roughly equal volumes from each location

° Fill anion vial directly from sampling line (not part of composite)

° Reserve water for field measurements

	Sulfide – preserve water

– Decant water from 500-mL Teflon® bottle into an empty 20-mL scintillation vial

– Use syringe to transfer 3 mL to scintillation vial containing 3 mL of SAOB-ascorbic acid 

mixture

– Cap and shake briefly to mix

– Label vial

– Store at ambient temperature in a cool, dark location

– Measure within 24 hours

	ORP – measure

– Decant water from 500-mL Teflon® bottle into an empty 20-mL scintillation vial

– Place short piece (approximately 5 cm) of plastic tube on syringe

– Draw water from scintillation vial into syringe

– Move sleeve away from filling hole in the electrode

– Place electrode partially into tube

– Expel water past electrode

 Take care not to get the filling hole wet

– Note mV readings, and record approximate median

 Pay particular attention to the last 1 mL of water

– Repeat

	pH – set aside water

– Decant water from 500-mL Teflon® bottle into an empty 20-mL scintillation vial

– Set aside and measure immediately after sample processing

° Process sample immediately

° Perform remaining field measurements

	pH

–	 Timing: immediately after sample processing

– Measure pH

 Lower electrode into sample

 Allow reading to stabilize

 Record value

 Repeat

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.
38 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Sampling strategy (continued)

	Sulfide 

–	 Timing: within 24 hours of sample collection

– Prepare electrode

 Remove from SAOB-ascorbic acid mixture

 Rinse with deionized water

 Blot dry with Kimwipe®

 Uncover filling hole

– Measure sulfide

 Stir preserved sample with 12.7-mm Teflon®-coated, magnetic stir bar

 Lower electrode into sample

 Allow readings to stabilize

 Record value in mV

 If sample is below detection limit (-700 mV), readings will not stabilize

 Keep electrode in sample for 5 to 10 minutes, then record value in mV

 Repeat

– Between samples, rinse electrode with deionized water, and blot dry with Kimwipe®

– Store electrode in SAOB-ascorbic acid mixture (prepared fresh daily) when not in use

– After sampling is completed

 Prepare electrode for shipment back to laboratory 

 Remove filling solution

 Rinse inside and outside with deionized water

 Convert mV readings to concentrations

b. Quality-control samples

•	 Blanks

° Frequency: 1 blank for every 10 regular samples (during early sampling events)

° Analyses: sulfide field measurement and all laboratory analyses performed for regular samples

° Blank waters to be used

	Sulfide

– Inorganic blank water

	THg and MeHg

– Milli-Q® water obtained from the WMRL

	DOC

– Certified organic-free water

	Nutrients and anions

– Inorganic blank water

•	 Replicates

° Type: sequential

° Frequency: 1 replicate for every 10 regular samples

° Analyses: all field measurements and laboratory analyses performed for regular samples

4. Piezometric-head measurements

a. Measure after sediment- and pore-water-sample collection

b. Making measurements

•	 Collect at multiple depths

° 10 cm

° 20 cm

° 30 cm

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.
Appendix 1 39

•	 Collect in the area sampled for sediment and pore water

5. Document sample information

a. Key sample identification information

•	 Station-identification number (STAID)

•	 Date

•	 Mean sample time

° Samples of the same medium collected from the same stream site on the same day are distinguished 

from each other on the basis of mean sample time in the NWIS database

•	 Medium code

° Sediment

	“H” for regular samples

	“W” for replicate samples

° Pore water

	“F” for regular samples

	“Z” for replicate samples

	“Q” for blank samples

b. Fill out all sample labels

c. Fill out forms

•	 Field forms

° Fill out all field forms completely in the field

° Draw map of stream reach

	Use orthophotos and topographic maps to assist in drawing stream

– http://www.terraserver-usa.com/

	Record stream and riparian features

	Draw, label, and classify the zone and sampling area

– Label it using the same sampling-area name (that is, letter-number combination) assigned 

to it during spatial sampling

– Briefly describe additional sediment characteristics

– Record any changes that have occurred in/near the sampling area

 Riparian area

 Grain size

 Observable organic content

 Other

– Indicate distance to reference location (for example, bridge/gage)

– Indicate flow direction

– Draw any other distinguishing features that will assist in finding sampling area location 

again

° Record relationship between sampling-area name and key sample-identification information for NWIS 

on MPP- and MDP-rates field form

•	 Shipping forms

° Fill out Wisconsin Mercury Research Laboratory (WMRL) analytical services request form

	Use a new sheet for each sample collected

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
40 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

° Remaining shipping forms may be filled out in the office, prior to shipping samples 

d. Verify that all labels and forms are in agreement regarding sampling-area names and key sample-identification 

information

Sample collection 

1. Bed-sediment-sample collection

a. Insert 2-cm-deep polycarbonate core (8-cm diameter) into the sediment until top edge is flush with sediment/water 

interface

b. Gently scoop away sediment downstream of the core ring

c. Insert stiff plastic sheet under the bottom of the core ring (where sediment has been scooped away)

d. Slide sheet under the core ring, keeping it flush with the core ring bottom

e. Slowly lift the resulting patty from the stream bottom

•	 Where flows are sufficiently fast to remove top layer of sediment, place a second plastic sheet on the core

ring before lifting

f. Divide patty for analysis

•	 Hold plastic sheet containing core ring and patty horizontal

•	 Lift core ring straight up, leaving sediment patty on plastic sheet

•	 Use core ring to parse patty for sample processing

2. Pore-water-sample collection

a. Sampling equipment preparation

•	 Attach acrylic disc to probe, 2 cm above vents

•	 Secure the C-flex and short Teflon® tubes together with cable tie

•	 Insert probe perpendicular to the sediment surface

° Acrylic disc should rest on top of sediment

° Avoid moving probe, as this can cause stream-water influx

•	 Pump water at a low flow rate to minimize depletion of pore water in the area

•	 Allow sediment slug to evacuate the line

•	 Once water runs fairly clear, attach cartridge filter (quartz fiber, 47-mm diameter, 0.7-μm nominal pore size)

•	 Hold filter upright to purge air from it

•	 Allow a few milliliters of water to flush it

b. Sample collection

•	 Pour acid (dilute hydrochloric acid (HCl)) from 500-mL Teflon® bottle into an acid-waste container

•	 Rinse three times with small aliquots of filtered pore water

•	 Deploy probe to a minimum of three, spatially separated locations in the sample area

° Each time probe is deployed, remove filter from line and allow sediment plug to evacuate before 

replacing

•	 Rinse anion vial three times and fill directly from line

•	 Fill 500-mL Teflon® bottle to the top

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sampling strategy (continued)
Appendix 1 41

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sample processing

Bed sediment: reach characterization

1. Use core ring to parse patty directly into sample jars (no compositing)

a. Leave headspace of approximately 20 to 30 percent of container volume (for expansion upon freezing)

b. Discard remaining sediment into stream

c.	 Fill jars for analyses:

•	 LOI

° 30-mL polypropylene jar (not acid-rinsed)

° Store on dry ice/in freezer

° Ship

	Timing: once all streams have been sampled

	To: WMRL

	Conditions: dry ice

•	 Percent fines

° 30-mL polypropylene jar (not acid-rinsed)

° Store at ambient temperature in a cool, dark location (don’t freeze)

° Ship

	Timing: once all streams have been sampled

	To: Sediment laboratory

	Conditions: ambient temperature (cool, dark location)

Bed sediment: spatial and temporal biogeochemical sampling

1. Bed-sediment-sample processing

a. Sieved MPP- and MDP-rates fraction

•	 Constitutes 7/8 of each patty collected in a sampling area

•	 Construct apparatus (fig. 5)

° Use brass lid-ring to secure 1-mm nylon mesh to a half-pint mason jar

° Cap mason jar with an upside-down, 250-mL beaker (with bottom cut out)

	This fits snugly over the lid-ring (overlapping it by ~1 cm) and forms an enclosure to contain 

sediment during sieving

•	 Sieve sample

° Add small amount of sediment (~1/4 of patty) to the enclosure formed by the upside-down beaker

° Tamp down on sediment using plastic bottle

° Remove larger pieces stuck on mesh and repeat with another small amount of sediment

•	 Continue collecting patties until the mason jar is filled to the top with sieved sediment and pore water

•	 Prepare sample for storage and shipment

° Remove mesh sieve and lid-ring

° Clean threads with Kimwipe®

° Secure lid on mason jar using lid-ring

° Wrap lid with Parafilm M®, to seal

° Place mason jar in foam sleeve
42 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sample processing (continued)

