Summary of Environmental Monitoring and 

Assessment Program (EMAP) Activities in 

South Dakota, 2000–2004

By Allen J. Heakin, Kathleen M. Neitzert, and Jeffrey S. Shearer

Prepared in cooperation with the 

South Dakota Department of Game, Fish and Parks and the 

U.S. Environmental Protection Agency

Scientific Investigations Report 2006-5007

U.S. Department of the Interior

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

Gale A. Norton, Secretary

U.S. Geological Survey

P. Patrick Leahy, Acting Director

U.S. Geological Survey, Reston, Virginia: 2006

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Suggested citation:

Heakin, A.J., Neitzert, K.M., and Shearer, J.S., 2006, Summary of Environmental Monitoring and Assessment 

Program (EMAP) activities in South Dakota, 2000–2004: U.S. Geological Survey Scientific Investigations 

Report 2006–5007, 45 p.
iii

Contents

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

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

Purpose and Scope ..............................................................................................................................2

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

Overview of the Environmental Monitoring and Assessment Program ...............................................3

EMAP Implementation in South Dakota............................................................................................3

Randomly Selected Sites............................................................................................................4

Candidate Reference Sites ........................................................................................................4

Availability of Data Sets.......................................................................................................................7

Methods and Activities...............................................................................................................................15

Methods for Characterization of Physical Stream Attributes .....................................................15

Reach Layout..............................................................................................................................15

Channel Dimensions and Bank Characteristics ...................................................................15

Thalweg Measurements...........................................................................................................16

Substrate Size and Type ...........................................................................................................16

Riparian Vegetation Cover and Structure..............................................................................17

Streamflow..................................................................................................................................17

Stream Gradient.........................................................................................................................18

Methods for Collecting Vertebrate Data.........................................................................................18

Seining.........................................................................................................................................19

Electrofishing..............................................................................................................................19

Methods for Collecting Invertebrate Data......................................................................................19

Benthic Macroinvertebrates ...................................................................................................20

Periphyton...................................................................................................................................20

Methods for Assessing Water Quality ............................................................................................21

Quality Assurance and Quality Control ..................................................................................21

Field Measurements..................................................................................................................21

Chemical Analysis......................................................................................................................22

Methods for Characterizing Geologic Influences on Stream Condition....................................22

Geologic Influences on Stream Condition...............................................................................................22

Basin Characteristics and Streamflow ...........................................................................................22

Water Quality.......................................................................................................................................24

Vertebrate Richness...........................................................................................................................24

Physical Habitat ..................................................................................................................................24

Vertebrate /Physical Habitat Associations.....................................................................................29

Summary........................................................................................................................................................29

References....................................................................................................................................................30

Supplemental Information..........................................................................................................................33
iv

Figures

1–3. Maps showing:

 1. Location of South Dakota EMAP randomly selected wadeable stream sites

visited during 2000–2003.......................................................................................................5

 2. Location of South Dakota EMAP candidate reference sites visited during 

2002–2004................................................................................................................................6

 3. Generalized geologic map showing surfical geology of a part of the White 

River Basin and location of multiple assessment sites in the study area..................14

4. Photograph showing field data were recorded on standardized field data sheets 

during field activities...........................................................................................................15

5. Diagram showing depiction of a stream reach layout. ........................................................16

6–13. Photographs showing:

 6. Field crew members laying out a transect......................................................................17

 7. Field crew members measured the wetted stream width to determine 

channel dimensions throughout the designated stream assessment reach. ...........17

 8. A field crew member making a stream discharge measurement at the 

“X-site.”.................................................................................................................................18

 9. Field crew biologists documented abnormalities visible on vertebrate 

specimens.............................................................................................................................18

 10. Vertebrate specimens, such as this Shorthead Redhorse, were measured 

following the collection and identification process. .....................................................19

 11. Field crew members identified vertebrate species while electrofishing. ...............19

 12. Field crew members processing benthic macro-invertebrates................................20

 13. Crew members calibrated water-quality instruments prior to collecting 

field measurements.............................................................................................................21

14–15. Graphs showing:

 14. Variations in annual, monthly, and daily mean streamflow for 

station 06446700, Bear-in-the-Lodge Creek near Wanblee, SD, water 

years 1995–2003...................................................................................................................25

 15. Variations in annual, monthly, and daily mean streamflow for 

station 06447230, Black Pipe Creek near Belvidere, SD, 

water years 1993–2003. ......................................................................................................26

16–18. Photographs showing:

 16. Examples of fish caught, identified, and measured at Bear-in-the-Lodge 

or Black Pipe Creeks include (A) channel catfish and (B) river carp sucker............27

 17. Bear-in-the-Lodge Creek, assessment sites: (A) upper site (site 1), 

(B) middle site (site 3), and (C) lower site (site 4)...........................................................28

 18. Upper Black Pipe Creek, assessment sites: (A) upper site (site 5), 

(B) middle site (site 6), and (C) lower site (site 8)...........................................................28
Tables

1. Stream assessment site information for South Dakota EMAP sites visited during

2000–2004. ......................................................................................................................................8

2. Information for sites used to characterize geologic influences.........................................23

3. General guidelines for consideration in selection of candidate reference sites ............34

4. Data reporting criteria for water chemistry analyses..........................................................35

5. Analytical methodologies for water chemistry......................................................................36

6. Water-quality data for sites on Bear-in-the-Lodge and Black Pipe Creeks. ....................38

7. Vertebrate information for Bear-in-the-Lodge Creek. ..........................................................39

8. Vertebrate information for Black Pipe Creek.........................................................................40

9. Physical habitat data for sites on Bear-in-the-Lodge Creek...............................................41

10. Physical habitat data for sites on Black Pipe Creek.............................................................43

11. Rapid habitat assessment ratings for sites on Bear-in-the-Lodge and Black Pipe

Creeks...........................................................................................................................................45

Conversion Factors and Datums

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 foot (ft2) 929.0 square centimeter (cm2)

square foot (ft2) 0.09290 square meter (m2)

square mile (mi2) 259.0 hectare (ha)

square mile (mi2) 2.590 square kilometer (km2) 

Flow rate

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

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 the North Geodetic Vertical Datum of 1929 

(NGVD 88).

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

Other abbreviations and acronyms used:

L liters

mL milliliters

μS/cm microsiemens per centimeter at 25 degrees Celsius

μm micron

DENR South Dakota Department of Environment and Natural Resources

EMAP Environmental Monitoring and Assessment Program

EMAP-West Environmental Monitoring and Assessment Program-West

GF&P South Dakota Department of Game, Fish and Parks

GPS Global Positioning System

NERL National Exposure Research Laboratory

NHEERL National Health and Environmental Effects Research Laboratory

USEPA U.S. Environmental Protection Agency

USGS U.S. Geological Survey

WED Western Ecology Division
Summary of Environmental Monitoring and Assessment 

Program (EMAP) Activities in South Dakota, 2000–2004

By Allen Heakin1, Kathleen M. Neitzert1, and Jeffrey S. Shearer2

Abstract

The U.S. Environmental Protection Agency (USEPA) 

initiated data-collection activities for the Environmental 

Monitoring and Assessment Program-West (EMAP-West) in 

South Dakota during 2000. The objectives of the study were 

to develop the monitoring tools necessary to produce unbiased 

estimates of the ecological condition of surface waters across 

a large geographic area of the western United States, and to 

demonstrate the effectiveness of those tools in a large-scale 

assessment.

In 2001, the U.S. Geological Survey (USGS) and the 

South Dakota Department of Game, Fish and Parks (GF&P) 

established a cooperative agreement and assumed responsibility for completing the remaining assessments for the perennial, wadable streams of the EMAP-West in the State. Stream 

assessment sites were divided into two broad categories—the 

first category of sites was randomly selected and assigned by 

the USEPA for South Dakota. The second category consisted 

of sites that were specifically selected because they appeared 

to have reasonable potential for representing the best available physical, chemical, and biological conditions in the State. 

These sites comprise the second category of assessment sites 

and were called “reference” sites and were selected following 

a detailed evaluation process. Candidate reference site data 

will serve as a standard or benchmark for assessing the overall 

ecological condition of the randomly selected sites.

During 2000, the USEPA completed 22 statewide stream 

assessments in South Dakota. During 2001–2003, the USGS 

and GF&P completed another 42 stream assessments bringing the total of randomly selected stream assessments within 

South Dakota to 64. In addition, 18 repeat assessments 

designed to meet established quality-assurance/quality-control 

requirements were completed at 12 of these 64 sites. During 

2002–2004, the USGS in cooperation with GF&P completed 

stream assessments at 45 candidate reference sites. Thus, 

109 sites had stream assessments completed in South Dakota 

for EMAP-West (2000–2004).

Relatively early in the EMAP-West stream-assessment 

process, it became apparent that for some streams in southcentral South Dakota, in-stream conditions varied considerably over relatively short distances of only a few miles. 

These changes appeared to be a result of geomorphic changes 

associated with changes in the underlying geology. For these 

streams, moving stream assessment sites short distances 

upstream or downstream had the potential to provide substantially different bioassessment data. In order to obtain a better 

understanding of how geology influences stream conditions, 

two streams located in south-central South Dakota were 

chosen for multiple stream sampling at sites located along 

their longitudinal profile at points where notable changes in 

geomorphology were observed. Subsequently, three sites on 

Bear-in-the-Lodge Creek and three sites on Black Pipe Creek 

were selected for multiple stream sampling using EMAP-West 

protocols so that more could be learned about geologic influences on stream conditions.

Values for dissolved oxygen and specific conductance 

generally increased from upstream to downstream locations 

on Bear-in-the-Lodge Creek. Values for pH and water temperature generally decreased from upstream to downstream 

locations. Decreasing water temperature could be indicative of 

ground-water inflows.

Values for dissolved oxygen, pH, and water temperature 

generally increased from upstream to downstream locations 

on Black Pipe Creek. The increase in temperature at the 

lower sites is a result of less dense riparian cover, and the 

warmer water also could account for the lower concentrations of dissolved oxygen found in the lower reaches of Black 

Pipe Creek. Values for specific conductance were more than 

three times greater at the lower site (1,342 microsiemens per 

centimeter (μS/cm)) than at the upper site (434 μS/cm). The 

increase probably occurs when the stream transitions from 

contacting the underlying Arikaree Formation to contacting 

the underlying Pierre Shale.

Vertebrate richness was found to be slightly higher for 

Bear-in-the-Lodge Creek than for Black Pipe Creek. On average, reaches on Bear-in-the-Lodge Creek had a deeper thalweg 

and wider wetted stream width than Black Pipe Creek. This 

resulted in a larger habitat volume of aquatic vertebrates in 

1 Bear-in-the-Lodge Creek than in Black Pipe Creek and prob- U.S. Geological Survey

2

South Dakota Department of Game, Fish and Parks.
ably is the reason for the slightly higher vertebrate richness 

found in Bear-in-the-Lodge Creek.

Average substrate size decreased in a downstream direction for Bear-in-the-Lodge Creek. In-stream fish cover also 

transitioned from woody debris to macrophytes in a downstream direction for Bear-in-the-Lodge Creek, whereas the 

predominate riparian cover transitioned from trees to barren 

dirt in the lower reaches. The stream channel for Bear-in-theLodge Creek largely consisted of riffles in the upper stream 

reaches and transitioned into glide or glide/riffle combinations 

in the lower reaches. Rapid habitat assessments metrics generally were scored as good except for sediment deposition and 

riffle frequency.

Average substrate size increased from silt to fine gravel 

in a downstream direction for Black Pipe Creek. In-stream 

fish cover was composed of overhanging vegetation and algae 

in the upper reaches and transitioned to macrophytes in the 

lower reaches. However, fish cover was sparse throughout 

all reaches. Riparian cover largely consisted of grasses and 

woody shrubs in the upper reaches of Black Pipe Creek and 

transitioned to grasses and bare dirt in the lower reaches. The 

stream channel was largely a glide in the upper reaches and 

transitioned to a glide/riffle in the middle reaches and to a 

series of interconnected pools in the lower reach. No rapid 

habitat assessments were completed for the upper reach, but 

the lower reaches were categorized as poor for most in-stream 

and near-stream conditions.

Introduction

The Environmental Monitoring and Assessment ProgramWest (EMAP-West) was initiated in South Dakota in 2000 

by the U.S. Environmental Protection Agency (USEPA). The 

two primary objectives of the surface-water component of the 

EMAP-West were to (1) develop the monitoring tools (biological indicators, stream survey design, and estimates of reference condition) necessary to produce unbiased estimates of the 

ecological condition of surface waters across a large geographic area of the West; and (2) demonstrate the effectiveness 

of those tools in a large-scale assessment (U.S. Environmental 

Protection Agency, 1998). Although not specifically defined as 

an objective, data collected during the EMAP-West also will 

help to establish a baseline for comparisons with data obtained 

from future monitoring efforts and could be used to document 

changing ecological conditions resulting from changing landuse or land-management practices associated with regulatory 

or restorative efforts.

Data collection for EMAP-West was generally limited to 

perennial streams and rivers; that is, those streams that maintain at least minimal flow throughout all but the driest climatic 

conditions. Two primary components of EMAP-West included 

assessments on wadeable streams and on larger, deeper rivers 

that typically cannot be waded. In South Dakota, all data collection on large rivers was completed by USEPA contractors 

using rafts. During 2000, USEPA employed contractors to 

collect data on wadeable streams. In 2001, the South Dakota 

Department of Game, Fish and Parks (GF&P) assumed the 

responsibility for overseeing Environmental Monitoring 

and Assessment Program (EMAP) activities that focused on 

wadable streams. GF&P subsequently initiated a cooperative 

agreement with the U.S. Geological Survey (USGS) to conduct the remaining assessments.

Through EMAP, USEPA, USGS, and GF&P have gained 

valuable information collected in a consistent manner that 

can be used to more accurately assess the condition of our 

Nation’s and South Dakota’s aquatic resources. Furthermore, 

bioassessment data obtained from EMAP may be used by 

the South Dakota Department of Environment and Natural 

Resources (DENR) to develop a set of biocriteria for South 

Dakota’s streams. Biocriteria are a set of narrative descriptions 

or numerical values that States and Tribes can include in their 

water-quality standards. The standards can be used along with 

the chemical and physical data routinely collected by States 

through their monitoring programs to better manage water 

resources (U.S. Environmental Protection Agency, 2002).

Purpose and Scope

The primary purpose of this report is to provide an overview of EMAP activities conducted in South Dakota during 

2000–2004. This report describes the activities and methods 

used to conduct assessments on wadable, perennial streams 

and presents information on the location of selected sites in 

South Dakota. It describes procedures for accessing the data 

sets, but does not provide a compilation of the exhaustive data 

sets.

This report also presents data collected as part of a 

special effort during 2004 for two streams, Bear-in-the-Lodge 

Creek and Black Pipe Creek, located in south-central South 

Dakota. Sampling was conducted at three points along each 

of these streams to demonstrate how changing geology along 

the longitudinal stream profiles substantially influences 

geomorphology and other associated stream conditions. Data 

pertaining to physical habitat, water chemistry, and vertebrate 

assemblages are presented. In addition, existing streamflow 

data available for Bear-in-the-Lodge and Black Pipe Creeks 

are summarized.

Acknowledgments

Numerous individuals from various agencies provided 

their assistance and support to the study. Specifically, Dennis Unkenholz of GF&P provided considerable guidance and 

expertise for fish identifications. Dr. Charles Berry of USGS 

coordinated the activities of several students who served on 

the field teams—most notably, Nathan Morey, Vaugn Wassink, 

Jason Kral, and Bryan Able who collected, field-identified, 

and enumerated most of the aquatic vertebrate samples. Ryan 

Thompson, John Clark, Kathy Converse, and Richard Hudson 

   Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
of the USGS collected the physical habitat data. Gene Stueven 

and Pat Snyder of the DENR, and Michael Kuck of the U.S. 

Department of Agriculture, Natural Resources Conservation 

Service, provided valuable assistance with the selection of 

potential candidate reference sites. The efforts of Tina Laidlaw, Karl Hermann, and David Peck of the USEPA also are 

greatly appreciated.

Overview of the Environmental 

Monitoring and Assessment Program

Historically, most of the data collected for USEPA to 

evaluate the condition of our Nation’s surface-water resources 

have consisted of physical and chemical data, which have been 

collected by States and Tribes using many different methods. 

These data have been compiled by USEPA and submitted to 

Congress in biennial reports called 305b reports (for section 

305b of the Clean Water Act).

