U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2012–5272

The Occurrence of Trace Elements in Bed Sediment 

Collected from Areas of Varying Land Use and 

Potential Effects on Stream Macroinvertebrates in 

the Conterminous Western United States, Alaska, 

and Hawaii, 1992–2000

National Water-Quality Assessment Program
Cover art: Collecting a macroinvertebrate sample on Big 

Wood River in southern Idaho, November 2010. 

Photo credit: Terry Maret
The Occurrence of Trace Elements in Bed 

Sediment Collected from Areas of Varying 

Land Use and Potential Effects on Stream 

Macroinvertebrates in the Conterminous 

Western United States, Alaska, and 

Hawaii, 1992–2000

By Angela P. Paul, Nicholas V. Paretti, Dorene E. MacCoy, Anne M.D. Brasher

National Water-Quality Assessment Program

Scientific Investigations Report 2012–5272

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2012

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Suggested citation:

Paul, A.P., Paretti, N.V., MacCoy, D.E., and Brasher, A.M.D., 2012, The occurrence of trace elements in bed sediment 

collected from areas of varying land use and potential effects on stream macroinvertebrates in the conterminous 

western United States, Alaska, and Hawaii, 1992–2000 : U.S. Geological Survey Scientific Investigations Report 

2012–5272, 55 p. Available at http://pubs.water.usgs.gov/sir/2012/5272.
iii

Foreword

The U.S. Geological Survey (USGS) is committed to providing the Nation with reliable 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, 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 water-quality 

management and policy (http://water.usgs.gov/nawqa). The NAWQA Program is designed to answer: 

What is the quality 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 to 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). 

In the second decade of the Program (2001–2012), a major focus is on regional assessments of 

water-quality conditions and trends. These regional assessments are based on major river basins and 

principal aquifers, which encompass larger regions of the country than the Study Units. Regional 

assessments extend the findings in the Study Units by filling critical gaps in characterizing the quality 

of surface water and ground water, and by determining water-quality status and trends at sites that have 

been consistently monitored for more than a decade. In addition, the regional assessments continue to 

build an understanding of how natural features and human activities affect water quality. Many of the 

regional assessments employ modeling and other scientific tools, developed on the basis of data collected at individual sites, to help extend knowledge of water quality to unmonitored, yet comparable 

areas within the regions. The models thereby enhance the value of our existing data and our understanding of the hydrologic system. In addition, the models are useful in evaluating various resourcemanagement scenarios and in predicting how our actions, such as reducing or managing nonpoint and 

point sources of contamination, land conversion, and altering flow and (or) pumping regimes, are likely 

to affect water conditions within a region.

Other activities planned during the second decade include continuing national syntheses of information on pesticides, volatile organic compounds (VOCs), nutrients, trace elements, and aquatic ecology; 

and continuing national topical studies on the fate of agricultural chemicals, effects of urbanization on 

stream ecosystems, bioaccumulation of mercury in stream ecosystems, effects of nutrient enrichment on 

stream ecosystems, and transport of contaminants to public-supply wells.

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 waterresource 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

Associate Director for Water
iv

Contents

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

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

Purpose and Scope ...................................................................................................................................... 4

Description of Study Areas ......................................................................................................................... 4

Methods ......................................................................................................................................................... 6

Site Selection ....................................................................................................................................... 6

Bed-Sediment and Surface-Water Collection and Chemical Analyses ..................................... 6

Macroinvertebrate Collection and Taxonomic Resolution ........................................................... 9

Land-Use Categorization .................................................................................................................... 9

Trace Elements and Macroinvertebrate Communities ................................................................. 9

Statistical Analyses............................................................................................................................10

Data Limitations ................................................................................................................................. 11

Trace-Element Concentrations in Bed Sediment .................................................................................. 12

Arsenic ................................................................................................................................................ 14

Cadmium, Lead, and Zinc ................................................................................................................. 14

Chromium and Nickel........................................................................................................................ 16

Copper ................................................................................................................................................. 17

Mercury............................................................................................................................................... 18

Selenium ............................................................................................................................................. 18

Cumulative Toxic Units ..................................................................................................................... 19

Macroinvertebrate Communities and Habitat Characteristics........................................................... 22

Trace Elements and Macroinvertebrates in the Hawaiian Islands .................................................... 24

Ecoregion and Land-Use Characterization ................................................................................... 25

Macroinvertebrate Community Response to Trace Elements ................................................... 27

Mountain Northern Rockies Ecoregion (MT-NROCK) ........................................................ 28

Mountain Southern Rockies Ecoregion (MT-SROCK) ........................................................ 33

Ozark Highlands Ecoregion (OH)............................................................................................ 36

Eastern Xeric Plateau Ecoregion (XE-EPLAT)...................................................................... 40

Summary and Conclusions ....................................................................................................................... 44

Acknowledgments...................................................................................................................................... 46

References Cited......................................................................................................................................... 47

Appendix 1-1................................................................................................................................................ 56

Appendix 1-2................................................................................................................................................ 56

Appendix 2-1................................................................................................................................................ 56

Apppendix 2-2.............................................................................................................................................. 56

Appendix 3-1................................................................................................................................................ 57

Figures

1. Maps showing ecoregions and bed-sediment and macroinvertebrate sampling locations

 in the A, conterminous western United States; B, island of Oahu, Hawaii; and C, 

Cook Inlet area near Anchorage, Alaska, 1992–2000 .............................................................. 5
v

2. Maps showing locations of bed-sediment and macroinvertebrate sampling sites 

representative of undeveloped and developed land uses for the A, conterminous 

western United States, B, Island of Oahu, Hawaii, and C, Cook Inlet area near 

Anchorage, Alaska, 1992–2000 .....................................................................................................8

3. Boxplots showing concentrations of arsenic in bed sediment collected from 201 sites 

representative of undeveloped and developed areas in the conterminous western 

United States and Alaska, 1992–2000 ........................................................................................14

4. Boxplots showing concentrations of A, cadmium, B, lead, and C, zinc in bed sediment 

collected from 201 sites representative of undeveloped and developed areas in the 

conterminous western United States and Alaska, 1992–2000 ..............................................15

5. Boxplots showing concentrations of A, chromium, and B, nickel in bed sediment 

collected from 201 sites representative of undeveloped and developed areas in the 

conterminous United States and Alaska, 1992–2000 ..............................................................16

6. Boxplots showing concentrations of copper in bed sediment collected from 201 sites 

representative of undeveloped and developed areas in the conterminous western 

United States and Alaska, 1992–2000 ........................................................................................17

7. Boxplots showing concentrations of mercury in bed sediment collected from 201 sites 

representative of undeveloped and developed areas in the conterminous western 

United States and Alaska, 1992–2000 ........................................................................................18

8. Boxplots showing concentrations of selenium in bed sediment collected from 201 

sites representative of undeveloped and developed areas in the conterminous 

western United States and Alaska, 1992–2000 ........................................................................19

9. Boxplots showing cumulative toxic units calculated for 201 bed-sediment samples 

collected from streams in undeveloped, agricultural, urban, mined, and mixed landuse areas within the conterminous western United States and Alaska, 1992–2000 ........ 20

10. Boxplots showing contribution of each of the eight trace elements used to determine 

the cumulative toxic units for bed sediment collected from selected streams and 

rivers in A, undeveloped; B, agricultural; C, urban; D, mined; and E, mixed landuse areas in the conterminous western United States and Alaska, 1992– 2000 .............. 21

11. Boxplots showing non-metric multidimensional scaling ordination representing 

A, aquatic-macroinvertebrate communities within the large-scale ecoregions; 

and B, associated distribution patterns in trace-element cumulative toxic units 

for the 208 samples collected from streams in the conterminous western United 

States, Alaska, and Hawaii, 1992–2000 .................................................................................... 23

12. Box plots showing general water-quality characterization of A, specific conductance; 

B, total dissolved solids concentration; C, water hardness; D, pH; and E, suspendedsediment concentration by large-scale ecoregion in the conterminous western 

United States, Alaska, and Hawaii, 1992–2000 ....................................................................... 26

13. Bar graph showing general land-use categories represented within the large-scale 

ecoregions within the conterminous western United States and Alaska, 1992–2000 ..... 27

14. Bar chart showing general land-use categories represented in intermediate-scale 

ecoregions in the conterminous western United States and Alaska, 1992–2000 ............. 28

15. Graph showing a non-metric multidimensional scaling ordination of macroinvertebrate communities in selected streams in the Mountain Northern Rockies 

ecoregion and distribution of cumulative toxic units, 1992–2000 ........................................ 29

16. Graph showing A, Average number of taxa and percent contribution from each of 

Ephemeroptera, Plecoptera, and Trichoptera, Diptera, Coleoptera, and other taxa 

to the overall richness; and B, average relative abundances of Ephemeroptera, 

Plecoptera, Trichoptera, Diptera, Coleoptera, and other taxa for macroinvertebrate communities in selected streams of the Northern Rocky Mountains 

ecoregion, 1992–2000 .................................................................................................................. 30
vi

17. Graph showing a non-metric multidimensional scaling ordination of macroinvertebrate communities in selected streams in the Mountain Southern Rockies 

ecoregion and distribution of cumulative toxic units, 1992–2000 ........................................ 33

18. Graph showing A, Average number of taxa and percent contribution from each of 

Ephemeroptera, Plecoptera, and Trichoptera, Diptera, Coleoptera, and other taxa 

to the overall richness; and B, average relative abundances of Ephemeroptera, 

Plecoptera, Trichoptera, Diptera, Coleoptera, and other taxa for macroinvertebrate 

communities in selected streams of the Mountain Southern Rockies ecoregion, 

1992–2000 ...................................................................................................................................... 35

19. Graph showing a non-metric multidimensional scaling ordination of macroinvertebrate 

communities in selected streams in the Ozark Highlands ecoregion and distribution 

of cumulative toxic units, 1992–2000 ........................................................................................ 37

20. Graphs showing A, Average number of taxa and percent contribution from each of 

Ephemeroptera, Plecoptera, and Trichoptera, Diptera, Coleoptera, and other taxa 

to the overall richness; and B, average relative abundances of Ephemeroptera, 

Plecoptera, Trichoptera, Diptera, Coleoptera, and other taxa for macroinvertebrate 

communities in selected streams of the Ozark Highlands ecoregion, 1992–2000 ............ 38

21. Graph showing a non-metric multidimensional scaling ordination of macroinvertebrate communities in selected streams in the Xeric Eastern Plateau ecoregion 

and distribution of cumulative toxic units, 1992–2000 ........................................................... 41

22. Graphs showing A, Average number of taxa and percent contribution from each of 

Ephemeroptera, Plecoptera, and Trichoptera, Diptera, Coleoptera, and other taxa 

to the overall richness; and B, average relative abundances of Ephemeroptera, 

Plecoptera, Trichoptera, Diptera, Coleoptera, and other taxa for macroinvertebrate communities in selected streams of the Xeric Eastern Plateau ecoregion, 

1992–2000 ...................................................................................................................................... 42

Tables

1. Average basin drainage area and slope and ranges in sampling-site elevation and 

average annual air temperature, precipitation, and potential evapotranspiration for 

sites within each intermediate-scale ecoregion included in this investigation for the 

conterminous western United States, Alaska, and Hawaii .....................................................6

2. Threshold Effect Concentration and Probable Effect Concentration values for trace 

elements of ecological significance and evaluated as part of this study .............................7

3. Minimum, maximum, average, and median baseline concentrations for nine selected 

trace elements determined using two methods of analysis for bed-sediment samples 

collected from streams and rivers within the conterminous western United States 

and Alaska, 1992 to 2000, and national median baseline concentrations ...........................12

4. Correlations among the nine trace elements in bed sediment samples collected at 

reference and non-reference streams and rivers in the conterminous western 

United States and Alaska, 1992–2000 ........................................................................................13

5. Cumulative toxic unit percentile enrichment thresholds used to characterize bed 

sediment samples collected from selected streams in the conterminous western 

United States and Alaska, 1992–2000 ....................................................................................... 20

6. Range in cumulative toxic unit values for each of the intermediate-scale ecoregions 

used to evaluate the influence of trace elements on macroinvertebrate community 

structure in selected streams in the conterminous western United States and 

Alaska, 1992–2000 ........................................................................................................................ 27
vii

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

square mile (mi2

) 2.590 square kilometer (km2) 

Volume

cubic-foot (ft3

) 28.316 liter (L)

Precipitation rate

inch per year (in/yr) 25.4 millimeter per year (mm/yr)

mass

pound, avoirdupois (lb) 0.4536 kilogram (kg)

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

°F=(1.8×°C)+32

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

°C=(°F-32)/1.8

Vertical coordinate information is referenced to North American Vertical Datum of 1988 (NAVD 88).

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

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

25 °C).

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

micrograms per liter (μg/L). 
viii

Abbreviations

As Arsenic

AVS Acid Volatile Sulfide

ANOVA Analysis of Variance

Cd Cadmium

CCU Cumulative Concentration Units

CERCLA Comprehensive Environmental Response, Compensation, and Liability Act

Cr Chromium

CTU Cumulative Toxic Units

Cu Copper

EPT Ephemeroptera, Plecoptera, Trichoptera

GIS Geographic Information System

HI Hawaiian Ecoregion

Hg Mercury

IDAS Invertebrate Data Analysis System

LC50 Lethal Concentration (50 percent)

MDL Method detection limit

MDS Multidimensional Scaling

MT Mountain Ecoregion (MT-NROCK, MT-SROCK, MT-SWEST, MT-PNW)

MT-NROCK Mountain Northern Rockies Ecoregion

MT-PNW Mountain Pacific Northwest Ecoregion

MT-SROCK Mountain Southern Rockies Ecoregion

MT-SWEST Southwestern Mountains Ecoregion

NAWQA National Water Quality Assessment Program

NLCDE Enhanced National Land Cover Data

NMS Non-metric multidimensional scaling

MRDS Mineral Resources Dataset

Ni Nickel

NWQL National Water Quality Laboratory

OH Ozark Highlands Ecoregion

Pb Lead

PCA Principal Components Analysis

PCO Polar Coordinate Ordination

PEC Probable-Effect Concentration

PEL Probable-Effect Level

PL Plains Ecoregion (PL-NCULT, PL-RANGE)

PL-NCULT Cultivated Northern Plains Ecoregion

PL-RANGE Rangeland Plains Ecoregion

SIMPROF Similarity Profile Test

Se Selenium

TDS Total Dissolved Solids

TEC Threshold-Effect Concentration

TEL Threshold-Effect Level

USEPA U.S. Environmental Protection Agency

XE Xeric Ecoregion (XECALIF, XE-NORTH, XE-SOUTH, XE-EPLAT)

XE-CALIF Xeric California Ecoregion

XE-NORTH Northern Xeric Basins Ecoregion

XE-SOUTH Southern Xeric Basins Ecoregion

XE-EPLAT Eastern Xeric Plateau Ecoregion

Zn Zinc 
The Occurrence of Trace Elements in Bed Sediment 

Collected from Areas of Varying Land Use and 

Potential Effects on Stream Macroinvertebrates in the 

Conterminous Western United States, Alaska, and 

Hawaii, 1992–2000 

By Angela P. Paul, Nicholas V. Paretti, Dorene E. MacCoy, and Anne M.D. Brasher 

distinctive pattern in Se concentrations with land use, median 

bed-sediment concentrations were slightly elevated in urbanized areas.

Macroinvertebrate community structure was influenced by 

topographic, geologic, climatic, and in-stream characteristics. 

To account for inherent distribution patterns resulting from 

these influences, samples of macroinvertebrates were stratified by ecoregion to assess the influence of trace elements on 

community structure. Cumulative toxic units (CTUs) were 

used to evaluate gradients in trace-element concentrations 

in mixture. Correlation analyses among the trace elements 

under different land-use conditions indicate that trace-element 

mixtures vary among bed sediment and can have a marked 

influence on CTU composition. Macroinvertebrate response to 

bed-sediment trace-element exposure was evident only at the 

most highly contaminated sites, notably at sites classified as 

contaminated by the Comprehensive Environmental Response, 

Compensation, and Liability Act (CERCLA) as a result of 

historic mining activities. Results of this study agree with the 

findings of other studies evaluating trace-element exposure 

to in-stream macroinvertebrate community structure in that 

generally lower richness metrics and taxa dominance occur in 

streams where high trace-element enrichment occurs; however, not all streams in all areas have the same characterizing 

taxa. In the mountain and xeric ecosystems, the mayfly, Baetis

sp.; the Diptera, Simulium sp.; caddisflies in the family Hydropsychiidae; midges in the family Orthocladiinae; and the 

worms belonging to Turbellaria and Naididae all demonstrated 

resilience to trace-element exposure and, in some cases, possible changes in physical habitat within stream ecosystems. 

The taxa characteristics within the Ozark Highland ecoregion 

were different than other ecoregions as evidenced by generally more diverse mayfly populations. In addition, Baetis sp. 

was common and dominated many of the mayfly populations 

found in the Rocky Mountain streams within the Mountain 

Southern Rockies and Mountain Northern Rockies ecoregions; 

however, within the Ozark Highland ecoregion, Tricorythodes

sp. appeared to be more common than Baetis sp. 

Abstract

As part of the National Water-Quality Assessment Program of the U.S. Geological Survey, this study examines the 

occurrence of nine trace elements in bed sediment of varying 

mineralogy and land use and assesses the possible effects of 

these trace elements on aquatic-macroinvertebrate community 

structure. Samples of bed sediment and macroinvertebrates 

were collected from 154 streams at sites representative of 

undeveloped, agricultural, urban, mined, or mixed land-use 

areas and 12 intermediate-scale ecoregions within the conterminous western United States, Alaska, and Hawaii from 

1992 to 2000. The nine trace elements evaluated during this 

study—arsenic (As), cadmium (Cd), chromium (Cr), copper 

(Cu), lead (Pb), mercury (Hg), nickel (Ni), selenium (Se), and 

zinc (Zn)—were selected on the basis of potential ecologic 

significance and availability of sediment-quality guidelines. 

At most sites, the occurrence of these trace elements in bed 

sediment was at concentrations consistent with natural geochemical abundance, and the lowest concentrations were in 

bed-sediment samples collected from streams in undeveloped 

and agricultural areas. With the exception of Zn at sampling 

sites influenced by historic mining-related activities, median 

concentrations of all nine trace elements in bed sediment collected from sites representative of the five general land-use 

areas were below concentrations predicted to be harmful to 

aquatic macroinvertebrates. The highest concentrations of As, 

Cd, Pb, and Zn were in bed sediment collected from mined 

areas. Median concentrations of Cu and Ni in bed sediment 

were similarly enriched in areas of mining, urban, and mixed 

land use. Concentrations of Cr and Ni appear to originate 

largely from geologic sources, especially in the western 

coastal states (California, Oregon, and Washington), Alaska, 

and Hawaii. In these areas, naturally high concentrations of 

Cr and Ni can exceed concentrations that may adversely affect 

aquatic macroinvertebrates. Generally, Hg concentrations were 

below the sediment-quality guideline for this trace element but 

appeared elevated in urbanized areas and at sites contaminated 

by historic mining practices. Lastly, although there was no 
2 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Introduction

Local, regional, and national studies have examined effects 

of agriculture, urbanization, and mining on trace-element 

occurrence in bed sediment (Horowitz and others, 1993; 

Rice, 1999; Seiler and others, 2003; Horowitz and Stephens, 

2008) and changes in macroinvertebrate community structure 

along pollution and (or) other stress gradients (Ourso and 

Frenzel, 2003; Brasher and others, 2004; Cuffney and others, 

2005; Carlisle and Hawkins, 2008). Changes in macroinvertebrate community structure can result from the invasion of 

non-indigenous fauna, alterations in physical habitat, and 

contamination, all of which can be influenced by human 

activities, making it difficult to ascertain cause and effect 

relations. In addition, it is oftentimes problematic to extrapolate from effects on individual taxa to the community level 

(Sheehan and Winner, 1984; Paul and Meyer, 2001; Griffith 

and others, 2004; Mahler and others, 2005; Pollard and Yuan, 

2006; Strayer, 2006). Evaluating benthic-macroinvertebrate 

community structure is an important component of assessing 

the health of stream ecosystems because stream invertebrates 

respond to water quality, sediment quality, and physicalhabitat characteristics of the system; as a result, biological 

assessments have become an integral component of waterquality and resource-management programs throughout the 

United States (Cain and others, 1992; Meador and Gurtz, 

1994; Hickey and Golding, 2002; U.S. Environmental Protection Agency, 2009). Understanding the interplay between 

aquatic assemblages and the influences of various land uses 

on ecosystem dynamics within the Nation’s rivers is important 

in assessing the health of streams and how to most effectively 

implement best-management practices; however, elucidating 

cause and effect between land use(s) and potential ecological impairments using data evaluated herein is not within the 

scope of this work.

Data in this report were collected as part of the National 

Water Quality Assessment (NAWQA) Program of the U.S. 

Geological Survey and are used to describe associations 

among physical, chemical, and biological components in 

stream ecosystems (Gilliom and others, 1995). The current 

report summarizes bed-sediment trace-element concentrations 

and macroinvertebrate assemblages in 208 samples from 154 

streams, representative of 12 ecoregions, across the conterminous western United States, Alaska, and Hawaii from 1992 to 

2000. The sites included in this evaluation varied in mineralogy, land use (urbanization, agriculture, and mining), and 

macroinvertebrate communities. Physiochemical influences 

of urbanization, agriculture, mining, and grazing of livestock 

on stream environments have been well characterized (Collins 

and Dunne, 1990; Tucker and Burton, 1999; Hawkins and others, 2000; Griffith and others, 2001; Paul and Meyer, 2001). 

General influences of these different land uses on occurrences 

of trace elements and stream conditions are briefly summarized below.

In the western United States, most freshwater withdrawal 

is used for irrigated agriculture (National Research Council, 

1989). Through leaching, erosion, and runoff, agricultural 

irrigation practices can introduce trace elements, nutrients, 

and sediment into streams and wetlands (Presser and Ohlendorf, 1987; Hoffman, 1994; National Research Council, 1989; 

Seiler and others, 2003). Streams in agricultural areas can 

also be susceptible to pesticide contamination (Gilliom and 

others, 2006). However, geology can also have a marked influence on the occurrence of trace-element concentrations. For 

instance, Seiler and others (2003) found that in the western 

United States surface-water samples with the highest median 

As concentrations were collected near Tertiary volcanic rocks. 

Elevated Se concentrations have been correlated to Upper Cretaceous marine shales, and high concentrations of boron and 

molybdenum are associated with evaporate deposits (Seiler 

and others, 2003). 

Streams within urban centers are influenced by point and 

nonpoint sources, such as treated wastewater discharge, urban 

runoff, and interbasin transfers of water that can introduce 

sediment, trace elements, nutrients, pesticides, and other 

contaminants into stream ecosystems (Paul and Meyer, 2001; 

Mahler and others, 2005; Short and others, 2005). Dry and 

wet deposition originating from industrial emissions, burning 

of fossil fuels, and dust can transport contaminants, including trace elements (Wilber and Hunter, 1977; Puckett, 1994; 

Coupe and others, 2000; Davis and others, 2001). Davis 

and others (2001) found that the amount of Cd, Cu, and Pb 

contained in precipitation contributed notably to the total 

trace-element loadings carried in urban streams. Since its 

elimination from gasoline in the late 1970s, the amount of Pb 

entering waterways has decreased; however, bed-sediment 

data collected from streams in high-traffic areas continue to 

show high levels of Zn (Callender and Rice, 2000; Davis and 

others, 2001; Councell and others, 2004). Impervious surfaces 

within urban environments can alter stream geomorphology 

and hydrology, and it has been estimated that 15 to 20 percent 

of the streams in the United States are ecologically impaired 

by roads (Schueler, 1994; Forman and Alexander, 1998; Paul 

and Meyer, 2001; Ourso and Frenzel, 2003).

Smelting and production of waste tailings can provide 

a source for airborne particulates that can contribute to the 

atmospheric deposition of trace elements to surrounding 

areas near and far from the sources (Evans, 1986; Maret and 

others, 2003; Peterson and others, 2007). Changes in physiochemical habitat caused by mining include changes in water 

chemistry and coating of streambed substrates resulting from 

the precipitation of metal oxides from solution (Theobald and 

others, 1963; Moore and others, 1991; Griffith and others, 

2001). Noted alterations in water chemistry have included 

decreased pH where acid mine drainage occurs, increased 

specific conductance and water hardness, and higher concentrations of sulfate, phosphate, and many trace elements (Moran 

and Wentz, 1974; McKnight and Feder, 1984; Clements and 

others, 2000). The effects from mining typically attenuate at 

some point downstream from the mining-related activities as a 

result of inflow of unaffected tributaries and (or) groundwater 

seepage, chemical precipitation, and particle settling (Moran 

and Wentz, 1974).
Introduction 3

Environmental concentrations of contaminants, such as 

trace elements, provide some indication of exposure, but the 

actual dose received by an organism depends on the amount 

actually assimilated (Forbes and Forbes, 1994). Landrum 

and Robbins (1990) define bioavailability as the amount of a 

contaminant that can be assimilated by an organism through 

all routes of uptake. Routes of uptake include absorption 

through the cuticle and respiratory membranes and (or) by 

ingestion (Selby and others, 1985; Hare, 1992; Michaud and 

others, 2005). These processes are all influenced by taxa 

characteristics, including physiology, trophic status, and habit. 

In streams and lakes, the partitioning of contaminants between 

the sediment matrix (solids) and interstitial (pore space) water, 

through a process called sorption, is important in determining 

bioavailability to aquatic biota (Luoma, 1989; Landrum and 

Robbins, 1990). The partitioning of a contaminant depends on 

the physiochemical characteristics of the environment and the 

properties of the contaminant (Krantzberg, 1989; Landrum and 

Robbins, 1990). Sediment characteristics important to sorption 

reactions include surface charge, exchange capacity, organiccarbon content, and particle-size distribution (Elder, 1989; 

Landrum and Robbins, 1990). Acid-volatile sulfide (AVS), 

typically composed mostly of iron sulfide, has been studied as 

a possible protective mechanism against exposure of benthic 

organisms to heavy metals in interstitial pore water and is 

considered in the determination of protective benchmarks 

for Cd, Cu, Pb, Ni, silver, and Zn by the U.S. Environmental Protection Agency (USEPA) (Hansen and others, 2005). 

Recent investigations have shown that ingested particulatebound trace elements are of biological importance (Griscom 

and others, 2000; Lee and others, 2000). Where ingestion 

is the primary route of exposure to an organism, analysis of 

fine-grained material can give a reasonable approximation of 

the amount of contaminant exposure (Landrum and Robbins, 1990). Identifying the biologically available fraction of 

trace elements associated with sediment particles is problematic when measured concentrations represent the lithogenic 

contribution (Luoma, 1989); however, the potential bioavailability of some trace elements has been shown to increase with 

decreasing sediment grain size (Stone and Droppo, 1996).