° Place wrapped jar in sealed Ziploc® bag

° Store on wet ice

° Ship

	Timing: as soon as possible (optimally within 24 hours of sampling)

	To: MPP- and MDP-rates laboratory

	Conditions: wet ice

b. Whole-sediment fraction

•	 Constitutes 1/8 of each patty collected in a sampling area

•	 Deposit sediment into a 120-mL polypropylene jar for compositing

•	 Mix sediment by stirring the sample

° Use a clean Teflon®, plastic, or glass device

° 30 to 60 seconds

° Try not to entrain air into sample

•	 Remove sediment for jars using an acid-cleaned plastic spoon or Teflon® policeman

° Leave headspace of approximately 20 to 30 percent of container volume (for expansion upon freezing)

° Fill jars for analyses:

	THg, MeHg, and Hg(II)R

– 20-mL Teflon® jar

 Alternatively an acid-cleaned, DI-rinsed 30-mL polypropylene jar may be used 

– Store on dry ice/in freezer

– Ship

 Timing: once all streams have been sampled

 To: WMRL

 Conditions: dry ice

	AVS

– 30-mL polypropylene jar (not acid-rinsed)

– (Do not add zinc acetate)

– Store on dry ice/in freezer

– Ship

 Timing: once all streams have been sampled

 To: Sulfur geochemistry laboratory

 Conditions: dry ice

	Percent fines

– 30-mL polypropylene jar (not acid-rinsed)

– Store at ambient temperature in a cool, dark location (don’t freeze)

– Ship

 Timing: once all streams have been sampled

 To: Sediment laboratory

 Conditions: ambient temperature (cool, dark location)

Pore water: spatial and temporal biogeochemical sampling

1. Pore-water-sample processing

a. Fill vial directly from sampling line

•	 Anions
Appendix 1 43

Appendix 1. Method summary sheets—Continued.

Appendix 1b. Method summary sheets: detailed studies—Continued.

Sample processing (continued)

° 6-mL high-density polyethylene vial

° Filtered sample, but not part of composite

° Store on wet ice/refrigerator

° Ship

	Timing: once all streams have been sampled

	To: Sulfur geochemistry laboratory

	Conditions: wet ice

b. Field measurements

•	 Decant water from the composite pore water bottle (500-mL Teflon®) for all measurements

c. Fill vials from the composite pore water collected in the 500-mL Teflon® bottle

•	 DOC

° 40-mL amber glass vial

° Do not rinse vial

° Fill vial

° Store on wet ice/refrigerator

° Ship

	Timing: once all streams have been sampled

	To: Carbon geochemistry laboratory

	Conditions: wet ice

•	 Nutrients

° 60-mL plastic vial

° Rinse vial three times

° Fill vial, but leave 20 to 30 percent of vial volume as headspace for expansion upon freezing

° Store on dry ice/in freezer

° Ship

	Timing: once all streams have been sampled

	To: Sulfur geochemistry laboratory

	Conditions: dry ice

•	 THg and MeHg

° 500-mL Teflon® bottle

	Minimum submission volume is 250 mL 

° After water has been poured off for other analyses, preserve sample

	Final volume of 1-percent HCl

– 10 mL of 6-normal (50-percent) HCl for ~500 mL of sample

– 5 mL of 6-normal (50-percent) HCl for ~250 mL of sample

	Mix

	Store at ambient temperature in a cool, dark location

	Ship

–	 Timing: once all streams have been sampled

–	 To: WMRL

–	 Conditions: ambient temperature (cool, dark location)
44 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury [NWIS, National Water Information System; --, constituent is incompatible with storage in the National Water Information System database; MeHg, methylmercury; MPP, methylmercury production potential; MDP, methylmercury degradation potential; Fe(II), ferrous iron; Fe(III), ferric iron; THg, total mercury; Hg(II)R, reactive mercury; nm, nanometer; S, sulfur; C, carbon; N, nitrogen; P, phosphorus] Medium Parameters Units (abbreviated) Units (full) NWIS database parameter code Field Stream water pH standard units standard units 00400 Specific conductance μS/cm at 25°C microsiemen per centimeter at 25 degrees Celsius 00095 Dissolved oxygen (DO) mg/L milligram per liter 00300 Temperature °C degree Celsius 00010 Streamflow, instantaneous ft3/s cubic feet per second 00061 Sediment Oxidation-reduction potential (ORP), relative to the standard hydrogen electrode mV millivolt 63002 pH standard units standard units 70310 Temperature °C degree Celsius -- Pore water Sulfide mg/L milligram per liter -- Oxidation-reduction potential (ORP), relative to the standard hydrogen electrode mV millivolt 63002 pH standard units standard units -- Hyporheic zone Piezometric head mm millimeter -- Methylmercury production- and degradation-potential-rates laboratory Sediment MeHg production-potential (MPP) rate pg/g dry wt/d picogram per gram, dry weight, per day -- MeHg degradation-potential (MDP) rate pg/g dry wt/d picogram per gram, dry weight, per day -- MPP rate:MDP rate ratio (unitless) (unitless) -- MeHg production rate constant 1/d per day -- MeHg degradation rate constant 1/d per day -- Microbial sulfate reduction nmol/g dry wt/d nanomole per gram, dry weight, per day -- Dry weight % wet wt percent, wet weight -- Loss on ignition (LOI)

% percent --

Bulk density g/cm3 wet sed gram per cubic centimeter, wet sediment --Porosity mL PW/cm3 wet sed milliliter of pore water per cubic centimeter, wet sediment --Acid-volatile sulfur μmol/g dry wt micromole per gram, dry weight --

Appendix 2. Primary and Ancillary Constituents Analyzed for in Bed Sediment and Pore Water Collected for the National Water-Quality Assessment (NAWQA) Program Detailed Mercury Studies. 
Appendix 2 45

Medium Parameters Units (abbreviated) Units (full) NWIS database parameter code

Methylmercury production- and degradation-potential-rates laboratory (cont.)

Sediment (cont.) Total-reduced sulfur μmol/g dry wt micromole per gram, dry weight --

Acid-extractable Fe(II) mg/g dry wt milligram per gram, dry weight --Amorphous Fe(III) mg/g dry wt milligram per gram, dry weight --Crystalline Fe(III) mg/g dry wt milligram per gram, dry weight --Sediment oxidation-reduction potential (ORP) at 

time of incubation

 mV millivolt --

Sediment pH at time of incubation standard units standard units --Incubation temperature °C degree Celsius --

Pore water1 Fe(II) mg/L milligram per liter --

Sulfate μmol/L micromole per liter --Chloride μmol/L micromole per liter --Acetate μmol/L micromole per liter --

Wisconsin Mercury Research Laboratory (WMRL)

Sediment THg ng/g dry wt nanogram per gram, dry weight 62978

MeHg ng/g dry wt nanogram per gram, dry weight 62979Hg(II)R ng/g dry wt nanogram per gram, dry weight --Loss on ignition (LOI) % percent 64178Dry weight % wet wt percent, wet weight 64177

Pore water THg, filtered water ng/L nanogram per liter 50287

MeHg, filtered water ng/L nanogram per liter 50285

Carbon geochemistry laboratory

Pore water Dissolved organic carbon (DOC) mg/L milligram per liter 00681

Ultraviolet (UV) absorbance at 254 nm units/cm units per centimeter 50624Specific ultraviolet absorbance (SUVA) at 254 nm L/(mg DOC*m) liter per (milligram of dissolved organic carbon * meter) 63162