In the late 1980s, USEPA began to re-evaluate the 

methods previously used to determine the condition of the 

Nation’s water resources. Several recommendations suggested 

that USEPA should collect data that could be used to evaluate 

environmental trends and identify potential problems in their 

infancy (U.S. Environmental Protection Agency, 1987a). This 

type of ecological “risk assessment” required development of 

a core set of indicators of ecological conditions that could be 

incorporated into the bioassessment process. A risk assessment can be defined as a process of assigning magnitudes and 

probabilities to the adverse effects of human activities (Suter, 

1993).

During the 1990s, USEPA conducted research and 

monitoring demonstrations through several regional studies, 

including the Mid-Atlantic Highlands Streams Assessment 

study, that helped to develop and refine many of the bioassessment monitoring techniques and designs used by EMAP-West 

(U.S. Environmental Protection Agency, 2000). However, for 

EMAP-West, some novel tools still had to be developed, primarily to address the large environmental variability encountered throughout the western States (U.S. Environmental 

Protection Agency, 1998).

In 2000, USEPA initiated EMAP-West with the primary 

purpose of developing the tools needed to measure the status 

and trends in the condition of the surface-water resources of 

the western United States. Special emphasis was placed on 

developing a core set of biological measurements that would 

provide reliable bioassessment data for the diverse stream 

conditions found throughout the West.

Bioassessments largely consist of surveys involving the 

collection, identification, and enumeration of aquatic biota 

(algae, invertebrates, and vertebrates) inhabiting a water body 

and often include estimates of areal density and a categorization of riparian vegetation. Current (2005) thinking is that 

when bioassessment data are combined with chemical and 

physical data, the ability to estimate the overall condition of a 

water body is enhanced, thereby providing more validity and 

usefulness to water-resources assessments, and a more factual 

representation of aquatic conditions to our Federal and State 

decisionmakers.

Physical changes occurring in a water body, such as 

fluctuations in temperature and sediment concentrations, or 

chemical changes, such as fluctuations in concentrations of 

nutrients or trace metals, can serve as stressors and result from 

both natural and anthropogenic sources. Even subtle changes 

in physical or chemical conditions can stress more sensitive 

members of the aquatic community. This can cause a shift 

in biological integrity that favors the less sensitive and more 

tolerant aquatic organisms over those that are more sensitive 

and less tolerant, thus providing the potential for lowering 

species diversity. Generally speaking, a water body with good 

biological integrity has the capacity to support a diverse and 

balanced community of organisms that are representative 

of the composition found in the natural habitat of the area. 

Therefore, reliable bioassessment data are required to make 

meaningful assessments of biological integrity, which in turn, 

is essential for providing accurate evaluations of the condition 

of our Nation’s surface-water resources.

The resource population of interest for EMAP-West was 

all perennial streams and rivers represented in USEPA’s River 

Reach File (RF3), with the exception of the lower portions of 

the “Great Rivers” (the Columbia, Snake, Colorado, and Missouri Rivers). Because it was neither economically feasible nor 

practical to sample all perennial streams, USEPA developed a 

probability design to randomly select stream assessment sites 

that would be statistically representative of the surface waters 

in the West. The design ensures that streams of all orders are 

included and that sites will be located throughout the region 

of interest (Stevens and Olsen, 2004). Thus, the probability of 

a stream site being selected for assessment is proportional to 

its length times the weight assigned for its order. EMAP also 

incorporated a systematic sampling grid, designed to provide 

a uniform spatial coverage, to ensure that each ecological 

resource is sampled in proportion to its geographical presence. By incorporating these two site selection processes into 

EMAP, USEPA believes it provides a valid mechanism that 

will allow for the extrapolation of results for streams within 

each State, and for streams in all regions that share similar 

ecological characteristics (Larsen, 1997).

EMAP Implementation in South Dakota

In 2004, DENR estimated that there were 10,298 mi of 

major rivers and streams in South Dakota, of which about 

7,360 mi or 71 percent have some sparse water-quality data 

available, largely as a result of compliance monitoring for 

305(b) reporting (http://www.state.sd.us/denr/document.htm). 

The GF&P and other cooperating agencies also have collected 

data related to the distribution and diversity of the State’s fish 

populations, especially in larger streams and rivers. However, 

for numerous other smaller order streams and tributaries, little 

Overview of the Environmental Monitoring and Assessment Program 
or no water quality or fish data are known to exist. Previous 

monitoring and stream assessment activities likely did not provide detailed data sets collected using consistent methods. Furthermore, the high level of effort associated with conducting 

complex data-collection activities in remote locations coupled 

with the costs associated with sample analysis would make indepth stream assessments impractical and cost prohibitive for 

the State without EMAP-West.

In South Dakota, data were collected for two different 

categories of sites: (1) randomly selected sites assigned for 

assessment by USEPA (fig. 1), and (2) candidate reference 

sites that were specifically selected for assessment (fig. 2). 

During 2000, USEPA completed sampling for 22 randomly 

selected sites (excluding repeat assessments) within South 

Dakota. During 2001–2003, the USGS and GF&P completed 

sampling for another 42 randomly selected sites assigned 

by USEPA, bringing the total to 64 sites. Eighteen repeat 

assessments were completed at 12 sites in accordance with 

the EMAP-West quality-assurance plan (U.S. Environmental 

Protection Agency, 1997b). During 2002–2004, the USGS and 

GF&P also completed stream assessments for 45 candidate 

reference sites. Thus, the total number of assessment sites 

in South Dakota during EMAP-West (2000–2004) was 109. 

Stream names and location information for assessment sites 

are summarized in table 1.

Relatively early in the EMAP-West stream assessment 

process, it became apparent that for some streams in southcentral South Dakota, in-stream conditions varied considerably over relatively short distances of only a few miles. These 

changes appeared to be a result of geomorphologic changes 

associated with changes in the underlying geology. For these 

streams, moving a stream assessment site short distances 

upstream or downstream had the potential to provide substantially different bioassessment data. In order to obtain a better 

understanding of how geology influences stream conditions, 

two streams located in south-central South Dakota were 

chosen for multiple stream sampling at sites located along 

their longitudinal profile at points where notable changes in 

geomorphology were observed. Subsequently, three sites on 

Bear-in-the-Lodge Creek and three sites on Black Pipe Creek 

were selected for multiple stream sampling so that more could 

be learned about the geologic influences on stream conditions 

(fig. 3).

A complete set of core ecological indicators established 

by USEPA were measured at each stream site whenever possible. The ecological indicators measured included (1) physical habitat (channel and riparian characterization), (2) instream characteristics (vegetation and frequency of riffles and 

pools), (3) aquatic vertebrate assemblages (fish, amphibians, 

and crayfish), (4) periphyton assemblages (algae), (5) benthic 

macroinvertebrate assemblages (aquatic organisms without 

backbones that can be seen with the naked eye), (6) field 

properties (water temperature, pH, dissolved oxygen, specific 

conductance, and streamflow), (7) water chemistry (major 

ions and nutrients), and (8) fish tissue contaminants. However, 

periphyton and macroinvertebrate samples were not collected 

for two sites on Bear-in-the-Lodge Creek and for two sites on 

Black Pipe Creek.

USEPA established an “index” period for stream assessments in an attempt to reduce the effects of temporal variations at selected sites. The index period in South Dakota was 

between June 1 and August 31, and was when most of the 

field work was completed during a 5-year period from 2000 

through 2004.

Field data were recorded on standardized data sheets 

(fig. 4) developed by the USEPA’s Western Ecology Division 

(WED) in Corvallis, Oregon. The completed data sheets were 

returned to WED, where they were optically scanned to facilitate quick entry of the data into the USEPA’s database and 

to minimize data entry errors. The WED also is responsible 

for tabulating, reviewing, and verifying the large volume of 

stream assessment data generated by field crews participating 

in EMAP-West.

Randomly Selected Sites

Once site location information for the randomly selected 

sites had been obtained from USEPA (coordinates for latitude 

and longitude in degrees, minutes, and seconds), the location of a site was plotted on a topographic map. The site was 

then field visited to confirm that the stream was representative of the target population (perennial and wadeable) and to 

determine the precise location of the site on the stream bank 

using maps and a Global Positioning System (GPS). Later, 

a field crew returned to the site to establish the length of the 

stream reach and to conduct the sampling. USEPA identified 

several alternate sites that could be substituted for assigned 

sites when reconnaissance visits indicated that they were 

unsafe (could not be waded), non-target, or dry, or because 

site access permission was denied. Sometimes alternate sites 

were substituted because errors in the sample selection process 

identified sample locations where no stream was present. 

These site selection errors were infrequent; however, they may 

represent a portion of the resource where no assessment data 

are available.

Samples were collected at 64 randomly selected sites 

during 2000–2003 (fig. 1; table 1). Twelve of these sites 

were selected for a total of 18 repeat assessments to provide 

estimates of important components of variability related to 

determining current status of the target population and trend 

detection.

Candidate Reference Sites

In order to provide a means for assessing the relative 

overall ecological condition of the randomly selected sites 

throughout South Dakota, it was necessary to establish some 

standard or benchmark for comparison purposes. Furthermore, 

estimates of reference condition are specifically included as 

part of objective 1 for the EMAP-West study design (U.S. 

Environmental Protection Agency, 1998). In South Dakota, 

   Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Figure 1. Location of South Dakota EMAP randomly selected wadeable stream sites visited during 2000–2003.

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S042

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S028

S012

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S061 S057

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S004

0 20 40 60 MILES

0 20 40 60 KILOMETERS

S061

Omernik level III ecoregions (Omernik, 1987) 

Northwestern Glaciated Plains 

Major Minor

Northwestern Great Plains 

Middle Rockies Northern Glaciated Plains 

Nebraska Sandhills Western Corn Belt Plains Lake Agassiz Plain Western High Plains 

EXPLANATION 

Site randomly selected—Number is site number 

Base from U.S. Geological Survey digital data, 1:100,000, 1979–1994Universal Transverse Mercator projection zones 13 and 14

Overview of the Environmental Monitoring and Assessment Program 
Figure 2. Location of South Dakota EMAP candidate reference sites visited during 2002–2004.

Cr

Grand

River 

River 

River 

River 

River 

River 

Keya 

James 

Big

East

West 

Sand

Crow 

Elm

Knoll

Platte

Medicine

Snake 

Fork 

Fork 

River 

River 

River 

Paha 

River 

RIVER

River 

White

Bad

Little

White

Moreau

L M. si os Riru .

Cheyenne

Belle

Fourche 

MISSOURI

L. Vermillion R

Vermillion

Sioux

L. Minnesota R

Maple

Elm

River River 

North

Fork 

Fork 

South

LaBelle Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Cr

Skunk

Brule

Wolf 

Turtle 

Rock 

Dry

Enemy

Choteau

Firesteel

Campbell

Medicine

Spring

Cr

Cr

Cr

Cottonwood

Cherry

Horsehead

Cr

Cr

Cr

Cr

Hat

White Clay Cr

Wounded Knee

Bear-in-the-Lodge

Black Pipe Cr

Antelope

Rosebud Cr

Lake 

Cr

Medicine

Cr

Battle

Cr

Spring

104o 103o 102o 101o 100o 99o 98o 97o

45o

44o

43o

S131

S130

S129

S128

S127

S126

S125

S124

S123

S122

S121

S120

S119

S118

S117

S116

S115

S114

S113

S112

S111

S110

S109

S108

S107

S106

S105

S104

S103

S102

S101

S100

S099

S098

S097

S096

S095

S094

S093 S092

S091

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S089

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S131

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S104

S103

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S101

S100

S099

S098

S097

S096

S095

S094

S093 S092

S091

S090

S089

S088

S087

0 20 40 60 MILES

0 20 40 60 KILOMETERS

S114 Candidate reference site —Number is site number 

EXPLANATION 

Omernik level III ecoregions (Omernik, 1987) 

Northwestern Glaciated Plains 

Major Minor

Northwestern Great Plains 

Middle Rockies Northern Glaciated Plains 

Nebraska Sandhills Western Corn Belt Plains Lake Agassiz Plain Western High Plains 

Base from U.S. Geological Survey digital data, 1:100,000, 1979–1994Universal Transverse Mercator projection zones 13 and 14

 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
this objective was accomplished by establishing a network 

of candidate reference sites. These sites were selected for 

assessment after preliminary field reconnaissance, when it was 

determined that they appeared to meet an established set of 

selection criteria, and appeared to have reasonable potential 

for representing the best available physical, chemical, and 

biological conditions within each of the four major Omernik 

Level III Ecoregions (Omernik, 1987) within the State (the 

Northern Glaciated Plains, the Northwestern Glaciated Plains, 

the Northwestern Great Plains, and the Middle Rockies). 

Basically, ecoregions can be defined as areas that share similar 

types of ecosystems and have similar environmental resources. 

Locations of the various Level III Ecoregions and locations of 

the 45 candidate reference sites where assessments were completed are shown in figure 2. Additional candidate reference 

site information is provided in table 1.

During 2002–2003, USGS and GF&P primarily were 

responsible for selecting candidate reference sites for assessment. However, assistance with site selection was provided by 

personnel from various State and Federal agencies, Tribal representatives, various water-resource professionals, and other 

interested parties. Potential candidate candidate reference sites 

were screened using criteria developed and agreed upon by 

representatives from the various agencies listed above. The 

list of candidate reference site screening criteria is provided in 

table 3 in the Supplemental Information section at the end of 

the report.

Once a list of viable candidate reference sites was created 

using the screening criteria, sites were field visited by a team 

of hydrologists and further evaluated using a field questionnaire. Candidate reference sites that passed the field screening 

were ranked by score and the sites with the highest scores 

were added to the site list, and those sites with lower scores 

were added to the list of alternate sites.

In 2004, USEPA provided USGS and GF&P with a list 

of additional candidate reference sites for assessment. The 

USEPA’s list of candidate reference sites was generated with 

a screening approach using Geographic Information System 

Technology, aerial photograph interpretation, and validation 

by field visits or best professional judgment. By the end of 

the 2004 field season, South Dakota’s candidate reference site 

network totaled 45 sites and included sites selected by both 

methods. As assessment data are made available, USEPA, 

GF&P, DENR, and USGS will further evaluate the data to 

determine if a site remains a viable candidate for the candidate 

reference site network or if it should be removed.

Availability of Data Sets

During 2000–2004, 109 stream assessments were completed in South Dakota as part of EMAP-West. After field 

activities were finished, field data sheets were sent to USEPA. 

The data sheets were scanned and compiled in a database 

in preparation for analysis. However, as of the date of this 

report, some of the data sets had not been verified and were 

not available. Eventually, all the data sets will be archived in 

the USEPA’s STOrage and RETrieval (STORET) database at 

http://www.epa.gov/storet. The EMAP Web site at http://www.

epa.gov/emap/html/dataI/index.html also contains a list of 

individuals that should be consulted prior to attempting data 

retrieval and acquisition. The USEPA currently (2005) is finalizing a report containing statistical summaries of the data sets 

that include an initial assessment of ecological condition for 

the entire United States. Plans also are underway to provide a 

more focused report that describes the data collected specifically for streams in the States comprising USEPA Region VIII.

Overview of the Environmental Monitoring and Assessment Program 
Table 1. Stream assessment site information for South Dakota EMAP sites visited during 2000–2004.