Some macroinvertebrate taxa possess various mechanisms 

of protection that enhance their ability to either inhabit or 

escape from contaminated areas, such as the ability to drift 

from contaminated areas or burrow into less-contaminated 

sediment (Cuffney and others, 1984; Courtney and Clements, 1998). Some taxa known to drift include the mayflies, 

Ameletus sp., Baetis tricaudatus, Drunella doddsi, Ephemerella infrequens, and Rithrogena hageni; the caddisfly, Lepidostoma sp.; and the dipteran, Atherix pachypus (Courtney 

and Clements, 1998). Avoidance behaviors, such as burrowing 

and drift, and acclimation to site-specific concentrations can 

obscure results pertaining to contaminant toxicity (Krantzberg and Stokes, 1989; Beltman and others, 1999; Clements, 

2004). Pre-exposure to metals has been shown to increase 

metal tolerance in some aquatic insects such as the mayfly, 

Rithrogena sp., and the midge, Chironomus riparius (Miller 

and Hendricks, 1996; Clements, 1999). Some invertebrate 

taxa possess a metal-binding glycoprotein that has a relatively 

high affinity for metals thereby enhancing their excretion from 

the organism (Clubb and others, 1975; Rainbow and Scott, 

1979; Yamamura and others, 1983; Petering and others, 1990; 

Cain and others, 2006). Cd-binding glycoproteins have been 

isolated from select stream macroinvertebrates including the 

mayfly, Hexagenia lambata; the midge, Chironomus yoshimatsui; the caddisfly, Hydropsyche californica; and the stonefly, 

Pteronarcys californica (Clubb and others, 1975; Yamamura 

and others, 1983; Michaud and others, 2005; Cain and others, 

2006; Janssens and others, 2007). Possessing metal-sequestering enzymes, such as this glycoprotein, can potentially give 

certain taxa an advantage over others when inhabiting metalenriched areas (Clubb and others, 1975; Yamamura and others, 

1983).

The interactions of trace elements in mixtures are important to consider when examining the biological effects of trace 

elements in natural systems (Oakden and others, 1984; Preston 

and others, 2000). Cd, Cu, and Zn have been shown to act 

synergistically (greatly enhance effects) on macroinvertebrate 

community structure (Moran and Wentz, 1974; Clements, 

2004). Antagonistic (inhibitory) interactions among contaminants have been observed in some studies. Se has been shown 

to influence the manner in which Hg is assimilated by aquatic 

organisms including the marine crab, Carcinus maenas, and 

the freshwater northern pike, Esox lucius (Rudd and others, 1980; Turner and Swick, 1983; Larsen and Bjeeregaard, 

1995). To account for trace elements in mixture, researchers 

have used indices such as cumulative concentration units 

(CCUs) and cumulative toxic units (CTUs) to quantify effects 

of aqueous and bed-sediment trace-element concentrations, 

respectively (Clements and others, 2000; McGuire, 2001; 

Maret and others, 2003; Clements, 2004). However, the use 

of these types of indices may overestimate or underestimate 

effects because this approach assumes additive toxicity among 

trace elements (Clements and others, 2000; Clements, 2004).

Chelating agents (e.g., dissolved organic carbon) and water 

hardness can influence the toxicity of some metals, such as 

Cu and Zn (Stiff, 1971; Oakden and others, 1984; Gauss and 

others, 1985; Santos and others, 2008). An inhibitory effect 

of water hardness has been attributed to the reduced effective concentration (activity) of trace elements in solution in 

relation to other solutes in hard water (Stiff, 1971; Drever, 

1988). Humic and fulvic acids are components of the dissolved organic material in natural waters, and the affinity of 

these acids to metal ions varies by metal, the ratio of acid to 

metal, water hardness, and pH (Morel and Hering, 1993). Cu 

toxicity to the cladoceran, Ceriodaphia silvestrii, was reduced 

in the presence of humic substances (Santos and others, 2008); 

however, in acute tests with the cladoceran, Simocephalus 

serrulatus, in soft water, the 24-hour LC50 (the concentration 

lethal to 50 percent of organisms exposed) for Cu was lower 

in the presence of organic matter than without (Giesy and 

others, 1983). Other organic molecules in natural waters may 

be capable of chelating trace elements and, in some cases, are 

necessary to facilitate the transport of these trace elements 

across cellular membranes (Luoma, 1983).
4 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Purpose and Scope

The purpose of this study was to describe, in a regional 

context, the differences in macroinvertebrate community 

structure in relation to concentrations of trace elements in bed 

sediment collected from selected streams in the conterminous 

western United States, Alaska, and Hawaii from 1992 to 2000. 

The nine trace elements targeted for investigation (As, Cd, 

Cr, Cu, Pb, Hg, Ni, Se, and Zn) were selected on the basis of 

their potential ecological significance and available sedimentquality guidelines (Van Derveer and Canton, 1997; MacDonald and others, 2000).Concentrations of trace elements were 

measured in 208 samples of bed sediment collected from 154 

streams in 15 states and 12 ecoregions. Watersheds associated with the 208 sampling sites had varying mineralogy and 

were influenced by different human-related activities (such 

as urbanization, mining, and agriculture). Land use was used 

to characterize the occurrence of trace elements as well as 

account for other potential influences (such as habitat alteration) that may affect macroinvertebrate communities. It is 

outside the scope of this report to evaluate cause-and-effect 

relations between land use and trace-element concentrations or 

effects of land use directly on macroinvertebrate populations. 

Ecoregions, as defined by other researchers (Omernick, 1987; 

Whittier and others, 2007), were used to reduce the inherent variability among aquatic-macroinvertebrate community 

distributions. This report evaluates:

• Trace-element concentrations at undeveloped (reference) 

sites and those representative of four generalized land uses 

(agricultural, urban, mined, and mixed use);

• Co-occurrence of trace elements in bed-sediment samples 

collected at sites representative of undeveloped, agricultural, urban, mining, and mixed land uses;

• Relations of trace-element concentrations in bed sediment 

to established probable-effect and threshold-effect concentrations;

• Macroinvertebrate community structure along bed-sediment 

trace-element (CTU) gradients;

• Regional evaluation of taxa resilience to trace-element 

concentrations.

Description of Study Areas

Study areas described in this report generally represent 

the diverse nature of groundwater and surface-water systems 

throughout the conterminous western United States, Alaska, 

and Hawaii (Shelton and Capel, 1994; Gilliom and others, 1995). The 154 streams targeted for examination in this 

investigation are in the states of Alaska, Arizona, California, 

Colorado, Hawaii, Idaho, Missouri, Montana, Nebraska, 

Nevada, New Mexico, Oregon, Utah, Washington, and Wyoming (fig. 1).

Carlisle and Hawkins (2008) identified season, latitude/

longitude, mean annual precipitation, basin area, channel 

slope, and mean annual air temperature as important environmental gradients explaining a substantial amount of the biological variability among macroinvertebrate samples collected 

from undeveloped (reference) areas. Study areas and sampling 

locations were examined within an ecoregional framework 

to ascertain whether or not ecoregional differences could be 

influencing distributional patterns among aquatic communities. The regional study area consisted of 5 large-scale (10 

intermediate-scale) ecoregions (table 1). Large-scale ecoregions were delineated by Omernick (1987) and Whittier and 

others (2007) by considering stream order, slope/relief, soil 

types, water quality, physical-habitat characteristics, forested/

agricultural land uses, and climate. Mountain ecoregions (MT) 

are generally those with steep slopes, shallow soil, and cooler 

climates, whereas xeric (XE) and plains (PL) ecoregions are 

flat and have deep soils and warmer temperatures (Stoddard 

and others, 2005).The intermediate-scale ecoregions, delineated by Whittier and others (2007), represent areas with 

greater similarities in climate, topography, and in-stream characteristics relative to the large-scale ecoregions. The characteristics of the intermediate-scale ecoregions in this dataset are 

summarized in table 1; the extent of the large-scale ecoregions 

is shown in figure 1. Assessment of general water-quality characteristics for the large-scale ecoregions is summarized in the 

section “Ecoregion and Land Use Characterization.”
Description of Study Areas 5

Figure 1. Ecoregions and bed-sediment and macroinvertebrate sampling locations in the A, conterminous western United States; B, 

island of Oahu, Hawaii; and C, Cook Inlet area near Anchorage, Alaska, 1992–2000.

Washington

Oregon

Montana North

Dakota Minnesota

Wisconsin South

Dakota Wyoming

Idaho

Nevada

Utah

California

Arizona

New

Mexico

Colorado

Nebraska

Iowa

Kansas

Oklahoma

Texas

Missouri

Arkansas

Louisiana

Illinois

Alabama

A

B C

Base from U.S. Geological Survey digital data, 1:10,000,000, 2006

Ecological Regions of North America, Commission for Environmental Cooperation, 2006

Albers Equal-Area Conic projection: Standard parallels 29°30', 45°30', central meridian -96°, 

latitude of origin 23°; North American Datum of 1983

Base from U.S. Geological Survey digital data, 1:10,000,000, 2006

Ecological Regions of North America, Commission for Environmental 

Cooperation, 2006

Albers Equal-Area Conic projection, Standard parallels 8°, 18°, central 

meridian -157°, latitiude of origin 13°; North American Datum of 1983

0 20 40 MILES

0 20 40 KILOMETERS

Are of map

Hawaii

EXPLANATION

Base from U.S. Geological Survey digital data, 1:10,000,000, 2006

Ecological Regions of North America, Commission for Environmental 

Cooperation, 2006

Albers Equal-Area Conic projection, Standard parallels 55°, 65°, central 

meridian -154°, latitiude of origin 50°; North American Datum of 1983

0 100 200 MILES

0 100 200 KILOMETERS

Area

of

map

58°

64°

158°30' 157°30' 154° 146°

21°30'

21°00'

0 200 400 600 MILES

2000 400 600 KILOMETERS

130° 90°

45°

30°

Oahu

Alaska

Ecoregion

Hawaii (HI)

Mountains (MT)

MT-Northern Rockies

MT-Southern Rockies

Ozark Highlands (OH)

Plains (PL)

Xeric (XE)

Eastern-XE Plateau

Uncharacterized

Sampling site
6 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Methods

Site Selection

A total of 208 bed-sediment and macroinvertebrate 

samples were collected from 154 streams and rivers across 15 

states and 12 ecoregions (fig. 1) to assess the occurrence and 

influence of trace elements on macroinvertebrate communities. 

Data used for this analysis were obtained from sites where 

macroinvertebrate and bed-sediment samples were collected 

within approximately 1 year (less than or equal to 450 days) 

of each other during the period 1992 to 2000 (appendix 1, 

table 1-1; appendix 2, table 2-2). Sites with basin areas greater 

than about 25,000 km2

 were not included in this study because 

these were considered to be large rivers (non-wadeable), 

requiring modified sampling protocols. In addition, stream 

sites influenced by wastewater outfalls and those containing 

the invasive New Zealand mudsnail were excluded from the 

dataset used in this investigation. The number of sites varied 

across intermediate ecoregions, ranging from 6 in the Southwestern Mountains to 47 in the Mountain Pacific Northwest 

(table 1). 

Bed-Sediment and Surface-Water Collection 

and Chemical Analyses

Samples of surface water and bed sediment were collected 

from streams and rivers in areas of differing land use and 

mineralogy using standard U.S. Geological Survey protocols 

(Shelton, 1994; Shelton and Capel, 1994; Mueller and others, 

1997). Samples for water quality were not collected at all sites. 

General water-quality characteristics (suspended-sediment 

concentration, pH, specific conductance, and hardness) are 

summarized where available (appendix 1, table 1–2). These 

water-quality characteristics are important in considering distribution patterns of aquatic macroinvertebrates because they 

influence the colonization of taxa with different physiological characteristics and in-stream habitat preferences (Hynes, 

1979; Merrit and Cummins, 1996; Hawkins and others, 2000). 

The ecoregional delineations used in this study have been 

described elsewhere (Whittier and others, 2007) and are evaluated in the section of this report “Ecoregion and Land Use 

Characterization.” 

Trace-element concentrations were assessed in bed-sediment samples representing undeveloped (reference) conditions 

and areas influenced by human-related activities (urbanization, agriculture, and mining). Although data were available 

for 45 trace elements, the 9 targeted for investigation (As, Cd, 

Table 1. Average basin drainage area and slope and ranges in sampling-site elevation and average annual air temperature, 

precipitation, and potential evapotranspiration for sites within each intermediate-scale ecoregion included in this investigation for the 

conterminous western United States, Alaska, and Hawaii.

[Abbreviations: °F, degrees fahrenheit; mi2, square miles; in, inches; yr, year; ±, plus or minus; NA, not available]

Large-scale ecoregion Intermediate-scale ecoregion Number 

of sites

Average basin 

drainage area 

± standard 

deviation

(mi2

)

Average 

annual 

watershed 

air 

temperature

(oF)1

Average 

annual 

watershed 

precipitation

(in/yr)2

Average 

annual 

potential 

evapotranspiration

(in/yr)3

Sampling-site 

elevation

(feet)4

Average 

basin slope 

(percent)4

Conterminous Western United States and Alaska

Mountain (MT)

Mountain Pacific Northwest (MT-PNW) 47 280 ± 1,757 40–53 8–125 17–6 7–6,244 0.2–53.2

Mountain Northern Rockies (MT-NROCK) 32 1,026 ± 1,894 32–45 22–65 14–22 1,627–7,405 13.3–44.6

Mountain Southern Rockies (MT-SROCK) 15 611 ± 1,192 32–47 21–37 13–24 5,230–9,505 18.0–38.7

Southwestern Mountains (MT-SWEST) 6 2,420 ± 2,544 43–54 19–40 18–28 2,097–6,267 9.6–32.9

Ozark Highlands (OH) NA 15 265 ± 417 55–56 44–46 31–32 456–1,024 1.6–10.8

Plains (PL) Cultivated Northern Plains (PL-NCULT) 10 2,023 ± 2,364 40–49 15–29 18–28 1,109–5,673 1.8–20.3

Rangeland Plains (PL-RANGE) 10 1,163 ± 1,224 41–50 15–27 20–28 1,444–3,442 0.5–18.5

Xeric (XE)

Eastern Xeric Plateaus (XE-EPLAT) 17 2,578 ± 2,756 34–50 9–31 14–27 4,521–7,989 1.4–36.6

Northern Xeric Basins (XE-NORTH) 22 665 ± 995 36–51 8–48 16–29 535–5,850 1.6–27.8

Southern Xeric Basins (XE-SOUTH) 9 2,024 ± 2,431 41–62 17–38 18–35 1,752–4,928 6.2–36.1

Xeric California (XE-CALIF) 18 1,789 ± 1,983 50–65 10–63 24–37 16–981 0.2–29.8

Hawaii

Hawaii (HI) NA 7 9 ± 16 76 63.7 NA 19–280 NA

1

 PRISM Data, 30 years (1961–1990), 2-kilometer grid size for temperature and relative humidity; Alaska temperature data are averages for Anchorage, Alaska (Western Regional 

Climate Center 2009a); Hawaii temperature data are averages for Honolulu, Hawaii (Western Regional Climate Center 2009a).

2

 PRISM Data, 30 years (1971–2000), 800-meter grid size; Alaska precipitation is statewide average, 1971–2000 (Western Regional Climate Center 2009b); Hawaii precipitation is 

statewide precipitation 1971–2000 (Western Regional Climate Center 2009b).

3

 PRISM Data, 30 years (1961–1990), 1-kilometer grid size for potential evaporation; data unavailable for Alaska and Hawaii.

4

 Elevation and basin slope data from National Elevation Dataset, 100-meter resolution; average basin slope data for Hawaii were unavailable.
Methods 7

Cr, Cu, Pb, Hg, Ni, Se, and Zn) were selected on the basis of 

their potential ecological significance and available sedimentquality guidelines (Van Derveer and Canton, 1997; MacDonald and others, 2000). Bed sediment at each sampling site was 

collected from 5 to 10 depositional areas, wet-sieved in the 

field through a 63-micron nylon mesh with ambient stream 

water, composited, and kept chilled until analysis (Shelton and 

Capel, 1994). Samples were analyzed by the U.S. Geological Survey Geologic Discipline, Colorado Minerals Program 

Laboratory, in Denver, Colo., using standardized analytical 

techniques for total (lithogenic) concentrations (Shelton and 

Capel, 1994; Horowitz, 1991; Arbogast, 1996). In circumstances where bed-sediment trace-element concentrations are 

sufficiently low to be considered below a detectable quantity, 

the Colorado Minerals Program Laboratory reports these 

concentrations as less than the method detection limit (MDL). 

The MDL is determined as three times the standard deviation 

of eight analyses for each trace element in method-blank water 

(Paul Lamothe, Research Chemist, U.S. Geological Survey, 

Geologic Discipline, Colo., written commun., 2011). When 

trace-element concentrations were below the MDL, representative values were calculated as half the MDL and that value 

used in all analyses. Concentrations of Cr, Cu, Ni, and Zn in 

bed-sediment samples were above their respective MDLs in 

all samples used in this study. Concentrations of As, Cd, Pb, 

Hg, and Se in bed-sediment samples were below the respective MDLs for these constituents in 1 to 13 samples (0.5 to 6 

percent of the samples) assessed in this study. Given the relatively low frequency of these occurrences, it is unlikely that 

the substitution of half the MDL in these cases substantially 

biased any conclusions made using this technique. Labile 

contaminants associated with bed sediment are generally 

considered more bioavailable to sediment-dwelling organisms 

than those contained in the lithogenic fraction (Luoma, 1989; 

Luoma and Rainbow, 2008). Weak-acid digestion methods 

have been employed to approximate the labile fraction of trace 

elements associated with bed sediment; however, of the 208 

sites evaluated in this study, only 21 (10 percent) had labile 

trace-element concentration information. Given the limited 

availability of this data, this information was not used in the 

analyses for this report.

Trace-element concentrations were evaluated for bed sediment collected from streams within undeveloped (reference) 

and developed (agricultural, urban, mined, and mixed land 

use) areas. Consensus-based Probable Effect Concentrations 

(PECs), the concentration of a substance above which adverse 

effects may likely occur, have been used to evaluate in-stream 

chemical conditions in aquatic ecosystems (MacDonald and 

others, 2000; Maret and others, 2003; Mebane and others, 

2003). In most cases, trace-element concentrations were 

compared to a PEC and threshold effect concentration (TEC). 

A TEC is the concentration below which adverse effects are 

unlikely to occur (MacDonald and others, 2000). TEC and 

PEC values were not available for Se; however, a probable 

effect level (PEL), similar to a PEC, of 4 μg/g was available 

from Van Derveer and Canton (1997) (table 2).

Two different methods were used to assess the reference 

and regional baseline concentrations for each of the nine trace 

elements assessed in this study. Reference bed-sediment concentrations of trace elements were determined from samples 

collected from undeveloped areas; regional baseline concentrations were determined without considering land use. These 

two methods were used because although sediment samples 

collected from areas of agriculture, urbanization, and mining 

can contain trace-element concentrations above those considered baseline, it does not necessarily follow that bed sediment 

from these areas will be above baseline. The seven sites in 

Hawaii were not included in the determination of either the 

regional reference or baseline trace-element concentrations 

in bed sediment because the concentrations of Cr, Cu, and Ni 

were 6 to 11 times higher in Hawaiian bed sediment than in 

bed sediment from other areas. The method used to determine 

regional reference trace-element concentrations was a summary of concentrations in bed sediment collected from streams 

at the 57 sites, in the conterminous western United States 

and Alaska, minimally influenced by human-related activities. Regional baseline concentrations were determined using 

methods similar to Velz (1984) and Rice (1999). To determine 

the regional baseline concentrations of the trace elements, 

probability distributions were used and trace-element concentrations were evaluated for each of 19 general study areas 

distributed among the 15 states (fig. 2). Trace-element baseline 

concentrations were considered those within each study area 

exhibiting a lower-linear range. Trace-element concentrations 

lying outside this lower-linear range, as indicated by a break 

in linearity, were considered above baseline for that area. This 

approach has two limitations: (1) the sometimes relatively limited number of data points available to determine the chemical baseline condition of bed sediment collected from some 

Table 2. Threshold Effect Concentration (TEC) and Probable 

Effect Concentration (PEC) values for trace elements of ecological 

significance and evaluated as part of this study.

[TEC and PEC values were obtained from MacDonald and others (2000); Thresholdeffect level (TEL) and probable-effect level (PEL) values obtained from Van Derveer and 

Canton (1997). Abbreviations: μg/g, microgram per gram]

Trace element

Threshold-effect 

concentration (TEC) 

(μg/g)

Probable-effect 

concentration (PEC) 

(μg/g)

Arsenic (As) 9.79 33

Cadmium (Cd) 0.99 4.98

Chromium (Cr) 43.4 111

Copper (Cu) 31.6 149

Lead (Pb) 35.8 128

Mercury (Hg) 0.18 1.06

Nickel (Ni) 22.7 48.6

Selenium (Se) 2.5 1 4 2

Zinc (Zn) 121 459

1

 Threshold-effect level. 

2

 Probable-effect level. 
8 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Figure 2. Locations of bed-sediment and macroinvertebrate sampling sites representative of undeveloped and developed (agricultural, 

urban, mined, and mixed) land uses for the A, conterminous western United States, B, Island of Oahu, Hawaii, and C, Cook Inlet area 

near Anchorage, Alaska, 1992–2000.

Green River

Formation

Washington

Oregon

Montana

North

Dakota Minnesota

Wisconsin

South

Wyoming Dakota

Idaho

Nevada

Utah

California

Arizona

New

Mexico

Colorado

Nebraska

Iowa

Kansas

Oklahoma

Texas

Missouri

Arkansas

Louisiana

Illinois

Alabama

A

B

C

Base from U.S. Geological Survey digital data, 1:10,000,000, 2006

Shaded-relief from ESRI Map Service

 http://server.arcgisonline.com/ArcGIS/services/World_Shaded_Relief, 2009

Albers Equal-Area Conic projection: Standard parallels 29°30', 45°30', central 

meridian -96°, latitude of origin 23°; North American Datum of 1983

Base from U.S. Geological Survey digital data, 1:10,000,000, 2006

Shaded-relief from ESRI Map Service

 http://server.arcgisonline.com/ArcGIS/services/

World_Shaded_Relief, 2009

Albers Equal-Area Conic projection

Standard parallels 8°, 18°, central meridian -157°, latitiude of origin 13°; 

North American Datum of 1983

0 20 40 MILES

0 20 40 KILOMETERS

Are of map

Hawaii

EXPLANATION

General study area

Site by land use

Undeveloped

Agriculture

Urban

1

CERCLA

Mined

Mixed

Base from U.S. Geological Survey digital data, 1:10,000,000, 2006

Shaded-relief from ESRI Map Service

 http://server.arcgisonline.com/ArcGIS/services/

World_Shaded_Relief, 2009

Albers Equal-Area Conic projection

Standard parallels 55°, 65°, central meridian -154°, latitiude of origin 

50°; North American Datum of 1983

0 100 200 MILES

0 100 200 KILOMETERS

Area

of

map

58°

64°

154° 146°

158°30' 157°30'

21°30'

21°00'

0 200 400 600 MILES

2000 400 600 KILOMETERS

130° 90°

45°

30°

Oahu

Alaska

1

Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA)
Methods 9

of the study areas, and (2) the visual assessment employed 

to ascertain the break in linearity. Trace-element concentrations reported among the various land-use categories were not 

adjusted for baseline concentrations. Baseline adjustment was 

not used because the purpose of this assessment is not to show 

a cause and effect between land use and trace-element concentrations but to indicate the relative trace-element exposure to 

macroinvertebrates at a given site. These results are discussed 

in further detail within the “Trace Element Concentrations in 

Bed Sediment” section of this report where regional baseline 

and reference concentrations derived from these assessments 

were compared to national baseline trace-element concentrations (Horowitz and Stephens, 2008).

Macroinvertebrate Collection and Taxonomic 

Resolution

Benthic-macroinvertebrate samples were collected following standard U.S Geological Survey NAWQA protocols (Cuffney and others, 1993). Sampling reaches for wadeable streams 

were typically between 150 and 300 m in length. Invertebrates 

were sampled during low-flow conditions and at targeted habitats expected to support the faunistically richest assemblages. 

In most cases, samples were collected from coarse-grained 

substrates in riffles, but occasionally, samples were collected 

from woody snags. Samples were collected using a 0.5 by 0.5 

m (0.25-m2 area) rectangular net with 425-micron mesh. Five 

discrete samples were collected from representative riffle or 

snag habitats in the sampling reach. After collection, macroinvertebrate samples were cleaned of extraneous material, composited into a single sample, preserved with 10-percent buffered formalin, and sent to the U.S. Geological Survey National 

Water Quality Laboratory (NWQL) Biological Unit in Denver, 

Colo., for identification and enumeration. A quantitative fixedcount (300 organisms) processing method was used to identify 

and estimate the abundance of each taxon sorted in the sample, 

and results were reported as relative abundance (the number 

of individuals per square meter; Moulton and others, 2000). 

Verification of problematic taxa and routine quality-assurance 

checks on taxonomic identification were performed. Taxonomic ambiguities were resolved by distributing ambiguous 

parents among children using the U.S. Geological Survey 

Invertebrate Data Analysis System (IDAS; Cuffney, 2003); the 

lowest taxonomic level considered was genus. IDAS was also 

used to generate a broad suite of macroinvertebrate metrics 

commonly used in water-quality assessment.

Land-Use Categorization

Land-use classifications were determined using enhanced 

U.S. Geological Survey National Land Cover Data (NLCDE) 

with a 30-m by 30-m grid dataset (Gilliom and others, 2006) 

and comparison with land-use characterizations by Horowitz 

and Stephens (2008). Land-use information was not available for Alaska; however, in this study, information regarding 

predominant land use near Alaskan stream sites was obtained 

from Timothy Brabets (U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, written commun., 2007). 

Land use was further refined to 250-m buffer areas along each 

bank of the stream segment from which macroinvertebrate 

and bed-sediment samples were collected (Maret and others, 2003; King and others, 2005). Available U.S. Geological 

Survey Mineral Resource Dataset (MRDS) data were sparse 

and varied by site, resulting in limited characterization of mining operations and associated mineralogy and dominant ore 

deposits within the regional study area (U.S. Geological Survey, 2004). Of the 208 sampling locations, which include the 

7 sites in Hawaii, 33 were in urbanized, 48 in agricultural, 41 

in mined, and 27 in mixed (urban, agriculture, and (or) mined) 

land-use areas. The remaining 59 sampling locations were in 

undeveloped areas considered to be relatively unaffected by 

human-related activities (fig. 2). 

Trace Elements and Macroinvertebrate 

Communities

CTU values were used to assess the relation between traceelement exposure and macroinvertebrate community structure 

in this study. CTU values were used in order to provide a 

means of addressing the occurrence of trace-element mixtures 

and to describe concentration gradients of these mixtures. 

Researchers have used indices such as CCUs and CTUs 

to quantify effects of aqueous and sediment trace-element 

concentrations, respectively (Clements and others, 2000; 

McGuire, 2001; Maret and others, 2003; Clements, 2004); 

however, the use of these types of indices may overestimate or 

underestimate effects because this approach assumes additive toxicity (Clements and others, 2000; Clements, 2004). 