Appendix 2. Primary and ancillary constituents analyzed for in bed sediment and pore water collected for the National Water-Quality Assessment (NAWQA) Program detailed mercury studies—Continued. [NWIS, National Water Information System; --, constituent is incompatible with storage in the National Water Information System database; MeHg, methylmercury; MPP, methylmercury production potential; MDP, methylmercury degradation potential; Fe(II), ferrous iron; Fe(III), ferric iron; THg, total mercury; Hg(II)R, reactive mercury; nm, nanometer; S, sulfur; C, carbon; N, nitrogen; P, phosphorus]
46 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury Appendix 2. Primary and ancillary constituents analyzed for in bed sediment and pore water collected for the National Water-Quality Assessment (NAWQA) Program detailed mercury studies—Continued. [NWIS, National Water Information System; --, constituent is incompatible with storage in the National Water Information System database; MeHg, methylmercury; MPP, methylmercury production potential; MDP, methylmercury degradation potential; Fe(II), ferrous iron; Fe(III), ferric iron; THg, total mercury; Hg(II)R, reactive mercury; nm, nanometer; S, sulfur; C, carbon; N, nitrogen; P, phosphorus] Medium Parameters Units (abbreviated) Units (full) NWIS database parameter code Sulfur geochemistry laboratory Sediment Acid-volatile sulfide (AVS) % wet wt percent, wet weight -- Disulfides % wet wt percent, wet weight -- Organic S % wet wt percent, wet weight -- Sulfate % wet wt percent, wet weight -- Total C % dry wt percent, dry weight -- Organic C % dry wt percent, dry weight -- Inorganic C % dry wt percent, dry weight -- Total N % dry wt percent, dry weight -- Total P % dry wt percent, dry weight -- Total S % dry wt percent, dry weight -- Pore water Specific conductance μS/cm at 25°C microsiemen per centimeter at 25 degrees Celsius -- Total dissolved solids (TDS) mg/L milligram per liter -- Sulfate mg/L milligram per liter -- Chloride mg/L milligram per liter -- Fluoride mg/L milligram per liter -- Bromide mg/L milligram per liter -- Nitrate mg/L milligram per liter -- Ammonium μg/L microgram per liter -- Phosphate μg/L microgram per liter -- Sediment laboratory Sediment Percent fines, percent of sediment less than 0.063 millimeters

% percent 80164

1 Pore water used for analyses in the Methylmercury production- and degradation-potential-rates laboratory was derived by centrifuging sediment collected for microbial rate assays.
Appendix 3 47

Appendix 3. Field Forms

Appendix 3a. Field forms common to reconnaissance and detailed studies.

3a–1. Stream water (not included in this report)

3a–2. General sampling form

This form is available for download at http://pubs.usgs.gov/ofr/2008/1279/

General sampling form

Field Data Sheet 

SAMPLE HEADER 

Station: Date (MM/DD/YYY):

Waterbody:

Station description: 

Station ID: Reach: Start time: h

Collector (leader): End time: h

Streambed-sediment temperature: oC

Sample and photographic notes: 

RELATED SAMPLING ACTIVITIES

(Circle all that apply) 

Water chemistry Streamflow Habitat Tissues 

Invertebrate survey Algae survey Other (specify): 

SKETCHES AND ADDITIONAL NOTES
48 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Appendix 3. Field forms—Continued.

Appendix 3b. Field forms specifically for detailed studies.

3b–1. Reach establishment

This form can be accessed at http://pubs.usgs.gov/ofr/2008/1279/

Collectors: _______________________________________________________

Station Name: _____________________________________________________

STAID: ________________

Date: __________________

Reach type (circle one): wadeable unwadeable

Representative wetted channel widths: 

1. ___________ m ft 

2. ___________ m ft 

3. ___________ m ft 

Mean: Mean wetted channel width (MCW) = _______ m ft 

Ideal reach length: MCW x 20 = __________ m ft 

Actual reach length: ________________ m ft

[wadeable reaches must be ≥150 m (492 ft)] 

[unwadeable reaches must be between ≥500 m (1,640 ft)] 

Distance between transects: Actual reach length / 14 = distance between transects

 ________ m ft / 14 = ________ m ft 

Reference location:

Description (circle one): gage bridge other _________________________ 

Location: latitude ____ ____ ____ longitude ____ ____ ____ 

 Datum: NAD 83 NAD 27 Other ______________ 

 (can be obtained from site header file, reference location for the STAID;

 all NWIS information is in NAD 27) 

Location of reach:

Distance from reference location to nearest reach boundary: ______ m ft 

 Boundary nearest reference location (circle one): upstream downstream 

Descriptors of reach-boundary locations 

 Upstream: 

 LEW:

Latitude (DMS):___________ Longitude (DMS): ___________ 

Datum:_________ (NAD 83 preferred) Accuracy: ______ m ft

Landmarks/reference points:_____________________________ 

 REW:

Latitude (DMS):___________ Longitude (DMS): ___________ 

Datum:_________ (NAD 83 preferred) Accuracy: ______ m ft

Landmarks/reference points:_____________________________ 

 Downstream:

 LEW:

Latitude (DMS):___________ Longitude (DMS): ___________ 

Datum:_________ (NAD 83 preferred) Accuracy: ______ m ft

Landmarks/reference points:_____________________________ 

 REW:

Latitude (DMS):___________ Longitude (DMS): ___________ 

Datum:_________ (NAD 83 preferred) Accuracy: ______ m ft

Landmarks/reference points:_____________________________ 

Comments:

__________________________________________________________________________________________

__________________________________________________________________________________________

__________________________________________________________________________________________

__________________________________________________________________________________________

__________________________________________________________________________________________

__________________________________________________________________________________________

__________________________________________________________________________________________

__________________________________________________________________________________________
Appendix 3 49

Appendix 3. Field forms—Continued.

Appendix 3b. Field forms specifically for detailed studies.

3b–2. Reach diagram

This form can be accessed at http://pubs.usgs.gov/ofr/2008/1279/

Station Name: ___________________ STAID:______________ Date:_________

(include: reference location, habitat types, flow direction, important features in area, substrate zones)
50 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Appendix 3. Field forms—Continued.

Appendix 3b. Field forms specifically for detailed studies.

3b–3. Transect sampling

This form can be accessed at http://pubs.usgs.gov/ofr/2008/1279/

Transect sampling

Station Name: __________________________ Collectors: __________________

STAID: ________________

Date: __________________ Transect: ______

Bed-Substrate Characterization

Description Size (mm) Basic categories Expanded categories 

Smooth bedrock/concrete/hardpan N/A >3 1

Fine-grained; organic-rich N/A 2 2

Mixed sand and fine-grained; intermediate organic content ≤ 2 2.5 2.5

Sand; organic-poor > 0.063–2 3 3

Fine/medium gravel > 2–16 >3 4

Coarse gravel > 16–32 >3 5

Very coarse gravel > 32–64 >3 6

Small cobble > 64–128 >3 7

Large cobble > 128–256 >3 8

Small boulder > 265–512 >3 9

Large boulder/irregular bedrock/irregular hardpan/irregular artificial surface > 512 >3 10

Method used for measurements (circle one):

rangefinder measuring tape other: _____________

Units of measurement (circle one): ft m

Substrate 

zone 

Position 

of rightmost

boundary

*

Width 

of zone

Position 

of zone

midpoint

**

Bedsubstrate 

category

(see table

above)

Core 

collected? 

(Y/N)

Time of 

sample

collection 

Method of core collection 

(circle)

LEW -- -- -- -- -- --

T__-1 Core Grab None

T__-2 Core Grab None

T__-3 Core Grab None

T__-4 Core Grab None

T__-5 Core Grab None

T__-6 Core Grab None

T__-7 Core Grab None

T__-8 Core Grab None

T__-9 Core Grab None

T__-10 Core Grab None

T__-11 Core Grab None

T__-12 Core Grab None

T__-13 Core Grab None

T__-14 Core Grab None

T__-15 Core Grab None

REW*** -- -- -- -- -- * “Position of right-most boundary” refers to the location of the right-most (when facing downstream) boundary of the substrate zone on the tape or rangefinder. With a tape, the left edge

of water may not be positioned at the zero point marked on the tape; record the measurement on the tape at the left edge of water (LEW) or at the boundary of the substrate zone. With a 

rangefinder, all measurements should be taken from the LEW; the LEW should be zero. 

** “Position of zone midpoint” refers to the location of the zone’s midpoint on the tape/rangefinder.

*** REW: right edge of water

Wetted Width (circle units): REW – LEW = ___________ ft m

Comments: _________________________________________________________

____________________________________________________________________

____________________________________________________________________

____________________________________________________________________
Appendix 3 51

Appendix 3. Field forms—Continued.

Appendix 3b. Field forms specifically for detailed studies.