[EMAP, Environmental Monitoring and Assessment Program]

Site 

number 

(number 

refers to 

fig. 1 or 

fig. 2) Sample ID Site name

Latitude Longitude

County

Date(s) visited

(degrees, minutes, 

seconds) Visit 1 Visit 2 Visit 3 Visit 4

Randomly selected sites sampled 2000–2003

S001 WSDP99-0502 Whitewood Creek EMAP site near Englewood, SD 441716 1034727 Lawrence 07-18-00 07-18-03S002 WSDP99-0503 High Bank Creek EMAP site near Timber Lake, SD 453416 1010059 Corson 07-20-00 07-30-00 06-14-01 07-19-01S003 WSDP99-0507 Sand Creek EMAP site below Keyapaha, SD 430708 1000604 Tripp 07-30-00 07-02-03S004 WSDP99-0508 White Thunder Creek EMAP site near Bad Nation, SD 434118 1002612 Mellette 07-16-00S005 WSDP99-0509 Hay Creek EMAP site near Belle Fourche, SD 443856 1035414 Butte 07-09-00 06-11-03S006 WSDP99-0510 Moreau River EMAP site near Dewey County line in SD 451200 1013025 Ziebach 06-04-03S007 WSDP99-0512 Platte Creek EMAP site above Platte, SD 432449 0985239 Charles 

Mix

07-31-00 06-24-03

S008 WSDP99-0514 Eagle Nest Creek EMAP site near Wanblee, SD 433231 1014305 Jackson 07-15-00 06-16-03S009 WSDP99-0515 Lone Tree Creek EMAP site near Bison, SD 452532 1022100 Perkins 07-06-00S010 WSDP99-0516 Spring Creek EMAP site near Pollock, SD 455120 1001251 Campbell 07-06-00 06-25-03S011 WSDP99-0525 Antelope Creek EMAP site near Date, SD 451836 1024113 Perkins 07-07-00 05-03-03S012 WSDP99-0526 Grand River EMAP site above Black Horse Butte Creek, SD 454114 1015021 Corson 06-27-02S013 WSDP99-0543 Stink Creek EMAP site near Bullhead, SD 454749 1011134 Corson 06-05-03S014 WSDP99-0544 No Name Creek EMAP site near Wilmot, SD 452745 0965621 Roberts 07-01-03S015 WSDP99-0546 Ponca Creek EMAP site near Herrick, SD 430258 0991052 Gregory 08-12-03S016 WSDP99-0547 White River EMAP site near Okaton, SD 434546 1005003 Mellette 07-16-00 08-12-03S017 WSDP99-0548 Belle Fourche River EMAP site above Belle Fourche, SD 444333 1035811 Butte 06-12-03S018 WSDP99-0561 Beaver Creek EMAP site near Norbeck Lake in SD 433504 1032747 Custer 06-29-00 07-17-03S019 WSDP99-0579 White River EMAP site near Redshirt, SD 431714 1024903 Shannon 09-04-01S020 WSDP99-0580 Elk Creek EMAP site near Nemo, SD 441636 1033944 Lawrence 06-08-01S021 WSDP99-0581 Louse Creek EMAP site near Timber Lake, SD 454033 1012757 Corson 07-18-01S022 WSDP99-0582 Dupree Creek EMAP site near Carlin Flat, SD 444458 1011834 Ziebach 06-26-01

 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Site 

number 

(number 

refers to 

fig. 1 or 

fig. 2) Sample ID Site name

Latitude Longitude

County

Date(s) visited

(degrees, minutes, 

seconds) Visit 1 Visit 2 Visit 3 Visit 4

Randomly selected sites sampled 2000–2003—Continued

S023 WSDP99-0585 Spring Creek EMAP site near Rapid City, SD 435915 1031931 Pennington 06-19-01S024 WSDP99-0586 Elk Creek EMAP site above Elm Springs, SD 441459 1023830 Meade 06-21-01S025 WSDP99-0587 South Fork of Grand River EMAP site near Buffalo, SD 453412 1033702 Harding 06-12-01S026 WSDP99-0588 Smith Creek EMAP site near Kimball, SD 435353 0990210 Brule 07-13-01S027 WSDP99-0589 Mud Creek EMAP site near Groton, SD 452419 0980332 Brown 07-12-01S028 WSDP99-0590 Turkey Ridge Creek EMAP site near Centerville, SD 430820 0970034 Turner 07-11-01 07-26-01 07-11-02 07-25-02S029 WSDP99-0593 Alkali Creek EMAP site near Sturgis, SD 442309 1031643 Meade 06-07-01S030 WSDP99-0594 Thunder Butte Creek EMAP site near Thunder Butte, SD 451656 1015542 Ziebach 06-26-01S031 WSDP99-0596 Whetstone Creek EMAP site near Bonesteel, SD 431047 0990235 Gregory 08-03-01S032 WSDP99-0599 White River EMAP site near Rockyford, SD 432903 1023039 Shannon 06-19-02S033 WSDP99-0602 Bear Butte Creek EMAP site near Sturgis, SD 442829 1031312 Meade 06-11-01S034 WSDP99-0603 Unnamed Creek EMAP site near Timber Lake, SD 453033 1010505 Corson 07-17-01S035 WSDP99-0604 Big Creek EMAP site near Oacoma, SD 434920 0992704 Lyman 07-10-01S036 WSDP99-0605 Ponca Creek EMAP site near Burke, SD 430919 0992156 Gregory 07-25-01S037 WSDP99-0657 Spring Creek EMAP site below Sheridan Lake in SD 435914 1032505 Pennington 06-05-02S038 WSDP99-0658 White River EMAP site near Jackson County line in SD 434148 1020949 Shannon 06-17-03S039 WSDP99-0660 Cottonwood Creek EMAP site near Presho, SD 434038 1000530 Tripp 07-10-02S040 WSDP99-0664 North Fork of Moreau River EMAP site, SD 452012 1032039 Harding 06-26-02S041 WSDP99-0665 Moreau River EMAP site, SD 450914 1023548 Perkins 06-25-02S042 WSDP99-0666 Bad River EMAP site near Capa, SD 440646 1005702 Jones 07-09-02S043 WSDP99-0667 Pipestone Creek EMAP site near Minnesota border in SD 435110 0963041 Moody 07-23-02S044 WSDP99-0669 Hat Creek EMAP site near Rumford, SD 430803 1033752 Fall River 06-06-02 06-18-02 06-10-03 08-13-03S045 WSDP99-0670 Spring Creek EMAP site above Little White River in SD 430509 1010225 Todd 07-12-02

Table 1. Stream assessment site information for South Dakota EMAP sites visited during 2000–2004.—Continued

Overview of the Environmental Monitoring and Assessment Program 
Site 

number 

(number 

refers to 

fig. 1 or 

fig. 2) Sample ID Site name

Latitude Longitude

County

Date(s) visited

(degrees, minutes, 

seconds) Visit 1 Visit 2 Visit 3 Visit 4

Randomly selected sites sampled 2000–2003—Continued

S046 WSDP99-0672 Grand River EMAP site below Black Horse Butte Creek, SD 453957 1014214 Corson 06-12-02S047 WSDP99-0674 Beaver Creek EMAP site above Beaver Lake in SD 430110 0972730 Yankton 07-24-02S048 WSDP99-0678 Little White River EMAP site at White River, SD 433415 1004545 Mellette 07-18-02S049 WSDP99-0679 Bad River EMAP site at Capa, SD 440624 1005814 Jones 07-09-02S050 WSDP99-0681 Moreau River EMAP site near Imogene, SD 450812 1024848 Perkins 06-13-02S051 WSDP99-0695 Cheyenne River EMAP site, 1.5 mile east of Edgemont, SD 431849 1034712 Fall River 06-18-02S052 WSDP99-0696 Little White River EMAP site near Soldier Creek, SD 432000 1005323 Todd 07-17-02S053 WSDP99-0697 Elk Creek EMAP site near Bend, SD 441459 1031022 Meade 06-04-02S054 WSDP99-0698 White Shirt Creek EMAP site near McIntosh, SD 454615 1011636 Corson 06-11-02S055 WSDP99-0501 Medicine Root Creek EMAP site below Kyle, SD 433149 1021355 Shannon 07-11-00S056 WSDP99-0505 Cobb Creek EMAP site near Brandt, SD 444148 0963351 Deuel 06-28-00S057 WSDP99-0506 Wolf Creek EMAP site near Bridgewater, SD 433015 0973229 McCook 06-30-00S059 WSDP99-0521 Bull Creek EMAP site above SD-NE State line in SD 430110 1005205 Todd 07-25-00S060 WSDP99-0522 Porcupine Creek EMAP site at Sharps Corner, SD 432256 1022320 Shannon 07-11-00S061 WSDP99-0523 Eagle Nest Creek EMAP site near Wanblee, SD 433837 1014659 Jackson 07-13-00S062 WSDP99-0527 Artichoke Creek EMAP site at Missouri River near Agar, SD 445353 1002118 Sully 07-22-00S063 WSDP99-0533 Turkey Ridge Creek EMAP site near Turkey Ridge, SD 431540 0971503 Turner 06-28-00S064 WSDP99-0540 Spring Creek EMAP site below Rockerville, SD 435611 1030914 Pennington 07-06-00S065 WSDP99-0541 Bear-in-the-Lodge Creek EMAP site near Potato Creek, SD 433140 1014749 Jackson 07-14-00

Candidate reference sites sampled 2002–2004

S087 WSDP02-R001 Firesteel Creek EMAP reference site near Firesteel, SD 453147 1011921 Corson 07-23-02S088 WSDP02-R002 Swan Creek EMAP reference site near Akasaka, SD 451923 1001137 Walworth 07-24-02

10 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004 Table 1. Stream assessment site information for South Dakota EMAP sites visited during 2000–2004.—Continued
Site 

number 

(number 

refers to 

fig. 1 or 

fig. 2) Sample ID Site name

Latitude Longitude

County

Date(s) visited

(degrees, minutes, 

seconds) Visit 1 Visit 2 Visit 3 Visit 4

Candidate reference sites sampled 2002–2004—Continued

S089 WSDP02-R003 Medicine Knoll Creek EMAP reference site near Canning, 

SD

442632 1000001 Hughes 07-25-02

S090 WSDP02-R004 Rock Creek EMAP reference site near Valentine, NE 430516 1003214 Todd 07-31-02S091 WSDP02-R005 Bear-in-the-Lodge Creek EMAP reference site near Wanblee, 

SD

433226 1014832 Jackson 07-30-02

S092 WSDP02-R006 East Fork Vermillion River EMAP reference site near Monroe, SD 432932 0970938 Turner 08-01-02S093 WSDP02-R007 Twelvemile Creek EMAP reference site near Ethan, SD 433148 0975546 Hanson 08-02-02S094 WSDP02-R008 Spring Creek EMAP reference site near Greenwood, SD 425421 0981520 Charles 

Mix

08-06-02

S095 WSDP02-R009 Choteau Creek EMAP reference site near Avon, SD 425402 0980702 Charles 

Mix

08-06-02

S096 WSDP02-R010 Emanuel Creek EMAP reference site near Springfield, SD 425133 0975638 Bon 

Homme

08-07-02

S097 WSDP02-R011 Peterson Creek EMAP reference site near Canton, SD 432053 0963236 Lincoln 08-08-02S098 WSDP02-R012 Chekapa Creek EMAP reference site near Grenville, SD 453051 0971329 Roberts 08-13-02S099 WSDP02-R013 West Fork Lac qui Parle River EMAP reference site near 

Gary, SD

444700 0962813 Deuel 08-14-02

S100 WSDP02-R014 Peg Munky Run EMAP reference site near Estelline, SD 443455 0964812 Deuel 08-14-02S101 WSDP02-R015 Stray Horse Creek EMAP reference site near Castlewood, SD 444402 0965709 Hamlin 08-14-02S102 WSDP02-R016 West Pipestone Creek EMAP reference site near Sherman, 

SD

434522 0963256 Minnehaha 08-16-02

S103 WSDP03-R017 Castle Creek EMAP reference site near Deerfield Lake in SD 440230 1035156 Pennington 07-07-03S104 WSDP03-R018 Turtle Creek EMAP reference site near confluence at Wolf 

Creek in SD

444313 0983743 Spink 07-16-03

S105 WSDP03-R019 Turkey Ridge Creek EMAP reference site near Turkey Ridge, 

SD

431530 0971428 Turner 07-31-03

Overview of the Environmental Monitoring and Assessment Program 11

Table 1. Stream assessment site information for South Dakota EMAP sites visited during 2000–2004.—Continued
Site 

number 

(number 

refers to 

fig. 1 or 

fig. 2) Sample ID Site name

Latitude Longitude

County

Date(s) visited

(degrees, minutes, 

seconds) Visit 1 Visit 2 Visit 3 Visit 4

Candidate reference sites sampled 2002–2004—Continued

S106 WSDP03-R020 Pass Creek EMAP reference site near Hwy 44 in SD 433801 1012723 Jackson 07-08-03S107 WSDP03-R021 Lake Creek EMAP reference site near Lacreek National 

Wildlife Refuge in SD

430448 1014004 Bennett 08-05-03

S108 WSDP03-R022 Blackpipe Creek EMAP reference site near Hwy 63 in SD 433005 1011200 Mellette 07-10-03S109 WSDP03-R023 Blackhorse Butte Creek EMAP reference site near Meadow, 

SD

453350 1015527 Corson 07-22-03

S110 WSDP03-R025 Owens Creek EMAP reference site near Ortley, SD 452055 0971232 Roberts 07-24-03S111 WSDP03-R026 Cain Creek EMAP reference site near confluence at James 

River in SD

441552 0981155 Beadle 07-15-03

S112 WSDP03-R027 Enemy Creek EMAP reference site below Mitchell, SD 433743 0980217 Davison 07-17-03S113 WSDP03-R028 Wolf Creek EMAP reference site near Wolf Creek Colony, 

SD

432305 0973620 Hutchinson 07-30-03

S114 WSDP03-R029 Keya Paha River EMAP reference site near Hidden Timber, 

SD

431130 1001859 Todd 08-06-03

S115 WSDP03-R032 Elm Creek EMAP reference site near Westport, SD 454002 0983111 Brown 07-29-03S116 WSDP04-R033 High Bank Creek EMAP reference site near Little Eagle, SD 453733 1005426 Corson 06-22-04S117 WSDP04-R034 Clarks Fork Creek EMAP reference site near Buffalo, SD 453256 1032255 Harding 06-03-04S118 WSDP04-R035 Little White River EMAP reference site south Hwy 44 near 

White River, SD

432851 1004548 Mellette 07-08-04

S119 WSDP04-R036 Little White River EMAP reference site at Ghost Hawk Park, 

near Rosebud, SD

431554 1005402 Todd 07-06-04

S120 WSDP04-R038 South Fork Grand River EMAP reference site near Buffalo, 

SD

453707 1032031 Harding 06-02-04

S121 WSDP04-R040 Eagle Nest Creek EMAP reference site near Interior, SD 434049 1014644 Jackson 06-14-04S122 WSDP04-R041 Black Pipe Creek EMAP reference site north Hwy 44 near 

Norris, SD

433822 1011255 Mellette 06-09-04

S123 WSDP04-R044 Plum Creek EMAP reference site near Cherry Creek, SD 443559 1012744 Haakon 06-21-04

12 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004 Table 1. Stream assessment site information for South Dakota EMAP sites visited during 2000–2004.—Continued
Site 

number 

(number 

refers to 

fig. 1 or 

fig. 2) Sample ID Site name

Latitude Longitude

County

Date(s) visited

(degrees, minutes, 

seconds) Visit 1 Visit 2 Visit 3 Visit 4

Candidate reference sites sampled 2002–2004—Continued

S124 WSDP04-R045 South Fork Grand River EMAP reference site above Buffalo, 

SD

453324 1033944 Harding 06-04-04

S125 WSDP04-R046 Pass Creek EMAP reference site near Kadoka, SD 434126 1012807 Jackson 06-07-04S126 WSDP04-R047 South Fork Moreau River EMAP reference site below Zeona, 

SD

450801 1025030 Perkins 06-01-04

S127 WSDP04-R048 Bear-in-the-Lodge Creek EMAP reference site below Wanblee, SD 433338 1014821 Jackson 06-05-04S128 WSDP04-R049 Little White River EMAP reference site near Spring Creek, 

SD

430631 1010613 Todd 07-07-04

S129 WSDP04-R050 West Fork Vermillion River EMAP reference site near Stanley Corner, SD 433240 0972115 McCook 07-09-04S130 WSDP04-R051 Flandreau Creek EMAP reference site near Flandreau, SD 440428 0962754 Moody 07-01-04S131 WSDP04-R052 Oak Creek EMAP reference site near Mahto, SD 454406 1003654 Corson 06-23-04

Overview of the Environmental Monitoring and Assessment Program 13

Table 1. Stream assessment site information for South Dakota EMAP sites visited during 2000–2004.—Continued
Figure 3. Generalized geologic map showing surficial geology of a part of the White River Basin and location of multiple 

assessment sites in the study area.