Although actual toxicity of bed sediment may not be directly 

elucidated, this technique has provided resource managers with a measure of the relative severity of trace-element 

contamination in streams (Maret and others, 2003). CTUs 

were determined for each site by calculating the ratio of each 

measured trace-element concentration to the appropriate PEC 

value and then summing the resulting ratios (Maret and others, 

2003). 

Previous investigations have shown that total counts (abundance) of macroinvertebrate individuals and taxa and abundance of Ephemeroptera (mayflies), Plecoptera (stoneflies), 

and Trichoptera (caddisflies), or EPT individuals and taxa, 

are sensitive indicators of trace-element effects on aquatic 

communities (Maret and others, 2003; Carlisle and others, 

2007). To examine the relation between mixtures of bedsediment trace-element concentrations and macroinvertebrate 

community structure, taxa occurring at 30 percent of the sites 

within each ecoregion and CTUs were evaluated (appendix 2, 

table 2-1). Using taxa occurring at a minimum of 30 percent 

of the sites within a given ecoregion was implemented to 

reduce the complexity of macroinvertebrate communities by 

de-emphasizing rarer taxa. Attributing a causal effect between 
10 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

trace-element exposure and community structure must be 

made with caution because habitat characteristics also play an 

important role in structuring macroinvertebrate communities 

(Vannote and others, 1980; Plafkin and others, 1989; Hawkins 

and others, 2000). In this study, ecoregions delineated previously by Omernick (1987) and Whittier and others (2007) 

were used to reduce the effects of varying gross-level habitat 

characteristics on the occurrence of macroinvertebrate taxa 

(table 1). 

Statistical Analyses

Relations among bed-sediment trace elements were evaluated using Spearman correlation analysis (SYSTAT, 2004), 

and correlations were considered significant at the 95-percent confidence level (α = 0.05). Significant differences in 

trace-element concentrations among land-use categories and 

general ecoregion characteristics were tested using Analysis of 

Variance (ANOVA) Fisher Least-Significant Difference Test 

with pairwise comparisons on ranked data (SYSTAT, 2004). 

The Fisher Least-Significant Difference Test procedure was 

selected because of the inconsistency in sample sizes within 

each land-use category and ecoregion (Ott and Longnecker, 

2001; Helsel, 2005).

Ordination (multivariate analysis) was used to describe 

similarities and differences in macroinvertebrate community 

structure among sites. Ordination is a way of transforming 

original data into a form that can be interpreted in two or three 

dimensions (low dimensional space) whereby data points are 

assessed for similarity (or dissimilarity) along gradients (trajectories or eigenvectors) of interrelated explanatory variables 

(McGarigal and others, 2000; Clarke and Warwick, 2001). 

Gradients are described by using scores, calculated by weighting possible explanatory variables, with which trajectories are 

created in multidimensional space. Each gradient is related to 

principal components representing the amount of variability 

(data scatter) accounted for by those components within the 

dataset. Ideally, only a few variables are necessary to account 

for most of the variability observed. The components most 

effective at describing the variability within the dataset are 

identified as those with higher eigenvalues (McGarigal and 

others, 2000).

Non-metric (nonparametric) multidimensional scaling 

(MDS) was the primary multivariate ordination technique used 

to examine the relative patterns in macroinvertebrate community structure. This method is similar to Principal Components 

Analysis (PCA); however, PCA is limited in its ability to 

handle dissimilarities among samples and maintain Euclidean Distances, the measurement of straight lines between 

data points in multidimensional space (Clarke and Warwick, 

2001). Unlike many of the available ordination methods, 

MDS preserves the relative distance in multivariate space 

by retaining the rank order of among-sample dissimilarities. 

Therefore, interpretation of the MDS plot in two-dimensional 

space is relatively straight forward; samples close in proximity 

are more similar in taxonomic composition than those that are 

farther apart (Clarke, 1993). 

In nonparametric MDS, if the rank order of the data points 

is perfectly preserved from high to low dimensional space, 

a perfect fit would be observed between the data points and 

the regression line portraying the distance between the most 

dissimilar samples. It is the deviation from this perfect fit that 

is termed “stress” within MDS analyses (Clarke and Warwick, 

2001). The measure of stress is provided from the MDS analysis as a diagnostic to determine how well the data fit the MDS 

ordination. Lower stress values are desired, and stress values 

below 0.20 generally indicate that the MDS ordination is 

providing an accurate representation of the data in multivariate 

space. In other words, lower stress values generally indicate 

that the MDS ordination is producing a true distribution that is 

not the result of random chance (Clarke and Warwick, 2001).

Transforming original data prior to analysis using MDS 

can help alleviate bias in similarity (or dissimilarity) that may 

arise from variables potentially dominating the system(s) 

evaluated. In this study, a square-root transformation was 

used to normalize the macroinvertebrate relative-abundance 

data before calculating the Bray-Curtis dissimilarity matrix. 

A Bray-Curtis dissimilarity matrix is a type of resemblance 

matrix that is well suited for species abundance data because 

of the flexibility to include zero taxa abundance information 

into the matrix. Dissimilarities are determined by comparing 

data points to a trajectory drawn between the two most dissimilar data points within the dataset. Data points falling away 

from the trajectory line indicate the presence of factors, other 

than those described by the trajectory, influencing the distribution of data within the dataset. This method of analysis is also 

known as polar coordination (PCO) or Bray-Curtis ordination 

(McGarigal and others, 2000; Anderson, 2008). MDS analysis 

was performed on the Bray-Curtis dissimilarity matrix and 

plotted in two-dimensional space to reduce misinterpretation 

of multivariate patterns. 

PCO can use any resemblance (or dissimilarity) matrix 

making it similar to but more flexible than PCA. PCO is 

a re-projection of the sample data in the form of axes that 

distinguish groupings on the basis of the maximum variation 

in the sample data. The number of PCO axes used is chosen to 

minimize the probability of misclassifying a new point to the 

wrong group. In this study, correlations between the compositions of macroinvertebrate communities were evaluated along 

trajectories generated within the two-dimensional space of the 

MDS. Characterizing taxa were identified as those that separated the communities along particular trajectories (gradients) 

from other communities lying along other similarly generated trajectories. To simplify the results of the MDS, only 

those taxa occurring at a minimum of 30 percent of the sites 

within a given ecoregion and found to be correlated to community distribution (α = 0.05) were identified within the MDS 

ordinations. Hawaii was included in the initial MDS ordination to demonstrate the ability of the MDS to identify aquatic 

communities distinctly different from the other communities 

included in this study. Unlike macroinvertebrate assemblages 
Methods 11

in the MT, PL, and XE ecoregions, mayflies and stoneflies are 

not found in Hawaiian streams. The absence of these taxa is 

not attributed to contaminant exposure but to the geographic 

isolation of the Hawaiian Islands (Brasher and others, 2004). 

While ordination was used to discern patterns of macroinvertebrate community distribution along trace-element 

concentrations gradients, cluster analysis was performed to 

identify groups of similar communities along those gradients. 

Cluster analysis identifies groups of similar communities by 

evaluating minimal within-group differences and maximum 

differences among groups. Similar to the MDS, a Bray-Curtis 

similarity matrix (the complement to the dissimilarity matrix 

described above) was used to assess similarities among the 

various macroinvertebrate assemblages. An agglomerative 

approach was used within the cluster analysis where similar 

macroinvertebrate communities were grouped together forming a cluster (McGarigal and others, 2000). To further evaluate the difference among clusters of similar communities, the 

similarity profile test (SIMPROF) was used (PRIMER v.6; 

Clarke and Gorley, 2006). 

A SIMPROF was used to test for statistically meaningful 

groups displayed in the dendrogram of the cluster analysis. 

SIMPROF is a permutation test that evaluates whether or not 

a specified set of samples, which are not a priori assigned into 

groups, do not differ from each other in multivariate structure 

(Clarke and others, 2008). SIMPROF first ranks the sample 

resemblances from smallest to largest and then plots these similarities against their ranks, serving as the basis for the shape 

of an expected curve. One-thousand curves were generated 

in this manner by randomly rearranging the variable entries 

across samples. The 1,000 iterations are averaged to generate a 

simulated curve. It is the departure from the expected shape of 

the curve that is used to determine the likelihood that individual groups were generated purely by chance. The sum of 

the absolute distances between the real similarity profile and 

the simulated mean profile of the 1,000 iterations is used as 

the test statistic. The significance of the groupings within the 

ordination was evaluated at 95-percent confidence (p = 0.05). 

Vector overlays were added to MDS graphical outputs 

as an additional exploratory tool to visualize potential linear (monotonic) relations between influential taxa and the 

ordination axes. Spearman rank correlations were restricted 

to vectors with lengths of plus or minus 0.50 or greater; plus 

or minus 1.0 indicates complete correlation. The length and 

direction of each vector indicates the strength and sign, respectively, of the relation between the taxa and the MDS axes 

(Anderson and others, 2008). As an additional exploratory 

tool, bubble plots of sediment CTUs were superimposed onto 

the MDS plot to better visualize patterns between the macroinvertebrate assemblages and trace-element concentrations. Each 

bubble is a site assemblage where the size of the bubble represents the magnitude of the CTUs for bed sediment collected 

from that site. All multivariate analyses were performed using 

PRIMER v.6 and PERMANOVA v. 1.1 (Clarke and Gorley, 

2006; Anderson and others, 2008).

Data Limitations

At large geographic scales, macroinvertebrate community structure varies substantially with natural and anthropogenic disturbance gradients (Whittier and others, 2006). The 

interrelated environmental and chemical factors occurring 

at multiple scales can confound the interpretation of a community response to a known pollution gradient (LaPoint and 

others, 1984; Griffith and others, 2001; Feld and Hering, 2007; 

Whitter and others, 2007). The regional study area was broken 

into ecoregions, previously described by Omernick (1987) 

and Whittier and others (2007), in order to minimize some 

of the natural habitat-related variability during data analyses. 

Although delineation into ecoregions did mitigate, to some 

degree, the variability in macroinvertebrate distributions patterns not associated with contamination, these groupings did 

not account for site-specific habitat characteristics which, in 

some cases, may have been influencing aquatic assemblages.

Trace elements are commonly transported in streams in 

association with suspended particulates, and in areas where 

flow velocities are sufficiently slow, suspended material 

can settle out (Moran and Wentz, 1974; Gibbs, 1977). Bedsediment samples collected from depositional areas containing large quantities of fine-grained materials commonly have 

higher trace-element concentrations than areas predominantly 

composed of coarse-grained substrates (Horowitz, 1991). 

Accordingly, bed-sediment samples collected from depositional areas may contain higher trace-element concentrations 

than bed sediment in erodible areas within the stream channel 

where macroinvertebrates sampling was largely targeted. As 

a result, the actual exposure of macroinvertebrates collected 

from riffles and woody snags to bed-sediment trace elements 

collected from depositional areas, where finer-grained material 

accumulates, remains uncertain. Additionally, data regarding the portion of bioavailable trace elements in sediment to 

the aquatic organisms were not available for most of the sites 

included in this assessment.
12 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Trace-Element Concentrations in Bed 

Sediment

 Reference and regional baseline trace-element concentrations in bed sediment were determined by two methods: 

evaluating concentrations for 57 undeveloped sites and using 

methods similar to Rice (1999) and Velz (1984), respectively. 

Reference and regional baseline trace-element concentrations 

in bed-sediment samples used for purposes of this study were 

similar to the national baseline concentrations described by 

Horowitz and Stephens (2008) (table 3). The following discussion pertains to each of the 9 selected trace elements, their 

association with other trace elements, and occurrence within 

Table 3. Minimum, maximum, average, and median baseline concentrations for nine selected trace elements determined using two 

methods of analysis for bed-sediment samples collected from streams and rivers within the conterminous western United States and 

Alaska, 1992 to 2000, and national median baseline concentrations.

[Abbreviations: μg/g, microgram per gram; <, less than; ±, plus or minus]

Trace element Number of sites Percent of sites 1, 2

Minimum 

concentration

(μg/g)

Maximum 

concentration

(μg/g)

Average

concentration

± standard 

deviation

(μg/g)

Median 

concentration

(μg/g)

National median 

baseline 

concentration, 

(μg/g) 5

Concentrations in Bed-Sediment Samples from Undeveloped (Reference) Sites 3

Arsenic 57 28 1.9 50 11 ± 10 7.2 6.6

Cadmium 57 28 0.1 1.8 0.4 ± 0.4 0.3 0.4

Chromium 57 28 26 190 64 ± 33 55 58

Copper 57 28 8.0 79 31 ± 17 26 20

Lead 57 28 < 4 200 29 ± 37 20 20

Mercury 57 28 < 0.02 0.34 0.06 ± 0.06 0.04 0.04

Nickel 57 28 10 72 26 ± 14 21 23

Selenium 57 28 0.1 2.5 0.7 ± 0.5 0.53 0.7

Zinc 57 28 34 430 112 ± 72 93 91

Regional Baseline Concentrations 4

Arsenic 145 72 <0.1 33 7.4 ± 4.8 6.3 6.6

Cadmium 140 70 <0.1 3.8 0.47 ± 0.64 0.3 0.4

Chromium 153 76 7.0 190 60 ± 30 53 58

Copper 160 80 7.0 80 32 ± 15 29 20

Lead 146 73 <4 37 18 ± 7 17 20

Mercury 139 69 <0.02 0.15 0.04 ± 0.03 0.03 0.04

Nickel 144 72 2.0 90 25 ± 14 21 23

Selenium 120 62 <0.1 1.30 0.50 ± 0.29 0.44 0.7

Zinc 145 72 34 210 100 ± 34 95 91

1

 Total number of sites is 201; Hawaii bed-sediment samples (n=7) were not included in these analyses because concentrations of chromium, copper, and nickel were four to eight 

times higher in these samples than all other samples included in this study.

2

 193 sites were sampled for selenium. 

3

 Concentrations of the nine selected trace elements reported in this table were determined as those concentrations in bed-sediment samples collected from the 57 undeveloped sites 

included in this study. These undeveloped sites are in the following states: Alaska, Arizona, California, Idaho, Missouri, Montana, Nebraska, Nevada, Oregon, Utah, Washington, and 

Wyoming.

4

 Regional baseline concentrations for the nine selected trace elements reported in this table were determined using methods similar to Rice (1999) and Velz (1984). Regional 

baseline concentrations reported here were calculated from bed-sediment trace-element concentrations for sites in the following states: Alaska, Arizona, California, Colorado, Idaho, 

Missouri, Montana, Nebraska, Nevada, New Mexico, Oregon, Utah, Washington, and Wyoming.

5

 National baseline concentrations from Horowitz and Stephens, 2008. 

each of the 5 general land-use categories for samples collected 

from within the conterminous western United States and 

Alaska. Trace elements that are discussed in groups are discussed as such on the basis of moderate to strong correlations 

among these trace elements in bed sediment collected from 

undeveloped areas (table 4). Moderate and strong correlations 

were found among concentrations of Cd, Pb, and Zn (0.544 ≤ 

rho ≤ 0.626) and between Cr and Ni (rho = 0.842) in reference bed-sediment samples. Although moderate correlations 

were also found between Zn and Cu (rho = 0.552) and Hg 

(rho = 0.541), moderate to strong correlations were not found 

between Cu and Hg (rho = 0.470) or between Cu or Hg with 

either Cd and Pb, with which Zn was moderately correlated 

(table 4). 
Trace-Element Concentrations in Bed Sediment 13

Table 4. Correlations among the nine trace elements in bed sediment samples collected at reference and non-reference (agricultural, 

urbanized, mined, and mixed) streams and rivers in the conterminous western United States and Alaska, 1992–2000.

[A mixed land-use classification indicates a combination of agricultural, urbanization, and (or) mining-related activities present at or near the sampling site. Because of the high 

concentrations of chromium, copper, and zinc beyond those of other areas included in this study, trace-element concentrations in bed-sediment samples collected from Hawaii were not 

included in the correlation analysis (n=7). Spearman rho values less than 0.5 were considered weak, between 0.5 and 0.7 considered moderate, and greater than 0.7 considered strong. 

Correlations greater than 0.5 are emphasized (shown in bold) in the table]

Trace element Arsenic Cadmium Chromium Copper Lead Mercury Nickel Selenium Zinc

Correlation Among Trace Elements in Bed Sediment Collected from Undeveloped (Reference) Sites, n=57

Arsenic 1.0

Cadmium 0.438 1.0

Chromium 0.238 0.027 1.0

Copper 0.265 0.164 0.381 1.0

Lead 0.311 0.626 –0.108 0.047 1.0

Mercury 0.339 0.274 0.049 0.470 0.219 1.0

Nickel 0.276 0.050 0.842 0.488 –0.041 0.156 1.0

Selenium –0.190 0.373 0.201 0.055 0.145 –0.064 0.222 1.0

Zinc 0.430 0.592 0.170 0.552 0.544 0.541 0.202 0.307 1.0

Correlation Among Trace Elements in Bed Sediment Collected from Agricultural Areas, n=47

Arsenic 1.0

Cadmium 0.237 1.0

Chromium 0.351 0.168 1.0

Copper 0.423 –0.048 0.522 1.0

Lead 0.225 0.474 0.053 –0.058 1.0

Mercury 0.244 0.088 0.544 0.665 0.086 1.0

Nickel 0.477 0.151 0.778 0.789 0.053 0.581 1.0

Selenium 0.233 0.506 –0.048 0.050 0.257 0.046 0.220 1.0

Zinc 0.473 0.373 0.337 0.608 0.372 0.388 0.476 0.294 1.0

Correlation Among Trace Elements in Bed Sediment Collected from Urban Areas, n=29

Arsenic 1.0

Cadmium 0.187 1.0

Chromium 0.575 –0.185 1.0

Copper 0.051 0.263 0.351 1.0

Lead 0.138 0.794 –0.031 0.476 1.0

Mercury 0.007 –0.277 0.488 0.305 –0.362 1.0

Nickel 0.556 –0.141 0.936 0.425 0.004 0.438 1.0

Selenium –0.231 –0.233 0.071 0.137 –0.454 0.666 –0.003 1.0

Zinc –0.015 0.783 –0.045 0.522 0.783 –0.070 –0.033 –0.207 1.0

Correlation Among Trace Elements in Bed Sediment Collected from Mined Areas, n=41

Arsenic 1.0

Cadmium 0.559 1.0

Chromium –0.097 –0.399 1.0

Copper 0.540 0.395 0.195 1.0

Lead 0.503 0.889 –0.584 0.301 1.0

Mercury 0.585 0.379 0.266 0.669 0.299 1.0

Nickel –0.418 –0.520 0.691 –0.090 –0.570 –0.042 1.0

Selenium 0.136 0.297 0.055 0.130 0.083 0.106 0.088 1.0

Zinc 0.568 0.917 –0.341 0.484 0.851 0.423 –0.423 0.279 1.0

Correlation Among Trace Elements in Bed Sediment Collected from Mixed Land Use Areas, n=27

Arsenic 1.0

Cadmium 0.256 1.0

Chromium –0.193 –0.558 1.0

Copper 0.053 –0.024 0.419 1.0

Lead –0.018 0.370 –0.297 0.001 1.0

Mercury 0.336 –0.038 0.342 0.581 0.134 1.0

Nickel –0.048 –0.313 0.744 0.572 –0.461 0.206 1.0

Selenium 0.329 0.434 –0.233 –0.198 0.191 –0.133 –0.161 1.0

Zinc 0.196 0.738 –0.396 0.162 0.475 0.227 –0.194 0.302 1.0
14 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Arsenic

Natural sources of As include weathering of As-bearing 

rocks (such as arsenopyrite), volcanic activity, and geothermal 

water (Boyle and Jonasson, 1973; Wilkie and Hering, 1998; 

Glass and Frenzel, 2001). The median As concentration at 

undeveloped (reference) sites was 7.2 μg/g, similar to the concentration determined by Horowitz and Stephens (2008) and 

the regional baseline concentration determined using methods 

similar to Rice (1999) and Velz (1984) (table 2). Seventy-two 

percent of the bed-sediment samples collected had As concentrations within regional baseline limits (<0.1 to 33 μg/g, 

table 2). As concentrations in reference bed sediment were not 

correlated to any appreciable extent (rho < 0.5) with the other 

eight trace elements included in this investigation; however, in 

bed sediment collected from streams in developed areas, there 

were stronger correlations between As and other select trace 

elements (0.503 ≤ rho ≤ 0.585) depending on the area from 

which the bed-sediment samples were collected (urban or 

mined) (table 3). Most moderate correlations between As and 

other trace elements were in bed-sediment samples collected 

from mined areas.

In this study, median As concentrations in bed sediment from streams within urbanized (9.10 μg/g) and mined 

(22.70 μg/g) areas were higher compared to bed sediment 

collected from areas that were largely undeveloped (7.20 μg/g) 

or influenced by either agriculture (5.59 μg/g) or a mixture 

(7.20 μg/g) of land uses (p ≤ 0.024, fig. 3). Of the 16 sites 

at which bed-sediment samples exceeded the PEC for As 

(33 μg/g), 75 percent of these sites were in mined areas. Eight 

of these 12 sites are associated with CERCLA areas listed 

as a result of historic mining activities in Colorado, Idaho, 

Montana, and Utah (U.S. Environmental Protection Agency, 

2010); As concentrations at these eight sites ranged from 42 

to 170 μg/g. Bed sediment collected from five of these eight 

sites also exceeded the PEC values for Cd, Cu, Pb, and Zn 

(table 2). Concentrations in bed sediment sampled from the 

other eight sites not associated with CERCLA areas, but where 

As concentrations exceeded 33 μg/g, ranged from 37 to 93 

μg/g; these eight sites were representative of undeveloped and 

mined areas. The median concentrations of As in bed sediment 

collected from areas influenced by human-related activities, 

other than mining, were below the TEC for this trace element 

(table 2; fig. 3).

Cadmium, Lead, and Zinc

The most common sources of Pb and Zn are the sulfide (S) ores of these trace elements that commonly occur 

together—PbS (galena) and ZnS (sphalerite). Although not 

widely distributed, the most common Cd-containing mineral, greenockite (CdS), can occur as a coating on sphalerite 

(Berry and Mason, 1959; Hurlbut, 1971; Helmuth, 1973). 

Median concentrations of Cd, Pb, and Zn in bed sediment 

collected from undeveloped areas were 0.3, 20, and 93 μg/g, 

respectively (table 3, figs. 4A–4C). Regionally, these reference concentrations are similar to those determined as part of 

a national study by Horowitz and Stephens (2008) and to the 

regional baseline concentrations determined using methods 

similar to Rice (1999) and Velz (1984) (table 2). Most bedsediment samples (70 to 73 percent) were within Cd, Pb, and 

Zn regional baseline concentrations (table 3). Cd, Pb, and Zn 

were moderately correlated in bed sediment collected from 

reference areas (0.544 ≤ rho ≤ 0.626) and strongly correlated 

at sites influenced by urbanization and mining (rho ≥ 0.783, 

table 4). Zn was the only one of these three trace elements 

moderately correlated to other trace elements (Cu and Hg) in 

bed sediment under undeveloped conditions. Cd (-0.558 ≤ rho 

≤ 0.559), Pb (-0.570 ≤ rho ≤ 0.503), and Zn (0.522 ≤ rho ≤ 

0.608) were correlated to other trace elements in bed-sediment 

samples collected from developed areas (table 4). The negative moderate correlations between Cd and Pb were for the 

correlations between these two trace elements and Cr and (or) 

Ni in bed sediment collected from streams in mined or mixed 

land-use areas, suggesting these trace elements do not cooccur at the regional scale used during this study.

Figure 3. Concentrations of arsenic (As) in bed sediment 

collected from 201 sites representative of undeveloped and 

developed (agricultural, urban, mined, and mixed land use) areas 

in the conterminous western United States and Alaska, 1992–2000.

Outlier

90th percentile

75th percentile

Median (50th percentile)

25th percentile

10th percentile

Outlier

EXPLANATION

Number of sites

57 47 29 41 27

1

10

100

1,000

0.1

Land-use category

Bed-sediment arsenic concentration, in micrograms per gram

PEC

(33 μg/g)

TEC

(9.79 μg/g)

A

B

C

D

A,B

Undeveloped Agricultural Urban Mined Mixed*

 Schematic boxplot *Mixed, sites with agricultural, urban, and (or) mining 

land uses represented

PEC, probable-effect concentration

TEC, threshold-effect concentration

μg/g, micrograms per gram

Median concentrations for boxplots with different 

letter designations are statistically different (p<0.05). 

Data from Hawaii were not included in this figure.
Trace-Element Concentrations in Bed Sediment 15

Number of sites

57 47 29 41 27

1

10

100

< 0.1

Land-use category

Bed-sediment cadmium concentration, in micrograms per gram

Bed-sediment lead concentration, in micrograms per gram

PEC

(4.98 μg/g)

TEC

(0.99 μg/g)

A

A

B,C

B,C

D

A,B

Undeveloped Agricultural Urban Mined Mixed*

Land-use category

Undeveloped Agricultural Urban Mined Mixed*

Land-use category

Undeveloped Agricultural Urban Mined Mixed*

Outlier

90th percentile

75th percentile

Median (50th percentile)

25th percentile

10th percentile

Outlier

EXPLANATION

 Schematic boxplot

Number of sites

57 47 29 41 27

10,000

1,000

100,000

10

100

< 4

PEC

(128 μg/g)

TEC

(35.8 μg/g)

A

B

B,C

C

D

A,B

Number of sites

57 47 29 41 27

10,000

1,000

100,000

10

100

Bed-sediment zinc concentration, in micrograms per gram

PEC

(459 μg/g)

TEC

(121 μg/g)

A

C

B

B

C

A

*Mixed, sites with agricultural, urban, and (or) mining 

land uses represented

PEC, probable-effect concentration

TEC, threshold-effect concentration

μg/g, micrograms per gram, <, less than.

Median concentrations for boxplots with different 

letter designations are statistically different (p<0.05). 

Data from Hawaii were not included in this figure.

in mined areas were 2.2, 110, and 460 μg/g, respectively. 

The median concentrations of Pb and Zn at these sites were 

approaching and equal to the respective PEC values for these 

trace elements (table 2; figs. 4B–4C).

The PEC values for Cd, Pb, and Zn were exceeded in bed 

sediment collected from 12, 24, and 25 sites, respectively 

(table 2; figs. 4A–4C). Most of these exceedences (83–92 

percent) were in bed sediment collected from streams in mined 

areas. The other bed-sediment samples (8 to 17 percent), 

where the PEC value for at least one of these trace elements 

was exceeded, were collected from undeveloped and urban 

Figure 4. Concentrations of A, cadmium, B, lead, and C, zinc in bed sediment collected from 201 sites representative of undeveloped 

and developed (agricultural, urban, mined, and mixed land use) areas in the conterminous western United States and Alaska, 1992–2000.