3b–4. Methylmercury production- and degradation-potential rates

This form can be accessed at http://pubs.usgs.gov/ofr/2008/1279/

Methylmercury production- and degradation-potential rates

NAWQA Mercury Detailed Studies 

Collected by: _____________________________________ 

Field Data Sheet Full date (dd/mm/yy): ______________________________ 

I. LOCATION 

Site (full name): _________________________________________ Site/Station ID: __________________________________ 

Latitude: ___________________ Longitude: ____________________ Datum: _____________ Accuracy: ___________ 

II. SEDIMENT SAMPLING

Begin time: ____________ End time: ____________ Median time: ____________ SW Temp (oC): __________ 

Mason jars filled (#): _______ mason jar size (#): _______ 

Depth interval (for example, 0–2 cm)

 D1 (cm): _______ D2 (cm): _______ D3 (cm): _______ D4 (cm): _______ 

Site description:_________________________________________________________________________________________ 

______________________________________________________________________________________________________ 

______________________________________________________________________________________________________ 

______________________________________________________________________________________________________ 

Sample collection:_______________________________________________________________________________________ 

______________________________________________________________________________________________________ 

______________________________________________________________________________________________________ 

______________________________________________________________________________________________________ 

Sample physical description (color, texture, smell, etc.):________________________________________________________ 

______________________________________________________________________________________________________ 

______________________________________________________________________________________________________ 

______________________________________________________________________________________________________ 

______________________________________________________________________________________________________ 

III. Analysis To Be Conducted (Check) IV. Electrode checks and calibrations

Reading 

(mV) 

_____ 203Hg-Methylation ORP electrode calibration 

_____ 14C-MeHg Degradation Std. Used

_____ 35S-Sulfate reduction Zobell’s

_____ TRS/AVS quinhydrone @ pH 4

_____ PW-SU quinhydrone @ pH 7

_____ PW-SO4, Ac Orion®

ORP std (bed-sediment electrode)

_____ LOI Orion® ORP std (pore-water electrode)

_____ Eh/pH 

_____ BS/PW-Fe pH electrode calibration

_____ PW-DOC (If auto-calibration, circle buffers used) Reading Temp. (

o

C) 

_____ other (specify): __________________ 4.0

_____ other (specify): __________________ 7.0

10.0

V. Minipiezometer measurements VI. On-Site Measurements

Depth of penetration (cm) ______ R1 R2 R1 R2 

in situ

or 

patty

Head difference (+/-)(mm) Bed-sediment ORP (mV)

Bed-sediment pH

Depth of penetration (cm) ______ R1 R2 Bed-sediment temperature (

o

C)

Head difference (+/-)(mm) R1 R2 

Pore-water ORP (mV)

Depth of penetration (cm) ______ R1 R2 Pore-water pH

Head difference (+/-)(mm) Pore water S2-(circle 1oor 2o) (mV)
52 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Appendix 3. Field forms—Continued.

Appendix 3b. Field forms specifically for detailed studies.

3b–5. Pore-water sulfide

This form can be accessed at http://pubs.usgs.gov/ofr/2008/1279/

Pore-water sulfide

Pore-water sulfide collection sheet 

Site Name: Site Number:

Project Name: Date:

Detection Limit of Electrode: -700 mV Electrode Used:

Sample ID Sulfide Reading (mV)
Appendix 4 53

Appendix 4. Sample Labels

All labels are 1 in. by 2-5/8 in., and designed to fit Avery© weather-proof mailing labels (Avery© label number 5520).

All labels are available online as pre-formatted Microsoft© Word templates at: http://pubs.usgs.gov/ofr/2008/1279/

Please note that Avery© labels 5520 use the same Microsoft© Word template as Avery© label number 5160.

Appendix 4a. Sample labels: reconnaissance studies.

WMIC – 05 04070720

South Branch Oconto R. nr. Breed, WI

Medium Code: H 

Sample Type: 9 

Date: ____________ Time: ____________

 Hg (THg and MeHg) – 30-mL Jar

WMIC – 05 04070720

South Branch Oconto R. nr. Breed, WI

Medium Code: H 

Sample Type: 9 

Date: ____________ Time: ____________

 AVS – 30-mL Jar

WMIC – 05 04070720

South Branch Oconto R. nr. Breed, WI

Medium Code: H 

Sample Type: 9 

Date: ____________ Time: ____________

 Sand/Fine – 30-mL Jar Acct. No.: XXXXX
54 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Appendix 4b. Sample labels: detailed studies.

Appendix 4. Sample labels—Continued.

All labels are 1 in. by 2-5/8 in., and designed to fit Avery© weather-proof mailing labels (Avery© label number 5520).

All labels are available online as pre-formatted Microsoft© Word templates at: http://pubs.usgs.gov/ofr/2008/1279/

Please note that Avery© labels 5520 use the same Microsoft© Word template as Avery© label number 5160.

Bed sediment for LOI 04075365

Evergreen River near Langlade, WI 

Date: ____________ Time: ____________ 

Medium: ______ Sample Type: ______

 Depth: ____________ Site: ____________

 Contact: <Contact name> (XXX/XXX-XXXX)

Bed sediment for percent fines 04075365

Evergreen River near Langlade, WI 

Date: ____________ Time: ____________ 

Medium: ______ Sample Type: ______

 Depth: ____________ Site: ____________

 Contact: <Contact name> (XXX/XXX-XXXX) 

Bed sed. for MeHg prod/degrad. 04075365

Evergreen River near Langlade, WI 

Date: ____________ Time: ____________ 

Medium: ______ Sample Type: ______

 Depth: ____________ Site: ____________

 Contact: <Contact name> (XXX/XXX-XXXX) 

 

Bed sediment sample for Hg 04075365

Evergreen River near Langlade, WI 

Date: ____________ Time: ____________ 

Medium: ______ Sample Type: ______

 Depth: ____________ Site: ____________

 Contact: <Contact name> (XXX/XXX-XXXX) 

 

Bed sediment for AVS 04075365

Evergreen River near Langlade, WI 

Date: ____________ Time: ____________ 

Medium: ______ Sample Type: ______

 Depth: ____________ Site: ____________

 Contact: <Contact name> (XXX/XXX-XXXX) 

 

Pore water for nutrients 04075365

Evergreen River near Langlade, WI 

Date: ____________ Time: ____________ 

Medium: ______ Sample Type: ______

 Depth: ____________ Site: ____________

 Contact: <Contact name> (XXX/XXX-XXXX) 

 

Pore water for anions 04075365

Evergreen River near Langlade, WI 

Date: ____________ Time: ____________ 

Medium: ______ Sample Type: ______

 Depth: ____________ Site: ____________

 Contact: <Contact name> (XXX/XXX-XXXX) 

 

Pore water for DOC 04075365

Evergreen River near Langlade, WI 

Date: ____________ Time: ____________ 

Medium: ______ Sample Type: ______

 Depth: ____________ Site: ____________

 Contact: <Contact name> (XXX/XXX-XXXX) 

 

Pore water for Hg 04075365

Evergreen River near Langlade, WI 

Date: ____________ Time: ____________ 

Medium: ______ Sample Type: ______

 Depth: ____________ Site: ____________

 Contact: <Contact name> (XXX/XXX-XXXX) 

 
Appendix 5 55

[cm, centimeter; M, molar; HCl, hydrochloric acid; mm, millimeter; mL, milliliter; WMRL, Wisconsin Mercury Research Laboratory; ®, registered 

trademark; THg, total mercury; MeHg, methylmercury; Hg(II)R, reactive mercury; USEPA, U.S. Environmental Protection Agency; AVS, acid-volatile 

sulfide; LOI, loss on ignition; n/a, not applicable; SW, stream water; PW, pore water; QFF, quartz fiber filter; μm, micrometer; N, normal; L, liter; DOC, 

dissolved organic carbon; HDPE, high-density polyethylene; ORP, oxidation-reduction potential; SAOB, sulfide antioxidant buffer; cm3, cubic centimeter; 

MPP, methylmercury production potential; MDP, methylmercury degradation potential; V, volt; m, meter; PVC, polyvinyl chloride; DI, deionized; %, percent; 

GPS, Global Positioning System; WAAS, wide area augmentation system; sample (to which quantities are related to) refers to all sediment and pore water 

(where applicable) collected from the same sampling area within a stream; study area (to which quantities are related to) refers to the NAWQA study area (for 

example, the Willamette Basin)]

Equipment Cleaning 

procedure

Quantity per study

Quantity 

relates to 

Reconnaissance each...