SOUTH DAKOTA

Study

area

White

Little

White

River 

Porcupine 

Medicine

Eagle Nest

Craven 

Long

Pass 

Red

Stone

Black 

Pipe

Root

Creek 

Creek 

Creek 

Creek 

Creek 

Creek 

Creek 

Creek 

Creek 

River 

Bear-in-the-lodge

MELLETTE COUNTY

JONES COUNTY

BENNETT COUNTY TODD COUNTY

PENNINGTON COUNTY JACKSON COUNTY

JACKSON COUNTY

SHANNON COUNTY

Base from U.S. Geolgoical Survey digital data 1:100,000 

Kadoka, 1980, Martin, 1983, Mission, 1982, and Wall, 1981 

Universal Transverse Mercator projection, zone 13 

Geology modified from Martin and others, 1:500,000, 2004 

102o15' 102o00' 101o45’ 101o30’ 101o15' 101o00' 100o45'

44o00'

43o45'

43o30'

43o15'

0 10 20 KILOMETERS

0 10 20 MILES

Middle White River Basin boundary 

Quaternary units 

Surficial geology 

Tertiary units 

Cretaceous units 

EXPLANATION 

Alluvium

Colluvium

Terrace deposits 

Gravel deposits 

Eolian deposits 

Ogallala Formation (Pliocene) 

Batesland Formation (Miocene) 

Arikaree Formation (Miocene) 

White River Group (Oligocene and Eocene) 

Pierre Shale (Upper Cretaceous) 

Fox Hills Sandstone (Upper Cretaceous) 

Qal

Qal

Qc

Qc

Qe

Qe Qe

Qe

Qe

Qe

Qe

Qe

Qt

Qt

Qt

Qt

Qt

Qt

Tg

Tg

To

To

To

To

Tb

Tb

Ta

Ta

Ta

Ta

Ta

Tw

Tw

Tw

Tw

Tw

Tw

Kfh

Kfh

Kfh

Kp

Kp

Kp

Kp

Kp

Kp

Tg

Qal

2004 EMAP

reference site

1

2

3

4

8

7

6

5

2004 EMAP

reference site

Continuous-record streamflow-gaging station— 

 Number indicates site number (table 2) 

Surface-water-quality sampling site—Number

 indicates site number (table 2) 

Stream assessment sites

1

2

14 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Figure 4. Field data were recorded on standardized field data 

sheets during field activities.

Methods and Activities

This section of the report contains an overview of EMAP 

methods for data collection and a description of the types 

of data collected during stream assessments. Methods are 

described for characterizing physical stream attributes, collecting vertebrate and invertebrate data, and assessing water 

quality. Methods used to characterize geologic influences on 

stream conditions also are described.

Methods for Characterization of Physical 

Stream Attributes

Most of the methods used for assessing stream condition 

during EMAP-West were developed during previous EMAP 

studies conducted by USEPA. The methods were developed 

jointly by investigators working at the USEPA’s National 

Exposure Research Laboratory (NERL) in Cincinnati, Ohio, 

and by the National Health and Environmental Effects 

Research Laboratory (NHEERL) in Corvallis, Oregon.

The methods described in this section of the report are 

taken from Peck and others (2003). A more thorough discussion of the following methods can be found in that document.

Reach Layout

One of the first tasks for characterization of physical stream attributes was for the field crew to establish the 

sampling reach. To ensure that an accurate representation of 

environmental conditions and biota are obtained, a sufficient 

stream length needs to be sampled. Previous studies conducted 

by USEPA have shown that assessing a stream reach that 

is equivalent to 40 channel widths in length will generally 

yield about 90 percent of the fish species present (Reynolds 

and others, 2003). Similar considerations for other factors 

led to development of EMAP protocol that stream reaches 

should be at least 40 channel-widths long or a minimum of 

150 meters (m), whichever is longer.

The randomly selected site location coordinates (latitude 

and longitude) provided by USEPA were designated as the 

“X-site.” For each stream site, the mean wetted width at the 

X-site was determined and then multiplied by 40 to get the 

total length of the stream reach to be assessed (fig. 5). The 

stream reach was then divided into 11 equally spaced transects, five upstream and five downstream from the X-site, 

creating 10 segments that were each four stream-widths long 

(fig. 6). In cases where the wetted width of the stream at 

the X-site was fairly narrow (less than 3.75 m), each of the 

10 segments was assigned a length of 15 m. Therefore, either 

process produced 10 equally spaced segments separated by 

11 transects that were subsequently labeled from A to K. Typically, the A transect represented the most downstream transect 

and K represented the most upstream transect. The middle or 

F transect typically represented the location of the X-site.

Channel Dimensions and Bank Characteristics

At each of the 11 stream transects (labeled A to K; fig. 5) 

the wetted width of the stream was measured and recorded on 

field forms in order to determine channel dimensions present 

throughout the designated stream assessment reach (fig. 7). 

Measurements of channel width allow for the determination 

of the stream’s structural complexity and when coupled with 

depth measurements, provide a mechanism for estimating 

stream volume throughout the reach.

Bank characteristics include several measurements such 

as estimates of bank angle, undercutting, and bankfull flow 

during base-flow conditions. Bank angle is determined for 

both banks at each of the 11 transects. To accomplish this, a 

rod was laid on the bank with one end at the water’s edge, then 

a clinometer was placed on the rod to obtain the bank angle.

Measurements of bank characteristics also include 

estimates of the extent of bank undercutting, channel incision, 

and height of bankfull flow above the present water-surface 

elevation. The extent of bank undercutting was determined 

by measuring the horizontal distance from the deepest point 

of the undercut to a point on the end of the protruding overhang of the bank to where a vertical plumb line would hit the 

water’s surface. The length of the measured section provides 

an estimate of the extent of bank undercutting.

An estimate of channel incision was obtained when a 

surveyor’s rod was held perpendicular to the water surface just 

at the edge of the water. Channel incision was determined to 

be the height up from the water’s surface to the first terrace of 

the valley floodplain. Height estimates generally were determined only by sighting.

Estimates for the height of bankfull flow above the present base-flow water level were made by placing a surveyor’s 

rod at the water’s edge while observing the physical evidence 

Methods and Activities 15
A

B

C

D

E

F G H

I

J

K

Total reach length = 40 times mean wetted width at X-site (minimum = 150 meters)

Distance between transects = 4 times

mean wetted width at X-site

SAMPLING POINTS

L = Left C = Center R = Right

First point (transect A)

determined at random

Subsequent points assigned

in order L, C, R

C

C

C

C

L

L

L

L R

R

R

FLOW

X-site

Figure 5. Depiction of a stream reach layout (reproduced from Environmental Monitoring and Assessment 

Program-Western Pilot field manual courtesy of U.S. Environmental Protection Agency).

Figure 6. Field crew members laying out a transect.

on the stream banks, then estimating their elevation using 

the rod. Physical evidence consisted of locating areas where 

stream sediments transitioned to terrestrial vegetation. Other 

examples of physical evidence include the presence of moss 

on rocks along the bank and the presence of drift material 

deposited along the bank and on the overhanging vegetation. 

After identifying areas of bankfull flow on each bank, the 

width of the stream was measured between the two points and 

recorded. This allowed for calculation of stream volume at 

bankfull flow.

Thalweg Measurements

The term “thalweg” refers to the deepest portion of the 

stream channel. Typically, depth measurements were collected 

at 100 to 150 equally spaced points throughout the reach, and 

the resulting data can be used to construct a thalweg profile, 

which provides a longitudinal representation of channel depth. 

The depth measurements also can provide valuable information about stream size and channel complexity as well as the 

location and relative size of riffles and pools. During thalweg 

measurements, the location and width of sand or gravel bars 

also were noted and recorded.

The number of depth measurements and spacing between 

them was based on the wetted width of the stream at each transect. At places where the pools were too deep to be waded, a 

calibrated surveyor’s rod was rested on the bottom of the pool, 

and a clinometer was laid on the rod to measure the angle of 

insertion. The depth reading from the rod also was recorded. 

Using those two values, a pool depth was calculated.

Substrate Size and Type

Characterization of the substrate is a critical component 

of any bioassessment because the substrate size and type (silt, 

sand, gravel, and cobbles) have a large influence on the composition and diversity of aquatic invertebrates and vertebrates 

inhabiting a stream. Substrate size also has a direct influence 

on both hydraulic roughness and stream velocity. Furthermore, 

a large percentage of fine sediments can provide an indication 

16  Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Figure 7. Field crew members measured the wetted stream 

width to determine channel dimensions throughout the designated 

stream assessment reach.

of the extent that erosional processes are occurring upstream, 

and sometimes can be linked to anthropogenic activities such 

as logging, mining, and farming within the drainage basin.

To provide an accurate determination of substrate size 

and type, bed materials were categorized into various classes 

and sizes according to classifications provided by the U.S. 

Environmental Protection Agency (2001). Determinations of 

substrate size and type were made at five locations along each 

transect (5-point pebble-counts), at points equal to 100 (right 

stream bank), 75, 50, 25, and 0 percent (left stream bank) of 

the wetted width of the individual transect. Five-point pebblecounts also were made at locations midway between established transects so that data were collected from 21 transects at 

a total of 105 points along the stream reach.

The extent (average percent) of embeddedness also 

was estimated at points where substrate size and type were 

measured, but only at transects A through K. At these points, 

embeddedness was estimated within the area of a circle 

approximately 10 centimeters (cm) in diameter. Embeddedness is an estimate of the extent that bed materials are buried 

in bottom sediments that are the size of sand grains (0.06–

2 millimeters (mm) in diameter) or smaller; thus, sands and 

silts were considered to be 100-percent embedded, whereas 

bedrock and hardpan were considered to be 0-percent embedded.

Riparian Vegetation Cover and Structure

Riparian vegetation has important influences on stream 

condition. Tall trees provide a canopy over the stream that provides shade and lowers water temperature. Leaves from overhanging trees fall into the stream and become food for aquatic 

insects and provide a source of particulate organic material 

for other organisms. Limbs from these trees also fall into the 

stream and provide additional organic material and habitat for 

insects, algae, and fish. Terrestrial vegetation provides bank 

stability that can reduce sediment loading. The presence of 

non-native or invasive species of plants or agricultural crops 

within the riparian corridor also provides a means of assessing 

potential effects of anthropogenic activities.

Stream canopy cover was measured using a spherical 

convex canopy densiometer. Measurements were made at 

mid-channel, right edge of water, and left edge of water on all 

11 transects (A–K). Readings were made holding the densiometer 0.3 m above the water surface while facing upstream, right 

bank, downstream, and left bank.

Terrestrial vegetation and structure were estimated for 

three conceptual layers near or above the stream—the canopy 

layer consisting of vegetation greater than 5 m in height, the 

understory layer consisting of vegetation from 0.5 to 5 m in 

height, and the ground cover layer consisting of vegetation less 

than 0.5 m in height. At the mid-channel point of each transect, an area was visualized that extended 5 m upstream and 

5 m downstream and 10 m out from both stream banks. Within 

these two areas, visual estimates were made to determine the 

dominant vegetation type and areal extent for each of the three 

layers. Various keys were used to assist with the identification 

of trees and non-native or invasive plants.

Streamflow

The EMAP study design established an index period 

for conducting stream assessments that roughly runs from 

the beginning of June through the end of August. The intent 

of establishing this index period was to conduct assessments 

under steady or base-flow conditions. Sampling during highflow conditions likely would produce different chemical and 

biological data than those obtained during stable base-flow 

conditions. Furthermore, it is difficult and potentially dangerous to conduct assessments when the water is high and turbid. 

No assessments were made when streams appeared to be 

approaching bankfull levels, or when streams where located in 

very remote areas where recent rainfall made access difficult. 

Visits to sites were rescheduled when unfavorable conditions 

were encountered.

Streamflow was determined at most assessment sites 

(fig. 8) at the Xsite coordinates provided by USEPA using 

methods established by USGS (Rantz and others, 1982). 

Streamflow at some sites could not be measured because the 

water level was too low to measure. For those sites, only visual 

estimates of streamflow were provided. Some sites consisted 

of only a series of intermittent pools of varying sizes and subsequently only estimates, or no streamflow data, were reported 

for those sites.

Stream Gradient

The velocity of a stream is greatly influenced by stream 

gradient. Increases in stream gradient increase velocity, 

thereby increasing the stream’s ability to erode and transport 

Methods and Activities 17
Figure 8. A field crew member making a stream discharge 

measurement at the “X-site.”

Figure 9. Field crew biologists documented abnormalities visible 

on vertebrate specimens.

sediments. Changes in gradient along the longitudinal profile 

of a stream also enhances the diversity and complexity of the 

aquatic habitat. As velocity increases, streamflow changes 

from laminar to turbulent flow. The resulting turbulent flow 

helps facilitate the exchange of gases between the stream and 

the atmosphere.

Measurement of stream gradient was completed by a twoperson team with each person having a surveyor’s pole flagged 

at exactly the same height. Measurements were made starting 

at the downstream end of the reach and were accomplished by 

backsiting. For example, one person would stand at the water’s 

edge at transect A while the other person would stand at the 

water’s edge at transect B. Team members used a clinometer 

to measure the percent slope between the two transects. One 

person would stand at the upstream transect and hold the clinometer at the previously flagged level on their pole and backsite to the flagged level on the downstream pole and record the 

percent slope between the two points. This process would be 

repeated by moving upstream until the gradient between each 

successive transect was measured. At points where there was 

no direct line of site between transects, intermediate measurements were made and recorded at points between transects.

Methods for Collecting Vertebrate Data

The purpose of collecting vertebrate data was to determine their relative abundance throughout the assessment reach 

and to identify any obvious external abnormalities present 

on the specimens (fig. 9). Trained biologists from GF&P or 

from South Dakota State University conducted the sampling 

and identification activities. Following identification, fish 

were measured, inspected, and returned to the stream as soon 

as possible (fig. 10). State or Federally listed species were 

photographed on a measuring board next to a card containing 

the stream name and date of collection, then were immediately 

returned to the water. Overall, mortality rates generally were 

very low. Some specimens that proved difficult to identify in 

the field were sent to the Smithsonian Institution in Washington, D.C., for identification. Only amphibians and fish were 

counted; reptiles were not included in the tallies. Crayfish also 

were tallied when collected to provide information related to 

potentially introduced species.

Voucher specimens were collected whenever possible. 

These specimens will provide a permanent, archived, historical record of fish collections. After the required data were 

recorded, selected specimens were anesthetized, placed in 

nylon mesh bags, then put into a labeled jar containing a 

formalin preservation solution. Some vouchered samples were 

used for analysis of fish tissue contaminants. All vouchered 

samples were shipped to the National Museum of Natural 

History in Washington, D.C., for confirmation of identification 

and for permanent cataloging.

All areas between established transects were sampled 

unless they were too deep to wade or the pools were to small 

and shallow to hold any targeted organisms. Vertebrate 

samples were collected using either seining or electrofishing 

18  Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Figure 10. Vertebrate specimens, such as this Shorthead 

Redhorse, were measured following the collection and 

identification process.

Figure 11. Field crew members identified vertebrate species 

while electrofishing.

methods. Seining was used when streams appeared turbid, 

when field measurements indicated that stream conductivity was too high for electrofishing, or when the presence of 

Topeka Shiners (an endangered species) was possible.

Seining

A two-person seine with a mesh size of 0.6 cm was used 

when stream conditions dictated. Seining began at the downstream end of the reach (A transect) and proceeded upstream. 

Riffle, pool, and snag habitats were sampled when present. As 

seining progressed to the next transect upstream, the contents 

of the seine were dumped into buckets and the biologists 

began tallying and recording the data. This procedure was 

repeated until the crew reached the final upstream (K) transect. 

Electrofishing

Most of the vertebrate samples were collected by seining. However, a Smith-Root model 12-B, P.O.W. backpack 

electrofishing unit (DC pulsed; volts 100 to 600; pulse rate of 

60 hertz and a pulse width of 2-6 milliseconds) was used at 

several stream assessment sites where conductivities generally were low and the water was clear (fig. 11). Electrofishing 

in large streams typically required the efforts of all four team 

members. Team members in the stream wore waders and rubber gloves to prevent being shocked. Netters were careful not 

to touch the water or the anode while the shocking unit was 

operating. The person operating the backpack shocker often 

held the anode in one hand and a dip net in the other hand 

(fig. 11) and typically worked a net from the middle of the 

stream over to the right bank, while a second person worked a 

net from the middle of the stream to the left bank. A third person followed behind the operator with yet another net. Netted 

vertebrates were placed in buckets carried along by the netters 

in the stream and were later emptied into larger buckets positioned on shore at the next upstream transect. The fourth team 

member stayed on the bank and initiated the identification and 

enumeration process. Shocking proceeded in a similar manner 

as seining, from downstream to upstream. Two people could 

complete the electrofishing on small creeks and streams.

Methods for Collecting Invertebrate Data

Aquatic invertebrate samples collected during EMAPWest consisted of both benthic and periphyton macroinvertebrates. Both of these macroinvertebrates serve as very useful 

indicators of aquatic condition because they tend to respond 

rapidly to changing environmental conditions, often in very 

different ways (Fore and others, 1996). The type of response 

can sometimes be linked to a particular type of stressor such as 

nutrient enrichment or exposure to toxic metals, herbicides, or 

other forms of aquatic contamination.

Because benthic macroinvertebrates are not very mobile, 

are relatively easy to catch, and often live in the aquatic environment for a year or more, they provide a convenient method 

for assessing the biological integrity of a stream. Therefore, 

much can be learned about the short-term history of in-stream 

conditions by looking at benthic macroinvertebrate species 

diversity and community composition.