The concentrations of Cd, Pb, and Zn in bed sediment collected from undeveloped and agricultural areas were not significantly different (0.070 ≤ p ≤ 0.290). Concentrations of Cd 

were similar among undeveloped and urbanized (p = 0.085) 

and mixed land-use (p = 0.229) areas, whereas Pb and Zn 

showed some degree of enrichment in mixed (p ≤ 0.016) and 

urbanized (p < 0.05) landscapes, respectively (figs. 4A–4C). 

The highest concentrations of all three of these trace elements 

were in bed-sediment samples collected from streams influenced by historic mining-related activities (p ≤ 0.004). Median 

concentrations of Cd, Pb, and Zn determined for bed sediment 
16 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

areas. Eleven bed-sediment samples contained concentrations 

of Cd, Pb, and Zn that exceeded the PEC values for all three 

trace elements, all within mined landscapes. Of these 11 sites, 

7 exceeded the PEC value for As, 6 exceeded the PEC for Cu, 

and 4 exceeded the PEC for Hg (table 2). Of these 11 sites, 9 

are associated with CERCLA areas in Colorado, Idaho, and 

Utah listed as a result of trace-element contamination from 

historic mining activities (U.S. Environmental Protection 

Agency, 2010).

Chromium and Nickel

Coastal mountain ranges in California, parts of the Sierra 

Nevada, and mountains in southern Oregon were formed by 

upward faulting of oceanic crustal deposits containing ophiolite-sequence formations and ultramafic rocks (Bateman and 

Wahrhaftig, 1966; Irwin, 1966; Kosanke and Harper, 1997; 

Godfrey and Dilek, 2000). Ni has been found to be enriched in 

ultramafic rocks and in chromite, which are important sources 

of naturally occurring Cr and the primary ore targeted by Cr 

mining operations (Hancock, 1991; Papp, 1994; Salminen and 

others, 2004). Serpentine soils, derived from the weathering 

of ultramafic rock, contain relatively large amounts of Cr and 

Ni. Although not widely distributed, areas noted for having 

serpentinitic rocks and soils are in California and Oregon 

(Oze and others, 2004). The high concentrations of Cr in bed 

sediment collected from streams in California are likely the 

result of the weathering and transport of material originating 

from the ultramafic serpentine rock exposed along the Coast 

Ranges and Sierra Nevada (Morrison and others, 2009). Areas 

within Washington and Alaska also have geologically derived 

Cr and (or) Ni (Fuhrer and others, 1999; Frenzel, 2002; Ourso 

and Frenzel, 2003). Median concentrations of Cr (55 μg/g) 

and Ni (21 μg/g) in bed sediment collected from streams in 

undeveloped areas were similar to median concentrations of 

these trace elements in bed sediment throughout the Nation 

(Horowitz and Stephens, 2008) and to regional baseline 

concentrations determined for this study. Most bed-sediment 

samples had concentrations of Cr (76 percent) and Ni (72 

percent) within regional baseline limits (table 3). Concentrations of Cr and Ni in bed sediment collected from streams in 

undeveloped and developed areas were strongly correlated 

(rho ≥ 0.691, table 3), a condition observed only for these two 

trace elements.

Median concentrations of Cr and Ni in bed sediment collected from undeveloped and agricultural areas (p ≥ 0.386) 

were not significantly different. Median concentrations of Cr 

in bed sediment from areas influenced by mining (48 μg/g) 

were statistically similar to those in bed sediment from undeveloped (55 μg/g) and agricultural (53 μg/g) areas (p ≥ 0.380); 

median concentrations of Cr were elevated but statistically 

similar in bed sediment from streams in urbanized (78 μg/g) 

and mixed (65 μg/g) land-use areas (p = 0.286, fig. 5A). Of 

the 19 bed-sediment samples exceeding the PEC for Cr (111 

μg/g), the fewest exceedences were in agricultural (10 percent) 

and urban (10 percent) landscapes; the most exceedences 

Number of sites

57 47 29 41 27

1,000

1

10

100

Land-use category

Bed-sediment chromium concentration, in micrograms per gram

PEC

(111 μg/g)

TEC

(43.4 μg/g)

A

A

B B

A A

Undeveloped Agricultural Urban Mined Mixed*

Land-use category

Undeveloped Agricultural Urban Mined Mixed*

Number of sites

57 47 29 41 27

1,000

1

10

100

Bed-sediment nickel concentration, in micrograms per gram

PEC

(48.6 μg/g)

TEC

(22.7 μg/g)

A

B

B

B B

A

Outlier

90th percentile

75th percentile

Median (50th percentile)

25th percentile

10th percentile

Outlier

EXPLANATION

 Schematic boxplot *Mixed, sites with agricultural, urban, and (or) mining 

land uses represented

PEC, probable-effect concentration

TEC, threshold-effect concentration

μg/g, micrograms per gram.

Median concentrations for boxplots with different 

letter designations are statistically different (p<0.05). 

Data from Hawaii were not included in this figure.

Figure 5. Concentrations of A, chromium, and B, nickel in bed 

sediment collected from 201 sites representative of undeveloped 

and developed (agricultural, urban, mined, and mixed land use) 

areas in the conterminous United States and Alaska, 1992–2000.
Trace-Element Concentrations in Bed Sediment 17

were in mined (38 percent) areas. These results indicate that 

relatively high concentrations of Cr are encountered in many 

bed-sediment samples from urban and mixed land-use areas; 

however, these concentrations are generally below the PEC for 

this trace element. In contrast, Cr concentrations in bed sediment collected from streams in mined landscapes contain generally lower concentrations than in urban and mixed land-use 

areas but have occasional samples with high concentrations 

exceeding the PEC for Cr. Although Cr can be mobilized when 

mined, Cr contained in waste tailings is relatively immobile 

(Papp, 1994; Salminen and others, 2004). Median concentrations of Cr and Ni in bed sediment collected from all land-use 

areas were between the TEC and PEC concentrations for these 

trace elements (figs. 5A-5B). Ninety-five percent of the bedsediment samples exceeding the PEC for Cr also exceeded 

the PEC for Ni (48.6 μg/g), 10 percent for As (33 μg/g), and 5 

percent each for Pb (128 μg/g) and Zn (459 μg/g).

Concentrations of Ni were elevated, and median concentrations similar in bed sediment collected from streams flowing 

through areas influenced by urbanization (35 μg/g), mining 

(29 μg/g), and mixed (29 μg/g) land uses (p ≥ 0.277, fig. 5B). 

The PEC for Ni was exceeded in 37 bed-sediment samples 

from all five land-use categories (undeveloped, agricultural, 

urban, mined, and mixed); the lowest number of exceedences 

was in streams in agricultural areas (11 percent), and the highest in streams influenced by historic mining-related activities 

(32 percent). Where PEC exceedences occurred for Ni, 47 

percent of those samples also exceeded the PEC for Cr; the 

PECs for As, Pb, and Zn were exceeded in 5 to 11 percent of 

these 37 samples. These results show a connection between Cr 

and Ni where sediment-quality guidelines generally exceeded 

for one of these trace elements may be exceeded for the other. 

There were a few instances where the PECs for Cr and (or) 

Ni were exceeded and concentrations of the other seven trace 

elements considered in this evaluation were also greater than 

respective PEC values. Of the 18 bed-sediment samples where 

concentrations of Cr and Ni exceeded their respective PEC 

values, 7 of these samples (39 percent) were collected from 

streams that have segments listed as impaired; none were 

associated with areas influenced by known CERCLA areas 

or considered impaired as a result of either Cr and (or) Ni 

contamination (table 2; Alaska Department of Environmental 

Conservation, 2010; California Environmental Protection 

Agency, 2010; State of Washington, Department of Ecology, 

2010).

Copper

Chalcopyrite (CuFeS2) is commonly associated with 

galena (PbS) and sphalerite (ZnS), which were all relatively 

common in areas where bed-sediment samples were collected 

and mineralogic data were available (Berry and Mason, 1959; 

Hurlbut, 1971); other researchers have noted the common 

co-occurrence of Cd, Cu, Pb, and Zn (Baker and Proctor, 

1990). Available U.S. Geological Survey Mineral Resource 

Dataset (MRDS) data were sparse and varied by site, resulting 

in limited characterization of the mineralogy associated with 

dominant ore deposits throughout the study area (U.S. Geological Survey, 2004). However, of the 117 sites for which MRDS 

information was available, chalcopyrite was identified at 77 

sites, and chalcopyrite, galena, and sphalerite co-occurred at 

61 (79 percent) of these 77 sites. The median Cu concentration in bed sediment collected from streams in undeveloped 

areas was 26 μg/g, similar to the regional baseline concentration and the national baseline concentration determined by 

Horowitz and Stephens (2008). Concentrations of Cu in 80 

percent of the samples collected throughout the regional study 

area were within regional baseline concentration limits (7 to 

80 μg/g, table 3). In undeveloped areas, bed-sediment Cu concentrations were moderately correlated to Zn concentrations 

(rho = 0.552). Concentrations of Cu in bed-sediment samples 

collected from streams in developed areas were at least moderately correlated to various other trace elements (0.522 ≤ rho ≤ 

0.789) depending on the land use (table 4). These results show 

that Cu commonly co-occurred with other trace elements in 

the bed-sediment samples.

The median Cu concentration in bed sediment collected 

from agricultural areas (21 μg/g) was statistically lower than 

concentrations in bed sediment collected from undeveloped 

areas (26 μg/g, p = 0.008, fig. 6). Although the median Cu 

Figure 6. Concentrations of copper (Cu) in bed sediment 

collected from 201 sites representative of undeveloped and 

developed (agricultural, urban, mined, and mixed land use) areas 

in the conterminous western United States and Alaska, 1992–2000.

Number of sites

57 47 29 41 27

1,000

1

10

100

Land-use category

Bed-sediment copper concentration, in micrograms per gram

PEC

(149 μg/g)

TEC

(31.6 μg/g)

B

C C

C

A

Undeveloped Agricultural Urban Mined Mixed*

Outlier

90th percentile

75th percentile

Median (50th percentile)

25th percentile

10th percentile

Outlier

EXPLANATION

 Schematic boxplot *Mixed, sites with agricultural, urban, and (or) mining 

land uses represented

PEC, probable-effect concentration

TEC, threshold-effect concentration

μg/g, micrograms per gram.

Median concentrations for boxplots with different 

letter designations are statistically different (p<0.05). 

Data from Hawaii were not included in this figure.
18 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

concentration appears to be the highest in bed sediment collected from areas influenced by mining, there was no strong 

statistical difference among median Cu concentrations in bedsediment samples collected from areas of mining (58.7 μg/g), 

urban (45 μg/g), and mixed (40 μg/g) land use (p ≥ 0.055, 

fig. 6). The PEC (149 μg/g) for Cu was exceeded in nine 

bed-sediment samples of which eight were associated with 

CERCLA areas listed because of historic mining activities 

in Colorado, Idaho, Montana, and Utah (U.S. Environmental Protection Agency, 2010). Concentrations of Cu at these 

eight sites ranged from 170 to 500 μg/g. In the nine instances 

where the PEC for Cu was exceeded, 44 to 89 percent of these 

samples also exceeded a PEC value for one or more of the 

other trace elements—As, Cd, Pb, Hg, and (or) Zn.

Mercury

Cinnabar (HgS) is the most important Hg-containing mineral and is commercially mined in only a few locations in the 

United States (Bailey and others, 1973). In the western United 

States, Hg deposits are found in Alaska, California, Idaho, 

Nevada, Oregon, and Utah (Hurlbut, 1971; Bailey and others, 

1973). Hg is a global-scale pollutant, widely distributed by 

atmospheric transport (Fitzgerald and others, 1998; Eisler, 

2000). Through atmospheric transport mechanisms, elevated 

Hg concentrations have been occurring in otherwise relatively 

“pristine” areas (Fitzgerald and others, 1998; Krabbenhoft 

and others, 1999). The use of Hg to facilitate the extraction of 

gold and silver from milled ore by a process called amalgamation can release large quantities of Hg to adjacent streams and 

rivers (Bevans and others, 1998; Alpers and others, 2005). 

Activities related to historic amalgamation operations continue 

to be an environmentally important source of Hg contamination within the western United States (Maret and others, 2003; 

Norman and others, 2008). Scudder and others (2009) found 

that concentrations of total Hg were higher in bed-sediment 

samples collected from streams in mined areas relative to 

samples collected from unmined areas in the western United 

States.

The median Hg concentration in bed sediment from undeveloped areas was 0.04 μg/g, similar to the regional baseline 

concentration determined as part of this study (0.03 μg/g) 

and the same as the national baseline value determined by 

Horowitz and Stephens (2008). Sixty-nine percent of the 

bed-sediment samples collected and analyzed for Hg contained concentrations of Hg within regional baseline limits 

(<0.02 to 0.15 μg/g, table 3). Concentrations of Hg in bed 

sediment were correlated with Zn concentrations in samples 

collected from streams at undeveloped sites (rho = 0.541, 

table 4). At developed sites, Hg was moderately correlated 

with bed-sediment concentrations of Cr, Cu, Ni, and Se 

(0.544 ≤ rho ≤ 0.669) depending on the predominant land 

use (table 4). Concentrations of Hg in bed sediment exceeded 

the PEC (1.06 μg/g) at seven sites, all influenced by historic 

mining-related activities (fig. 7). At these seven sites, 57 to 

86 percent of these samples also exceeded the PECs for As, 

Cd, Pb, and Zn. Six of these seven sites were associated with 

three CERCLA areas in Idaho, Montana, and Nevada. Concentrations of Hg associated with bed-sediment samples from 

these CERCLA areas ranged from 1.7 to 17 μg/g; the highest 

concentration was in bed sediment collected from a river in 

Nevada. Scudder and others (2009) indicate that a more accurate estimate of Hg toxicity in bed sediment would be represented by concentrations of methyl mercury (methyl-Hg), the 

more toxic form of Hg; however, sediment-quality guidelines 

for methyl-Hg are currently unavailable. 

Selenium

The most common Se-containing mineral is clausthalite 

(PbSe); however, Upper Cretaceous marine sedimentary 

deposits are the most prominent Se-containing material in the 

western United States (Bear, 1957; Berry and Mason, 1959; 

Seiler and others, 2003; Mineral Data Publishing, 2005). Cutter and Bruland (1984) suggest a biogeochemical cycle of Se 

in the marine environment that involved Se uptake by marine 

Figure 7. Concentrations of mercury (Hg) in bed sediment 

collected from 201 sites representative of undeveloped and 

developed (agricultural, urban, mined, and mixed land use) areas 

in the conterminous western United States and Alaska, 1992–2000.

Number of sites

57 47 29 41 27

100

< 0.02

0.1

1

10

Land use category

Bed-sediment mercury concentration, in micrograms per gram

PEC

(1.06 μg/g)

TEC

(0.18 μg/g)

B

C

A

C

A

Undeveloped Agricultural Urban Mined Mixed*

Outlier

90th percentile

75th percentile

Median (50th percentile)

25th percentile

10th percentile

Outlier

EXPLANATION

 Schematic boxplot

*Mixed, sites with agricultural, urban, 

and(or) mining land uses represented

PEC, probable-effect concentration

TEC, threshold-effect concentration

μg/g, micrograms per gram

Median concentrations for boxplots 

with different letter designations are 

statistically different (p<0.05). Data from 

Hawaii were not included in this figure.
Trace-Element Concentrations in Bed Sediment 19

organisms and subsequent deposition of biogenic organicselenide particulate matter. Areas within the western United 

States with noted Upper Cretaceous marine shales include 

California, Colorado, eastern Utah, Montana, parts of New 

Mexico, and Wyoming (Byers, 1935; Seiler and others, 2003). 

Concentrations of Se in seleniferous soils derived from these 

deposits have been found to range from 5 to 80 μg/g (Bear, 

1957). The world’s largest deposit of oil shale, a bituminous 

sedimentary rock containing trace elements including Se, is 

the Green River Formation in Colorado, Utah, and Wyoming 

(Stollenwerk and Runnells, 1981; Spackman and others, 

1990). The median Se concentration in bed sediment collected 

from undeveloped sites was 0.53 μg/g, similar to the regional 

baseline concentration of 0.44 μg/g and that determined in 

the national study by Horowitz and Stephens (2008) (table 3). 

Of the 201 sites within the conterminous western United 

States and Alaska included in this study, 193 bed-sediment 

samples were analyzed for Se; 62 percent of those samples 

had concentrations within baseline limits (<0.1 to 1.3 μg/g, 

table 3). Concentrations of Se were not substantially correlated 

(rho ≤ 0.373) to any of the other eight trace elements evaluated in bed-sediment samples collected from undeveloped 

areas (table 4). Concentrations of Se in bed sediment from 

streams in agricultural areas were moderately correlated to Cd 

(rho = 0.506), and in urban areas, there was a moderate correlation between Se and Hg (rho = 0.666); all other correlations 

between Se and the remaining five other trace elements within 

developed areas were weak (rho ≤ 0.339). 

Compared to undeveloped (reference) sites, significantly 

higher concentrations of Se in bed sediment were observed 

only in streams in urban land-use settings (p = 0.012, fig. 8). 

Sources of Se to receiving streams include municipal wastewater discharges and runoff from agricultural lands, coal and 

metal mining operations, and oil refineries (Renner, 1998). 

The highest concentrations of Se observed in this study, and 

the only two instances where concentrations exceeded the PEL 

(4 μg/g; Van Derveer and Canton, 1997), were in bed-sediment samples collected from a wash influenced by agricultural 

practices in Colorado (5.6 μg/g) and a creek in an urbanized 

landscape in Alaska (5.8 μg/g). Geological sources, such as 

coal deposits, exist within the Cook Inlet area near Anchorage, 

Alaska, and could be contributing to elevated Se concentrations in the area (Frenzel, 2000). In all land-use categories, 

median Se concentrations were below the threshold-effect 

level (TEL) of 2.5 μg/g.

Cumulative Toxic Units

The interactions among trace elements in mixture are 

important to consider when examining the effects of trace 

elements in natural systems (Dunlop and Chapman, 1981; 

Oakden and others, 1984; Preston and others, 2000; Griffith 

and others, 2004). Enhanced trace-element interactions can 

be additive, where toxicity among trace elements increases in 

proportion to the number of trace elements present, or synergistic, where a trace element enhances the toxicity of others 

by a factor greater than the number of trace elements present. 

Alternatively, trace-element interactions can be antagonistic (inhibitory), whereby a trace element can decrease the 

expressed toxicity of another (Larsen and Bjeeregaard, 1995; 

Andrewes and others, 2000). The use of CTUs assumes 

additive toxicity among trace elements. The use of CTUs 

to characterize the degree of bed-sediment impairment can 

potentially underestimate or overestimate the harmful quality 

of the sediment being evaluated and should be considered an 

indicator of impairment, not an actual measure of impairment. 

CTUs were used to evaluate trace-element concentrations 

in bed sediment in mixture with respect to available sedimentquality guidelines (MacDonald and others, 2000). CTU values 

were calculated using available bed-sediment concentration 

data for eight of the nine trace elements examined in this 

study. Se was not used in the determination of CTUs because 

data were not available for all bed-sediment samples collected. There were only two instances where Se concentrations 

exceeded the PEL of 4 μg/g, and with the exception of two 

instances, Se was at best weakly correlated with other trace 

elements. Median CTU values for bed sediment collected from 

streams in undeveloped (2.04) and agricultural (1.57) landscapes were below the 50th percentile for the entire study area 

(2.5). Bed sediment collected from urban and mixed land-use 

Figure 8. Concentrations of selenium (Se) in bed sediment 

collected from 201 sites representative of undeveloped and 

developed (agricultural, urban, mined, and mixed land use) areas 

in the conterminous western United States and Alaska, 1992–2000.

Number of sites

57 47 29 41 27

10

< 0.1

1

Land-use category

Bed-sediment selenium concentration, in micrograms per gram

PEL

(4 μg/g)

TEL

(2.5 μg/g)

B

C

A,C

A,B

A,B

Undeveloped Agricultural Urban Mined Mixed*

Outlier

90th percentile

75th percentile

Median (50th percentile)

25th percentile

10th percentile

Outlier

EXPLANATION

*Mixed, sites with agricultural, urban, and (or) mining Schematic boxplot land uses represented

PEL, probable-effect level

TEL, threshold-effect level

μg/g, micrograms per gram, <, less than.

Median concentrations for boxplots with different 

letter designations are statistically different (p<0.05). 

Data from Hawaii were not included in this figure.
20 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

areas had median CTU values (2.9 and 2.7, respectively) 

exceeding the 50th percentile for the entire regional dataset 

(fig. 9). All median CTU values were statistically different 

(p ≤ 0.002) except those for bed sediment from urban and 

mixed (p = 0.35) landscapes. The highest CTU values were 

calculated for bed sediment collected from streams in mined 

areas. The median CTU value for mined landscapes (7.5) 

was equal to the 90th percentile for the entire regional dataset. 

Only bed sediment from mined landscapes had CTU values 

exceeding the 90th percentile (fig. 9). For the purposes of this 

study, sediment with CTU values less than or equal to the 

25th percentile for the regional dataset (1.71) were considered 

unenriched in trace elements (table 5). Sediment with CTU 

values ranging between the 26th and 50th percentiles (1.72 to 

2.52) were considered to have low trace-element enrichment. 

Moderately and moderately-high enriched sediment were 

classified as those sediment samples with CTU values ranging from the 51st to 75th percentiles (2.52 to 3.9) and from the 

76th and 89th percentiles (4.1 to 7.2), respectively. Sediment 

samples with CTU values greater than the 90th percentile of 

the regional dataset (less than or equal to 7.5) were considered 

highly enriched.

Bed sediment collected from different locations can have 

different trace-element compositions. Generally, Hg contributed the least to CTU values determined for bed sediment collected from undeveloped, agricultural, mined, and mixed landuse areas (figs. 10A–10E). Hg contributed over 50 percent to 

the calculated CTU value in two instances; both were associated with bed sediment collected from a river in Nevada where 

contamination of bed sediment resulted from historic mining 

practices involving the use of Hg to amalgamate gold from 

ore (figs. 10D–10E). Hg contributions to overall CTU values 

in bed sediment in urban areas showed greater variability than 

in other landscapes evaluated as part of this study (fig. 10C). 

Cd contributed the least to CTU values determined for bed 

sediment collected from streams in urbanized areas (fig. 10C). 

With a few subtle differences, the relative contribution of each 

of the eight trace elements to respective CTU values calculated for undeveloped, agricultural, urban, and mixed land 

uses were similar (figs. 10A–10E). Given the regional perspective of the analysis, the most important point here is the 

relative pattern(s) in trace-element contributions among these 

various land uses. These analyses do not take into account 

site-specific differences in actual CTU composition that occur 

and should be addressed on a case-by-case basis. In samples 

evaluated as part of this study, Cr and Ni were identified as 

contributing substantially more to the overall CTU values than 

the remaining six trace elements (figs. 10A–10E). The pattern 

observed for samples collected from mined areas differs markedly from the other land-use areas (fig. 10D). In these samples, 

median contributions of Pb and Zn are of greater significance 

than those for either Cr or Ni.

Concentrations of Cr and Ni were strongly correlated in all 

bed-sediment samples evaluated in this study (rho ≥ 0.691). 

Of the 29 bed-sediment samples collected from urbanized 

areas, Cr and Ni comprised 24 to 61 percent of the CTU 

values (range 1.8 to 6.4). Bed sediment from streams in areas 

of mixed land use had CTU values similar to those in urbanized areas (range 1.7 to 7.3); Cr and Ni contributed 12 to 84 

percent. The general pattern observed in CTU contributions 

among the various land uses, except mined, shows that Cr 

and Ni contribute variable and oftentimes the most to the 

overall CTU values in undeveloped, agricultural, urban, and 

Figure 9. Cumulative toxic units (CTUs) calculated for 201 

bed-sediment samples collected from streams in undeveloped, 

agricultural, urban, mined, and mixed land-use areas within the 

conterminous western United States and Alaska, 1992–2000.

Number of sites

57 47 29 41 27

1,000

100

10

0.1

1

Land-use category

B

C C

D

A

Undeveloped Agricultural Urban Mined Mixed*

Cumulative toxic units (unitless)

90th percentile

25th percentile

75th percentile

Median (50th percentile)

Outlier

90th percentile

75th percentile

Median (50th percentile)

25th percentile

10th percentile

Outlier

EXPLANATION

 Schematic boxplot *Mixed, sites with agricultural, urban, and (or) mining 

land uses represented

Median concentrations for boxplots with different 

letter designations are statistically different (p<0.05). 

Data from Hawaii were not included in this figure.

Table 5. Cumulative toxic unit (CTU) percentile enrichment 

thresholds used to characterize bed sediment samples collected 

from selected streams in the conterminous western United States 

and Alaska, 1992–2000.

[Abbreviations: ≤, less than or equal to; ≥, greater than or equal to]

Percentile threshold Value (unitless) Description

≤ 25 1.71 No enrichment

26–50 1.72–2.52 Low enrichment

51–75 2.53–3.9 Moderate enrichment

76–89 4.1–7.2 Moderately-high enrichment

≥ 90 ≥ 7.5 High enrichment
Trace-Element Concentrations in Bed Sediment 21

Figure 10. Contribution of each of the eight trace elements used to determine the cumulative toxic units (CTUs) for bed sediment 

collected from selected streams and rivers in A, undeveloped; B, agricultural; C, urban; D, mined; and E, mixed land-use areas in the 

conterminous western United States and Alaska, 1992– 2000.

Trace element

Contribution of trace element to cumulative

toxic unit, in percent

As Cd Cr Cu Pb Hg Ni Zn 0

10

20

30

40

50 A Undeveloped (n=57)

A

B

C

D,F D

E

C

A,F

Trace element

Contribution of trace element to cumulative

toxic unit, in percent

As Cd Cr Cu Pb Hg Ni Zn

Trace element

As Cd Cr Cu Pb Hg Ni Zn

0

10

20

30

40

60

50

A

B Agricultural (n=47)

D Mined (n=41)

E

A

B

C

D D

C

Trace element

Contribution of trace element to cumulative

toxic unit, in percent

Contribution of trace element to cumulative

toxic unit, in percent

As Cd Cr Cu Pb Hg Ni Zn 0

10

20

30

40

50

E

D

A,E

B

C

A,E

A

C

C Urban (n=29)

0

20

40

80

60

100

A

B

D

A A,C

C

A,C

D

Trace element

Contribution of trace element to cumulative

toxic unit, in percent

As Cd Cr Cu Pb Hg Ni Zn

0

20

60

40

80

E

B

A,D

B

C

A,E D

C

E Mixed (n=27) Outlier

90th percentile

75th percentile

Median (50th percentile)

25th percentile

10th percentile

Outlier

EXPLANATION

 Schematic boxplot

n, number of samples

Arsenic (As)

Cadmium (Cd)

Chromium (Cr)

Copper (Cu)

Lead (Pb)

Mercury (Hg)

Nickel (Ni)

Selenium (Se)

Zinc (Zn)

Median concentrations for boxplots with 

different letter designations are statistically 

different (p<0.05). Data from Hawaii were not 

included in this figure.
22 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

mixed land-use areas. Given the essentially unwavering strong 

correlation between Cr and Ni, areas where PEC values are 

exceeded for these trace elements are of particular interest. 