Detailed

Reach 

characterization1 Spatial Temporal

Methylmercury production- and degradation-potential-rates laboratory

2-cm sections of polycarbonate core tube 

(8-cm diameter)

Laboratory 

method2

0 1 1 1 Stream

Flexible solid plastic sheets Laboratory 

method2

0 2 2 2 Stream

Half-pint mason jars Laboratory 

method2

0 0 1 1 Sample

Lids (for half-pint mason jars) New 0 0 1 1 Sample

Nylon 1-mm mesh (10 cm x 10 cm) New 0 0 1 1 Stream

Plastic beakers with bottom cut off 

(250-mL)

Laboratory 

method2

0 0 1 1 Stream

Plastic bottle that fits through small end 

of cut-off beaker

Laboratory 

method2

0 0 1 1 Stream

Wisconsin Mercury Research Laboratory (WMRL)

 20-mL Teflon® jar (acid rinsed)

(for sediment THg/MeHg/Hg(II)R)

USEPA, 2002 1 0 1 1 Sample

 30-mL polypropylene jar (not acidrinsed) (for sediment AVS, percent 

fines, and LOI)

New 2 2 2 2 Sample

Zinc-acetate solution

(for preserving AVS samples)

n/a 1 0 0 0 Trip

Disposable pipets (graduated at 0.1-mL 

increments) (for delivering zincacetate solution to AVS samples)

New 1 0 0 0 Sample

Pore-water probe USEPA, 2002 0 0 1 1 Trip

Acrylic disc (for minimizing the flow of 

SW into the PW-sampling area)

Laboratory 

method3

0 0 1 1 Trip

Long Teflon® sampling line

(1/4-inch outside diameter)

USEPA, 2002 0 0 1 1 Stream

Short C-flex pump-head tube Laboratory 

method4

0 0 1 1 Stream

Short Teflon® sampling line

(1/4-inch outside diameter)

USEPA, 2002 0 0 1 1 Stream

Loaded filter cartridges (QFF: 47-mm 

diameter, 0.7-μm nominal pore size)

USEPA, 2002 0 0 3 3 Sample

Appendix 5. Equipment Required for Bed-Sediment and Pore-Water Sampling 

in Association with the National Water-Quality Assessment (NAWQA) Program 

Reconnaissance and Detailed Mercury Studies. 
56 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Equipment Cleaning 

procedure

Quantity per study

Quantity 

relates to 

Reconnaissance each...

Detailed

Reach 

characterization1 Spatial Temporal

Zip ties New 0 0 1 1 Sample

500-mL coded Teflon® sample bottle

(for filtered THg and MeHg)

USEPA, 2002 0 0 1 1 Sample

Spare filters (QFF: 47-mm diameter, 

0.7-μm nominal pore size)

Laboratory 

method5

0 0 5 5 Sample

Tweezers

(for loading spare filters into 

cartridges)

USEPA, 2002 0 0 2 2 Trip

Cartridge wrench n/a 0 0 2 2 Trip

Bottle of 6N-HCl with jar

(for filtered THg and MeHg 

preservation)

n/a 0 0 1 1 Study area

1-L bottle of Milli-Q® water

(for pore water THg and MeHg 

blanks)

n/a 0 0 Varies Varies Trip

Carbon geochemistry laboratory

40-mL amber baked glass bottles with 

Teflon®-lined lids (for DOC)

New or baked 

using 

laboratory 

method6

0 0 1 1 Sample

Sulfur geochemistry laboratory

Anion vials New 0 0 1 1 Sample

Nutrient vials New 0 0 1 1 Sample

20-mL HDPE scintillation vials

(for pore-water sulfide, ORP, and pH)

New 0 0 2 2 Sample

SAOB in vials (pre-measured) n/a 0 0 1 1 Day

Ascorbic acid in vials (pre-measured) n/a 0 0 1 1 Day

5-cm3 syringe (for pore-water ORP 

and sulfide)

New 0 0 2 2 Sample

C-flex tube (for ORP) New 0 0 1 1 Sample

Sulfide electrode (Orion® model 

9616BN)

n/a 0 0 1 1 Kit

Filling solution A (for sulfide electrode) n/a 0 0 1 1 Kit

Sediment-ORP electrode (Orion® model 

9180BN)

n/a 0 0 1 1 Kit

Pore-water-ORP electrode 

(Microelectrodes, Inc. model 

MI-800/710)

n/a 0 0 1 1 Kit

Appendix 5. Equipment required for bed-sediment and pore-water sampling in association with the National Water-Quality 

Assessment (NAWQA) Program reconnaissance and detailed mercury studies—Continued. 

[cm, centimeter; M, molar; HCl, hydrochloric acid; mm, millimeter; mL, milliliter; WMRL, Wisconsin Mercury Research Laboratory; ®, registered 

trademark; THg, total mercury; MeHg, methylmercury; Hg(II)R, reactive mercury; USEPA, U.S. Environmental Protection Agency; AVS, acid-volatile 

sulfide; LOI, loss on ignition; n/a, not applicable; SW, stream water; PW, pore water; QFF, quartz fiber filter; μm, micrometer; N, normal; L, liter; 

DOC, dissolved organic carbon; HDPE, high-density polyethylene; ORP, oxidation-reduction potential; SAOB, sulfide antioxidant buffer; cm3, cubic 

centimeter; MPP, methylmercury production potential; MDP, methylmercury degradation potential; V, volt; m, meter; PVC, polyvinyl chloride; DI, 

deionized; %, percent; GPS, Global Positioning System; WAAS, wide area augmentation system; sample (to which quantities are related to) refers to all 

sediment and pore water (where applicable) collected from the same sampling area within a stream; study area (to which quantities are related to) refers 

to the NAWQA study area (for example, the Willamette Basin)]
Appendix 5 57

Appendix 5. Equipment required for bed-sediment and pore-water sampling in association with the National Water-Quality 

Assessment (NAWQA) Program reconnaissance and detailed mercury studies—Continued. 

[cm, centimeter; M, molar; HCl, hydrochloric acid; mm, millimeter; mL, milliliter; WMRL, Wisconsin Mercury Research Laboratory; ®, registered 

trademark; THg, total mercury; MeHg, methylmercury; Hg(II)R, reactive mercury; USEPA, U.S. Environmental Protection Agency; AVS, acid-volatile 

sulfide; LOI, loss on ignition; n/a, not applicable; SW, stream water; PW, pore water; QFF, quartz fiber filter; μm, micrometer; N, normal; L, liter; 

DOC, dissolved organic carbon; HDPE, high-density polyethylene; ORP, oxidation-reduction potential; SAOB, sulfide antioxidant buffer; cm3, cubic 

centimeter; MPP, methylmercury production potential; MDP, methylmercury degradation potential; V, volt; m, meter; PVC, polyvinyl chloride; DI, 

deionized; %, percent; GPS, Global Positioning System; WAAS, wide area augmentation system; sample (to which quantities are related to) refers to all 

sediment and pore water (where applicable) collected from the same sampling area within a stream; study area (to which quantities are related to) refers 

to the NAWQA study area (for example, the Willamette Basin)]

Equipment Cleaning 

procedure

Quantity per study

Quantity 

relates to 

Reconnaissance each...

Detailed

Reach 

characterization1 Spatial Temporal

Orion® ORP standard n/a 0 0 1 1 Kit

ORP filling solution n/a 0 0 1 1 Kit

Low-maintenance pH/temperature triode 

(Orion® model 9107BN)

n/a 0 0 1 1 Kit

pH calibration standards n/a 0 0 1 1 Kit

Magnetic stir plate n/a 0 0 1 1 Kit

Stir bars (12.7-mm length) n/a 0 0 1 1 Kit

Orion® meter model 250 A+ n/a 0 0 1 1 Kit

Study area

Guillotine sampler/10-cm section of 

1.5-inch diameter Teflon® tube/Teflon®

spoon, scoop or spatula/plastic spoon 

or scoop (can be made by cutting 

plastic sample bottle)

Shelton and 

Capel, 1994; 

Wilde, 2004

1 0 0 0 Sample

Glass/Teflon®/plastic bowl (for 

compositing samples)

Shelton and 

Capel, 1994; 

Wilde, 2004

1 0 0 0 Sample

120-mL polypropylene jar (for 

compositing samples)

Shelton and 

Capel, 1994; 

Wilde, 2004

0 0 1 1 Sample

Plastic spoon/Teflon® policeman 

(WMRL) (for mixing sediment)

Shelton and 

Capel, 1994; 

Wilde, 2004

1 0 1 1 Sample

Grab sampler (Birge-Ekman, 9-inch 

square)

Shelton and 

Capel, 1994; 

Wilde, 2004

1 1 1 1 Trip

Soft rope (in meters) (for grab sampler, 

clipboards, and float boats)

n/a 6 15–30 6 6 Trip

Sieve (0.063-mm pore size) (for assisting 

in categorizing substrate zones)

n/a 0 1 1 1 Trip

Parafilm M® roll (for sealing mason jars) n/a 0 0 1 1 Study area

Foam sleeves (for protecting the MPPand MDP-rates samples in storage and 

shipment)

New 0 0 1 1 Sample

Floating cooler/tub boats for equipment 

towing on stream

n/a 0 0 2 2 Trip

Peristaltic pump n/a 0 0 1 1 Trip

12-V battery n/a 0 0 1 1 Trip
58 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Equipment Cleaning 

procedure

Quantity per study

Quantity 

relates to 

Reconnaissance each...