Methods and Activities 19
Figure 12. Field crew members processing benthic macroinvertebrates.

Benthic Macroinvertebrates

The term “benthic macroinvertebrate” generally is used 

to describe organisms that live in the bottom substrate of freshwater environments during part of their life cycle. For many 

years, the usefulness of benthic macroinvertebrate data for 

assessing stream conditions was not fully appreciated. However, recent advances associated with quantitative sampling 

methods, analytical processes, taxonomy, and identification 

methodology, followed by the compilation of toxicological 

data related to species’ response to pollution, have all served 

to strengthen the case for making benthic macroinvertebrate 

data an integral part of biomonitoring programs. Although 

the costs of collecting benthic macroinvertebrate samples are 

relatively low, large numbers of organisms are needed in order 

to provide more precise estimates of population abundance, 

and substantial costs can be incurred as a result of sample 

processing and identification (Rosenberg and Resh, 2001). 

The USEPA has recognized the importance of benthic macroinvertebrate data for assessing stream condition and biological 

integrity and has incorporated data-collection and analysis 

activities into the EMAP stream assessment process (Klemm 

and others, 1990).

Two types of benthic macroinvertebrate samples were 

collected—reach-wide and targeted riffle. The reach-wide 

samples were collected at the same time and from the same 

locations where periphyton samples were collected. Samples 

were collected using a 500-micron (μm) mesh D-frame kick 

net that had an opening width of 12 in. The opening of the net 

was placed facing upstream so that the current swept dislodged 

organisms into the net. A 1-ft2 area directly in front of the 

net was visualized, and all loose rocks and substrate particles 

(larger than a golf ball) that were more than halfway inside 

the 1-ft2 area were picked up and scrubbed with a brush so 

that any dislodged organisms were carried into the net by the 

current. Cleaned rocks were then returned to the stream bed 

outside the 1-ft2 area in front of the net. The substrate area in 

front of the net was then vigorously disturbed for 30 seconds 

by kicking. Samples were rinsed into a bucket and composited 

with reach-wide samples obtained from the other transects.

Targeted riffle samples were collected using methods 

described for reach-wide samples. However, a minimum of 

eight 1-ft2 areas were required for a sample to be collected. 

Multiple areas on a single riffle could be sampled to obtain the 

eight samples necessary in the event that the reach consisted 

largely of pool-glide type habitat. All eight targeted riffle 

samples were combined into a single composite sample prior 

to processing.

Sample processing for reach-wide and targeted riffle 

samples consisted of screening samples of each type through 

a 500-μm mesh sieve (fig. 12) to remove as much debris and 

sediment as possible. Rinse bottles filled with stream water 

were used to facilitate this process. Samples were then rinsed 

into containers labeled as reach-wide or targeted riffle and 

preserved with 95-percent ethanol.

Periphyton

Periphyton encompasses several types of aquatic organisms including algae, fungi, bacteria, protozoans, and other 

organic matter. For EMAP, periphyton samples were collected from both erosional and depositional habitats and then 

composited into a single reach-wide sample for processing. 

Erosional habitats consisted of rapidly flowing areas of the 

stream such as riffles where submerged rocks or woody debris 

were present. Depositional habitats consisted mostly of pools 

where flows were diminished.

Sampling started at the most downstream (A) transect and 

proceeded upstream. The starting position on the A transect 

was randomly selected from one of three positions (right 

bank, left bank, center channel) and alternated as sampling 

progressed upstream. Thus, if the right bank was randomly 

selected for the A transect, periphyton would be collected 

from the B transect at the left bank position and from the 

C transect at the center channel position alternating until all 

11 transects were sampled (fig. 5).

For riffle habitats, a delimeter with an inside area of 

12 square centimeters (cm2) was placed on the upper surface 

of a rock that was completely submerged, and the area was 

brushed with a toothbrush for about 30 seconds and then the 

scrubbed area was rinsed through a funnel into a 500-milliliter (mL) bottle and composited. For depositional areas, the 

delimeter was placed on the stream bed, and the top 1 cm of 

bottom material within the delimited area was sucked into a 

60-mL syringe and composited.

After sampling, a 50-mL aliquot of the composite was put 

into a small sealable container and preserved with a 10-percent 

formalin solution and labeled “identification and enumeration” 

sample. Another 50-mL aliquot of the composite was placed 

in another small sealable container and labeled “acid/alkaline 

20 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Figure 13. Crew members calibrated water-quality instruments 

prior to collecting field measurements.

phosphatase activity,” and the sample was placed on ice. A 

third aliquot consisting of 25 mL of the composite sample 

was filtered through a glass fiber filter, and the filter and 

filtrate were placed into a small sealable container and labeled 

“biomass sample” then placed on ice. A fourth aliquot consisting of 25 mL of the composite sample was filtered through a 

glass-fiber filter, and the filter and the filtrate were placed in 

another small resealable container and labeled “chlorophyll 

sample,” then put in a resealable bag and placed on ice.

Methods for Assessing Water Quality

Two methods were used to assess stream-water quality 

for EMAP-West. Field measurements were made using submersible multi-probe instrumentation that provided instantaneous in situ measurements of stream-water quality for four 

properties: (1) dissolved oxygen, (2) pH, (3) specific conductance, and (4) water temperature. Field measurements were 

made at the approximate location of the centroid of flow at the 

X-site (F transect; fig. 5).

Aliquots of stream water also were collected and sent 

to WED for analysis. Water samples were collected by team 

members wearing latex surgical gloves to prevent sample 

contamination. Samples were collected from the centroid of 

flow and put into a 4-liter (L) acid rinsed container that was 

completely filled to remove any trapped air. The container 

was tightly sealed, labeled, and placed immediately on ice. 

Samples were shipped in a cooler filled with ice to USEPA 

by an express service. Following receipt, the chilled water 

sample was filtered and preserved by USEPA, generally 

within 72 hours of sample collection. Concentrations of trace 

elements, major ions, nutrients, and turbidity were measured 

from aliquots taken from this sample.

Additional water samples were collected in two 50-mL 

sterile syringes that were held underwater and filled, and 

then held upright while the air was ejected from the syringe. 

Syringe water was used largely for the analysis of pH and 

dissolved inorganic carbon. Specially designed teflon syringe 

locks were used to protect samples from exchanging carbon 

dioxide with the atmosphere. Filled and locked syringes were 

labeled, sealed into special shipping containers, placed in the 

ice chest, and sent with the other time-dependant samples to 

USEPA.

Quality Assurance and Quality Control

Quality assurance is a required element of all USEPAsponsored studies that involve the collection and analysis 

of environmental samples (U.S. Environmental Protection 

Agency, 2003). This meant that all participants of the field 

teams received in-depth training on methods and procedures 

from USEPA or from experienced USGS personnel that had 

successfully completed the training and had previously served 

as field crew members. All field crew members also were 

provided with copies of the EMAP-West field manual and 

the quality-assurance plan (U.S. Environmental Protection 

Agency, 1997). Field team leaders also were provided with 

phone numbers of USEPA contacts that could provide additional guidance and information.

Twelve sites (approximately 15–20 percent) were revisited for repeat assessments, either during the same field season 

or during successive field seasons, to assess the variability and 

precision of the various methods used to measure ecological 

indicators (Larsen, 1997). Furthermore, annual field audits 

were conducted by USEPA personnel during actual stream 

visits, and the entire stream assessment process was evaluated 

for compliance with EMAP methods and protocols.

Field Measurements

Field measurements were completed using submersible 

multi-probe water-quality instruments that were calibrated 

each time they were used (fig. 13). Instrument calibration followed guidelines established by the manufacturer and guidelines for field measurements outlined in the USGS National 

Field Manual for the Collection of Water-Quality Data (U.S. 

Geological Survey, 1997–2004). All calibration data were 

recorded in logbooks that accompanied each instrument into 

the field and included the operator’s observations about instrument performance and maintenance. USGS employees with 

the responsibility of collecting water-quality data generally 

receive 2 weeks of intensive training at the USGS National 

Training Center in Denver, Colorado, where they learn the 

theories and methods used for the collection of ground-water 

and surface-water samples. USGS field personnel that routinely collect field measurement data that are entered into 

the national database also are required to participate in the 

National Field Quality Assurance Program that audits the 

performance of instruments and operators on at least an annual 

basis (Stanley, 1996).

Methods and Activities 21
Calibration standards were purchased from the USGS 

Quality of Water Service Unit in Ocala, Florida, or from the 

National Water Quality Laboratory in Denver, Colorado. 

Prior to calibration, an aliquot of stream water was analyzed, 

and then calibration standards were selected that bracketed 

the expected value for the stream water. The instrument was 

then calibrated using the appropriate standard(s). Only valid 

standards were used for instrument calibration; standards that 

exceeded expiration dates were discarded. Standards for pH 

and specific conductance were immersed in the stream for 

about 20 minutes prior to instrument calibration so that the 

temperature of the stream and the standards were similar. 

Generally, two-point calibrations were used for pH and 

specific conductance. Measurements generally were recorded 

on field sheets when the instrument stabilized and when two 

consecutive readings varied by less than 0.3 milligram per 

liter for dissolved oxygen, 0.1 pH unit, 5 percent for specific 

conductance, and 0.2°C for water temperature.

Chemical Analysis

The chemical analysis of stream water samples was 

completed by the USEPA or their contract laboratories. A list 

of associated data reporting criteria and methods used for the 

chemical analysis of water samples are presented in tables 4 

and 5, respectively, in the Supplemental Information section 

(U.S. Environmental Protection Agency, written commun., 

2005). That communication also summarizes the methods for 

the collection, handling, processing, analysis, and management of EMAP data.

Methods for Characterizing Geologic Influences 

on Stream Condition

Geology can have a substantial influence on the natural 

conditions of a stream and further complicates the evaluation 

of human influences on stream condition. One obvious example of this occurs when streams transition from mountainous 

reaches with steep gradients to plains reaches with lesser gradients. More subtle changes can occur in other settings as well. 

A series of field surveys, incorporating many of the methods 

previously described for conducting stream assessments for 

the EMAP-West, were conducted at several predetermined 

points along the longitudinal profile of two streams—Bear-inthe-Lodge and Black Pipe Creeks—in order to demonstrate 

the geologic influences on stream condition.

Physical habitat and vertebrate data were collected at 

three sites along the longitudinal profiles of Bear-in-theLodge Creek and Black Pipe Creek (fig. 3) during a one-time 

assessment in 2004, in order to document differences between 

upstream sites and downstream sites with respect to in-stream 

and near-stream conditions. Along with physical habitat and 

vertebrate data, water chemistry data were collected only at 

the middle site on each stream. Site number and site type are 

provided in table 2.

The middle site on each stream was selected by USEPA 

as an assessment site for EMAP-West. Data-collection 

activities at these two sites (table 2, sites 3 and 6) included 

assessments of physical, chemical, and biological conditions. Samples for the analysis of water chemistry and benthic 

macroinvertebrate assemblages were collected by the USGS at 

these two sites and sent to USEPA for analysis. Data-collection activities at the other four stream assessment sites (table 2, 

sites 1, 4, 5, and 8) included similar assessments of physical 

habitat and vertebrate identification and enumeration; however, only field properties were measured to determine basic 

water quality, and no samples were submitted to the USEPA 

for the analysis of water chemistry.

Geologic Influences on Stream 

Condition

This section describes the results of assessments conducted on two streams in south-central South Dakota—Bearin-the-Lodge and Black Pipe Creeks. These assessments were 

conducted in order to demonstrate the geologic influences on 

stream conditions. Basin characteristics, streamflow, water 

quality, vertebrate richness, and physical habitat are described.

Basin Characteristics and Streamflow

The drainage basins for Bear-in-the-Lodge Creek 

includes portions of the Western High Plains and the Northern 

Great Plains ecoregions, while the drainage basin for Black 

Pipe Creek lies entirely within the Northern Great Plains 

ecoregion (fig. 2). A series of benches and buttes, underlain 

by Tertiary sandstones, siltstones, and shale is present in the 

southern portion of the study area (Malo, 1997). Silts and 

clays of the White River Group of Tertiary-age (Oligocene 

and Eocene) are present in the northern part of the study area 

(fig. 3).

The drainage basin of Bear-in-the-Lodge Creek encompasses approximately 365 mi2

. The elevation at the assessment site on upper Bear-in-the-Lodge (site 1) is about 2,570 ft 

above NGVD 29, and the elevation at the lower site (site 4) is 

about 2,280 ft above NGVD 29. The drainage basins of both 

streams are entirely within a single hydrologic unit (fig. 3) as 

designated by the hydrologic unit map for the State of South 

Dakota (U.S. Geological Survey, 1978). The headwaters of 

Bear-in-the-Lodge Creek are located in northwestern Bennett County in an area where intermittent eolian deposits and 

remnants of the Pliocene-age Ogallala Formation overlie 

the Miocene-age Arikaree Formation (fig. 3). The Ogallala 

Formation is a fine- to medium-grained sandstone containing 

some silty clay; the Arikaree Formation is an interbedded calcareous sand, silt, and clay (Ellis and Adolphson, 1971). The 

stream flows to the southeast and then abruptly turns north 

and flows northwest through Jackson County where it crosses 

22 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Table 2. Information for sites used to characterize geologic influences.

[USGS, U.S. Geological Survey; USEPA, U.S. Environmental Protection Agency; EMAP, Environmental Monitoring and Assessment Program]

Site number

(fig. 3) USGS station number Site name Site type

1 433151101480700 Upper Bear-in-the-Lodge Creek USGS stream assessment site 

2 06446700 Bear-in-the-Lodge Creek near Wanblee, SD USGS streamflow gaging station (not a stream 

assessment site)

3 433338101482100 Bear-in-the-Lodge Creek USEPA/EMAP reference site

4 434027101502600 Lower Bear-in-the-Lodge Creek USGS stream assessment site

5 432735101100300 Upper Black Pipe Creek USGS stream assessment site

6 433822101125500 Black Pipe Creek USEPA/EMAP reference site

7 06447230 Black Pipe Creek near Belvidere, SD USGS streamflow gaging station (not a stream 

assessment site)

8 434633101134000 Lower Black Pipe Creek USGS stream assessment site

the White River Group just prior to joining the White River. 

The White River Group is a poorly consolidated siltstone and 

claystone containing some beds of fine-grained sand (Ellis and 

Adolphson, 1971).

The drainage basin of Black Pipe Creek encompasses 

approximately 250 mi2. Elevations range from about 2,530 ft 

above NGVD 29 (site 5) at upper Black Pipe Creek to about 

2,020 ft above NGVD 29 at the lower site (site 8). The headwaters of Black Pipe Creek are located in northeast Bennett 

County, in an area where intermittent eolian deposits overlie the Arikaree Formation. Some remnants of the Ogallala 

Formation also are present in the area. The stream flows to 

the northeast into Mellette County where it flows across the 

outcrop of the White River Group. The stream turns north and 

then makes contact with isolated outcrops of terrace deposits 

of Quaternary age. The stream turns and flows to the northwest across outcrops of the Late Cretaceous-age Pierre Shale. 

The Pierre Shale is a dark gray marine shale and mudstone 

containing some layers of bentonite (Ellis and Adolphson, 

1971). The stream then flows across various isolated outcrops 

consisting of alluvium or eolian deposits just prior to joining 

the White River near the Jackson and Mellette County line.

The climate, which is characteristic of the northern Great 

Plains, is semi-arid with cold winters and hot summers. The 

following climate data was obtained from the South Dakota 

State University (2005). Most of the precipitation falls during 

the growing season between April and September. Climatological data available for Martin, South Dakota (located about 

20 miles south of the study area), for the period 1971–2000 

indicate that May is typically the wettest month with an average of 3.36 in. of precipitation, and December typically is the 

driest month with an average of 0.3 in. of precipitation. The 

average annual air temperature for the period 1971–2000 is 

about 47.3°F, with an average of 72.8°F for July and an average of 22.0°F for January.

Much of western South Dakota has been in a persistent 

drought since the latter part of the 1990s. Hydrologic conditions for water year 2004 (October 1, 2003, through September 30, 2004) were much different than the wetter conditions 

experienced during the mid- to early 1990s, and generally 

resulted in precipitation and streamflow levels that were well 

below normal throughout much of western South Dakota. The 

2004 U.S. drought monitor map (National Oceanographic and 

Atmospheric Administration, 2004) showed that the lower 

one-third of South Dakota, which includes the study area, was 

under severe to extreme drought conditions at the time the 

stream assessments were conducted during June 2004. As a 

result, most perennial streams probably experienced reduced 

streamflow due to extended period of intense drought conditions.