Median concentrations of Cr and Ni were relatively low in bed 

sediment collected from streams in undeveloped and agricultural areas; concentrations were elevated in samples of bed 

sediment from urban and mixed land-use areas and, in the case 

of Ni, also in mined landscapes (figs. 5A–5B). Most of the 

PEC exceedences for Cr and Ni were in bed-sediment samples 

collected from mined areas.

Regionally, As, Cd, Pb, and Zn were moderately correlated 

(rho ≥ 0.503) in bed sediment collected from mined areas. The 

CTUs determined for bed sediment collected from the mined 

landscapes varied in composition from those in undeveloped, 

agricultural, urban, and mixed land-use areas where the 

contribution of As, Cd, Pb, and Zn (as a group) ranged from 7 

to 98 percent, commonly exceeding the relative contributions 

of Cr and Ni. Generally, CTUs determined for bed sediment in mined areas were primarily composed of Pb and Zn 

(fig. 10D). In the mined landscapes, CTU values ranged from 

0.89 to 125.7 units. Non-CERCLA associated mined areas 

(23 sites) had CTU values ranging from 1.7 to 28.8 units. The 

trace elements As, Cd, Pb, and Zn comprised from 7 to 95 

percent of these CTU values, and Cr and Ni comprised 3 to 85 

percent. Mined areas associated with CERCLA sites had CTU 

values ranging from 0.89 to 125.7 units. The trace elements 

As, Cd, Pb, and Zn comprised from 9 to 98 percent of these 

CTU values, and Cr and Ni comprised 0.3 to 37 percent. It is 

apparent from these results that a combination of CTU composition, PEC exceedences, and site-by-site variability exists, 

and although composition patterns may be similar, relative 

contributions of trace elements vary.

Macroinvertebrate Communities and 

Habitat Characteristics

To assess the relation between bed-sediment trace-element 

concentrations and macroinvertebrate community structure, 

habitat characteristics of the sampling site must be taken into 

account. For example, macroinvertebrate taxa have different 

habitat preferences for water velocity, substrate, and general 

water-quality characteristics. Additionally, the introduction of 

contaminants to streams may coincide with physical alterations that themselves can cause changes in aquatic communities (Sheehan and Winner, 1984; Landrum and Robbins, 

1990; Cuffney and others, 2005). A preliminary assessment of 

aquatic-macroinvertebrate community structure using MDS 

showed little distinction among macroinvertebrate assemblages at sampling sites representing the large-scale PL and 

XE ecoregions; however, the Hawaii (HI), MT, and Ozark 

Highlands (OH) ecoregions were distinctly different from each 

other and the PL and XE ecoregions (fig. 11). Stratification 

of macroinvertebrate communities by ecoregion for statistical analysis can, at least to some degree, minimize inherent 

variability in aquatic community composition that results from 

differences in climate, topography, geology, and general instream characteristics.

The grouping of Hawaiian macroinvertebrate communities illustrates the ability of MDS analysis to distinguish these 

very different macroinvertebrate communities from those in 

the other ecoregions within the conterminous western United 

States and Alaska. A primary distinguishing feature of the 

aquatic communities in Hawaiian streams is that taxa belonging to the insect orders Ephemeroptera (mayflies) and Plecoptera (stoneflies) are absent. Bed sediment collected from the 

seven Hawaiian streams also had a different chemical signature; median concentrations of Cu, Cr, and Ni ranged from 

about 6 to 11 times higher than in bed sediment sampled from 

streams in the other ecoregions (see Hawaii Box; figs. 5A–5B

and 6).
Macroinvertebrate Communities and Habitat Characteristics 23

Figure 11. Non-metric multidimensional scaling ordination representing A, aquatic-macroinvertebrate communities within the largescale ecoregions; and B, associated distribution patterns in trace-element cumulative toxic units for the 208 samples collected from 

streams in the conterminous western United States, Alaska, and Hawaii, 1992–2000.

Larger bubble size indicates increase in Cumulative Toxic Unit.

Multi-dimensional Scaling Axis 2

MDS Axis 1

-1

0 

1 

2 

-1.5

-0.5

-2

0.5

1.5

-2 -1.5 -1 -0.5 0 0.5 1 1.5 2

Two-Dimensional Stress = 0.26

Mountains Ecoregion

Plains Ecoregion

Xeric Ecoregion

Ozark Highlands

Hawaii

Multi-dimensional Scaling Axis 2

Multi-dimensional Scaling Axis 1

-1

0 

1 

2 

-1.5

-0.5

-2

0.5

1.5

-2 -1.5 -1 -0.5 0 0.5 1 1.5 2

Two-Dimensional Stress = 0.26

Mountains Ecoregion

Plains Ecoregion

Xeric Ecoregion

Ozark Highlands

Hawaii

A

B
24 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Trace Elements and Macroinvertebrates in the Hawaiian Islands

0.01

1

10

100

1,000

10,000

0.1

Trace element

Trace-element concentration, in micrograms per gram

Arsenic Cadmium Chromium Copper Lead Mercury Nickel Selenium Zinc

(Brasher and Wolff, 2007). Cr, Cu, and Ni in bed-sediment 

samples from these seven Oahu sites exceeded the sediment-quality guidelines for these trace elements.

Because of the extreme isolation of the Hawaiian 

islands, macroinvertebrate assemblages in these streams 

are relatively depauparate and considerably different than 

in the other areas included in this study (Brasher and others, 2004). Most notably, none of the three insect orders, 

Ephemeroptera (mayflies), Plecoptera (stoneflies), and Trichoptera (caddisflies), that are routinely used as indicators 

of water quality in the continental United States occur naturally in Hawaii. Only caddisflies, which were introduced, 

now occur at high abundance in most Hawaiian streams 

(Brasher and others, 2004). The non-metric MDS model 

(fig. 11) shows how different the Hawaii macroinvertebrate 

samples are in comparison to the other samples in this study 

and consequently helps illustrate how an MDS performs. 

Seven stream sites on the island of Oahu, Hawaii, representing undeveloped, urban, and agricultural landscapes 

were sampled for bed sediment and macroinvertebrates. In 

general, median concentrations of As (6.4 μg/g), Cd (0.57 

μg/g), Pb (23 μg/g), Hg (0.15 μg/g), Se (1.8 μg/g), and Zn 

(270 μg/g) in bed sediment collected from the seven Oahu 

sites were similar to those determined for bed-sediment 

samples collected from streams in the conterminous western United States and Alaska; however, median concentrations of Cr (440 μg/g), Cu (190 μg/g), and Ni (280 μg/g) 

were about 6 to 11 times higher in the Oahu bed sediment. 

The relatively high concentrations of Cr and Ni in Hawaiian sediment originate from the volcanic rocks and soils 

of the islands (De Carlo and others, 2005). De Carlo and 

others (2004) suggest an urban source of Cu in sediment 

samples from Oahu. Concentrations of As, Cd, Pb, and Zn 

in sediment from urban areas were substantially higher than 

concentrations measured in undeveloped areas on Oahu 
Macroinvertebrate Communities and Habitat Characteristics 25

Ecoregion and Land-Use Characterization

To characterize some of the differences among the ecoregions (HI, MT, OH, PL, and XE), general water quality (pH, 

specific conductance, total dissolved solids (TDS), hardness, and suspended-sediment concentrations) was evaluated (figs. 12A–12D). These water-quality characteristics 

are important in considering distribution patterns of aquatic 

macroinvertebrates because they influence the colonization of 

taxa with different physiologic characteristics and in-stream 

habitat preferences (Hynes, 1979; Merrit and Cummins, 1996; 

Hawkins and others, 2000). With the exception of the HI 

ecoregion, the MT ecoregion had lower median pH, specific 

conductance, TDS, and hardness than the other ecoregions 

(figs. 12A–12D). The OH ecoregion had similar general waterquality characteristics to the XE ecoregion (figs. 12A–12D); 

however, suspended-sediment concentrations of the OH 

ecoregion closely resembled those observed in the MT ecoregion (fig. 12E). Sites within the PL ecoregion had the highest 

median specific conductance, TDS, and suspended-sediment 

concentration (fig. 12A–12B and 12E).

Impairments in habitat can result in conditions unfavorable to sensitive taxa, resulting in similar macroinvertebrate 

community structure to that found at sites with elevated 

trace-element concentrations (another type of impairment). 

Sampling sites in streams within the PL (45 percent) and XE 

(44 percent) ecoregions were primarily characterized as agriculture (fig. 13). Agricultural runoff has been found to transport higher quantities of nitrogen and phosphorus than forested 

areas, and elevated concentrations of these constituents can 

cause increased algal growth, reduced light permeability, and 

depleted dissolved oxygen concentrations, resulting in gradual 

changes in downstream aquatic communities (Stevenson and 

others, 1986; Staver and others, 1988). Additional physiochemical alterations downstream from agricultural drainage 

inputs include increased salinity, siltation of streambed materials, and turbidity (National Research Council, 1989; Tucker 

and Burton, 1999). Grazing cattle can create streambank instability and reduced riparian vegetation resulting in increased 

erosion, siltation, nutrient input, and fecal coliform bacteria 

(Forest Practices Board, 2002; Murray, 2007). Streams 

influenced by urban and mixed land-use-related activities 

accounted for 6 to 23 percent of the sites within the PL and 

XE ecoregions (fig. 13). Mined areas were not represented in 

the PL ecoregion; however, samples collected from the XE 

ecoregion included some sites representative of areas associated with mining-related activities (17 percent, fig. 13).

Streams within the MT ecoregion were representative of 

mainly undeveloped (42 percent), urbanized (22 percent), and 

mined (22 percent) conditions (fig. 13). The agricultural landscape is represented in about 6 percent of the sites. Streams 

within urban centers are influenced by point and nonpoint 

sources, such as treated wastewater discharge, urban runoff, 

and interbasin transfers of water that can introduce sediment, 

trace elements, nutrients, pesticides, and other contaminants 

into stream ecosystems (Paul and Meyer, 2001; Mahler and 

others, 2005; Short and others, 2005). Impervious surfaces 

within urban environments can alter stream geomorphology 

and hydrology, and it is estimated that 15 to 20 percent of 

the streams in the United States are ecologically affected by 

roads (Schueler, 1994; Forman and Alexander, 1998; Paul and 

Meyer, 2001; Ourso and Frenzel, 2003). In addition, losses of 

pools and riffles, reduced vegetative cover, greater fluctuations 

in stream temperature, diminished base flows, channel enlargement, and siltation resulting from stream-channel erosion have 

been recognized as ecological issues in urbanized watersheds 

(Wolman and Schick, 1967; Schueler, 1994; Trimble, 1997; 

Tucker and Burton, 1999). Short and others (2005) found that 

streambed instability, remnant bed armoring, channel incision, 

periods of drought and high-flow conditions, and basin slope 

can all influence streambed embeddedness.

Fifty-three percent of the stream sites sampled in the 

OH ecoregion were in areas that have been mined (fig. 13). 

Changes in physiochemical habitat caused by mining can 

include changes in water chemistry and coating of streambed 

substrates from the precipitation of metal oxides from solution (Theobald and others, 1963; McKnight and Feder, 1984; 

Moore and others, 1991; Clements and others, 2000; Griffith 

and others, 2001). Changes in water chemistry have included 

increased specific conductance and water hardness and higher 

concentrations of sulfate, phosphate, and many trace elements (Moran and Wentz, 1974; Clements and others, 2000). 

Where acid mine drainage occurs, receiving waters can also 

undergo acidification (Moran and Wentz, 1974; McKnight and 

Feder, 1984). The effects from mining typically attenuate at 

some point downstream from mining activities as a result of 

inflow of unaffected tributaries and (or) groundwater seepage, chemical precipitation, and particle settling (Moran and 

Wentz, 1974). Trace elements are commonly transported in 

streams and rivers in association with suspended organic and 

inorganic particulates (Moran and Wentz, 1974; Gibbs, 1977). 

In areas where flow velocities are sufficiently slow, suspended 

material can settle out (Moran and Wentz, 1974). Sediment 

samples collected from depositional areas containing large 

quantities of fine-grained materials commonly have high traceelement concentrations (Horowitz, 1991). In-stream dredging 

can cause physical alterations to stream channels such as bank 

instability, lowering of stream channels, increased erosion, and 

sedimentation (Collins and Dunne, 1990). 
26 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Figure 12. General water-quality characterization of A, specific conductance; B, total dissolved solids concentration; C, water 

hardness; D, pH; and E, suspended-sediment concentration by large-scale ecoregion in the conterminous western United States, 

Alaska, and Hawaii, 1992–2000.

Number of sites

7 99 14 20 65

10,000

1,000

100

10

A

A

B

C

A

B

HI MT OH PL XE

Specific conductance, in microsiemens per centimeter

Large-scale ecoregion

Number of sites

7 71 14 14 65

10,000

1,000

100

10

A

B

B

C

A

B

HI MT OH PL XE

Large-scale ecoregion

Total dissolved solids, in milligrams per liter

Outlier

90th percentile

75th percentile

Median (50th percentile)

25th percentile

10th percentile

Outlier

EXPLANATION

 Schematic boxplot

Number of sites

7 84 14 15 57

10,000

1,000

100

1

10

A,C

C

B

C

A

B

HI MT OH PL XE

Large-scale ecoregion

Water hardness, in milligrams per liter

as calcium carbonate

Number of sites

3 99 14 20 65

10

9

8

6

7

A

D

B

A A

B

HI MT OH PL XE

Large-scale ecoregion

pH, in standard units

Number of sites

None 41 14 18 42

100,000

10,000

1,000

1

100

10

A

E

A

C

B

HI MT OH PL XE

Large-scale ecoregion

Suspended sediment, in milligrams per liter

Median concentrations for boxplots with different 

letter designations are statistically different (p<0.05). 

Data from Hawaii were not included in this figure.

Mountain (MT), Ozark Highlands (OH), Plains (PL), 

Xeric (XE), Hawaii (HI)
Macroinvertebrate Communities and Habitat Characteristics 27

Macroinvertebrate Community Response to 

Trace Elements

Cuffney and others (2005) found that climate, topography, 

geology, and chemistry all influence macroinvertebrate community structure, making it difficult to separate out the independent effects of land use on macroinvertebrate assemblages. 

These factors, which vary across the regional study area, could 

also make it difficult to evaluate independent effects of trace 

elements on macroinvertebrate communities investigated 

as part of this study. To help alleviate some of the abiotic 

variability among the different areas of the regional study 

(fig. 1), community structure was examined within individual 

ecoregions. To account for known differences in climatic, 

topographic, and in-stream characteristics, an intermediatescale ecoregion was chosen as the regional scale at which the 

possible influences of trace elements on macroinvertebrate 

community patterns were evaluated (Whittier and others, 

2007) (fig. 14). The intermediate-scale ecoregional designation allowed for maximizing trace-element gradients while 

minimizing variability in land uses within a given ecoregion 

(fig. 14). 

The evaluation of CTUs described previously within this 

report showed that the CTU values calculated for bed sediment collected from streams in mined areas not only exhibited the widest range in values (0.89 to 126) but included 

the highest values (fig. 9). Four of the 12 intermediate-scale 

ecoregions are discussed in detail in this report because bed 

sediment collected from these areas varied in their ranges in 

CTU values and, for the most part, also represented the highest 

values. Samples were evaluated from the four intermediatescale ecoregions, MT-SROCK, MT-NROCK, OH, and XEEPLAT (table 6).

Given the complex interactions among physical, chemical, 

and biological characteristics in an ecosystem, MDS ordinations developed for the four intermediate-scale ecoregions 

were used in conjunction with richness and relative-abundance 

assessments. The error associated with the MDS ordinations, as evidenced by the stress levels, ranged from 0.11 to 

0.2. These stress levels result from bringing the distribution 

patterns of the macroinvertebrate community from multidimensional space into two-dimensional space and indicate 

that the observed distributions are unlikely due to random 

chance. Multiple lines of evidence from the MDS plots and 

the richness and relative-abundance data were used to develop 

data interpretations. Associations between CTU values and 

macroinvertebrate community structure were evaluated using 

two-dimensional MDS analysis and are presented with average taxonomic characteristics described in bar charts with 

standard deviation error bars.

Table 6. Range in cumulative toxic unit (CTU) values for each of 

the intermediate-scale ecoregions used to evaluate the influence 

of trace elements on macroinvertebrate community structure in 

selected streams in the conterminous western United States and 

Alaska, 1992–2000.

[Abbreviations: MT-NROCK, Mountain Northern Rockies ecoregion; MT-SROCK, 

Mountain Southern Rockies ecoregion; OH, Ozark Highlands ecoregion; XE-EPLAT, 

Eastern Xeric Plateau ecoregion]

Intermediate-Scale 

Ecoregion

Number of samples 

included in the 

intermediate-scale 

ecoregion

Range in CTU values 

for bed sediments in 

each intermediate-scale 

ecoreigon

MT-NROCK 32 1.1–126

MT-SROCK 15 0.89–50

OH 15 1.3–25

XE-EPLAT 17 1.0–7.5

Figure 13. General land-use categories (undeveloped, 

agricultural, urban, mined, and mixed) represented within the 

large-scale ecoregions within the conterminous western United 

States and Alaska, 1992–2000.

Land-use category

Undeveloped Agricultural Urban Mined Mixed*

0

10

20

30

40

50

60

Land use represented in each large-scale ecoregion, in percent

MT

OH

PL

XE 

Mountain (MT), Ozark Highlands (OH), Plains (PL), Xeric (XE)

*Mixed, sites with agricultural, urban, and (or) mining land uses represented
28 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Mountain Northern Rockies Ecoregion 

(MT-NROCK)

Samples collected from streams in the MT-NROCK 

ecoregion represented undeveloped (56 percent), agricultural (6 percent), urban (3 percent), mined (31 percent), and 

mixed (3 percent) land uses with CTU values ranging from 

1.1 to 125.7, the greatest range in values of bed-sediment 

CTUs in this study (figs. 14 and 15). The highest CTU values 

were associated with bed-sediment samples collected from 

streams in mined areas. Using agglomerative hierarchical 

cluster analysis for data from the intermediate-scale ecoregion 

MT-NROCK, the MDS ordination shows five distinct clusters 

(I–V) and three unclustered Samples (A–C) (fig. 15). Generally, richness characteristics in all macroinvertebrate communities (clustered and unclustered) consisted predominantly of 

EPT and dipteran taxa (fig. 16A)

Cluster I consists of three macroinvertebrate communities 

inhabiting streams with very high CTU values for bed sediment (range 61.1–126). The median CTU value (74.9) is well 

above the 90th percentile (7.5) for the entire regional dataset 

(fig. 9). These CTU values indicate that these bed-sediment 

samples are highly enriched in trace elements (table 5). Pb and 

Zn, together, contributed from 74 to 83 percent to the CTU 

Figure 14. General land-use categories (undeveloped, agricultural, urban, mined, and mixed) represented in intermediate-scale 

ecoregions in the conterminous western United States and Alaska, 1992–2000.

Undeveloped

Agricultural

Urban

Mined

Mixed*

Number of sites representing land-use category

Intermediate-scale ecoregion

0

5

10

15

20

25

MT-NROCK1

MT-PNW

MT-SROCK1

MT-SWEST OH1

PL-NCULT

PL-RANGE

XE-CALIF

XE-EPLAT1

XE-NORTH

XE-SOUTH

*Mixed, sites with agricultural, urban, and (or) mining land uses represented

Mountain Northern Rockies (MT-NROCK)1

Mountain Pacific Northwest (MT-PNW)

Mountain Southern Rockies (MT-SROCK)1

Southwestern Mountains (MT-SWEST)

Ozark Highlands (OH)1

Cultivated Northern Plains (PL-NCULT)

Rangeland Plains (PL-RANGE)

Xeric California (XE-CALIF)

Eastern Xeric Plateaus (XE-EPLAT)1

Northern Xeric Basins (XE-NORTH)

Southern Xeric Basins (XE-SOUTH)

1 These ecoregions were evaluated for macroinvertebrate community response to 

gradients in trace-element concentrations
Macroinvertebrate Communities and Habitat Characteristics 29

values, and Cr and Ni, together, contributed about 1 percent. 

The three sites from which these samples were collected 

were on streams associated with a designated CERCLA area 

(listed as a result of historic mining-related activities) where 

mine tailings are known to have contaminated bed sediment with high concentrations of As, Cd, Cu, Pb, Hg, and Zn 

(Horowitz and others, 1993; Maret and others, 2003). In all 

three samples, concentrations of As, Cd, Cu, Pb, Hg, and Zn 

exceeded their respective PEC values; concentrations of Cr 

and Ni remained below their respective PEC values (table 2). 

Generally, macroinvertebrate communities included in Cluster 

I had the lowest overall richness (average 17 taxa) of all 

clusters within the MT-NROCK ecoregion (fig. 16A). Most of 

the relative abundance (percent contribution of taxa to total 

number of organisms) was composed of mayflies (41 percent), 

dipterans (31 percent), and caddisflies (26 percent) (fig. 16B). 

The macroinvertebrate communities included in Cluster I were 

largely characterized and dominated by one to two taxa—a 

black fly (Simulium sp.), caddisflies (Arctopsyche sp. or Ceratopsyche sp.), and (or) a mayfly (Baetis sp.). Ordination results 

from the MT-NROCK ecoregion support the findings of other 

studies that have shown elevated trace elements from mining 

activities influence macroinvertebrate community structure 

(Canfield and others, 1994; Clements, 1994; Maret and others, 2003) and that these taxa are likely tolerant to elevated 

concentrations of trace elements (Clements, 1994; Clements 

and others, 2000). 

Six samples with bed-sediment CTU values ranging from 

1.3 to 27.5 are included in Cluster II. The sites from which 

these samples were collected included streams in undeveloped 

(reference) areas and areas representing various land-use activities (fig. 15). The bed-sediment samples included in Cluster II 

have trace-element concentrations representing unenriched to 

highly enriched conditions (table 5, fig. 15). The median CTU 

value for bed-sediment samples in this cluster (2.6) is slightly 

higher than the 50th percentile (2.5) for the entire regional 

Multi-dimensional Scaling Axis 2

Multi-dimensional Scaling Axis 1

-1

0

1

-1.5

-0.5

0.5

1.5

-2.5 -2 -1.5 -1 -0.5 0 0.5 1 1.5 2

Two-Dimensional Stress = 0.20

 Taxa Vectors

 1 Arctopsyche sp.

 2 Simulium sp.

 3 Hydropsyche sp.

 4 Ceratopsyche sp.

 5 Acentrella sp.

 6 Claassenia sp.

 7 Glossosoma sp.

 8 Optioservus sp.

 9 Zaitzevia sp.

 10 Rhithrogena sp.

 11 Drunella sp.

 12 Ameletus sp.

 13 Epeorus sp.

 14 Stempellinella sp.

 15 Rheocricotopus sp.

 16 Sweltsa sp.

 17 Rhyacophila sp.

 18 Zapada sp.

 19 Baetis sp.

Agriculture

Mined

Mined, CERCLA1

Mixed*

Undeveloped

Urban

III

I

II

IV

V

19

10

11

1

17

2

5 4

16

7

8

18

13

9

15

12 14

6

3

A C

B

*Mixed, sites with agricultural, urban, and (or) mining land uses represented

1 Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA)

Larger bubble size indicates a higher value Cumulative Toxic Unit

Figure 15. A non-metric multidimensional scaling (MDS) ordination of macroinvertebrate communities in selected streams in the 

Mountain Northern Rockies (MT-NROCK) ecoregion and distribution of cumulative toxic units (CTUs), 1992–2000.
30 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Figure 16. A, Average number of taxa (richness) and percent contribution from each of Ephemeroptera, Plecoptera, and Trichoptera 

(EPT), Diptera, Coleoptera, and other taxa to the overall richness; and B, average relative abundances of Ephemeroptera, Plecoptera, 

Trichoptera, Diptera, Coleoptera, and other taxa for macroinvertebrate communities in selected streams of the Northern Rocky 

Mountains ecoregion, 1992–2000.

Number of samples in each cluster

0

10

20

30

40

50

60

70

80

3 6 7 6 7 1 1 1

Unclustered Communities

Number of samples in each cluster

3 6 7 6 7 1 1 1

Unclustered Communities

Mountain Northern Rockies Ecoregion (MT-NROCK) Cluster

I II III IV V A B C

Mountain Northern Rockies Ecoregion (MT-NROCK) Cluster

I II III IV V A B C

Average contribution of EPT, Diptera, Coleoptera, and

other taxa to richness, in percent 

Average richness, in number of taxa

Number of Taxa (RICH)

Percent EPT/RICH

Percent DIPTERA/RICH

Percent COLEOPTERA/RICH

Percent OTHER TAXA/RICH 

0

10

20

30

40

50

60

70

80

90

Relative abundance of taxa, in percent

Ephemeroptera

Plecoptera

Trichoptera

Diptera

Coleoptera

Other Taxa

A

B

Standard deviation

Standard deviation
Macroinvertebrate Communities and Habitat Characteristics 31

dataset (fig. 9). Together, Pb and Zn contributed from 15 to 

72 percent to the CTU values; Cr and Ni contributed about 4 

to 63 percent for the six bed-sediment samples. These results 

indicate no clear pattern in regional trace-element composition of CTU values that is characteristic of a particular land 

use. Concentrations of As, Cd, Cu, Pb, and Hg exceeded their 

respective PEC values in at least one bed-sediment sample 

collected from the sites included in Cluster II; however, only 

occasionally did exceedences occur in the same sample. The 

PEC value for Zn (table 2) was exceeded in two bed-sediment 

samples. The stream included in Cluster II that was influenced 

by historic mining-related activities with the highest CTU 

value (27.5) was likely enriched in trace elements (Antimony, 

As, Cd, Cu, Pb, Hg, silver, and Zn) from mine tailings transported downstream from the CERCLA area in Idaho mentioned above in Cluster I (Horowitz and others, 1993; Maret 

and others, 2003). The second mined area in this cluster was 

associated with a different CERCLA site listed as a result of 

elevated As, Cd, Cu, Pb, and Zn resulting from historic mining 

and smelting operations in the watershed (U.S. Environmental 

Protection Agency, 2010). In both cases, bed sediment from 

these two rivers in mined areas is highly enriched with trace 

elements. It is unlikely that trace-element exposure is the sole 

cause of the clustering of these macroinvertebrate samples 

within Cluster II because the other CTU values (1.3 to 2.9) 

within the cluster indicate unenriched and moderately enriched 

conditions (table 5). Generally, the overall richnesses of Cluster II (24 taxa), Cluster V (27 taxa), and unclustered Sample 

C (24 taxa) were similar (fig. 16A). The most abundant taxa 

comprising the macroinvertebrate communities included in 

Cluster II were Diptera (39 percent), caddisflies (36 percent), 

and mayflies (22 percent) (fig. 16B). The macroinvertebrate 

communities included in Cluster II are primarily characterized 

by Diptera (Simulium sp.), Orthocladiinae midges (Cardiocladius sp., Eukiefferiella sp., and Tvetenia sp.), and caddisflies 

(Hydropsyche sp., Ceratopsyche sp., and Cheumatopsyche 

sp.). These taxa have been found to not only show tolerance to 

trace-element concentrations but have also exhibited tolerance 

to physical-habitat alterations such as sedimentation (Carlisle 

and others, 2007). On average, the mayfly communities in the 

macroinvertebrate samples in Cluster II were dominated by 

Baetis sp. (50 percent) (appendix 3, fig. 3-2).