Detailed

Reach 

characterization1 Spatial Temporal

Lead for 12-V battery (for connection to 

the peristaltic pump)

n/a 0 0 1 1 Trip

Clear zip ties (for attaching C-flex tube 

to short Teflon® tube)

New 0 0 1 1 Sample

 Rangefinder (for measuring reach 

length, distance from reference 

location, distance between transects; 

best if has at least a 

10-m minimum range)

n/a 1 1 1 1 Trip

Stream measuring tape [metric preferred] 

(for measuring stream width, point 

locations)

n/a 0 1 0 0 Trip

Stakes for measuring tape n/a 0 2 0 0 Trip

Stake flags (for marking transects on 

both sides of stream)

n/a 0 30 Varies Varies Stream

Flagging tape roll

(in case stake flag is hard to see)

n/a 0 1 1 1 Trip

4-person inflatable raft

(for carrying transect-sampling 

equipment)

n/a 0 1 0 0 Trip

Inflators (for inflating raft(s)) n/a 0 1 0 0 Trip

Small, inexpensive calculator n/a 0 1 0 0 Trip

PVC Pipe (1-inch inside diameter or 

larger)

New 0 1 0 0 Trip

Cooler with wet ice (for storing and 

shipping sediment samples for MPP 

and MDP rates; for storing PW 

samples for DOC and anions)

n/a 0 0 2 2 Trip

Cooler with dry ice (for storing sediment 

THg, MeHg, Hg(II)R, AVS, and LOI 

samples; for storing PW-nutrient 

samples)

n/a 1 3 1 1 Trip

Empty cooler/box (for storing sediment 

percent fines, and PW THg and MeHg 

samples) 

n/a 1 2 1 1 Trip

Minipiezometers n/a 0 0 1 1 Stream

Shovel (for retrieving the minipiezometer 

tip, if needed)

n/a 0 0 1 1 Trip

Hand vacuum pump n/a 0 0 1 1 Trip

C-flex tube (for connecting hand vacuum 

pump to minipiezometer tubes) 

n/a 0 0 1 1 Trip

Appendix 5. Equipment required for bed-sediment and pore-water sampling in association with the National Water-Quality 

Assessment (NAWQA) Program reconnaissance and detailed mercury studies—Continued. 

[cm, centimeter; M, molar; HCl, hydrochloric acid; mm, millimeter; mL, milliliter; WMRL, Wisconsin Mercury Research Laboratory; ®, registered 

trademark; THg, total mercury; MeHg, methylmercury; Hg(II)R, reactive mercury; USEPA, U.S. Environmental Protection Agency; AVS, acid-volatile 

sulfide; LOI, loss on ignition; n/a, not applicable; SW, stream water; PW, pore water; QFF, quartz fiber filter; μm, micrometer; N, normal; L, liter; 

DOC, dissolved organic carbon; HDPE, high-density polyethylene; ORP, oxidation-reduction potential; SAOB, sulfide antioxidant buffer; cm3, cubic 

centimeter; MPP, methylmercury production potential; MDP, methylmercury degradation potential; V, volt; m, meter; PVC, polyvinyl chloride; DI, 

deionized; %, percent; GPS, Global Positioning System; WAAS, wide area augmentation system; sample (to which quantities are related to) refers to all 

sediment and pore water (where applicable) collected from the same sampling area within a stream; study area (to which quantities are related to) refers 

to the NAWQA study area (for example, the Willamette Basin)]
Appendix 5 59

Equipment Cleaning 

procedure

Quantity per study

Quantity 

relates to 

Reconnaissance each...

Detailed

Reach 

characterization1 Spatial Temporal

Meter stick/ruler

(for minipiezometer-head 

measurements)

n/a 0 0 1 1 Trip

Multiparameter instrument

(for example, Hydrolab® Quanta®)

n/a 1 1 1 1 Trip

Barometer n/a 1 1 1 1 Trip

Set of pH calibration standards n/a 1 1 1 1 Trip

Specific-conductance calibration 

standards 

n/a 1 1 1 1 Trip

Squirt bottle (for rinsing electrodes) n/a 1 1 1 1 Trip

1-L bottle of dilute Liquinox®

(for cleaning in the field)

New 1 1 1 1 Trip

Tap-water carboy (for cleaning in the 

field 

and for multiparameter-probestorage)

New 1 1 1 1 Trip

DI-water carboy (for cleaning equipment 

in the field and for rinsing the 

electrodes during calibrations)

New 1 1 1 1 Trip

Carboy of 5% HCl (for cleaning in the 

field)

New 1 1 1 1 Trip

Carboy for waste acid New 1 1 1 1 Trip

Plastic shoulder-length veterinary gloves 

(boxes)

New 1 2 1 1 Trip

Non-powder nitrile gloves (boxes) New 1 6 3 1 Trip

Ziploc® bags (boxes) (for storing 

samples)

New 1 3 1 1 Trip

Large clear/white garbage bags (boxes) New 1 1 1 1 Trip

Kimwipes (boxes) n/a 1 3 2 1 Trip

Chairs (for calibrations and processing) n/a 1 2 2 2 Trip

Tarp (for covering equipment if it rains) n/a 1 2 2 2 Trip

Table (for calibrations and processing) n/a 1 1 1 1 Trip

GPS unit with WAAS, time-averaging 

capabilities, andan external antenna

n/a 0 1–2 1 1 Trip

Digital camera n/a 1 1 1 1 Trip

Appendix 5. Equipment required for bed-sediment and pore-water sampling in association with the National Water-Quality 

Assessment (NAWQA) Program reconnaissance and detailed mercury studies—Continued. 

[cm, centimeter; M, molar; HCl, hydrochloric acid; mm, millimeter; mL, milliliter; WMRL, Wisconsin Mercury Research Laboratory; ®, registered 

trademark; THg, total mercury; MeHg, methylmercury; Hg(II)R, reactive mercury; USEPA, U.S. Environmental Protection Agency; AVS, acid-volatile 

sulfide; LOI, loss on ignition; n/a, not applicable; SW, stream water; PW, pore water; QFF, quartz fiber filter; μm, micrometer; N, normal; L, liter; 

DOC, dissolved organic carbon; HDPE, high-density polyethylene; ORP, oxidation-reduction potential; SAOB, sulfide antioxidant buffer; cm3, cubic 

centimeter; MPP, methylmercury production potential; MDP, methylmercury degradation potential; V, volt; m, meter; PVC, polyvinyl chloride; DI, 

deionized; %, percent; GPS, Global Positioning System; WAAS, wide area augmentation system; sample (to which quantities are related to) refers to all 

sediment and pore water (where applicable) collected from the same sampling area within a stream; study area (to which quantities are related to) refers 

to the NAWQA study area (for example, the Willamette Basin)]
60 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Equipment Cleaning 

procedure

Quantity per study

Quantity 

relates to 

Reconnaissance each...

Detailed

Reach 

characterization1 Spatial Temporal

Tap-water carboy with spigot

(for hand washing)

New 1 1 1 1 Trip

Bottle of antimicrobial hand soap

(for hand washing)

n/a 1 1 1 1 Trip

Paper towels (boxes) n/a 1 3 3 1 Trip

Two-way radios n/a 0 2–3 2–3 0 Trip

Sharp knife and toolbox n/a 1 1 1 1 Trip

Clipboard n/a 1 2 2 1 Trip

First-aid kit n/a 1 1 1 1 Trip

Copies of old sediment field forms

(for locating previously sampled 

areas)

n/a 0 1 0 1 Trip

Copies of orthophotos and topographic 

maps of stream

n/a 0 1 1 1 Stream

Blank field form – Reach-establishment 

sheet

n/a 0 1 0 0 Stream

Blank field form – Transect sheet n/a 0 20 0 0 Stream

Blank field form – Reach-diagram sheet n/a 0 1 0 0 Stream

Blank field form – General sediment 

form

n/a 1 1 1 1 Stream

Blank field form – MPP- and MDP-rates 

field form

n/a 0 0 1 1 Sample

Blank field form – Pore-water-sulfide 

datasheet

n/a 0 0 1 1 Stream

Blank field form – USGS Stream-water 

field form

n/a 1 1 1 1 Stream

Waterproof labels – Avery© label number 

5520 (1 by 2 5/8 inches)

n/a 3 2 8 8 Sample

Pens n/a 4 10 10 4 Trip

Sharpies n/a 4 10 10 4 Trip

1

 Assume 100 grab samples for each reach characterization.