The USGS has operated streamflow gaging stations on 

Bear-in-the-Lodge and Black Pipe Creeks (fig. 3) for several 

years. Streamflow data have been collected at continuous gaging station 06446700, Bear-in-the-Lodge Creek near Wanblee, 

SD (table 2, site 2), for water years 1995 through 2003 and are 

presented graphically in figure 14. Streamflow data also have 

been collected at continuous gaging station 06447230, Black 

Pipe Creek near Belvidere, SD (table 2, site 7), from 1993 to 

2003 and are presented graphically in figure 15. The annual 

mean streamflow is 24.3 ft3/s at site 2 and 32.1 ft3/s at site 7 

(Burr and others, 2004).

Stream assessment sites on Bear-in-the-Lodge Creek 

were visited during June 15–16, 2004, and at that time, 

streamflow at the upper site (site 1 in fig. 3) measured 

Geologic Influences on Stream Condition 23
6.83 ft3

/s. Streamflow at site 3, the candidate reference site 

selected by USEPA, measured 7.13 ft3/s, and streamflow 

at site 4 measured 5.92 ft3/s. Streamflow data presented in 

graph B of figure 14 indicate that the monthly mean streamflow for June at the streamflow gaging station (site 2) for the 

period of record is about 50 ft3/s. Measured streamflow at all 

three sites on Bear-in-the-Lodge Creek was less than the 10th 

percentile of values recorded for June at site 2 for the period of 

record.

Sites on Black Pipe Creek were visited during June 8–9, 

2004, and at that time, streamflow at the upper site (site 5 in 

fig. 3) measured 1.45 ft3/s. Streamflow at site 6, the candidate reference site selected by USEPA, measured 0.38 ft3

/s, 

and streamflow at site 8 was estimated visually as 0.01 ft3/s. 

Streamflow data presented in graph B of figure 15 indicate 

that the monthly mean streamflow for June at site 7 for the 

period of record is about 68 ft3/s. The streamflow measurement for site 5 fell between the 10th and 25th percentiles of 

the June values; however, streamflow measurement for sites 6 

and 8 were less than the 10th percentile of values recorded at 

the streamflow gaging station site on Black Pipe Creek during 

the period of record.

Water Quality

Full sets of samples for the characterization of streamwater chemistry were collected only at site 3 on Bear-in-theLodge Creek and at site 6 on Black Pipe Creek. These two 

sites were selected by USEPA because they met their preliminary candidate reference site screening criteria. Results 

of the water-quality analyses are provided in table 6 in the 

Supplemental Information section. A summary of the analytical methodologies used for determination of stream-water 

chemistry are provided in table 5. Field measurements were 

completed for all six sites and also are included in table 6.

Values for dissolved oxygen and specific conductance 

generally increased from upstream to downstream locations on 

Bear-in-the-Lodge Creek. Values for pH and water temperature generally decreased from upstream to downstream locations. Decreasing water temperatures could be an indication of 

ground-water inflows.

Values for dissolved oxygen, pH, and water temperature 

generally increased from upstream to downstream locations on 

Black Pipe Creek. Most notably, values for specific conductance increased from 434 microsiemens per centimeter at 

25 degrees Celsius (μS/cm) at site 5 to 1,342 μS/cm at site 8, 

probably as a result of contact with the underlying Pierre 

Shale.

Vertebrate Richness

Vertebrate data collected from three reaches on Bearin-the-Lodge Creek and three reaches on Black Pipe Creek 

during June 2004 are provided in tables 7 and 8, respectively, 

in the Supplemental Information section. Overall, Bear-in-theLodge Creek had a slightly larger richness of vertebrate species than Black Pipe Creek. The total number of fish (excluding crayfish) caught from all three reaches also was much 

higher at Bear-in-the-Lodge Creek (547) than at Black Pipe 

Creek (147). More fish were found at the lower site (site 4) on 

Bear-in-the-Lodge Creek than at sites farther upstream. Proximity of site 4 to the confluence with the White River might 

help to explain the high number of fish caught. Relatively 

large fish ranging from 183 mm at the upper site to 532 mm at 

the lower site were found in Bear-in-the-Lodge Creek.

Black Pipe Creek had slightly lower species richness 

overall than Bear-in-the-Lodge Creek. A slightly larger richness of vertebrate species was found at the lower site (site 8) 

on Black Pipe Creek than at the two upstream sites. Proximity 

of site 8 to the confluence with the White River might help 

to explain the higher richness. Fish such as channel catfish 

(310 mm) and river carpsucker (152 mm) were found only at 

the lower site. These fish are common to the main stem White 

River (Fryda, 2001) and tended to be some of the larger fish 

caught in Black Pipe Creek. Examples of fish caught, identified, and measured at Bear-in-the-Lodge Creek or Black Pipe 

Creek are shown in figure 16.

Physical Habitat

Physical habitat data collected from three reaches on 

Bear-in-the-Lodge Creek (fig. 17) and three reaches on Black 

Pipe Creek (fig. 18) during June 2004 are provided in tables 9 

and 10, respectively, in the Supplemental Information section. 

In addition to the physical measurements and determinations, 

rapid habitat assessments also were used to characterize the 

habitat of both streams. Table 11 contains the responses of the 

field crews to their visual assessment of stream habitat and 

the area immediately adjacent to the stream. The procedures 

used for the rapid habitat assessment follow those originally 

described by Barbour and others (1999).

Substrate particle size for each site was characterized by 

averaging the 5-point pebble counts collected at 11 transects. 

Similar measurements also were made at points midway 

between established transects so that data were collected from 

21 transects at a total of 105 points along the stream reach. 

Average substrate particle size for each site was the mean 

of size class for the 105 total pebble counts. Upper Bear-inthe-Lodge Creek (site 1, table 2 and fig. 17A) has an average 

substrate composition generally consisting of coarse to fine 

gravels that gradually transitions to silt and clays at site 3. 

The substrate largely is composed of hardpan and silt and clay 

at site 4. Thus, average substrate sizes decreased in a downstream direction.

Fish cover at the upper site largely is composed of 

overhanging vegetation and woody debris. The predominant 

fish cover at site 3 (fig. 17B) is composed of woody debris 

and macrophytes and then transitions to macrophytes at site 4 

(fig. 17C).

24 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Figure 14. Variations in annual, monthly, and daily mean streamflow for station 06446700, Bear-in-the-Lodge Creek near Wanblee, SD, water years 1995–2003.

1

10

100

STREAMFLOW, IN CUBIC FEET PER SECOND

A. Annual mean flow B. Distribution of monthly mean flow

1995 1996 1997 1998 1999 2000 2001 2002 2003

FLOW, IN CUBIC FEET PER SECOND FLOW, IN CUBIC FEET PER SECOND

OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP

0.1

1

10

100

1,000

0.1

1

10

100

1,000

OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP

0.1

1

10

100

1,000

D. Duration hydrographs of daily mean flow

DISCHARGE, IN CUBIC FEET PER SECOND

C. Duration curve of daily mean flow

PERCENT OF TIME INDICATED VALUE WAS EQUALED OR EXCEEDED

1 0.1 2 5 10 20 30 40 50 60 70 80 90 95 98 99 99.9

Percent

of time

Flow, in

cubic feet

per second

959075502510

5

2.64.37.5

13.023.040.066.0

Maximum90th percentile75th percentileMean50th percentile25th percentile10th percentileMinimum

Maximum75 percent50 percent25 percentMinimum

Geologic Influences on Stream Condition 25
Figure 15. Variations in annual, monthly, and daily mean streamflow for station 06447230, Black Pipe Creek near Belvidere, SD, water years 1993–2003.

1

10

1,000

100

STREAMFLOW, IN CUBIC FEET PER SECOND

A. Annual mean flow B. Distribution of monthly mean flow

1993 1994 1995 1996 1997 1998 1999 2002 2000 2001 2003

FLOW, IN CUBIC FEET PER SECOND FLOW, IN CUBIC FEET PER SECOND

OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP

0.01

1

10

0.1

100

1,000

10,000

0.01

1

10

0.1

100

1,000

10,000

OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP

0.01

0.1

1

10

100

1,000

D. Duration hydrographs of daily mean flow

DISCHARGE, IN CUBIC FEET PER SECOND

C. Duration curve of daily mean flow

PERCENT OF TIME INDICATED VALUE WAS EQUALED OR EXCEEDED

1 0.1 2 5 10 20 30 40 50 60 70 80 90 95 98 99 99.9

Percent

of time

Flow, in

cubic feet

per second

959075502510

5

0.310.80

2.78.4

23.087.0

199.0

Maximum90th percentile75th percentileMean50th percentile25th percentile10th percentileMinimum

Maximum75 percent50 percent25 percentMinimum

26  Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Figure 16. Examples of fish caught, identified, and measured at Bear-in-the-Lodge or Black Pipe Creeks include (A) channel 

catfish and (B) river carp sucker.

A B

Riparian cover consisted of sparse to moderate densities 

of big and small trees and grasses at the upper site on Bear-inthe-Lodge Creek. The predominate riparian cover transitioned 

to grasses at site 3 and was largely composed of barren dirt at 

the lower site (table 9).

Thalweg depths and wetted widths varied among sites on 

Bear-in-the-Lodge Creek and showed no trend in relation to 

stream size. The average maximum thalweg depth for all transects at the upper site (site 1) was 42.8 cm. The largest maximum thalweg depth measurement at this site was 62 cm at 

transect J, and the smallest maximum thalweg depth measurement at this site was 23 cm at transect H. The average wetted 

width of the reach was 3.9 m, with a minimum width of 2.6 m 

at transect D and a maximum width of 5.3 m at transect I.

The average maximum thalweg depth for all transects at 

the middle site (site 3) was 79.7 cm. The largest maximum 

thalweg depth measurement at this site was 120 cm at transect I, and the smallest maximum thalweg depth measurement 

at this site was 38 cm at transect J. The average wetted width 

of site 3 was 4.0 m, with a minimum width of 2.9 m at transect 

H and a maximum width of 5.5 m at transect I.

The average maximum thalweg depth for all transects 

at the lower site (site 4) was 51.4 cm. The largest maximum 

thalweg depth measurement recorded at this site was 90 cm at 

transect I, and the smallest maximum thalweg depth measurement at this site was 30 cm at transects A, B, and C. The 

average wetted width of site 4 was 5.7 m, with a minimum 

width of 4.4 m at transect C and a maximum width of 7.2 m at 

transect J.

The stream channel was characterized as largely consisting of riffles at site 1, and transitioned into a glide throughout 

most of the transects at site 3. Site 4 was characterized as 

either a glide or glide/riffle combination throughout the reach.

Rapid habitat assessments for Bear-in-the-Lodge Creek 

tended (table 11) to rate this stream between optimal and 

sub-optimal for most categories. Bank stability and vegetative 

protection tended to decline somewhat at the middle and lower 

sites.

Upper Black Pipe Creek (site 5) generally had a substrate composition of silt and sand. Substrate composition was 

largely silt and clay at the middle site (site 6), and consisted 

of sand and fine gravel at the lower site (site 8). Thus, average 

substrate size increased from silt to fine gravel in a downstream direction (table 10).

Fish cover at site 5 on Black Pipe Creek primarily was 

composed of overhanging vegetation and filamentous algae 

(fig. 18A). Overhanging vegetation was the predominant fish 

cover at site 6 (fig. 18B), whereas macrophytes provided the 

dominant fish cover at site 8 (fig. 18C). Fish cover was largely 

categorized as sparse throughout the three reaches on Black 

Pipe Creek.

Riparian cover at the upper and middle sites on Black 

Pipe Creek was a mixture of grasses and woody shrubs. Riparian cover was largely absent at the lower site and consisted of 

grasses and bare dirt.

The average maximum thalweg depth for all transects at 

upper Black Pipe Creek (site 5) was 30.8 cm. The largest maximum thalweg depth measurement at this site was 41 cm at 

transect I, and the smallest maximum thalweg depth measurement at this site was 22 cm at transect D. The average wetted 

width of the reach was 2.4 m, with a minimum width of 1.6 m 

at transect A and a maximum width of 3.9 m at transect F.

The average maximum thalweg depth for all transects 

at the middle site on Black Pipe Creek (site 6) was 54.8 cm. 

The largest maximum thalweg depth measurement at this site 

was 87 cm at transect E, and the smallest maximum thalweg 

Geologic Influences on Stream Condition 27
A

B

C

A

B

C

Figure 17. Bear-in-the-Lodge Creek, assessment sites: 

(A) upper site (site 1), (B) middle site (site 3), and (C) lower 

site (site 4).

Figure 18. Upper Black Pipe Creek, assessment sites: 

(A) upper site (site 5), (B) middle site (site 6), and (C) lower 

site (site 8).

28  Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
depth measurement at this site was 16 cm at transect J. The 

average wetted width of the reach was 2.0 m, with a minimum 

width of 1.2 m at transect J and a maximum width of 2.8 m at 

transect C.

The average maximum thalweg depth for all transects at 

lower Black Pipe Creek (site 8) was 14.1 cm. The largest maximum thalweg depth measurement at this site was 26 cm at 

transect D, and the smallest maximum thalweg depth measurement at this site was 6 cm at transect G. The average wetted 

width of the reach was 2.2 m, with a minimum width of 0.7 m 

at transect H and a maximum width of 4.2 m at transect A.

The stream channel at site 5 on upper Black Pipe Creek 

was categorized as a glide that transitioned into a glide/riffle 

throughout the reach at site 6. The stream channel at the lower 

site (site 8) consisted largely of a series of interconnected 

pools throughout the reach.

No rapid habitat assessment rating was completed for 

upper Black Pipe Creek (site 5, table 11 in the Supplemental 

Information section). Sites 6 and 8 generally received ratings 

that ranged from suboptimal to poor for most categories that 

evaluated in-stream and near-stream conditions.

Vertebrate /Physical Habitat Associations

Differences in thalweg depth and wetted width between 

Bear-in-the-Lodge and Black Pipe Creeks may explain patterns in vertebrate diversity and abundance. On average, Bearin-the-Lodge Creek had a deeper thalweg and wider wetted 

width than Black Pipe Creek. Therefore, habitat volume for 

aquatic vertebrates (that is, fish) was greater in Bear-in-theLodge Creek than Black Pipe Creek. A longitudinal thalweg 

profile was plotted in relation to transect location for each site. 

Because vertebrate location to nearest transect was recorded 

during sampling, vertebrate location to thalweg depth could 

be determined. Accordingly, most vertebrates were collected 

nearest transects that represented the deepest pools in the sample reach for all sites. Given the intermittent nature of streams 

in the White River drainage basin, pools provide critical refuge for fish during low-flow periods. The continuing drought 

during this study period likely strengthened the importance of 

pool habitat for fish. The greater availability of pool habitat, 

and thus refuge area, in Bear-in-the-Lodge Creek would allow 

this stream to support a greater diversity and abundance of fish 

than Black Pipe Creek.

Summary

During 2000, the U.S. Environmental Protection Agency 

(USEPA) initiated a 5-year study called the Environmental 

Monitoring and Assessment Program-West (EMAP-West). 

The two primary objectives of the surface-water component 

of the EMAP-West were to (1) develop the monitoring tools 

(biological indicators, stream survey design, and estimates of 

reference condition) necessary to produce unbiased estimates 

of the ecological condition of surface waters across a large 

geographic area of the West; and (2) demonstrate the effectiveness of those tools in a large-scale assessment.

The resource population of interest for EMAP-West was 

all perennial streams and rivers represented in USEPA’s River 

Reach File (RF3), with the exception of the lower portions of 

the “Great Rivers” (the Columbia, Snake, Colorado, and Missouri Rivers). Assessments sites were selected randomly using 

a probability design where each site had a known probability 

for selection.

 This was done to ensure that all types of streams are 

included in the final list of sites and to allow for adequate 

spacial representation.

During 2000, USEPA completed assessments at 22 randomly selected wadeable stream sites in South Dakota. In 

2001, the South Dakota Department of Game, Fish and Parks 

(GF&P) and the U.S. Geological Survey (USGS) entered into 

a cooperative agreement to complete the remaining stream 

assessments in South Dakota for the duration of the EMAPWest study. During 2001–2003, USGS and GF&P completed 

another 42 stream assessments bringing the total number of 

randomly selected stream assessments to 64. USGS personnel 

used several monitoring techniques developed by the USEPA 

for conducting the ecological assessments. Many chemical, 

physical, and biological indicators were assessed at selected 

sites that included water chemistry, physical habitat, periphyton assemblages, benthic macroinvertebrate assemblages, 

aquatic vertebrate communities, and fish tissue contaminants.