Overall, Cluster III had bed sediment with the lowest 

overall range of CTU values (1.5–4.8) of all the clusters in 

the MT-NROCK ecoregion. The median CTU value (1.7) is 

equal to the 25th percentile for the entire dataset (fig. 9). Traceelement enrichment in bed sediment ranged from unenriched 

to moderately-high at these sites (table 5). Together, Pb and 

Zn contributed from 8 to 52 percent to the CTU values; Cr 

and Ni contributed about 22 to 64 percent in these seven bedsediment samples. The regional trace-element composition of 

CTU values indicated no clear pattern found to be characteristic of a particular land use, although bed-sediment samples 

were collected from streams predominantly in undeveloped 

(reference) areas (fig. 15). Concentrations of Pb, Cr, and Ni 

exceeded their respective PEC values in one bed-sediment 

sample collected from the sites included in Cluster III; in two 

samples, concentrations of As exceeded the PEC for this trace 

element (table 2). On average, the overall richness of macroinvertebrate communities represented in Cluster III (33 taxa) 

was similar to those in cluster IV (34 taxa) and in the unclustered Samples A (30 taxa) and B (36 taxa), indicating that 

overall richness is unlikely a defining characteristic for these 

communities (fig. 16A). 

The relative abundance of taxa in macroinvertebrate 

samples included in Cluster III showed a fairly even distribution among mayflies (29 percent), caddisflies (33 percent), and 

dipterans (23 percent) (fig. 16B). Macroinvertebrate communities in Cluster III were largely characterized by three caddisfly 

(Ceratopsyche sp., Glossosoma sp., and Hydropsyche sp.), 

two beetle (Optioservus sp. and Zaitzevia sp.), two mayfly 

(Drunella sp. and Rhithrogena sp.) and one stonefly (Claassenia sp.) taxa. The caddisfly, Glossosoma sp., and the Heptageniidae mayflies, Drunella sp. and Rhithrogena sp., are frequently reported as trace-element sensitive taxa (Clements and 

others, 2000; Carlisle and others, 2007). Beetle abundances 

have been reported as being reduced at locations with high 

trace-element concentrations (Clements and others, 2000). 

Macroinvertebrate communities in Clusters IV and V have 

similar taxa composition, contributing to their proximity to 

each other in the MDS ordination (fig. 15). The sites included 

in Cluster IV are from predominantly undeveloped (reference) 

sites; however, one site is associated with a CERCLA area 

and is listed as impaired because of water temperature and 

concentrations of Cd, Pb, and Zn (U.S. Environmental Protection Agency, 2010; Idaho Division of Environmental Quality, 

2008). The CTU values for Cluster IV ranged from 1.1 to 5.4; 

the median CTU value was 1.9. These results indicate that 

enrichment of trace-element concentrations in these bedsediment samples range from unenriched to moderately-high 

(table 5). Pb and Zn contributed from 11 to 54 percent to the 

CTU values; Cr and Ni contributed about 17 to 62 percent 

for the six bed-sediment samples. The regional trace-element 

composition of CTU values indicated no clear pattern found 

to be characteristic of a particular land use. Concentrations 

of trace elements in bed-sediment samples associated with 

communities represented in Cluster IV seldom exceeded their 

respective PEC values. Concentrations of As, Ni, and Zn 

exceeded their respective PEC values (table 2) in one sample 

each. 

 Generally, Cluster IV had a similar overall taxa richness 

(34 percent) to Cluster III (33 percent) and the unclustered 

Samples A and B (fig. 16A), suggesting that, on average, overall richness is not necessarily a defining characteristic for these 

communities. The macroinvertebrate communities included in 

Cluster IV were primarily composed of dipterans (51 percent) 

and mayflies (30 percent) (fig. 16B). Taxa characterizing the 

macroinvertebrate communities in Cluster IV were somewhat 

similar to Cluster V; however, the differences in the relative 

abundances between mayflies and dipterans appear to be the 

features distinguishing these two clusters. In general, Cluster 

IV had lower relative abundances of Baetis sp., Drunella sp., 
32 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Epeorus sp. mayflies, lower relative abundances of Zapada sp. 

stoneflies, and higher relative abundances of Simulium sp. flies 

than did Cluster V.

Cluster V included macroinvertebrate communities collected from seven sites associated with the CERCLA area 

mentioned above, in Clusters I and II, representing undeveloped (reference) and mined landscapes (fig. 15). The CTU 

values (range 2.2–14.1) were not as high as those in Cluster I, 

but the median CTU value for Cluster V (4.1) was above the 

75th percentile (3.9) for the entire regional dataset. Regionally, 

the range in CTU values indicates low to high trace-element 

enrichment at these sites (table 5, fig. 9). Together, Pb and 

Zn contributed from 35 to 75 percent to the CTU values; Cr 

and Ni contributed about 5 to 30 percent for the seven bedsediment samples. These results show a distinctive pattern 

in the contribution of these trace elements to the CTU values representative of a regional mining signature (fig. 10D). 

Five of the seven bed-sediment samples in Cluster V had Pb 

concentrations exceeding the PEC for this trace element. The 

PECs for As and Zn were exceeded in 14 and 43 percent, 

respectively, of the bed-sediment samples collected from 

these seven sites. The PECs for the other trace elements (Cd, 

Cr, Cu, Hg, and Ni) (table 2) were not exceeded in any of the 

bed-sediment samples associated with Cluster V. On average, 

Cluster V had a similar overall richness (27 percent) to Cluster 

II (24 percent) and the unclustered Sample C (fig. 16A). 

The most abundant macroinvertebrates in Cluster V were 

mayflies (60 percent) and dipterans (19 percent) (fig. 16B). 

Macroinvertebrate communities grouped in Cluster V were 

characterized by several taxa of mayflies (Baetis sp., Epeorus 

sp., and Ameletus sp.), two midges (Stempellinella sp. and 

Rheocricotopus sp.), a caddisfly (Rhyacophila sp.), and two 

stoneflies (Sweltsa sp. and Zapada sp.) (fig. 15). Heptageniidae mayflies (e.g., Epeorus sp.) are generally regarded as very 

sensitive to elevated trace-element concentrations (Mize and 

Deacon, 2002; Maret and others, 2003; Clark and Clements, 

2006); however, this family of mayflies comprised more than 

10 percent of the relative abundance of the three macroinvertebrate communities collected from streams associated with 

the CERCLA area (CTU values ranging from 4.1 to 14.1). 

Stoneflies were an important component of these macroinvertebrate communities; the relative abundance of these taxa 

(about 11 percent) was higher than the other Clusters I–IV and 

the unclustered Samples A and B. These results suggest that 

these taxa are at least moderately tolerant to the trace elements 

present in the bed sediment. Previous studies by Clements and 

others (2000) and Pollard and Yuan (2006) found several of 

these taxa at sites with CCUs in the moderate range of 2 to 10. 

Three sites did not significantly group during the cluster 

analysis (A, B, and C; fig. 15); unclustered Samples A and B 

represented undeveloped (reference) sites with CTU values of 

1.4 and 3.5 indicative of unenriched and moderately enriched 

conditions, respectively (table 5, fig. 9). Sample C represented 

a site influenced by historic mining practices with a CTU 

value of 4.1, exceeding the 75th percentile (3.9) for the entire 

regional dataset. The contribution of Pb and Zn, together, to 

the bed-sediment sample collected from unclustered Sample 

C was only 8 percent; Cr and Ni contributed 82 percent to this 

CTU value. This pattern in CTU composition deviates from 

the general pattern for trace-element contributions to CTU values for bed-sediment samples collected from streams in mined 

areas (fig. 10D). Together, Cr and Ni contributed more (58 and 

82 percent) to the CTU composition in reference Samples B 

and C than did Pb and Zn (18 and 8 percent), characteristic of 

undeveloped landscapes (fig. 10A). 

A distinguishing feature of the macroinvertebrate community represented by unclustered Sample C is the relative 

abundance of stoneflies. Three taxa (Zapada sp., Megarcys sp., and those belonging to the family Chloroperlidae) 

accounted for 92 percent of the stoneflies present in the 

sample (fig. 16B). The CTU value of 3.5 associated with the 

unclustered Sample B, representing an undeveloped (reference) condition, approached the 75th percentile for the entire 

dataset, suggesting that this bed sediment is naturally enriched 

in trace elements. The communities in unclustered Samples A 

and B represent reference conditions and show similar overall 

richnesses (30 and 36 taxa, respectively) to those of Clusters 

III and IV (33 and 34 taxa, respectively). However, the macroinvertebrate community for unclustered Sample A is markedly different from Sample B and Clusters III and IV in that 

about 80 percent of the community is composed of mayflies 

(fig. 16B). The mayfly community in unclustered Sample A is 

primarily composed of the Heptageniidae mayflies, Epeorus

sp. (36 percent) and Rhithrogena sp. (17 percent), and the 

Ameletidae mayfly, Ameletus sp. (20 percent). The macroinvertebrate community of unclustered Sample B had about half 

the number of mayflies as Sample A. One of the distinguishing 

characteristics of unclustered Sample B was the number of 

Coleoptera (beetle) individuals. Beetles from the family Elmidae (riffle beetles) comprised almost 30 percent of the relative 

abundance in Sample B, the highest of all samples collected 

from the MT-NROCK ecoregion (fig. 16B). 

The structure of macroinvertebrate communities clustering within the MT-NROCK ecoregion appears to be associated with trace-element concentration and land-use activities. 

Generally, macroinvertebrate samples collected from streams 

where historic mining-related activities greatly enriched bed 

sediment with trace elements (Cluster I) showed communities 

dominated by a few resilient taxa resulting in a lower richness 

metric. Trace-element enrichment in bed-sediment samples 

associated with macroinvertebrate communities grouped 

together in Cluster II is not strongly evident. The diverse 

nature of land uses in this group suggests that something other 

than exposure to trace elements is contributing to the macroinvertebrate community structure in these samples. Cluster 

II communities exhibit a slight depression in taxa richness 

relative to the other clusters, except Cluster I, and are dominated largely by tolerant mayfly, caddisfly, and dipteran taxa. 

The richness and relative abundance metrics determined for 

Clusters IV and V are interesting in that generally more traceelement sensitive taxa (e.g., Heptageniidae mayflies) were in 

macroinvertebrate communities included in Cluster V where 
Macroinvertebrate Communities and Habitat Characteristics 33

bed sediment had CTU values exceeding the 75th percentile 

for the entire regional study area, indicating moderately-high 

enrichment at these sites. It is unlikely that trace-element 

exposure is driving the macroinvertebrate community structure at these sites. Macroinvertebrate communities included in 

Cluster III, with the lowest bed-sediment CTUs representing 

predominantly undeveloped (reference) conditions, are distinguished by a relatively diverse community of taxa including 

tolerant and sensitive mayflies and caddisflies. 

Mountain Southern Rockies Ecoregion 

(MT-SROCK)

Samples collected from streams in the MT-SROCK ecoregion represented undeveloped (33 percent), mined (47 percent), and mixed (20 percent) landscapes. Within this ecoregion, CTU values ranged from 0.89 to 50.3 units; the highest 

CTU values were associated with bed sediment collected 

from streams in mined areas (fig. 17). Using hierarchical 

agglomerative clustering, three significant Clusters (I-III) of 

macroinvertebrate communities emerged in the MT-SROCK 

MDS ordination, each containing from three to seven samples 

(fig. 17).

The highest CTU value (50.3) was at a site (Sample A) 

that did not cluster with others and had a macroinvertebrate 

community characteristically different from the rest in the MTSROCK ecoregion (fig. 17). This site is on a stream associated 

with a CERLA area listed as a result of historic mining-related 

activities. The contamination of bed sediment with As, Cd, Pb, 

and Zn as a result of these mining-related activities resulted in 

the listing of this area on the National Priorities List in 2008 

(U.S. Environmental Protection Agency, 2010). The contribution of Pb and Zn to the bed-sediment sample associated with 

this unclustered sample was 78 percent; Cr and Ni contributed 

0.3 percent to this CTU value. These results show a distinctive 

Figure 17. A non-metric multidimensional scaling (MDS) ordination of macroinvertebrate communities in selected streams in the 

Mountain Southern Rockies (MT-SROCK) ecoregion and distribution of cumulative toxic units (CTUs), 1992–2000. Multi-dimensional Scaling Axis 2

Multi-dimensional Scaling Axis 1

-1

0

1

-1.5

-0.5

0.5

1.5

-2.5 -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5

Two-Dimensional Stress = 0.14

Mined

Mined, CERCLA1

Mixed*

Undeveloped III

I

II

19

10

11

1

17 2

5

4

16

7

8

18

13

9

15

14

12

6

3

Taxa Vectors

 1 Ceratopsyche sp.

 2 Brachycentrus sp.

 3 Rheotanytarsus sp.

 4 Eukiefferiella sp.

 5 Pagastia sp.

 6 Turbellaria

 7 Clinocera sp.

 8 Rheocricotopus sp.

 9 Rhyacophila sp.

 10 Heterlimnius sp.

 11 Epeorus sp.

 12 Ephemerella sp.

 13 Glossosoma sp.

 14 Hexatoma sp.

 15 Claassenia sp.

 16 Simulium sp.

 17 Atherix sp.

 18 Cardiocladius sp.

 19 Arctopsychesp.

 20 Optioservus sp. 

20

A

*Mixed, sites with agricultural, urban, and (or) mining land uses represented

1 Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA)

Larger bubble size indicates a higher value Cumulative Toxic Unit
34 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

pattern in the contribution of these trace elements to the CTU 

values representative of a regional mining signature (fig. 10D). 

Cr, Cu, Hg, and Ni did not exceed their respective PEC values 

in this bed-sediment sample (table 2). The overall taxa richness (16 taxa) of Sample A was the lowest in the MT-SROCK 

ecoregion (fig. 18A). Mayflies (42 percent) and dipterans (42 

percent) accounted for about 84 percent of the individuals in 

this sample (fig. 18B). The mayfly community in this sample 

was dominated by the family Ephemerellidae (99 percent). 

Eighty percent of the dipteran individuals were midges, 

mainly in the family Orthocladiinae (88 percent) (appendix 3, 

fig. 3-4). Orthocladiinae midges have been identified as being 

tolerant to trace elements and other physical-habitat disturbances; however, mayflies belonging to the family Ephemerellidae have exhibited varied responses to elevated trace-element exposure. Clements (1994) showed that Ephemerellidae 

mayflies were sensitive to aqueous Zn concentrations, and 

Carlisle and others (2007) associated low (less tolerant) indicator values to this family of mayflies with respect to chemical and physical stressors. Results from this study are more 

similar to the findings from Beasley and Kneale (2003), which 

identified Ephemerellidae mayflies as tolerant to trace-element 

exposure. 

CTU values for bed-sediment samples from the seven 

sites included in Cluster I ranged from 1.92 to 28.85 (fig. 17). 

These sites are predominantly influenced by historic miningrelated activities and mixed (urban and agriculture) land uses. 

The median CTU value (2.8) is only slightly higher than the 

50th percentile (2.52) for the entire dataset (fig. 9). The CTU 

values indicate that bed-sediment samples collected from the 

sites included in Cluster I were minimally enriched in trace 

elements, and others were highly enriched (table 5, fig. 9). 

The contribution of Pb and Zn to the bed-sediment samples 

ranged from 21 to 69 percent; Cr and Ni contributed about 3 to 

59 percent to these values. The regional trace-element composition of CTU values indicated no clear pattern found to be 

characteristic of a particular land use. Concentrations of As, 

Cd, Cu, Pb, Hg, and Zn exceeded their respective PEC values 

(table 2) in one to three samples collected from these seven 

sites but not necessarily in the same samples; there were no 

PEC exceedences for either Cr or Ni in these samples. 

The overall richness of macroinvertebrate communities represented in Cluster I (36 taxa) was the highest in 

the MT-SROCK ecoregion (fig. 18A). On average, Diptera 

(49 percent), mayflies (24 percent), and caddisflies (15 percent) accounted for most of the relative abundance (fig. 18B). 

Most of the taxa in Cluster I are known to be tolerant to elevated trace elements and other physical disturbances (Beltman 

and others, 1999; Mize and Deacon, 2002; Clements, 2004; 

Carlisle and others, 2007). The EPT taxa were dominated by 

a resilient mayfly, Baetis sp., and caddisflies belonging to the 

family Hydropsychidae (Arctopsyche sp. and Ceratopsyche

sp.) (appendix 3, fig. 3-4); however, Baetis sp. was not found 

to be characteristic of the macroinvertebrate communities 

within the MT-SROCK ecoregion. It is possible there were not 

enough differences among the Baetis sp. contributions among 

the clusters to elucidate a significant difference among them, 

thereby resulting in the lack of correlation with this taxon. 

Other characteristic taxa included two Diptera (Atherix sp. and

Simulium sp.), two Orthocladiinae midges (Cardiocladius sp. 

and Eukiefferiella sp.), and the caddisfly, Brachycentrus sp. 

The stonefly, Claassenia sp., accounts for 3.7 percent of the 

relative abundance at the only undeveloped site in Cluster I 

and 0.2 percent or less at the other two sites. Rheotanytarsus

sp., a member of the Tanytarsini midges, was characteristic 

of communities in Cluster I; however, Swansburg and others (2002) indicated that the Tanytarsini midges are sensitive 

to trace-element exposure. Alternatively, Canfield and others 

(1994) found that Tanytarsini midges were somewhat tolerant 

to trace-element exposure in bed sediment. Carlisle and others 

(2007) listed high indicator values (tolerance) for Rheotanytarsus sp. to concentrations of suspended sediment and 

nutrients. The results found in this study are similar to those of 

Canfield and others (1994) in that it appears Rheotanytarsus

sp. displays some degree of resilience to trace-element exposure in bed sediment. 

Cluster II consists of three sites; two sites are in a watershed associated with a CERCLA site (listed as a result of 

past dredge-mining practices) with Cd and Zn enrichment 

in bed sediment as well as impaired habitat conditions (U.S. 

Environmental Protection Agency, 2010); the other site is 

predominantly undeveloped but is influenced by a combination of urban and mining-related activities. CTU values in 

Cluster II range from 2.4 to 38.8 (median 16.7). Compared to 

regional values, these bed-sediment samples range from low 

enrichment to high enrichment conditions (table 5, fig. 9). 

The contribution of Pb and Zn to the bed-sediment samples 

collected from streams in mined areas included in Cluster II 

was substantially different that those collected from streams 

in areas with mixed landscapes. Pb and Zn contributed 69 and 

80 percent to the CTU values in bed sediment in the mined 

areas but only contributed 27 percent to the CTU value in bed 

sediment collected from the area of mixed land use. Cr and Ni 

contributed less than 10 percent (3 and 8 percent) to the CTU 

values for bed sediment collected from the streams in mined 

areas; these trace elements contributed 53 percent of the CTU 

value in samples collected from the mixed land-use site. Concentrations of As, Cd, Pb, and Zn exceeded their respective 

PEC values (table 2) in bed-sediment samples from the mined 

area. No trace-element concentrations from the mixed land-use 

site exceeded their respective PEC values. 

On average, the overall richness of macroinvertebrate 

communities in Cluster II (25 taxa) was the same as that 

for Cluster III (25 taxa); however, Cluster II had less EPT 

taxa relative to dipteran taxa than did Cluster III (fig. 18A). 

Although variable, on average, 63 percent of the organisms in 

Cluster II were flies (Diptera). The dipteran community was 

composed of about 95 percent midges of which taxa belonging 

to the family Orthocladiinae dominated (77 percent) (appendix 

3, fig. 3-4). Flatworms (Turbellaria), midges (Rheocricotopus 

sp.), and diptera belonging to the genus Clinocera sp. distinguished the macroinvertebrate communities in Cluster II 
Macroinvertebrate Communities and Habitat Characteristics 35

Figure 18. A, Average number of taxa and percent contribution from each of Ephemeroptera, Plecoptera, and Trichoptera (EPT), 

Diptera, Coleoptera, and other taxa to the overall richness; and B, average relative abundances of Ephemeroptera, Plecoptera, 

Trichoptera, Diptera, Coleoptera, and other taxa for macroinvertebrate communities in selected streams of the Mountain Southern 

Rockies ecoregion, 1992–2000.

Number of samples in each cluster

7 3 4 1

Mountain Southern Rockies Ecoregion (MT-SROCK) Cluster

Mountain Southern Rockies Ecoregion (MT-SROCK) Cluster

I II III A

I II III A

Number of Taxa (RICH)

Percent EPT/RICH

Percent DIPTERA/RICH

Percent COLEOPTERA/RICH

Percent OTHER TAXA/RICH 

Unclustered

Number of samples in each cluster

7 3 4 1

Unclustered

Average richness, in number of taxa

0

10

20

30

40

50

60

70

Average contribution of EPT, Diptera, Coleoptera,

and other taxa to richness, in percent

Ephemeroptera

Plecoptera

Trichoptera

Diptera

Coleoptera

Other Taxa

0

10

20

30

40

50

60

70

80

90

Relative abundance of taxa, in percent

A

B

Standard deviation

Standard deviation
36 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

(fig. 17). Turbellaria worms and Orthoclaniinae midges were 

the most abundant taxa in Cluster II. Studies have found these 

taxa tolerate a wide range of physical and chemical stressors 

(Carlisle and others, 2007). The habitat impacts from dredgerelated mining activities in combination with higher CTUs 

may be influencing the community structure in Cluster II and 

may be playing a role in the separation of these communities from the other clusters. These results are consistent with 

other investigations that have documented the loss of richness 

corresponding with an increase in the abundance of fewer, 

but tolerant, taxa at sites affected by trace-element pollution 

(Canfield and others, 1994; Clements and others, 2000; Maret 

and others, 2003).

Overall, Cluster III had the lowest CTU values (0.89 to 

2.4; median 1.9), indicating unenriched to low enrichment 

conditions, of the three clusters identified by the MDS ordination in the MT-SROCK ecoregion (table 5, fig. 9). Of the four 

sites included in this cluster, three were in undeveloped (reference) areas and one was associated with a CERCLA site listed 

as a result of As, Cd, Pb, and Zn contamination (U.S. Environmental Protection Agency, 2010). Given the relatively low 

CTU value for bed sediment collected from the site associated 

with the CERCLA area, it is apparent that mine tailings near 

the site have not contaminated the bed sediment at this site to 

the extent that they have contaminated bed sediment collected 

from another site associated with the same CERCLA area 

(Sample A, fig. 17). The contribution of Pb and Zn to the four 

bed-sediment samples included in Cluster III ranged from 22 

to 50 percent; Cr and Ni accounted for about the same amount, 

23 to 57 percent. Trace-element concentrations did not exceed 

any PEC value (table 2) in any of the four samples included in 

Cluster III. 

The overall richness of macroinvertebrate communities 

represented in Cluster III (25 taxa) was the same as that for 

Cluster II (25 taxa); however, Cluster III richness was comprised of a greater proportion of EPT taxa (fig. 18A). The most 

abundant taxa in the macroinvertebrate samples included in 

Cluster III were mayflies (39 percent), dipterans (28 percent), and caddisflies (16 percent) (fig. 18B). Cluster III also 

contained a substantial number of Elmidae beetles (dominated 

by Heterlimnius sp.), which contributed on average 13 percent 

(range 7.5 to 14.7 percent) to the overall relative abundance 

of these communities. Mayflies (Epeorus sp. and Ephemerella 

sp.), a caddisfly (Rhyacophila sp.), and beetles were the distinguishing taxa for these sites (fig. 17). 

Macroinvertebrate communities in the MT-SROCK ecoregion significantly grouped into three clusters and appear to be 

influenced by trace-element concentrations and, in some cases, 

possibly physical-habitat disturbances. The lowest taxa richness was observed for the sample which had the highest CTU 

value (50.3; unclustered Sample A). The macroinvertebrate 

community sample collected from this site was dominated by 

Ephemerellidae mayflies and midges belonging to the family 

Orthocladiinae. It appears that mayflies within the Ephemerellidae family may be tolerant to trace-element exposure in this 

stream; however, information in the literature regarding the 

overall resiliency of this family to chemical stress appears to 

be conflicting. Cluster I includes macroinvertebrate samples 

collected from a variety of landscapes including undeveloped (reference), mined, and mixed. On average, individuals belonging to the order Diptera constitute 50 percent and 

mayflies constitute 24 percent of the relative abundance of 

organisms in macroinvertebrate communities in Cluster I. 

Midges are the dominant taxa within the Diptera community 

in this cluster; about 45 percent of these midges belong to the 

family Orthocladiinae. Of the EPT taxa in Cluster I, relative 

abundance was generally dominated by a resilient mayfly, 

Baetis sp., and caddisflies belonging to the family Hydropsychidae (Arctopsychide sp. and Ceratopsyche sp.). Clusters II 

and III had similar richness metrics; however, Cluster II had 

more dipteran taxa (Orthocladiinae midges), and Cluster III 

had a greater number of EPT taxa and Elmidae beetles. 

Ozark Highlands Ecoregion (OH)

Sediment samples from streams in the OH ecoregion were 

representative of undeveloped (27 percent), agricultural (20 

percent), and mined (53 percent) land uses and had CTU 

values ranging from 1.3 to 24.9. The highest CTU values were 

from bed sediment collected from streams in mined areas. 

Using hierarchical agglomerative clustering, three significant 

clusters (I-III) of macroinvertebrate communities emerged in 

the OH MDS ordination, each containing from two to six communities (fig. 19). Four macroinvertebrate samples collected 

from streams in two undeveloped and two mined areas did not 

significantly group with any of the three clusters. 

Cluster I is the most distinct cluster of the OH ecoregion 

MDS ordination. CTU values for the three bed-sediment 

samples in this cluster ranged from 1.3 to 1.5 (median 1.4) and 

were collected from streams in agricultural landscapes. All 

CTU values lie below the 25th percentile (1.7) for the entire 

regional dataset (figs. 9 and 19). These results indicate these 

bed-sediment samples are not enriched in trace elements compared to other sites in this study. The contribution of Pb and 

Zn to the CTU values for these three samples ranged from 17 

to 23 percent; Cr and Ni accounted for 55 to 60 percent. The 

relative contributions of Cr, Pb, Ni, and Zn were consistent 

with bed sediment collected from other streams in agricultural 

areas in this study (fig. 10B). Concentrations of trace elements 

did not exceed PEC values in any of these samples (table 2). 