2

 Equipment is washed in a bath of 4-M HCl. 

3

 Equipment is washed with dilute Liquinox®. It is then rinsed three times with tap water, three times with Milli-Q® water, and allowed to air dry.

4

 Tube is filled with 50% nitric acid, the ends of the tube are sealed, and it is soaked in a room temperature 10% HCl bath for a minimum of 7 days.

5

 Equipment is ashed in a muffle furnace at 550o C for a minimum of 2 hours.

6

 Bottles and caps are rinsed three times with tap water, and three times with DI water. Bottles are then baked at 450o C for 4 hours. Caps are dried at 

room temperature, and then secured onto clean, cooled bottles.

Appendix 5. Equipment required for bed-sediment and pore-water sampling in association with the National Water-Quality 

Assessment (NAWQA) Program reconnaissance and detailed mercury studies—Continued. 

[cm, centimeter; M, molar; HCl, hydrochloric acid; mm, millimeter; mL, milliliter; WMRL, Wisconsin Mercury Research Laboratory; ®, registered 

trademark; THg, total mercury; MeHg, methylmercury; Hg(II)R, reactive mercury; USEPA, U.S. Environmental Protection Agency; AVS, acid-volatile 

sulfide; LOI, loss on ignition; n/a, not applicable; SW, stream water; PW, pore water; QFF, quartz fiber filter; μm, micrometer; N, normal; L, liter; 

DOC, dissolved organic carbon; HDPE, high-density polyethylene; ORP, oxidation-reduction potential; SAOB, sulfide antioxidant buffer; cm3, cubic 

centimeter; MPP, methylmercury production potential; MDP, methylmercury degradation potential; V, volt; m, meter; PVC, polyvinyl chloride; DI, 

deionized; %, percent; GPS, Global Positioning System; WAAS, wide area augmentation system; sample (to which quantities are related to) refers to all 

sediment and pore water (where applicable) collected from the same sampling area within a stream; study area (to which quantities are related to) refers 

to the NAWQA study area (for example, the Willamette Basin)]
Appendix 6 61

[USGS, U.S. Geological Survey; MS, mail stop; CA, California; CO, Colorado; IA, Iowa; VA, Virginia; WI, Wisconsin]

USGS laboratory Shipping address Contact 

Methylmercury productionand degradation-potential-rates 

laboratory

USGS Branch of Regional Research

attn: Jennifer Agee

345 Middlefield Road

Building 15, McKelvey Building

MS 480

Menlo Park, CA 94025-3561

Mark Marvin-DiPasquale

Wisconsin Mercury Research 

Laboratory (WMRL)

USGS Wisconsin Water Science Center

attn: John DeWild

8505 Research Way

Middleton, WI 53562-3586

David Krabbenhoft

Carbon geochemistry laboratory USGS Branch of Regional Research

attn: Kenna Butler

3215 Marine Street

Suite E-127

Boulder, CO 80303-1290

George Aiken

Sulfur geochemistry laboratory USGS Branch of Regional Research

attn: Margo Corum

12201 Sunrise Valley Drive

MS 956

Reston, VA 20192-0002

William Orem

Sediment laboratory USGS Iowa City Sediment Laboratory

attn: Julie Nason

400 South Clinton Street

Room #269

Iowa City, IA 52240-4105

Julie Nason

Appendix 6. Laboratory Contact Information for U.S. Geological 

Survey Laboratories Performing Analyses for the National 

Water-Quality Assessment (NAWQA) Program Reconnaissance 

and Detailed Mercury Studies.
62 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Appendix 7. Shipping Forms for Reconnaissance and Detailed Studies.

Appendix 7a. Generic shipping form for the methylmercury production- and degradation-potential-rates laboratory, the 

Wisconsin Mercury Research Laboratory (for transect samples only), the carbon geochemistry laboratory, and the sulfur 

geochemistry laboratory.

This form is available for download at http://pubs.usgs.gov/ofr/2008/1279/

Generic shipping form

Filename: Shipper instructions: 

t eehsdaer ps si ht ot ni at ad ni gol el p masr et nE) 1( :t cat noc aer a ydut S

. sel p mas hti w

mr of si ht f o ypoc dr ah pi hs dna, et ad, ngi S) 2( :r eb mun xaF

. ni- gol bal et atili caf ot yr ot ar obal ot ypoc ci nort cel eli a mE) 3( : yb deppi hS

Shipping date: Lab Instructions:

. sel p masf ot pi ecer nopu st ne m

moc et on dna, et ad, ngi S) 4( : yb devi ece R

.t cat noc aer a ydut s ot ypocli a mr o xaF. mr of evaS) 5( : et ad devi ece R

Station-identification

number

(STAID)

Date

(DATES)

Time

(TIMES)

Medium

code

(MEDIM)

Station name

(SNAME)

05 1 4 9 51 General description

Sample data

Analyses

requested

Number of 

containers

Lab notes / condition of samples:

HgStudy_SUID_YYYYMMDD.xls
Appendix 7 63

Appendix 7. Shipping forms for reconnaissance and detailed studies—Continued.

Appendix 7b-1. Analytical services request form for the Wisconsin Mercury Research Laboratory (WMRL).

These forms are available for download at http://pubs.usgs.gov/ofr/2008/1279/

Analytical services request form, page 1

_ _ _ _

_

_ _

WISCONSIN MERCURY RESEARCH LABORATORY REQUEST FOR ANALYSIS

SITE NAME:___________________________________________ SITE NUMBER:________________________________

PROJECT NAME:_____________________________________ PROJECT NUMBER:____________________________

DATE:_______________ TIME:_____________ DEPTH (M):____________ REPLICATE:___________

sample analysis filter volume <-------------preservative--------------->

container identification medium type type filtered type identification volume

COMMENTS:

SPECIAL REQUESTS

LABORATORY FILTERING LABORATORY SPLITTING

container identification analysis types filter type container identification analysis types

LABORATORY USE ONLY

LOGIN DATE: ANALYST:

COMMENTS:

PAGE 1 OF ____ WMRL FORM F03 REVISION 4 , 7/25/07
64 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Appendix 7. Shipping forms for reconnaissance and detailed studies—Continued.

Appendix 7b-1. Analytical services request form for the Wisconsin Mercury Research Laboratory (WMRL).

These forms are available for download at http://pubs.usgs.gov/ofr/2008/1279/

Analytical services request form, page 2

SAMPLE MEDIUM -- REGULAR SAMPLE MEDIUM -- QUALITY ASSURANCE

1 suspended sediment Q artificial

6 ground water R surface water

7 wet deposition S ground water

9 surface water T wet deposition

C animal tissue V suspended sediment

D plant tissue W bottom material (sediment)

F interstitial (pore) water X animal tissue

G soil Y plant tissue

H bottom material (sediment) Z interstitial (pore) water

ANALYSIS TYPE

UTHG unfiltered total mercury

UMHG unfiltered methyl mercury

FTHG filtered total mercury

FMHG filtered methyl mercury

PTHG suspended sediment (particulate) total mercury

PMHG suspended sediment (particulate) methyl mercury

STHG bottom sediment total mercury

SMHG bottom sediment methyl mercury

BTHG biological total mercury

BMHG biological methyl mercury

UTHGI unfiltered total mercury isotopes

UMHGI unfiltered methyl mercury isotopes

FTHGI filtered total mercury isotopes

FMHGI filtered methyl mercury isotopes

PTHGI suspended sediment (particulate) total mercury isotopes

PMHGI suspended sediment (particulate) methyl mercury isotopes

STHGI bottom sediment total mercury isotopes

SMHGI bottom sediment methyl mercury isotopes

BTHGI biological total mercury isotopes

BMHGI biological methyl mercury isotopes

URHG unfiltered reactive mercury

FRHG filtered reactive mercury

HG0 gaseous mercury

SPM suspended particulate matter

AVS acid volatile sulfide

UV ABS uv absorbance

DOC dissolved organic carbon

TOC total organic carbon

LOI loss on ignition

FILTER TYPE PRESERVATION TYPE

Q quartz fiber filter A acidification

C22 0.22um capsule F freezing

C45 0.45um capsule N none

M45 0.45um meissner

N22 0.22um nitrocellulose

N45 0.45um nitrocellulose

PC40 0.45um polycarbonate

OTHER please describe
Appendix 7 65

Appendix 7. Shipping forms for reconnaissance and detailed studies—Continued.