EMAP-West was expanded beginning in 2002 to include 

the selection and sampling of candidate reference sites 

throughout South Dakota. Candidate reference sites were not 

selected randomly but were specifically selected because it 

was generally believed that they possessed the best attainable aquatic conditions within the major Level III Ecoregions 

present in South Dakota. Inclusion of candidate reference sites 

into EMAP-West provided a valuable mechanism for assessing the overall health of sites randomly selected by USEPA 

throughout the State by providing standards or benchmarks 

that could be compared against existing aquatic conditions at 

randomly selected sites. Guidelines for selecting candidate 

reference sites were developed jointly by several State and 

Federal agencies to ensure that sites were representative of a 

variety of hydrogeological, ecological, and land-use settings 

found throughout South Dakota. During 2002–2004, USGS 

and GF&P completed stream assessments for 45 candidate 

reference sites. Thus, for the 5-year duration of EMAP-West 

(2000–2004), assessments were completed at 109 sites. 

Eighteen repeat assessments were completed at 12 of the 64 

randomly selected assessment sites to provide estimates of 

important components of variability and for quality-assurance 

purposes. Repeat assessments were not included in the 109 site 

assessment total.

This report provides an overview of EMAP-West activities in South Dakota during 2000–2004. It presents stream 

assessment site locations and describes the methods used to 

collect the chemical, physical, and biological data that will be 

Summary 29
used by USEPA to estimate the ecological conditions of our 

Nation’s stream and river resources in the 12 western States 

included in EMAP-West.

Relatively early in the EMAP-West stream-assessment 

process, it became apparent that for some streams in southcentral South Dakota, in-stream conditions varied considerably over relatively short distances of only a few miles. 

These changes appeared to be a result of geomorphic changes 

associated with changes in the underlying geology. For these 

streams, moving stream assessment sites short distances 

upstream or downstream had the potential to provide substantially different bioassessment data. In order to obtain a better 

understanding of how geology influences stream conditions, 

two streams located in south-central South Dakota were 

chosen for multiple stream sampling at sites located along 

their longitudinal profile at points where notable changes in 

geomorphology were observed. Subsequently, three sites on 

Bear-in-the-Lodge Creek and three sites on Black Pipe Creek 

were selected for multiple stream sampling using EMAP-West 

protocols so that more could be learned about the geologic 

influences on stream conditions.

Values for dissolved oxygen and specific conductance 

generally increased from upstream to downstream locations 

on Bear-in-the-Lodge Creek. Values for pH and water temperature generally decreased from upstream to downstream 

locations. Decreasing water temperature could be indicative of 

ground-water inflows.

Values for dissolved oxygen, pH, and water temperature 

generally increased from upstream to downstream locations 

on Black Pipe Creek. The increase in temperature at the lower 

sites is a result of less dense riparian cover, and the warmer 

water also could account for the lower concentrations of dissolved oxygen found in the lower reaches of Black Pipe Creek. 

Values for specific conductance were more than three times 

greater at the lower site (1,342 microsiemens per centimeter 

(μS/cm)) than at the upper site (434 μS/cm). The increase 

probably occurs when the stream transitions from contacting 

the underlying Arikaree Formation to contacting the underlying Pierre Shale.

Vertebrate richness was found to be slightly higher for 

Bear-in-the-Lodge Creek (547 total number of fish) than for 

Black Pipe Creek (147 total number of fish). On average, 

reaches on Bear-in-the-Lodge Creek had a deeper thalweg 

and wider wetted stream width than Black Pipe Creek. This 

resulted in a larger habitat volume of aquatic vertebrates in 

Bear-in-the-Lodge Creek than in Black Pipe Creek and probably is the reason for the higher vertebrate richness found in 

Bear-in-the-Lodge Creek.

Average substrate size decreased in a downstream direction for Bear-in-the-Lodge Creek. In-stream fish cover also 

transitioned from woody debris to macrophytes in a downstream direction for Bear-in-the-Lodge Creek, whereas the 

predominate riparian cover transitioned from trees to barren 

dirt in the lower reaches. The stream channel for Bear-in-theLodge Creek largely consisted of riffles in the upper stream 

reaches and transitioned into glide or glide/riffle combinations 

in the lower reaches. Rapid habitat assessments metrics generally were scored as good except for sediment deposition and 

riffle frequency.

Average substrate size for Black Pipe Creek increased 

from silt to fine gravel in a downstream direction. In-stream 

fish cover was composed of overhanging vegetation and algae 

in the upper reaches and transitioned to macrophytes in the 

lower reaches. However, fish cover was sparse throughout 

all reaches. Riparian cover largely consisted of grasses and 

woody shrubs in the upper reaches of Black Pipe Creek and 

transitioned to grasses and bare dirt in the lower reaches. The 

stream channel was largely a glide in the upper reaches and 

transitioned to a glide/riffle in the middle reaches and to a 

series of interconnected pools in the lower reach. No rapid 

habitat assessments were completed for the upper reach, but 

the lower reaches were categorized as poor for most in-stream 

and near-stream conditions.

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western pilot study field operations manual for wadable 

streams: accessed February 14, 2005, at www.epa.gov/emap/

html/pubs/docs/groupdocs/surfwatr/field/fomws.html

U.S. Environmental Protection Agency, 2002, Biological 

assessments and criteria—crucial components of water 

quality programs: U.S. Environmental Protection Agency 

Fact Sheet 822–F–02–006, 6 p.

U.S. Environmental Protection Agency, 2003, Overview of 

the EPA quality system for environmental data and technology: Washington, D.C., EPA/240/R–02/00, accessed 

December 5, 2005, at http://www.epa.gov/quality1/qs-docs/

overview-final/pdf

U.S. Geological Survey, 1978, Hydrologic unit map State of 

South Dakota: 1 sheet, scale 1:500,000.

References  31
U.S. Geological Survey, 1997–2004, National field manual for 

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

Techniques of Water-Resources Investigations, book 9, 

chaps. A1–A9, 2 v., variously paged. [Available online at 

http://pubs.water.usgs.gov/twri9A]. Chapters were originally published from 1997–1999; updates and revisions are 

ongoing and are summarized at http://water.usgs.gov/owq/

FieldManual/mastererrata.html.

32 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Supplemental Information
Table 3. General guidelines for consideration in selection of candidate reference sites.

1. General flow characteristics—Two specific criteria: (A) Sufficiently perennial to maintain viable aquatic communities during most years; 

and (B) can be waded in all but deepest of holes. Also a general guideline that tributaries near confluence with larger stream may make 

ideal candidates.

2. Geographic distribution and representative characteristics—Reference sites need to have a wide geographic distribution within the 

State and represent the best attainable aquatic conditions within the designated area. In addition to having good representation for the four 

major Omernik level III ecoregions (Omernik, 1987) within the State, a variety of different hydrogeologic/land-use/landscape settings need 

to be addressed. Target areas might include:

• Black Hills

• Badlands (parts of White River and some of its tributaries)

• Sand Hills (Little White/Keya Paha Rivers)

• Western South Dakota shales (Cheyenne/Bad Rivers)

• Western South Dakota sandstones/siltstones (Grand/Moreau Rivers)

• Missouri River breaks

• Upper James River

• Lower James/Lower Big Sioux/Vermillion Rivers

• Coteau des Prairies

• Upper Big Sioux River

3. Consideration of core factors listed in U.S. Environmental Protection Agency Region 7 document—The 11 core factors listed should 

be an excellent starting point for evaluating candidate sites—wastewater treatment plants (and other point sources of pollution), combined 

animal feeding operations (CAFOs), instream habitat, raparian habitat, land use/land cover (broad scale), land use/land cover (site specific), 

physical and chemical properties, altered hydrologic regime, biological metrics, faunal assemblages, and representativeness.

4. Geographic information system (GIS) analysis using selected coverages (land use, conservation easements, CAFOs, wastewater 

discharges, and others)—Again, no specific approach envisioned; however, numerous insights probably can be obtained by consideration 

of available GIS coverages.

5. Long-term viability/security/accessibility—Long-term potential for maintenance in a minimal-influence condition would be beneficial. 

Best prospects might include public ownership and permanent conservation easements, which also could be conducive to future site accessibility. Physical accessibility of sites also could be a consideration.

6. Parallelism with other programs—Another desirable quality would be parallelism with other environmental programs such as various 

Nataural Resource Conservation Service programs, availability of long-term water-quality data (305B monitoring sites, U.S. Geological 

Survey or Tribal data), and biological data from previous surveys. Expressed interest from land-management agencies (see item 7) would 

be beneficial.

7. Multiple recommendations—Recommendations from multiple sources (District Conservationists in overlapping areas, interested agencies, collaborating agencies) would be indicative of high potential for candidate sites.

8. Professional judgment—It is envisioned that no rigid method can be established to identify or score potential sites. Professional judgment 

and discussions leading to consensus among collaborating agencies may be an important factor in finalizing selections.

34 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Table 4. Data reporting criteria for water chemistry analyses.

[From U.S. Environmental Protection Agency, written commun., 2005. mg/L, milligrams per liter; °C, degrees Celsius; 

μeq/L, microequivalents per liter; μS/cm, microsiemens per centimeter at 25 degrees Celsius; μg/L, micrograms per liter; 

NTU, nephelometric turbidity units; PCU, platinum cobalt units]

Measurement Units

Number of

significant figures

Maximum number of 

decimal places

Dissolved oxygen mg/L 2 1

Temperature °C 2 1

pH pH units 3 2

Carbon, dissolved inorganic mg/L 3 2

Carbon, dissolved organic mg/L 3 1

Acid neutralizing capacity μeq/L 3 1

Aluminum (total dissolved, total monomeric, and organic monomeric)μeq/L 3 1

Specific conductance μS/cm 3 1

Calcium, magnesium, sodium, and 

potassium

μeq/L 3 2

Ammonium, chloride, nitrate, and 

sulfate

μeq/L 3 2

Silica mg/L 3 2

Total phosphorus and total nitrogen μg/L 3 2

Turbidity NTU 3 2

True color PCU 2 0

Total suspended solids mg/L 3 1

Supplemental Information  35
Table 5. Analytical methodologies for water chemistry.

[Quality-assurance classification: C, critical; N, non-critical. μeq/L, microequivelents per liter; CO2, carbon dioxide; mg/L, milligrams per liter; μS/cm, microsiemens per centimeter at 25 degrees Celsius; μg/L, micrograms per liter; ppm, parts per million; UV, ultraviolet; PCU, platinum cobalt units; NTU, nephelometric 

turbidity units; USEPA, U.S. Environmental Protection Agency; APHA, American Public Health Association; EDTA, ethylenediamine-tetraacetic acid]

Property or 

constituent

Qualityassurance 

classification Expected range Summary of method References

pH, closed system C 3 to 9 pH units Sample collected and analyzed without exposure 

to atmosphere; electrometric determination

(pH meter and glass combination electrode)

USEPA 150.6 (modified); 

USEPA (1987)

pH, equilibrated N 3 to 9 pH units Equilibration with 300 ppm CO2 for 1 hour prior 

to analysis; electrometric determination (pH 

meter and glass combination electrode)

USEPA 150.6 (modified); 

USEPA (1987)

Acid neutralizing 

capacity (ANC)

C -100 to 5,000 μeq/L Acidimetric titration to pH 3.5, with modified 

Gran plot analysis

USEPA 310.1 (modified); 

USEPA (1987)

Carbon, dissolved

inorganic (DIC)1

N 0.1 to 50 mg C/L Sample collected and analyzed without exposure 

to atmosphere; acid-promoted oxidation to 

CO2, with detection by infrared spectrophotometry

USEPA (1987)

Carbon, dissolved 

organic (DOC)

C 0.1 to 30 mg C/L UV-promoted persulfate oxidation, detection by 

infrared spectrophotometry

USEPA 415.2; 

USEPA (1987)

Conductivity C 1 to 500 μS/cm Electrolytic (conductance cell and meter) USEPA 120.6; 

USEPA (1987)

Aluminum, total dissolvedC 10 to 1,000 μg/L Atomic absorption spectroscopy (graphite 

furnace)

USEPA 202.2; 

USEPA (1987)

Aluminum, monomeric and organic 

monomeric

N 0 to 500 μg/L Collection and analysis without exposure to 

atmosphere. Portion of sample passed through

a cation exchange column before analysis to 

obtain estimate of organic-bound fraction. 

Colorimetric analysis (automated pyrocatechol 

violet)

APHA 3000-Al E.; 

APHA (1989); 

USEPA (1987)

Major cations, dissolved

Calcium C 0.02 to 76 mg/L 

(1 to 3,800 μeq/L)

Atomic absorption spectroscopy (flame) USEPA 200.6; 

USEPA (1987)

Magnesium C 0.01 to 25 mg/L 

(1 to 2,000 μeq/L)

Sodium C 0.01 to 75 mg/L 

(0.4 to 3.3 μeq/L)

Potassium C 0.01 to 10 mg/L 

(0.3 to 250 μeq/L)

Ammonium N 0.01 to 5 mg/L 

(0.5 to 300 μeq/L)

Colorimetric (automated phenate) USEPA 350.7; 

USEPA (1987)

36  Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Property or 

constituent

Qualityassurance 

classification Expected range Summary of method References

Major anions, dissolved

Chloride C 0.03 to 100 mg/L 

(1 to 2,800 μeq/L)

Ion chromatography

Sulfate C 0.05 to 25 mg/L 

(1 to 500 μeq/L)

Silica, dissolved N 0.05 to 15 mg/L Automated colorimetric (molybdate blue) USEPA 370.1 (modified); 

USEPA (1987)

Phosphorus, total C 0 to 1,000 μg/L Acid-persulfate digestion with automated colorimetric determination (molybdate blue)USGS I-4600-78; 

Skougstad and others 

(1979); 

USEPA (1987)

Nitrogen, total N 0 to 25,000 μg/L Alkaline persulfate digestion with determination 

of nitrate by cadmium reduction and determination of nitrite by automated colorimetry 

(EDTA/sulfanilimide)

USEPA 353.2 (modified); 

USEPA (1987)

True color N 0 to 300 PCU Visual comparison to calibrated glass color disks USEPA 100.2 (modified); 

APHA 204 A.; 

USEPA (1987)

Turbidity N 1 to 100 NTU Nephelometric APHA 214 A.; 

USEPA 180.1; 

USEPA (1987)

Total Suspended 

Solids (TSS)

N 1 to 200 mg/L Gravimetric USEPA 160.3; 

APHA (1989)

1

For DIC, dissolved is defined as that portion passing through a 0.45-micron nominal pore-size filter. For other constituents, dissolved is defined as that 

portion passing through a 0.4-micron pore-size filter (Nucleopore or equivalent).

Table 5. Analytical methodologies for water chemistry.—Continued

Supplemental Information  37
Table 6. Water-quality data for sites on Bear-in-the-Lodge and Black Pipe Creeks.

[NTU, nephelometric turbidity units; mg/L, milligrams per liter; μS/cm, microsiemens per centimeter at 25 degrees Celsius; deg. C, degrees Celsius; μeq/L, microiequivelents per liter; ft3/s, cubic feet per second; --, no data]

Site name 

(table 1)

Site 

number 

(fig. 3)

Date 

sampled

Turbidity 

(NTU)

Dissolved 

oxygen 

(mg/L)

pH, whole, 

field 

(standard 

units)

Specific 

conductance, 

field 

(μS/cm)

Temperature, air 

(deg. C)

Temperature, 

water 

(deg. C)

Calcium, 

dissolved 

(μeq/L)

Magnesium, 

dissolved 

(μeq/L)

Potassium, 

dissolved 

(μeq/L)

Sodium, 

dissolved 

(μeq/L)

ANC 

(μeq/L as 

CaCO3

)

Chloride, 

dissolved 

(μeq/L)

Upper Bear-in-theLodge Creek

1 06-15-04 -- 9.3 7.7 503 24.0 22.1 -- -- -- -- -- --

Bear-in-the-Lodge 

Creek

3 06-15-04 168 9.1 7.4 507 25.0 20.5 2,146.1 428.4 295.5 2,790.1 5,103.4 114

Lower Bear-in-theLodge Creek

4 06-16-04 -- 10.3 7.6 519 17.0 17.7 -- -- -- -- -- --

Upper Black Pipe 

Creek

5 06-08-04 -- 9.3 7.1 434 18.0 17.4 -- -- -- -- -- --

Black Pipe Creek 6 06-09-04 43.7 8.2 7.4 590 14.0 17.0 2,248.1 440.4 306.3 3,811.0 5,997.3 174.6Lower Black Pipe 

Creek

8 06-09-04 -- 9.6 7.6 1,342 17.0 18.7 -- -- -- -- -- --

Site 

number 

(fig. 3)

Silica, 

dissolved 

(μeq/L)

Sulfate, 

dissolved 

(μeq/L)

Ammonia, 

dissolved 

(μeq/L)

Nitrate, 

dissolved 

(μeq/L)

Nitrogen, 

total

(μg/L)

Phosphorous, 

total 

(μeq/L)

Selenium, 

dissolved 

(μeq/L)

Zinc, 

dissolved 

(μeq/L)

Color 

(PCU)

Dissolved 

organic 

carbon 

(mg/L)

Dissolved 

inorganic 

carbon 

(mg/L)

Hydroxide 

(μeq/L)

Bicarbonate 

(μeq/L)

Carbonate 

(μeq/L)

Total suspended 

solids 

(mg/L)

Discharge 

(ft3/s)

1 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 6.83

3 44.9 417.4 2.5 15 1,223 444 0.1 0.0 20 5.34 56.1 2.4 4,574.8 105.3 344.8 7.13

4 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 5.92

5 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 1.45

6 34.5 376.6 1.7 .0 872 147 .0 6.0 40 9.8 68.1 3.2 5,545.8 168.3 58.6 .383

8 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- .001

38  Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Table 7. Vertebrate information for Bear-in-the-Lodge Creek.