The overall richness of macroinvertebrate communities in 

Cluster I (36 taxa) was similar to that observed for Cluster II 

and unclustered Sample B; EPT taxa contributed the most to 

richness (fig. 20A). On average, mayflies (56 percent) and Diptera (16 percent) accounted for most of the relative abundance 

of individuals collected from macroinvertebrate communities included in Cluster I (fig. 20B). Cluster I is characterized 

by two taxa of midges (Polypedilum sp. and Stempellinella

sp.), two taxa of mayflies (Tricorythodes sp. and Stenacron

sp.), a dragonfly family (Gomphidae), and a caddisfly (Chimarra sp.). Tricorythodes sp. appears to be relatively common in macroinvertebrate samples collected throughout the 
Macroinvertebrate Communities and Habitat Characteristics 37

OH ecoregion and was found at about 87 percent of the sites 

(appendix 2, table 2-1). Tricorythodes sp. was a distinguishing taxon for Cluster I and Cluster III (where it was common 

in a sample from a mined area). Other mayfly taxa that were 

found at higher relative abundances in the agricultural areas 

were Caenis sp. (0 to 24.1 percent), Leucrocuta sp. (0 to 11.1 

percent), and Stenonema sp. (14.5 percent). Heptageniidae 

mayflies contributed, on average, 15.7 percent to the overall 

abundance of individuals collected from macroinvertebrate 

samples included in Cluster I. Many of the taxa in Cluster 

I are considered tolerant of fine sediment, low dissolved 

oxygen, and relatively high temperature conditions (Carlisle 

and others, 2007). Tricorythodes sp. and Stenacron sp. have 

been previously reported as tolerant of the effects of agricultural land-use activities on stream habitat and water chemistry 

(Griffith and others, 2001; Dance and Hynes, 1980). 

Clusters II and III are close to one another in the MDS 

ordination (fig. 19). Cluster II consists of six macroinvertebrate samples from streams in either undeveloped (reference) 

or mined landscapes. The CTU values for bed-sediment 

samples in Cluster II ranged from 1.7 to 3.6 (median 2.6). This 

range in CTU values represents trace-element concentrations 

in bed sediment that are unenriched to moderately enriched 

(table 5, fig. 9). The contribution of Pb and Zn to the CTU 

values for these four samples ranged from 18 to 54 percent; 

Cr and Ni accounted for 28 to 56 percent. This pattern in Cr, 

Pb, Ni, and Zn contributions to CTU values does not follow 

any particular pattern associated with a given land use (figs. 

10A–10E). Concentrations of Pb and Ni exceeded their PEC 

values in one bed-sediment sample each (in different samples); 

concentrations of As, Cd, Cr, Cu, Hg, and Zn did not exceed 

their respective PEC values (table 2) in any of the bed-sediment samples associated with Cluster II sites. 

The overall taxa richness (37 taxa) of the macroinvertebrate community in Cluster II was similar to Cluster I (fig. 

20A). Mayflies (54 percent) and caddisflies (17 percent) 

accounted for about 71 percent of the individuals in these samples (fig. 20B). Macroinvertebrate communities included in 

Cluster II were characterized by the mayfly, Plauditus sp.; the 

caddisfly, Ceratopsyche sp.; and the riffle beetle, Optioservus

sp. The close proximity of Clusters II and III and the presence 

of unclustered samples made it somewhat difficult to identify 

distinguishing taxa. On average, Cluster II communities had 

Figure 19. A non-metric multidimensional scaling (MDS) ordination of macroinvertebrate communities in selected streams in the Ozark 

Highlands (OH) ecoregion and distribution of cumulative toxic units (CTUs), 1992–2000.

Larger bubble size indicates a higher value Cumulative Toxic Unit

Multi-dimensional Scaling Axis 2

Multi-dimensional Scaling Axis 1

-1

0

1

-1.5

-0.5

0.5

1.5

-3.3 -2.3 -1.3 -0.3 0.7 1.7

Two-Dimensional Stress = 0.11

Agriculture

Mined

Undeveloped

III

I

II

10

11

1

2

5

4

16

7

8

13

9

15

14

12

6

3

Taxa Vectors

 1 Stenacron sp.

 2 Tricorythodes sp.

 3 Helicopsyche sp. 

 4 Plauditus sp.

 5 Leuctra sp.

 6 Optioservus sp.

 7 Pentaneura sp.

 8 Ceratopsyche sp.

 9 Atherix sp.

 10 Cardiocladius sp.

 11 Cheumatopsyche sp.

 12 Polypedilum sp.

 13 Pentaneurini

 14 Stempellinella sp.

 15 Gomphidae

 16 Chimarra sp.

D

C

B

A
38 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Figure 20. A, Average number of taxa (richness) and percent contribution from each of Ephemeroptera, Plecoptera, and Trichoptera

(EPT), Diptera, Coleoptera, and other taxa to the overall richness (RICH); and B, average relative abundances of Ephemeroptera, 

Plecoptera, Trichoptera, Diptera, Coleoptera, and other taxa for macroinvertebrate communities in selected streams of the Ozark 

Highlands (OH) ecoregion, 1992–2000.

Number of samples in each cluster

3 6 2 1 1 1 1

Ozark Highlands Ecoregion (OH) Cluster

Ozark Highlands Ecoregion (OH) Cluster

I II III A B C D

I II III A B C D

Number of Taxa (RICH)

Percent EPT/RICH

Percent DIPTERA/RICH

Percent COLEOPTERA/RICH

Percent OTHER TAXA/RICH 

Number of samples in each cluster

Average richness, in number of taxa

0

10

20

30

40

50

60

70

Average contribution of EPT, Diptera, Coleoptera,

and other taxa to richness, in percent

Ephemeroptera

Plecoptera

Trichoptera

Diptera

Coleoptera

Other Taxa

0

10

20

30

40

50

60

70

80

Relative abundance of taxa, in percent

A

B

Unclustered Communities

3 6 2 1 1 1 1

Unclustered Communities

Standard deviation

Standard deviation
Macroinvertebrate Communities and Habitat Characteristics 39

higher relative abundances of Heptageniidae mayflies (18 

percent) than did Cluster III (6.5 percent). 

Cluster III consists of only two sites, both influenced by 

historic mining-related activities (fig. 19). The CTUs for 

bed-sediment samples grouped in Cluster III were 2.6 and 

8.6 (average 5.6) and ranked from near the 50th percentile 

to exceeding the 90th percentile for the entire regional study 

area (fig. 9), indicating the bed-sediment samples ranged from 

moderately enriched to highly enriched in trace elements 

(table 5, fig. 9). The average contribution of Pb and Zn to the 

CTU values for these bed-sediment samples was 44 percent; 

Cr and Ni averaged 40 percent. Although both sites were influenced by mining-related activities, the pattern in the combined 

contribution of Pb and Zn relative to the combined contribution of Cr and Ni to the CTU values was not characteristic of 

the regional mining signature (fig. 10D). Concentrations of Pb, 

Ni, and Zn exceeded their respective PEC values in one bedsediment sample (the same bed-sediment sample); As, Cd, Cr, 

Cu, and Hg did not exceed their PEC values (table 2) in either 

bed-sediment sample in this cluster. 

The overall taxa richness (32 taxa) of the macroinvertebrate communities associated with Cluster III was a little 

lower than that for either Cluster I or II (fig. 20A). Mayflies 

(65 percent) and caddisflies (9.6 percent) accounted for about 

75 percent of the individuals in these samples (fig. 20B). Both 

macroinvertebrate samples in Cluster III are dominated by 

mayflies—55.5 and 74.5 percent, respectively. The mayfly 

community for the sample with the higher CTU value (8.6) 

was dominated by Tricorythodes sp. (62 percent); the other 

was dominated by Isonychia sp. (26 percent) and was generally more diverse. 

Four of the macroinvertebrate samples did not significantly 

cluster with any of the samples during the cluster analysis 

(A-D, fig. 19). Two of these samples were collected from 

streams in mined areas and two from streams with undeveloped (reference) conditions. Bed sediment collected from the 

two streams in mined areas, Samples A and B, had high CTU 

values (24.9 and 11.5). CTU values for bed-sediment samples 

collected from the two reference sites were low (1.6 and 1.9). 

Both CTU values for the bed-sediment samples collected 

from the streams in mined areas exceeded the 90th percentile 

(7.5) for the entire regional dataset (fig. 9), indicating high 

trace-element enrichment was present at both sites. Unclustered Sample A had the highest CTU value (24.9) for the OH 

ecoregion and was dominated by Pb and Zn (61 percent); 

Cr and Ni contributed 4 percent to this CTU. These results 

show a distinctive pattern in the contribution of these trace 

elements to the CTU values representative of a regional 

mining signature (fig. 10D). Concentrations of Cd, Pb, and 

Zn exceeded their respective PEC values (table 2) in this 

sample. This site (unclustered A) is listed on the 2008 303-d 

list for impaired water bodies, in part, because of elevated 

concentrations of Cd, Pb, and Zn in bed sediment resulting 

from abandoned mine tailings within the watershed (Missouri 

Department of Natural Resources, 2010). This site had the 

lowest overall richness (17 taxa) for samples collected from 

the OH ecoregion. Diptera dominated the taxa richness (59 

percent) and relative abundance (67 percent) for this sample 

(figs. 20A–20B). The relative abundance of Diptera individuals 

is the distinguishing characteristic of this macroinvertebrate 

community (fig. 20B). Just about half the relative abundance 

(55 percent) was comprised of midges belonging to the family 

Orthocladiinae (Cardiocladius sp. and Chaetocladius sp.) and 

tribe Tanytarsini (Cladotanytarsus sp.). Cardiocladius sp. was 

more abundant in unclustered Sample A than at any of the 

other sites in the OH ecoregion.

The CTU value for bed sediment associated with unclustered Sample B (11.5) was primarily composed of Pb and Zn 

(73 percent), and Cr and Ni contributed 16 percent to this 

value. These results show a distinctive pattern in the contribution of these trace elements to the CTU values representative 

of a regional mining signature (fig. 10D). Concentrations of 

Pb, Ni, and Zn exceeded their respective PEC values (table 2) 

in this sample. The overall richness for unclustered Sample B 

was similar to the taxa richness for Clusters I and II (fig. 20A). 

EPT taxa contributed most (47 percent) to the taxa richness of 

the community, and the relative abundance of individuals was 

fairly well distributed among mayfly (26 percent), caddisfly 

(19 percent), Diptera (22 percent), and beetle (24 percent) taxa 

(figs. 20A–20B). Most of the caddisflies belonged to the family 

Hydropsychidae (82 percent); most of the Diptera belonged to 

the family Chironomidae (71 percent) (appendix 3, fig. 3-6). 

The primary taxon characterizing unclustered Sample B was 

Atherix sp. (fig. 19). This taxon was found at about 33 percent 

of the samples collected from the OH ecoregion (appendix 2, 

table 2-1). Although occurring at very low relative abundances 

(0 to 0.75 percent), Atherix sp. was more abundant in this sample than in any other samples from this ecoregion and can be 

considered a distinguishing taxon of this community (fig. 19). 

Optioservus sp. was the most abundant taxon in unclustered 

Sample B (13.5 percent).

The CTU values for the bed sediment in samples (C and D) 

from the reference areas were near the 25th percentile (1.7) for 

the regional dataset, indicating that trace-element enrichment 

was not present at these sites. The CTU values for the bed-sediment samples from these reference areas were primarily composed of Cr and Ni (53 and 57 percent); Pb and Zn contributed 

20 and 17 percent to these values. The relative contributions of 

Cr, Pb, Ni, and Zn to these CTU values is consistent with the 

regional composition patterns for bed-sediment samples collected from streams in undeveloped areas (fig. 10A). Concentrations of trace elements did not exceed their respective PEC 

values (table 2) in either bed-sediment sample collected from 

streams in these undeveloped landscapes. 

The overall taxa richness of unclustered Samples C and D 

was the same (41 percent); however, unclustered Sample C 

had a lower number of EPT and a higher number of dipteran 

taxa (fig. 20A). Chironomidae comprised most of the Diptera 

population (relative abundance of 94 percent) in unclustered 

Sample C (appendix 3, fig. 3-6). Unclustered Samples C and 

D were dominated by mayflies (44 and 40 percent, respectively); unclustered Sample D had a higher relative abundance 
40 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

of “other taxa” (26 percent) than did Sample C (1.64 percent, 

fig. 20B). The category, “other taxa”, is comprised of taxa that 

are not mayflies, stoneflies, caddisflies, beetles (Coleoptera), 

or true flies (Diptera). Mesogastropoda (Elimia sp.) dominated 

the “other taxa” composition occurring at about 23 percent 

relative abundance in unclustered Sample D (appendix 2, table 

2-2). The caddisfly, Helicopsyche sp., was characteristic of 

Sample D (fig. 19). The relative abundance of this taxon in this 

community was 9.25 percent, the highest relative abundance 

of this taxon in streams sampled within the OH ecoregion. The 

caddisfly population in unclustered Sample D differed from 

other samples because it was not dominated by taxa belonging 

to the family Hydropsychidae (appendix 3, fig. 3-6).

Generally, macroinvertebrate distribution patterns in the 

OH ecoregion, represented by the MDS ordination, included 

more unclustered communities than the other three ecoregions 

evaluated for this study. The macroinvertebrate communities in the OH ecoregion that significantly group into three 

clusters appear to be influenced by trace-element concentrations and possibly land use. The possible influence of land use 

on macroinvertebrate community structure is suggested by the 

distinct grouping of the three macroinvertebrate communities, collected from streams in agricultural settings, in Cluster 

I. For comparison purposes, macroinvertebrate communities 

sampled from agricultural streams in the XE-EPLAT did not 

distinctly group into one particular cluster, and the agricultural 

landscape was uncommon in the mountain ecoregions. The 

characterizing features of macroinvertebrate communities 

were the contributions of various mayfly taxa (Caenis sp., 

Leucrocuta sp., Stenacron sp., and Stenonema sp.) to the overall relative abundance at these sites. The lack of trace-element 

enrichment in the bed sediment at these sites should be noted. 

Generally, the mayfly communities appear to be relatively 

diverse compared to samples from the other ecoregions in this 

study.

The macroinvertebrate communities included in Clusters 

II and III shared many common taxa, resulting in their close 

proximity in the MDS ordination. Cluster II included samples 

collected from undeveloped (reference) and mined areas, 

whereas Cluster III represented conditions of only mined 

locations. Concentrations of trace elements in bed-sediment 

samples were different between these two clusters. Bed sediment in Cluster II was unenriched to enriched in trace elements, whereas Cluster III bed sediment was low to highly 

enriched. Four taxa distinguished the Cluster II community 

structure (Ceratopsyche sp., Cheumatopsyche sp., Optioservus

sp., and Plauditus sp.). Tricorythodes sp. dominated the relative abundance (62 percent) of the community in Cluster III 

with the higher CTU value (8.6). 

Four macroinvertebrate samples within the OH ecoregion 

did not group with any of the three clusters. The lowest taxa 

richness was observed for the unclustered Sample A that had 

the highest CTU value (24.9). This community was heavily 

dominated by Diptera, primarily Chironomidae (Cardiocladius sp., Chaetocladius sp., and Cladotanytarsus sp.). This 

site has been influenced by historic mining practices, and the 

dominance of Diptera taxa is the defining characteristic of this 

community. The other unclustered macroinvertebrate community collected from a stream in a mined landscape also had 

bed sediment enriched in trace elements; however, the community structure was markedly different than that described 

for unclustered Sample A. Two taxa were characteristic of 

the unclustered Sample B (Atherix sp. and Optioservus sp.). 

Sample B had a fairly balanced representation of relative 

abundances of mayflies, caddisflies, and Diptera. The taxon 

Optioservus sp. was the most abundant in this sample. The 

most distinguishing feature of Samples C and D (unclustered 

communities) from reference sites was the relative contribution of mayflies and “other taxa” to the overall relative abundances observed in these communities. Generally, the taxa 

within the OH ecoregion were somewhat different than those 

in the other ecoregions.

Eastern Xeric Plateau Ecoregion (XE-EPLAT)

Samples were collected from streams in the XE-EPLAT 

ecoregion in undeveloped (12 percent), agricultural (41 

percent), urban (6 percent), mined (23 percent), and mixed 

(18 percent) landscapes. CTU values ranged from 1.0 to 7.5. 

The MDS ordination and hierarchical agglomerative cluster 

analysis identified three significant clusters of macroinvertebrate communities (I–III) and two unclustered Samples A and 

B (fig. 21). 

Cluster I consists of four macroinvertebrate communities collected from sites in agricultural and mixed landscapes 

(fig. 21). CTU values for bed-sediment samples associated 

with these macroinvertebrate communities included in Cluster 

I ranged from 1.3 to 2.1; the median CTU value was 1.7, equal 

to the 25th percentile for the entire regional dataset (fig. 9). 

These results generally indicate a lack of trace-element enrichment in the bed sediment. The contribution of Pb and Zn to 

the CTU values in Cluster I ranged from 23 to 69 percent; 

together, Cr and Ni contributed from 8 to 47 percent (figs. 10B

and 10E). Trace-element concentrations did not exceed PEC 

values (table 2) in any of the bed-sediment samples collected 

from these four sites. 

The overall richness of macroinvertebrate communities 

represented in Cluster I (20 taxa) was similar to the richness 

of the other two clusters and the unclustered Samples A and 

B (21–24 taxa, fig. 22A). This is the only ecoregion examined 

where this occurred. Although the overall richness values are 

very similar among clusters, the contributions of the various 

taxonomic groups differ (fig. 22B). Macroinvertebrate community richness in Cluster I primarily consisted of Diptera 

(48 percent), EPT (26 percent), and “other taxa” (24 percent) 

(fig. 22A). The contribution of Ephemeroptera, Trichoptera, 

and “other taxa” to the relative abundance in the macroinvertebrate communities in Cluster 1 was highly variable (fig. 22B). 

Taxa characteristic of Cluster I were the Oligochaeta worms 

(Tubficidae and Naididae) and the Orthocladiinae midge, 

Cricotopus sp. (fig. 21). The contribution of caddisfly taxa to 

community structure in Cluster I also was highly variable. On 
Macroinvertebrate Communities and Habitat Characteristics 41

average, caddisflies contributed about 11 percent to the overall 

number of individuals in these samples; about 48 percent of 

the caddisflies were Hydropsychidae (appendix 3, fig. 3-8). 

The abundance and taxa composition of mayflies in this 

cluster also were highly variable; however, Leptohyphidae (14 

percent) taxa and Acentrella sp. (52 percent) did occur at relatively high abundances in two agricultural samples. Given the 

low CTU values for the bed-sediment samples, other factors 

are likely influencing the macroinvertebrate community structure in these areas. Streams draining agricultural watersheds 

are susceptible to nutrient enrichment and deposition of excess 

fine sediments (Maret and others, 2010; Sidle and Sharma, 

1996), and the taxa Tubificidae, Naididae, and Cricotopus sp. 

are documented as having high thresholds to these stresses 

(Carlisle and others, 2007). Leptohyphidae are present at several of the agricultural sites within the XE-EPLAT ecoregion 

but particularly at one site included in Cluster I. Even though 

the information on taxa identification is limited to family, 

evidence sugggests that these mayflies are likely resilient in 

Figure 21. A non-metric multidimensional scaling (MDS) ordination of macroinvertebrate communities in selected streams in the Xeric 

Eastern Plateau (XE-EPLAT) ecoregion and distribution of cumulative toxic units (CTUs), 1992–2000. Multi-dimensional Scaling Axis 2

Multi-dimensional Scaling Axis 1

-1

0

1

-1.5

-0.5

0.5

1.5

-2 -1.5 -1 -0.5 0 0.5 1 1.5

Two-Dimensional Stress = 0.20

III

I

II

10

11

1

2

5

4

7

8

9

6

3

Taxa Vectors

 1 Tubificidae

 2 Cricotopus sp.

 3 Naididae

 4 Eukiefferiella sp.

 5 Baetis sp.

 6 Brachycentrus sp.

 7 Rhithrogena sp.

 8 Hydropsyche sp.

 9 Acentrella sp.

 10 Ceratopsyche sp.

 11 Leptohyphidae 

Agriculture

Mined

Mined, CERCLA1

Mixed*

Undeveloped

Urban

B

A

*Mixed, sites with agricultural, urban, and (or) mining land uses represented

1 Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA)

Larger bubble size indicates a higher value Cumulative Toxic Unit

ecosystems influenced by agricultural practices (Griffith and 

others, 2001; Dance and Hynes, 1980). 

Five macroinvertebrate samples are included in Cluster II, 

and the bed sediment at these sites had the highest CTU values 

(2.3 to 7.5; median 4.5) for the XE-EPLAT ecoregion. Regionally, these bed-sediment samples range from low enrichment 

to high enrichment conditions (table 5, fig. 9). The streams 

from which these samples were collected represent a variety 

of land uses—agriculture, mined, and mixed (fig. 21). The 

three bed-sediment samples collected from mined areas had 

the highest CTU values (4.5 to 7.5). Two of the three stream 

sites included in Cluster II that were influenced by historic 

mining-related activities were associated with waters listed 

as CERCLA because of the contamination of bed sediment 

with a variety of trace elements (aluminum, As, Cd, Cr, cobalt, 

Cu, fluoride, iron, Pb, manganese, molybdenum, sulfate, and 

Zn; Colorado Department of Public Health and Environment, 2009; U.S. Environmental Protection Agency, 2010). 

The contribution of Pb and Zn to the CTU values for these 
42 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Figure 22. A, Average number of taxa (richness) and percent contribution from each of Ephemeroptera, Plecoptera, and Trichoptera

(EPT), Diptera, Coleoptera, and other taxa to the overall richness (RICH); and B, average relative abundances of Ephemeroptera, 

Plecoptera, Trichoptera, Diptera, Coleoptera, and other taxa for macroinvertebrate communities in selected streams of the Xeric Eastern 

Plateau ecoregion, 1992–2000.

Number of samples in each cluster

4 5 6 1 1

4 5 6 1 1

I II III A B

Number of Taxa (RICH)

Percent EPT/RICH

Percent DIPTERA/RICH

Percent COLEOPTERA/RICH

Percent OTHER TAXA/RICH 

Number of samples in each cluster

Average richness, in number of taxa

0

10

20

30

40

50

60

70

Average contribution of EPT, Diptera, Coleoptera,

and other taxa to richness, in percent

Ephemeroptera

Plecoptera

Trichoptera

Diptera

Coleoptera

Other Taxa

0

10

20

30

40

50

60

70

90

80

Relative abundance of taxa, in percent

A

B

Unclustered Communities

Unclustered Communities

Eastern Xeric Plateau Ecoregion (XE-EPLAT) Cluster

Eastern Xeric Plateau Ecoregion (XE-EPLAT) Cluster

I II III A B

Standard deviation

Standard deviation
Macroinvertebrate Communities and Habitat Characteristics 43

bed-sediment samples included in Cluster II ranged from 17 to 

48 percent; Cr and Ni contributed from 6 to 45 percent. These 

results show about the same contributions of both Pb and Zn 

and Cr and Ni to CTU values, indicating no pattern associated 

with regional land use (figs. 10B, 10D, 10E). Concentrations 

of As, Cu, Ni, and Se each exceeded their respective PEC 

values, or PEL value in the case of Se, in one bed-sediment 

sample. However, these exceedences were rarely in the same 

sample. The PEC value for Pb and Zn (table 2) were exceeded 

in two bed-sediment samples. 

As previously mentioned, the overall taxa richness in 

Cluster II was similar to the other clusters generated by MDS 

for this ecoregion. On average, EPT (36 percent) and dipteran 

(48 percent) taxa contributed the most to overall richness in 

Cluster II macroinvertebrate communities (fig. 22A). Although 

highly variable, samples included in Cluster II were primarily 

composed of dipterans, mayflies, and caddisflies (fig. 22B).

The distinguishing characteristic of macroinvertebrate communities in Cluster II was the presence of the Orthocladiinae 

midge (Eukiefferiella sp.). Some researchers have found 

that the Orthocladiinae midges such as Eukiefferiella sp. are 

relatively tolerant of trace-element exposure (Gower and others, 1994; Clements and others, 2000; Swansburg and others, 

2002). Alternatively, other researchers have found Eukieferiella sp. most frequently in streams with relatively low concentrations of trace elements (Pollard and Yuan, 2006). 

In Cluster II, the three streams influenced by mining 

showed some differences in macroinvertebrate community 

structure. It is likely that the subtle differences in the composition of the CTU values among these sites and possibly 

site-specific habitat conditions may be contributing to the 

differences among these macroinvertebrate communities. 

About half (53 percent) of the relative abundance of individuals comprising the macroinvertebrate community at one of the 

sites influenced by historic mining activities was composed 

of the caddisfly, Brachycentrus sp. Clements (1994) showed 

that Brachycentrus sp. was positively associated with Zn and 

elevation, suggesting some degree of tolerance of this taxon to 

trace elements. Eukieferiella sp. was found at all sites included 

in Cluster II, and the relative abundance of this taxon contributed about 27 percent to the overall abundance of individuals at the two CERCLA sites. The overall stress of the MDS 

ordination (0.20) suggests that there may be some ambiguity 

in comparing these macroinvertebrate communities. 

The six macroinvertebrate samples included in Cluster III 

were collected from streams in all five land-use categories—

undeveloped, agricultural, urban, mined, and mixed (fig. 21). 

The CTU values in this cluster range from 1.0 to 3.0 (median 

1.7). The highest CTU value (3.0) was for bed sediment collected from the stream influenced by historic mining-related 

activities indicating moderate enrichment. The remaining 

CTU values do not exceed the 50th percentile (2.52) of the 

regional dataset, indicating that trace-element enrichment in 

these bed-sediment samples was minimal (table 5, fig. 9). The 

contribution of Pb and Zn to the CTU values in Cluster III 

ranged from 16 to 33 percent; together, Cr and Ni contributed 

from 36 to 60 percent. The higher contribution of Cr and Ni 

to the CTU values suggests a resemblance to regional patterns observed in CTU values representative of undeveloped, 

agricultural, urban, and mixed land uses (figs. 10A–10C, 10E). 

Trace-element concentrations did not exceed their respective 

PEC values (table 2) in bed-sediment samples collected from 

these sites. The overall richness of macroinvertebrate communities represented in Cluster III (21 taxa) was similar to the 

other clusters for this ecoregion (fig. 22A). On average, EPT 

taxa contributed the most (44 percent) to the taxa richness for 

macroinvertebrate communities included in Cluster III. The 

contribution to taxa richness was similar for Diptera taxa (42 

percent). The macroinvertebrate communities in Cluster III 

were dominated by caddisfly (52 percent), Diptera (26 percent), and mayfly (18 percent) taxa (fig. 22B). Generally, the 

macroinvertebrate community structure represented in Cluster 

III is characterized by relatively tolerant EPT taxa. Caddisflies 

(Brachycentrus sp., Hydropsyche sp., and Ceratopsyche sp.) 

were characteristic of the macroinvertebrate communities 

included in Cluster III. In addition to these tolerant caddisfly 

taxa, Acentrella sp., Baetis sp., and Rhithrogena sp. mayflies 

were also important in the characterization of these communities; however, these mayfly taxa have a much lower contribution to the total relative abundance than the caddisflies (fig. 

22B). 