Appendix 7b-2. Cooler inventory form for the Wisconsin Mercury Research Laboratory (WMRL).

These forms are available for download at http://pubs.usgs.gov/ofr/2008/1279/

Cooler inventory form

 COOLER INVENTORY FORM

page _____ of _____ USGS -- WISCONSIN MERCURY

PROJECT:

NUMBER TOTAL

CONTAINERS OF

TEFLON ML 125

TEFLON ML 250

TEFLON ML 500

TEFLON L 1

TEFLON L 2

TEFLON L 5

DISHES PETRI

GLASS ML 40

L VIA SEDIMENT RESEARCH LABORATORY 8505 RESEARCH WAY SAMPLERS: MIDDLETON, WI 53562 SITE NAME DATE TIME DEPTH SAMPLE MEDIA LABORATORY CHECK-IN COMMENTS

Relinquished by: date/time: Received by: date/time: COMMENTS:Relinquished by: date/time: Received by: date/time:Relinquished by: date/time: Received by: date/time:

WMRL F02 REVISION 4 JULY 25, 2007
66 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

Appendix 7. Shipping forms for reconnaissance and detailed studies—Continued.

Appendix 7c. Shipping form for the Iowa City Sediment Laboratory (ISCL).

This form is available for download at http://pubs.usgs.gov/ofr/2008/1279/

ISCL shipping form, page 1

This is____ of ____ sites [cases] in this case [shipment]. ____total bottles in this case.

U. S. GEOLOGICAL SURVEY SEDIMENT LAB ANA

LYSIS RE

Q

UEST

SW / SEDIMENT SAMPLE INFORMATION AT

A SITE (SL

A

R v. 1.04) 

Lab

________ Date Shipped _____________ Date Rec’d ____________by_____

Possibly Hazardous? Yes No Explain_________________________________

INDIVID

UAL BOT

TLE I

NFORMATION -- 1 line for each bottle (arrow/ditto do

wn to duplicate) 

Grey colu

mns required

(for Lab use only)

Pos.

No.

in

Case

Sample Start 

Date

(mm-dd-yy ) 

Start or 

Mean

Time 

(24hr) 

Sample End 

Date

(mm-dd-yy)

OPTIONAL 

End

Time 

(24hr) 

OPT.

m Mediu

e Sampl

e yp T

Set

ID

Bottle

No. in

Set

Gage

Height

Water

Temperatur

e

 (° C) 

Sampling

Method

(see

codes

above)

Lab

Analysis

Code(s)

Requested

(above)

Collector

Initials

Remarks

Bottle

Condition

codes

Lab Sample ID 

123

45

6

7

8

9

10

11

12

13

141516

1718

19

20

Enter in table below: Sampling Method (82398) Bedload: Single Equal Width Increment (1000) Multiple Equal Width Increment (1010) Unequal Width Increment (1020)

Suspended: EWI(10) EDI(20) Single-Vertical(30) Multiple-vertical (40) Fixed Single Vertical-BOX (920) Pumping (900) Single-stage (910) Partial-Depth (930) Partial-Width (940) Point (50) Grab (70)

Lab Analysis Codes Requested: (C) Concentration (SF) Sand-Fine (SA) Sand (Z) Full-Size (BD) Bulk-Density (LOI) Loss-on-Ignition (DS) Dissolved-Solids (T) Turbidity

(CC) Composite-Concentration (CSF) Composite Sand-Fine (CSA) Composite Sand-Analysis (CZ) Composite Full-Size (SC) Specific Conductance

Station No._______________________________ Station Name_________________________________________________________________ Time Datum ________ [ie., PDT]

Shipped by___________________@usgs.gov Phone No __________________________ Billing Account No.________________________ Project Chief________________________@usgs.gov

Parameter Family: Suspended Bed-Material Bedload Total Hydrologic Condition:_____ Hydrologic Event:_____ District Code_____ 
Appendix 7 67

Appendix 7. Shipping forms for reconnaissance and detailed studies—Continued.

Appendix 7c. Shipping form for the Iowa City Sediment Laboratory (ISCL).

This form is available for download at http://pubs.usgs.gov/ofr/2008/1279/

ISCL shipping form, page 2

U. S. GEOLOGICAL SURVEY SEDIMENT LAB ANALYSIS REQUEST

BACK OF FORM – EXPLANATION (SLAR v. 1.04)

Lab: Sediment lab you are shipping sample to.

Shipped by: email_id@usgs.gov or phone will be used for login questions.

Project Chief: email_id@usgs.gov will be used for data transmittal information or questions.

District Code: NWQL “Users code” for NWIS host computer for data return to NWIS. Usually the same as the "State Postal

code" (although some districts have a modified postal code for multiple NWIS hosts in a District, e.g. CA1 or FL1). Enter 

NONE for non-USGS collectors 

Parameter Family: Check the box for the appropriate type of sediment, each of which has its own group of NWIS Parameter 

codes for size fractions.

NWIS codes:

Medium: 9 = Surface Water, R = Surface Water QC, H = Bottom Material, W = Bottom Material QC,

1 = Suspended Sediment, V = Suspended Sediment QC, B = Solids, E = Core Material, G = Soil, J = Sludge,

3 = Dry Deposition, 8 = Bulk Deposition, U = Bulk Deposition QC, Q = Artificial QC (ie., equip. blank) 

Sample Type: 9 = Regular, 7 = Replicate, B = Other QA, H = Composite (time), 1 = Spike, 2 = Blank, 3 = Reference, 4=Blind

Hydrologic Condition: A = Not determined, 4 = Stable, low stage, 5 = Falling stage, 6 = Stable, high stage, 7 = Peak stage, 

8 = Rising stage, 9 = Stable, normal stage, X = Not applicable 

Hydrologic Event: A = Spring breakup, B = Under ice cover, C = Glacial lake outbreak, D = Mudflow, E = Tidal action,

F = Fire, H = Dam break, J = Storm, K = Backwater, 1 = Drought, 2 = Spill, 3 = Regulated flow, 4 = Snowmelt, 5 = 

Earthquake, 6 = Hurricane, 7 = Flood, 8 = Volcanic action, 9 = Routine sample, X = Not applicable

Sampling Method: Enter one numeric NWIS fixed-value sampling method (NWIS Pcode 82398) per sample. 

NOTE THAT ONE LINE ON THE BOTTOM TABLE IS USED FOR EACH BOTTLE. 

DUPLICATE INFORMATION MAY BE DITTOED DOWN OR SHOWN BY ARROWS. 

Analysis Codes Requested – Enter code[s] for analyses requested in the column next to the remarks. 

Remarks – add remarks pertaining to the sample set or bottle. 

SHIPP I N G INSTRUCTI O N S

Follow placement guide for packing – Bottle #1 information on the form should match Bottle #1 in case. 

Collection date (mm-dd-yy) and time (military) on the information sheet matches the bottle(s) 

Please include both Shipper and Project Chief’s email userids 

Please make sure the containers are properly labeled and sealed. 

Enclose paperwork in a Ziploc type bag. Ship samples and accompanying 

paperwork in a well-padded and securely-strapped case. 

S H I P PI N G CASE B O T T L E

PL ACEMENT G U I D E

 

Guide “C” Fill-in

GUIDE “B” 

1 0 1 1 1 2

7 8 9

4 5 6

1 2 3

GUIDE “A” 

1 7 1 8 1 9 2 0

1 3 1 4 1 5 1 6

9 1 0 1 1 1 2

5 6 7 8

1 2 3 4

(Lab use only) 

Bottle Condition Codes: use on front side, 2nd to last column

 NWL = Water Line NOT Marked 

 WBL = Water level below water line 

 NTP = Tape NOT Properly Applied 

 BRK = Broken or Spilled 

Sender will be notified by email when leakage or breakage is noted.
68 Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury

This page intentionally left blank.
Publishing support provided by:

Columbus and Tacoma Publishing Service Centers

For more information concerning this publication, contact:

Chief, USGS National Water Quality Assessment Program

MS 413 National Center

Reston, VA 20192

(703) 648–5716

Or visit the National Water Quality Assessment Program site at:

http://water.usgs.gov/nawqa/
Lutz and others— Procedures for Collecting and Processing Streambed Sediment and Pore Water for Analysis of Mercury—Open-FIle Report 2008–1279