[--, no data]

Date Species collected Tally

Minimum length

(millimeters)

Maximum length

(millimeters) Transect where found

Upper Bear-in-the-Lodge Creek (site 1 in fig. 3)

06–15–04 Flathead chub 26 69 143 A, B, C, D, E, I, J

Longnose Dace 1 52 -- I

Sand shiner 52 44 68 A, B, C, D, E G, I, J

Shorthead redhorse 5 163 175 A, C, D

Stonecat 4 121 183 D, E

Unknown crayfish 12 -- -- A, D, E, I, J

Bear-in-the-Lodge Creek (site 3 in fig. 3)

06–15–04 Channel catfish 15 57 255 E, I, J

Flathead chub 3 75 125 E

Green sunfish 1 53 -- E

Sand shiner 3 49 63 E, I, J

Shorthead redhorse 3 156 159 A, D, I

Stonecat 2 115 146 A, I

Unknown crayfish 1 -- -- F

Lower Bear-in-the-Lodge Creek (site 4 in fig. 3)

06–16–04 Black bullhead 4 52 130 F, G, I

Channel catfish 3 170 532 G, I

Flathead chub 114 57 127 A, B, C, D, E, F, G, H, I, J

Hybognathus spp 161 62 93 A, B, C, D, E, F, G, H, I, J

Sand shiner 103 50 62 A, B, C, D, E, F, G, H, I, J

Longnose dace 45 57 89 A, B, C, D, E, F, I, J

Red shiner 1 47 -- I

River carpsucker 1 241 -- I

Supplemental Information  39
Table 8. Vertebrate information for Black Pipe Creek.

[--, no data]

Date Species collected Tally

Minimum length

(millimeters)

Maximum length

(millimeters)

Transect where 

found

Upper Black Pipe Creek (site 5 in fig. 3)

06–08–04 Creek Chub 6 64 142 G, I, F, H

Long nose dace 5 55 84 F, H

Sand shiner 1 69 -- G

Unknown tapole 1 -- -- G

Black Pipe Creek (site 6 in fig. 3)

06–09–04 Flathead chub 13 78 115 A, C, E, G, F, H

Hybognathus spp 10 70 82 C, E, G, F

Lower Black Pipe Creek (site 8 in fig. 3)

06–09–04 Channel catfish 5 155 310 B

Flathead chub 38 62 100 B

Hybognathus spp 56 51 69 B

River carpsucker 4 144 152 B

Sand shiner 8 40 59 B

40 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Table 9. Physical habitat data for sites on Bear-in-the-Lodge Creek.

[cm, centimeter; OV, overhanging vegetation; ST, small trees; G, grasses; BT, big trees; WD, woody dedris; NDC, no dominant cover; BD, barren dirt; M, marophytes; R, roots; WS, woody shrubs; --, no data]

Transect

Substrate 

composition

Fish cover 

(dominant)

Riparian cover 

left bank 

Riparian cover 

right bank

Human 

influence

Maxiumum 

thalweg 

depth 

(cm)

Wetted 

width 

(meters)

Channel 

type

Upper Bear-in-the-Lodge Creek (site 1 in fig. 3)

A Silt/Clay Absent/Sparse

(OV)

Sparse/Moderate (ST,G) Sparse/Moderate (G) Pasture 50 3.6 Glide

B Fine Gravel Absent/Sparse

(OV)

Sparse/Moderate (BT,G) Sparse/Moderate (ST,G) Pasture 35 3.4 Riffle

C Coarse Gravel Absent/Sparse

(WD)

Sparse (NDC) Sparse (BD) Pasture 52 4.0 Riffle

D Silt/Clay Absent/Sparse

(OV,WD,M)

Sparse/Moderate (NDC) Sparse(G) Pasture 45 2.6 Riffle

E Fine/Coarse 

Gravel

Absent/Sparse(OV,WD,M)

Sparse/Moderate (G) Sparse (BD) Pasture 38 4.1 Riffle

F Silt/Clay Sparse/Moderate 

(OV,WD,M)

Moderate (BD) Moderate (G,WS) Pasture 40 3.3 Rapid

G Coarse Gravel Absent/Sparse

(WD,R,OV)

Sparse/Moderate (G,WS) Sparse/Moderate (G) Pasture 30 4.8 Riffle

H Coarse Gravel Absent/Sparse

(OV)

Sparse/Moderate (G,BD) Sparse (G) Pasture 23 4.5 Riffle

I Fine Gravel Sparse/Moderate 

(OV,WD,M)

Sparse/Moderate (G,WS) Sparse/Moderate (G) Pasture 53 5.3 Glide

J Fine Gravel Absent/Sparse

(OV)

Sparse/Moderate (G) Sparse/Moderate (G) Pasture 62 4.0 Glide

K Fine Gravel Sparse/Moderate Absent/Sparse Sparse/Moderate Pasture -- -- --

 Bear-in-the-Lodge Creek (site 3 in fig. 3)

A Silt/Clay Absent/Sparse

(NDC)

Moderate (NDC) Moderate (NDC) Pasture 77 3.9 Glide

B Silt/Clay Moderate (WD,OV) Sparse (G) Sparse (G) Pasture 72 4.3 GlideC Silt/Clay Sparse (NDC) Sparse/Moderate (G) Sparse/Moderate (G,BD) Pasture 94 4.2 Glide

D Silt/Clay Absent/Sparse (NDC) Sparse/Moderate (G) Sparse/Moderate (G) Pasture 67 3.7 Glide

E Silt/Clay Absent/Sparse

(WD,OV)

Sparse/Moderate (G) Sparse/Moderate (G) Pasture 99 3.9 Glide

F Silt/Clay Sparse (M,OV) Sparse/Moderate (ST,G) Sparse/Moderate (G) Pasture 71 3.3 Glide

Supplemental Information 41
Transect

Substrate 

composition

Fish cover 

(dominant)

Riparian cover 

left bank 

Riparian cover 

right bank

Human 

influence

Maxiumum 

thalweg 

depth 

(cm)

Wetted 

width 

(meters)

Channel 

type

 Bear-in-the-Lodge Creek (site 3 in fig. 3)—Continued

G Silt/Clay Sparse/Moderate 

(WD,OV)

Moderate (G) Sparse/Moderate (G) Pasture 75 3.6 Glide

H Silt/Clay Absent/Sparse

(NDC)

Sparse/Moderate (NDC) Sparse/Moderate (G) Pasture 84 2.9 Glide

I Silt/Clay Absent/Sparse

(M.WD,OV)

Sparse (G) Sparse (ST,G) Pasture 120 5.5 Glide

J Silt/Clay Absent/Sparse

(OV)

Moderate (NDC) Moderate (G) Pasture 38 4.5 Riffle

K Silt/Clay Absent/Sparse Sparse Sparse Pasture -- -- --

Lower Bear-in-the-Lodge Creek (site 4 in fig. 3)

A Sand/Coarse 

Gravel

Absent (M,OV) Sparse (BD) Sparse (BD) Pasture 30 6.1 Riffle

B Hardpan/Silt Absent/Sparse

(M,OV)

Moderate (NDC) Absent (BD) Pasture 30 5.5 Glide

C Hardpan Absent (R,OV) Sparse (BD) Sparse (BD) Pasture 30 4.4 Glide

D Coarse Gravel Absent (OV) Absent/Sparse (BD) Absent/Sparse (BD) Pasture 36 4.9 Glide/Riffle

E Silt/Clay Absent (OV) Sparse (BD) Absent/Sparse (BD) Pasture 64 5.6 Glide/Riffle

F Hardpan/Silt Absent (NDC) Absent/Sparse (BD) Sparse (BD) Pasture 35 5.6 Glide

G Sand Absent (M,OV) Sparse (BD) Sparse (BD) Pasture 76 6.0 GlideH Silt/Sand Absent (M,OV) Sparse (BD) Sparse/Moderate (BD) Pasture 63 6.2 Glide

I Silt/Clay Absent (OV) Absent/Sparse (G,BD) Absent/Sparse (G,BD) Pasture 90 5.7 Glide

J Silt/Clay Absent/Sparse (M,OV) Sparse/Moderate (G,BD) Sparse/Moderate (G,BD) Pasture 60 7.2 Glide/Riffle

K Silt/Sand Absent/Sparse Absent/Sparse Absent Sparse -- -- --

Table 9. Physical habitat data for sites on Bear-in-the-Lodge Creek.—Continued

42 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Table 10. Physical habitat data for sites on Black Pipe Creek.

[cm, centimeter; OV, overhanging vegetation; ST, small trees; G, grasses; BT, big trees; WD, woody dedris; NDC, no dominant cover; BD, barren dirt; M, macrophytes; R, roots; WS, woody shrubs; --, no data; FA, filamentous algae]

Transect

Substrate 

composition

Fish cover 

(dominant)

Riparian cover

left bank 

(dominant)

Riparian cover 

right bank 

(dominant)

Human 

influence

Maxiumum 

thalweg 

depth (cm)

Wetted width 

(meters) Channel type

Upper Black Pipe Creek (site 5 in fig. 3)

A Silt/Clay Sparse/Moderate (M,WD) Absent/Sparse (G) Absent/Sparse (G) Pasture 36 1.6 Riffle

B Fine Gravel Absent/Sparse (FA,WD) Sparse/Moderate (G) Sparse/Moderate (WS,G) Pasture 39 1.9 RiffleC Sand Sparse (FA) Moderate (WS,G) Moderate (WS,G) Pasture 33 2.1 Glide

D Silt/Sand Sparse (NDC) Sparse (G) Sparse (G) Pasture 22 2.7 Glide

E Silt/Sand Sparse/Moderate 

(FA,M,OV)

Sparse/Moderate (G) Sparse (WS) Pasture 25 2.4 Glide

F Silt/Sand Sparse/Moderate 

(FA,M,OV)

Sparse (G) Sparse (G) Pasture 30 3.9 Glide

G Silt/Sand Sparse/Moderate (WD,OV) Sparse/Moderate (WS,G) Sparse/Moderate (WS,G) Pasture 35 2.1 GlideH Silt/Sand Sparse (OV) Sparse/Moderate (WS) Absent (G) Trash/Pasture 23 2.5 Glide

I Sand Absent/Sparse (OV) Sparse (WS,G) Sparse (WS,G) Pasture 41 2.3 Glide

J Silt/Sand Sparse (OV) Sparse (G) Sparse (G) Trash/Pasture 24 2.1 Glide/Riffle

K Silt/Gravel Sparse Sparse/Moderate Sparse Trash/Pasture -- -- --

Black Pipe Creek (site 6 in fig. 3)

A Silt/Clay Sparse (NDC) Sparse (G) Sparse (G) Pasture 47 2.0 Glide

B Silt/Clay Sparse (NDC) Sparse (G) Sparse (G) Pasture 66 2.4 GlideC Silt/Clay Sparse (NDC) Sparse (G) Sparse (G) Pasture 50 2.8 Riffle

D Coarse Gravel Sparse/Moderate (WD,OV) Sparse/Moderate (WS,G) Sparse/Moderate (WS,G) Pasture 78 2.2 Glide/Riffle

E Silt/Clay Sparse (OV) Sparse/Moderate (WS,G) Sparse/Moderate (WS,G) Pasture 87 1.8 Glide

F Coarse Gravel Sparse (OV) Moderate/Heavy (WS,G) Sparse (G) Pasture 50 1.8 Glide/Riffle

G Silt/Clay Sparse/Moderate (WD,OV) Sparse (G,BD) Sparse (WS,G) Trash/Pasture 82 1.9 GlideH Silt/Clay Sparse (OV) Sparse (G) Sparse (G) Pasture 36 2.0 Glide

I Sand/Silt Sparse (OV) Sparse (NDC) Sparse (NDC) Trash/Pasture 36 1.7 Riffle

J Fine Gravel Sparse (OV) Moderate (G,WS) Sparse (BD) Pasture 16 1.2 Glide

K Coarse Gravel Sparse Moderate Sparse Pasture -- -- --

Supplemental Information 43
Transect

Substrate 

composition

Fish cover 

(dominant)

Riparian cover

left bank 

(dominant)

Riparian cover 

right bank 

(dominant)

Human 

influence

Maxiumum 

thalweg 

depth (cm)

Wetted width 

(meters) Channel type

Lower Black Pipe Creek (site 8 in fig. 3)

A Sand Sparse (M,OV) Absent/Sparse (G,BD) Absent (BD) Trash/Pasture/

Riprap/Bridge

22 4.2 Pool

B Sand Absent/Sparse (M,OV) Absent/Sparse (G,BD) Absent (BD) Trash/Pasture/

Riprap/Bridge

15 2.1 Pool

C Sand Absent/Sparse (M,OV) Absent/Sparse (G,BD) Absent (BD) Trash/Pasture/

Riprap/Bridge

13 3.5 Pool

D Fine Gravel Absent (OV) Sparse (G,BD) Absent (BD) Trash/Pasture/

Riprap/Bridge

26 2.1 Pool

E Hardpan/Sand Absent/Sparse (G) Absent/Sparse (G) Absent (BD) Trash/Pasture/

Riprap/Bridge

20 2 Pool/Riffle

F Sand Absent/Sparse (M,OV) Absent/Sparse (G,BD) Absent (BD) Trash/Pasture/

Riprap/Bridge

7 2.2 Pool

G Sand Absent/Sparse (M) Absent/Sparse (G,BD) Absent/Sparse (BD) Trash/Pasture/

Riprap/Bridge

6 1 Pool

H Fine Gravel Absent/Sparse (M,OV) Sparse/Moderate (G,BD) Absent/Sparse (BD) Trash/Pasture/

Riprap/Bridge

10 0.7 Glide/Riffle

I Fine Gravel Absent/Sparse (M,OV) Sparse/Moderate G,BD) Absent/Sparse (BD) Trash/Pasture/

Riprap/Bridge

12 2.6 Pool

J Sand Absent/Sparse (M,OV) Sparse/Moderate (G,BD) Absent/Sparse (BD) Trash/Pasture/

Riprap/Bridge

10 1.4 Pool/Riffle

K Sand Absent/Sparse Sparse/Moderate Absent/Sparse Trash/Pasture/

Riprap/Bridge

-- -- --

Table 10. Physical habitat data for sites on Black Pipe Creek.—Continued

44 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000–2004
Table 11. Rapid habitat assessment ratings for sites on Bear-in-the-Lodge and Black Pipe Creeks.

[O, optimal; SO, sub-optimal; M, marginal; P, poor; --, no data]

Site

number

Epifaunal 

substrate 

cover Embeddedness

Velocity/depth 

regime

Sediment 

deposition

Channel flow

status

Channel 

alteration

Riffle 

frequency

Bank stability 

right/left

Vegetative 

protection 

right/left

Riparian 

vegetative 

zone width

right/left

Bear-in-the-Lodge Creek

1 O O O SO O SO SO O/O O/O SO/SO3 O P M O O O P SO/SO O/O O/O4 O O O SO SO O O P/M P/M O/O

Black Pipe Creek

5 -- -- -- -- -- -- -- -- -- --6 O SO O SO SO O O SO/SO O/O O/SO8 P SO M P P M M SO/SO M/M M/M

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