Two macroinvertebrate communities did not group with 

any of the three clusters in the XE-EPLAT ecoregion—one 

sample from a reference site (undeveloped landscape) and the 

other an agricultural setting (fig. 21). The CTU values (1.3 

and 1.2) for the bed sediment were below the 25th percentile 

(1.7) for the entire regional dataset, indicating trace-element 

enrichment is not occurring at these sites (table 5, fig. 9).The 

CTU values for these two bed-sediment samples were primarily composed of Cr and Ni (47 and 53 percent); Pb and Zn 

contributed 19 and 24 percent. These results are consistent 

with the relative contributions of Cr, Pb, Ni, and Zn to CTU 

compositions for samples collected from streams in undeveloped and agricultural landscapes (figs. 10A–10B). Traceelement concentrations did not exceed their respective PEC 

values (table 2) in either bed-sediment sample collected from 

either stream associated with these unclustered communities. 

Overall taxa richness was similar among clusters within 

this ecoregion; however, the taxa contributing to the overall 

richness for these two unclustered communities were markedly different from the clustered samples and from each other 

(fig. 22A). On average, Diptera (35 percent) and “other taxa” 

(35 percent) influenced the richness at unclustered Sample A 

(undeveloped landscape); however, the relative abundances of 

Diptera (39 percent) and caddisflies (44 percent) dominated 

this sample. The relative abundances of the “other taxa” were 

relatively small (9.8 percent). In Sample A, Diptera were 

dominated by Ceratopogoninae (6.13 percent) and the midge, 

Parametriocnemus sp. (22.45 percent); the relative abundance of caddisflies was entirely composed of Hydropsyche 

sp. (43.57 percent). EPT taxa (59 percent) contributed the 

most to taxa richness in the unclustered Sample B collected 
44 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

at an agricultural site. EPT for Sample B was dominated by 

caddisflies (relative abundance of 65 percent) of which most 

belonged to the family Hydropsychidae (Ceratopsyche sp. 

and Cheumatopsyche sp.) (appendix 3, fig. 3-8). Mayflies 

accounted for about 21 percent of the individuals collected 

from unclustered Sample B, and Leptophlebiidae mayflies 

(Choroterpes sp.) contributed the most (9.3 percent) to the 

mayfly portion of this community.

The distribution patterns of macroinvertebrate communities within the XE-EPLAT ecoregion reflect exposure to trace 

elements and possibly land-use activities. The XE-EPLAT 

ecoregion had the highest level of similarity in richness among 

clusters of any of the ecoregions included in this study. The 

relative abundances of mayflies, caddisflies, and ”other taxa” 

were highly variable for communities in Cluster I. Agricultural 

settings were represented by two of the three streams included 

in Cluster I, and bed-sediment samples were not enriched in 

trace elements. Cluster I was mostly characterized by “other 

taxa” (Tubificidae and Naididae worms). The midge, Cricotopus sp., was also characteristic of the macroinvertebrate community structure of Cluster I. Generally, macroinvertebrate 

samples collected from streams where historic mining-related 

activities have bed sediment enriched with trace elements 

grouped into Cluster II. The relative abundances of mayflies, 

caddisflies, and “other taxa” were highly variable in Cluster II, 

which was characterized by the presence of the Chironomidae 

midge, Eukieferiella sp. Cluster III, consisting of sites from a 

variety of land uses, was characterized primarily by mayflies 

(Acentrella sp., Baetis sp., and Rhithrogena sp.) and caddisflies (Brachycentrus sp., Ceratopsyche sp., and Hydropsyche

sp.). The bed sediment samples collected at the sites included 

in this cluster were minimally enriched in trace elements. The 

diverse nature of land uses represented by the streams sampled 

in the XE-EPLAT ecoregion and the distribution patterns 

observed in general macroinvertebrate communities suggest 

that something other than trace-element exposure alone is 

likely contributing to macroinvertebrate community structure 

in these samples. 

Summary and Conclusions

The objective of this regional-scale study was to characterize trace-element concentrations and occurrence in streambed 

sediment and to determine the influence of trace elements on 

aquatic-macroinvertebrate communities. The nine trace elements included in this study—arsenic (As), cadmium (Cd), 

chromium (Cr), copper (Cu), lead (Pb), mercury (Hg), nickel 

(Ni), selenium (Se), and zinc (Zn)—were selected on the 

basis of their ecological significance and the availability of 

sediment-quality guidelines.

Each of the nine trace elements was first evaluated within 

each of the five general land-use categories (undeveloped, 

agricultural, urban, mined, and mixed) for range in concentration and comparison with available sediment-quality 

guidelines. It was outside the scope of this study to determine 

a cause and effect relation between land use and trace-element occurrence; however, it was necessary to evaluate the 

trace elements in the context of land use in order to address 

ranges in concentrations in bed sediment within each of these 

landscapes and, if necessary, consider generally accepted 

influences, other than trace-element contamination, on macroinvertebrate assemblages. Most of the 208 bed-sediment 

samples (62 to 80 percent) collected from selected streams in 

the conterminous western United States, Alaska, and Hawaii 

had trace-element concentrations within natural geochemical concentrations, regardless of land use. Regional baseline 

and reference-site trace-element concentrations determined 

in this investigation were similar to baseline concentrations 

previously reported for bed sediment collected throughout the 

Nation.

Median concentrations of all nine trace elements were lowest in bed sediment collected from undeveloped (reference) 

and agricultural landscapes. With the exception of Cr and Ni, 

median concentrations of the remaining seven trace elements 

in bed sediment collected from streams in these areas were 

below the threshold effect concentrations. Median concentrations of Cr and Ni in bed sediment in undeveloped and agricultural areas were between the threshold and probable-effect 

concentrations for these trace elements. Bed-sediment samples 

from streams in mined areas were enriched in concentrations 

of As, Cd, Cu, Pb, Hg, Ni, and Zn. Concentrations of many 

of these trace elements were elevated in urban (As, Cr, Cu, 

Hg, Ni, Se, and Zn) and mixed (Cd, Cr, Cu, Pb, Ni, Se, and 

Zn) landscapes. In most cases, median concentrations of As, 

Cd, Cr, Cu, Pb, Hg, Ni, Se, and Zn were within the threshold 

and probable-effect concentrations for these trace elements. 

A noted exception was observed for Zn in bed-sediment 

samples collected from streams influenced by mining-related 

activities, where this trace element was at its probable-effect 

concentration.

Assessing co-occurrence of trace elements in bed sediment is helpful in identifying areas where toxic effects may be 

enhanced. Generally, only moderate and strong correlations 

(rho ≥ 0.5, p ≤ 0.05) are discussed herein. Commonly, concentrations of Cr and Ni were strongly correlated in the bedsediment samples. This was observed only for these two trace 

elements. In a few instances, concentrations of Cr and Ni were 

moderately and positively correlated with other trace elements 

examined in this study. Cr and Ni exceeded probable-effect 

concentrations in 9 and 18 percent, respectively, of all bedsediment samples collected throughout the regional study area. 

Ni exceeded the probable-effect concentration more frequently 

than Cr; however, in all but one instance, when bed-sediment 

concentrations of Cr exceeded the probable-effect concentration for this trace element, Ni concentrations also exceeded 

its probable-effect concentration. In very few samples, when 

both Cr and Ni exceeded the probable-effect concentrations, 

the other seven trace elements also exceeded their respective 

probable-effect concentrations. Although natural or anthropogenic sources of trace elements were not directly evaluated 
Summary and Conclusions 45

as part of this study, results suggest that in many instances 

concentrations of Cr and Ni are naturally high in bed sediment 

in western streams. Concentrations of Zn were moderately 

correlated with Cd, Cu, Pb, and Hg in bed-sediment samples 

collected from undeveloped (reference) sites and with Cu in 

agricultural areas. Bed sediment from streams in undeveloped 

areas occasionally had concentrations of As, Cr, Pb, and Ni 

exceeding probable-effect concentrations, indicating that some 

areas may be naturally enriched in these trace elements above 

concentrations expected to cause ecosystem impairment. 

Concentrations of Cd, Pb, and Zn were moderately correlated in bed sediment collected from urbanized and mined 

areas. Of the 70 sites evaluated in urban and mined landscapes, concentrations of all three of these trace elements 

exceeded the probable-effect concentrations in 16 percent 

of the samples, all of which were from mined areas. As was 

moderately correlated to Cd, Pb, and Zn in bed sediment 

from streams in mined areas. Concentrations of As and Cu in 

these areas commonly exceeded probable-effect concentrations in the same samples where Cd, Pb, and Zn concentrations exceeded probable-effect concentrations. Although Hg 

concentrations were high in selected bed-sediment samples 

from areas influenced predominantly by historic mining activities, concentrations exceeding the probable-effect concentration occurred infrequently (3 percent of all samples). All 

exceedences were in samples collected from areas influenced 

by mining. With the exception of the moderate correlations 

between Se and Cu in agricultural bed sediment and with 

Hg in urban bed sediment, Se was only weakly correlated 

with the other six trace elements evaluated during this study. 

The median Se concentration was elevated in urban bedsediment samples. The only instances where Se concentrations 

exceeded the probable-effect level were in one sample each 

from an agricultural and urban stream. These exceedences of 

the Se probable-effect level did not co-occur with any other 

exceedences.

Cumulative toxic units (CTUs) were used to evaluate the 

influence of trace-element mixtures on aquatic-macroinvertebrate community structure. The use of CTUs assumes additive 

toxicity, which may or may not be the case. Se was not used 

in the determination of CTU values because this trace element 

was not analyzed in all bed-sediment samples, rarely exceeded 

concentrations expected to be harmful to macroinvertebrates, 

and was seldom correlated to other trace elements included in 

this study. Gradients in trace-element mixtures were evaluated 

by examining the range in CTU values. Generally, the lowest 

CTU values were in bed sediment collected from reference 

and agricultural areas; the highest CTUs were in bed sediment 

from mined areas. The median CTU values between undeveloped (reference) and agricultural landscapes and between 

urban and mixed land-use areas were not statistically different. 

Median CTU values for bed sediment collected from reference and agricultural areas were below the 50th percentile for 

the regional dataset indicating minimal enrichment; urban and 

mixed land-use areas were above the 50th percentile, indicating moderate enrichment in trace elements. Bed sediment 

collected from streams in mined areas had the widest range in 

CTU values; the median value was equal to the 90th percentile 

for the regional dataset indicating conditions of high enrichment. For most landscapes, median contributions of Cr and Ni 

to CTUs predominated over each contribution of the other six 

trace elements included in the CTU determinations. In mined 

areas, CTUs were predominantly composed of Pb and Zn.

Evaluating the results of large-scale regional investigations 

that rely on macroinvertebrates as indicators is challenging. 

Regional variability resulting from differences in topography, 

climate, water quality, and habitat characteristics affects the 

ability to detect changes in the macroinvertebrate communities in response to an environmental-stressor gradient, especially when multiple environmental stressors are present and 

biological responses are commonly confounded by additive or 

dominant effects from one or more stressors. For this investigation, the large-scale MDS ordination of macroinvertebrate 

community structure was influenced more by regional spatial 

variability rather than the effects caused by a gradient of trace 

elements in bed sediment. Even after the analysis was reduced 

to a sub-regional level, the effects of trace elements in bed 

sediment on macroinvertebrate community structure were only 

apparent at ecoregions with the greatest CTUs resulting from 

past mining activities. Regional patterns in CTU composition 

determined for general land uses oftentimes did not appear to 

be reflected in distinguishable macroinvertebrate distribution 

patterns.

To account for some of the natural variability in distribution patterns of aquatic macroinvertebrates across the study 

region, ecoregions were used to stratify analyses of macroinvertebrate community structure. Communities within a given 

ecoregion were expected to be similar enough to distinguish 

stress-induced changes in structure from other influences on 

distribution and abundance. Intermediate-scale ecoregions 

(sub-regional scale) were used to minimize differences in 

factors such as climate, topography, general geology, and 

general in-stream habitat characteristics such as water quality 

and channel substrate. The four intermediate-scale ecoregions 

used in this investigation were the Mountain Northern Rockies 

(MT-NROCK), Mountain Southern Rockies (MT-SROCK), 

Ozark Highlands (OH), and Eastern Xeric Plateau (XEEPLAT). Each of the four intermediate-scale ecoregions used 

to evaluate the influence of trace elements on macroinvertebrate community structure had different ranges in CTU values, 

and the community distribution pattern in each ecoregion 

appeared to be influenced, at least to some degree, by trace 

elements. In many cases, macroinvertebrate communities associated with bed-sediment samples with a given trace-element 

enrichment condition (no enrichment to high enrichment) and 

collected from a stream in a given landscape showed similar 

structure. 

The four intermediate-scale ecoregions were evaluated 

using multidimensional scaling (MDS) ordination and cluster 

analysis with significance testing of the selected clusters. 

Similar patterns were observed within all four ecoregions. 

Clusters of sites with the greatest CTUs had greater relative 
46 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

abundances of taxa that are generally considered tolerant 

to trace-element exposure when compared to clusters with 

lower CTUs. The common taxa to community composition in 

macroinvertebrate communities exposed to elevated trace-element concentrations in bed sediment among ecoregions were 

those belonging to the subfamily of midges, Orthocladiinae. 

Other taxa resilient to trace-element exposure in bed sediment 

included the mayflies, Baetis sp. and Tricorythodes sp.; the 

Hydropsychidae caddisflies; and the dipteran, Simulium sp. 

In addition, sensitive EPT taxa were generally absent from 

clusters with higher CTUs. 

Given that trace-element concentrations in bed sediment 

collected throughout the regional study area were predominantly within geochemical baseline concentrations, it is not 

unexpected that potential trace-element effects on macroinvertebrate communities were observed only at the most-contaminated sites, namely those associated with CERCLA areas. 

Results of this study are similar to other studies assessing the 

influence of trace-element exposure to in-stream macroinvertebrate communities in Rocky Mountain streams and in the 

XE-EPLAT ecoregion. Across the three intermediate-scale 

ecoregions—MT-NROCK, MT-SROCK, and XE-EPLAT—

the mayfly, Baetis sp.; the dipteran, Simulium sp.; caddisflies 

in the family Hydropsychiidae; and midges in the family 

Orthocladiinae were common, demonstrating some tolerance 

to trace-element exposure. In some cases, the observed results 

suggest some degree of resilience to possible changes in 

physical-habitat conditions within stream ecosystems as well. 

Generally, community composition in samples collected from 

the OH ecoregion was considerably different. For example, the 

mayfly community from streams sampled in the OH ecoregion 

appeared to be relatively more diverse in comparison to the 

other intermediate-scale ecoregions. One taxon that appeared 

to indicate possibly impaired conditions by occurring in 

relatively high relative abundances in the OH ecoregion was 

the mayfly, Tricorythodes sp. The presence of Tricorythodes

sp. at impaired sites within the OH ecoregion was similar to 

how Baetis sp. dominated the mayfly communities at impaired 

sites in the MT ecoregions. Given the regional perspective and 

retrospective nature of this evaluation, site-specific differences 

in trace-element composition (CTUs) and concentrations and 

the relative influence on macroinvertebrate communities could 

not be discussed in greater detail other than by gross generality, and these findings should not be extrapolated outside this 

context. 

In general, the findings of this investigation are consistent 

with previous studies analyzing the impacts of trace elements 

on macroinvertebrates. The primary difference between this 

study and many of the previous investigations is the scale 

at which patterns in macroinvertebrate community structure 

were observed. Most of the previous studies have focused on 

the characterization of macroinvertebrate communities in a 

single river basin or stream reach. This investigation evaluated macroinvertebrate responses on a larger regional scale. 

Although many interesting patterns were found, the analyses 

were limited because of the small number of samples spread 

across a large ecoregion, with little or no replication at individual sites. The findings of this investigation are useful in 

that it highlights relations between trace-element exposure and 

macroinvertebrate response that can be characterized outside 

local scales. In addition, this study emphasizes the importance 

of considering the complicated relations between physical and 

chemical influences that may be imparted on aquatic-macroinvertebrate communities. Natural-resource managers are 

required to implement best-management strategies intended to 

balance and maintain necessary resources of adequate quality 

to maintain healthy ecological systems while simultaneously 

allowing for continued human development in areas within 

which these ecosystems reside.

Natural systems are inherently complex and dynamic, 

and an evaluation of physical and (or) contaminant stress(es) 

on fauna necessarily will involve an assessment of many 

components important to the ecosystem being investigated. 

As described earlier, many studies have investigated isolated 

components of aquatic systems. When elucidating potential 

impairments to natural systems, it is important to consider the 

complicated, integrated, and oftentimes highly variable components of the system in order to place possible impairments 

into proper perspective. 

Acknowledgments

The authors of this report gratefully acknowledge the contributions from the following U.S. Geological Survey personnel: Christine Albano and Karen Thomas, for aiding in dataset 

preparation; Toby Welborn, for obtaining GIS-related datasets, 

extrapolating GIS data into buffer areas, and creating the 

ACCESS database where all the data used for analyses were 

stored; Justin Mayers, for writing script necessary for use in 

creating an inventory of mining-related mineralogic data from 

U.S. Geological Survey Mineral Resource Datasets; Tim Brabets, for information on land-use characterization in and near 

Anchorage, Alaska; Stephen Frenzel, for information regarding selenium occurrence in and near the Cook Inlet area, near 

Anchorage, Alaska; Quinn Cannon, for efforts during initial 

macroinvertebrate data analysis; Daren Carlisle, Terry Short, 

Terry Maret, and Dennis Wentz for helpful guidance; Jocelyn 

Gretz, for editorial assistance; and Dennis Wentz, Terry Short, 

Tim Rowe, and Michael Rosen for their respective reviews of 

this report. 
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56 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Appendix 1-1.

Trace element, land use, and cumulative toxic unit data 

used to assess the influence of trace elements on macroinvertebrate community structure in selected streams in the conterminous western United States, Hawaii, and Alaska, 1992–2000.

Appendix 1-2.

Average specific conductance, dissolved solids, calcium, 

magnesium, hardness, pH, and suspended-sediment concentration for each sampling site used to assess the difference in 

general water-quality characteristics among the five largescale ecoregions in the conterminous western United States, 

Hawaii, and Alaska, 1992–2000.

Appendix 2-1.

Relative abundance of taxa occurring at a minimum of 30 

percent of the sampling sites within each ecoregion included 

in this investigation within the conterminous western United 

States and Alaska, 1992–2000.

Apppendix 2-2.

Phylogony and relative abundance of taxa in macroinvertebrate samples collected as part of this study from selected 

streams in the western United States, Alaska, and Hawaii, 

1992–2000.
Appendix 3. 57

Figure 3-1. Average contribution of each Order, Ephemeroptera (E), Plecotpera (P), and Trichoptera (T), to EPT richness for 

macroinvertebrate communities in selected streams of the Mountain Northern Rockies (MT-NROCK) ecoregion, 1992–2000. Taxa 

represented in this figure include rare and common taxa occurring at sites within these MT-NROCK ecoregion streams. Clusters 

correspond to clusters of macroinvertebrate assemblages within the multidimensional scaling (MDS) ordination for this ecoregion (fig. 

15). Clusters identified as “Unclustered Communities” did not group significantly during the cluster analysis. 

Number of samples in each cluster

3 6 7 6 7 1 1 1

I II III IV V A B C

0

10

20

30

40

50

60

70

Unclustered Communities

Mountain Northern Rockies Ecoregion (MT-NROCK) Cluster

Relative contribution of Ephemeroptera, Plecoptera,

and Trichoptera taxa to EPT index, in percent

Ephemeroptera

Plecoptera

Trichoptera

Standard deviation

Appendix 3.

Community-structure metrics used to evaluate characteristics for macroinvertebrate samples collected from selected 

streams in four intermediate-scale ecoregions: Mountain 

Northern Rockies (MT-NROCK), Mountain Southern Rockies (MT-SROCK), Ozark Highlands (OH), and Eastern Xeric 

Plateau (XE-EPLAT) evaluated in this investigation. 
58 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Figure 3-2. Average relative abundance of selected taxa to Ephemeroptera, Trichoptera, Diptera, and Chironomidae relative 

abundances in macroinvertebrate communities in selected streams of the Mountain Northern Rockies (MT-NROCK) ecoregion, 

1992–2000. Taxa represented in this figure include rare and common taxa occurring at sites within these MT-NROCK ecoregion 

streams. Clusters identified as I-UNCLUSTERED correspond to clusters of macroinvertebrate assemblages within the MDS 

ordination for this ecoregion (fig. 15). Clusters identified as “Unclustered Communities” did not group significantly during the 

cluster analysis.

Number of samples in each cluster

7 3 1 4

0

20

40

60

80

100

120

140

Unclustered

Mountain Northern Rockies Ecoregion (MT-NROCK) Cluster

Baetis/Ephemeroptera

Hydropsychidae/Trichoptera

Chironomidae/Diptera 

Orthocladiinae/Chironomidae

Average relative abundance metric, in percent

I II III IV V A B C

Standard deviation
Appendix 3. 59

Figure 3-3. Average contribution of each Order, Ephemeroptera (E), Plecotpera (P), and Trichoptera (T), to EPT richness for 

macroinvertebrate communities in selected streams of the Mountain Southern Rockies (MT-SROCK) ecoregion, 1992–2000. 

Taxa represented in this figure include rare and common taxa occurring at sites within these MT-SROCK ecoregion streams. 

Clusters correspond to clusters of macroinvertebrate assemblages within the multidimensional scaling (MDS) ordination for this 

ecoregion (fig. 17). Clusters identified as “Unclustered Communities” did not group significantly during the cluster analysis. 

Number of samples in each cluster

7 3 1 4

I II III A

0

10

20

40

60

50

70

30

Unclustered

Ephemeroptera

Plecoptera

Trichoptera

Relative contribution of Ephemeroptera, Plecoptera,

and Trichoptera taxa to EPT index, in percent

Standard deviation

Mountain Southern Rockies Ecoregion (MT-SROCK) Cluster
60 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Number of samples in each cluster

7 3 1 4

I II III A

0

20

40

60

80

100

120

140

Unclustered

Baetis/Ephemeroptera

Hydropsychidae/Trichoptera

Chironomidae/Diptera 

Orthocladiinae/Chironomidae

Average relative abundance metric, in percent

Standard deviation

Mountain Southern Rockies Ecoregion (MT-SROCK) Cluster

Figure 3-4. Average relative abundance of selected taxa to Ephemeroptera, Trichoptera, Diptera, and Chironomidae relative 

abundances in macroinvertebrate communities in selected streams of the Mountain Southern Rockies (MT-SROCK) ecoregion, 

1992–2000. Taxa represented in this figure include rare and common taxa occurring at sites within these MT-SROCK ecoregion 

streams. Clusters identified as I-UNCLUSTERED correspond to clusters of macroinvertebrate assemblages within the MDS 

ordination for this ecoregion (fig. 17). Clusters identified as “Unclustered Communities” did not group significantly during the 

cluster analysis. 
Appendix 3. 61

Figure 3-5. Average contribution of each Order, Ephemeroptera (E), Plecotpera (P), and Trichoptera (T), to EPT richness for 

macroinvertebrate communities in selected streams of the Ozark Highlands (OH) ecoregion, 1992–2000. Taxa represented in this 

figure include rare and common taxa occurring at sites within these OH ecoregion streams. Clusters correspond to clusters 

of macroinvertebrate assemblages within the multidimensional scaling (MDS) ordination for this ecoregion (fig. 19). Clusters 

identified as “Unclustered Communities” did not group significantly during the cluster analysis.

Number of samples in each cluster

3 6 2 1 1 1 1

I II III A B C D

0

20

40

60

80

Unclustered Communities

Ozark Highlands Ecoregion (OH) Cluster

Ephemeroptera

Plecoptera

Trichoptera

Relative contribution of Ephemeroptera, Plecoptera,

and Trichoptera taxa to EPT index, in percent

Standard deviation
62 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Figure 3-6. Average relative abundance of selected taxa to Ephemeroptera, Trichoptera, Diptera, and Chironomidae relative 

abundances in macroinvertebrate communities in selected streams of the Ozark Highlands (OH) ecoregion, 1992–2000. Taxa 

represented in this figure include rare and common taxa occurring at sites within these OH ecoregion streams. Clusters identified 

as I-UNCLUSTERED correspond to clusters of macroinvertebrate assemblages within the MDS ordination for this ecoregion 

(fig. 19). Clusters identified as “Unclustered Communities” did not group significantly during the cluster analysis.

Number of samples in each cluster

3 6 2 1 1 1 1

I II III A B C D

0

20

40

60

80

100

120

140

Unclustered Communities

Ozark Highlands Ecoregion (OH) Cluster

Baetis/Ephemeroptera

Hydropsychidae/Trichoptera

Chironomidae/Diptera 

Orthocladiinae/Chironomidae

Average relative abundance metric, in percent

Standard deviation
Appendix 3. 63

Figure 3-7. Average contribution of each Order, Ephemeroptera (E), Plecotpera (P), and Trichoptera (T), to EPT richness for 

macroinvertebrate communities in selected streams of the Eastern Xeric Plateau (XE-EPLAT) ecoregion, 1992–2000. Taxa 

represented in this figure include rare and common taxa occurring at sites within these XE-EPLAT ecoregion streams. Clusters 

correspond to clusters of macroinvertebrate assemblages within the multidimensional scaling (MDS) ordination for this 

ecoregion (fig. 21). Clusters identified as “Unclustered Communities” did not group significantly during the cluster analysis.

Number of samples in each cluster

4 5 6 1 1

I II III A B

0

20

40

80

100

60

Unclustered Communities

Ephemeroptera

Plecoptera

Trichoptera

Eastern Xeric Plateaus (XE-EPLAT) Cluster

Relative contribution of Ephemeroptera, Plecoptera,

and Trichoptera taxa to EPT index, in percent

Standard deviation
64 Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Macroinvertebrates 

Figure 3-8. Average relative abundance of selected taxa to Ephemeroptera, Trichoptera, Diptera, and Chironomidae relative 

abundances in macroinvertebrate communities in selected streams of the Eastern Xeric Plateau (XE-EPLAT) ecoregion, 1992–

2000. Taxa represented in this figure include rare and common taxa occurring at sites within these XE-EPLAT ecoregion streams. 

Clusters identified as I-UNCLUSTERED correspond to clusters of macroinvertebrate assemblages within the MDS ordination for 

this ecoregion (fig. 21). Clusters identified as “Unclustered Communities” did not group significantly during the cluster analysis. 

Number of samples in each cluster

4 5 6 1 1

I II III A B

0

20

40

60

80

100

120

140

Unclustered Communities

Baetis/Ephemeroptera

Hydropsychidae/Trichoptera

Chironomidae/Diptera 

Orthocladiinae/Chironomidae

Average relative abundance metric, in percent

Standard deviation

Eastern Xeric Plateaus (XE-EPLAT) Cluster

Paul and others—The Occurrence of Trace Elements in Bed Sediment Collected from Areas of Varying Land Use and Potential Effects on Stream Macroinvertebrates in the Conterminous Western United States, Alaska, and Hawaii, 1992–2000—Scientific Investigations Report 2012–5272