U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2006–3001

January 2006

Prepared in cooperation with the South Dakota Department of Game, Fish and Parks and the U.S. Environmental Protection Agency

The Environmental Monitoring and Assessment 

Program (EMAP)-West—Summary of Activities and 

Accomplishments in South Dakota, 2000–2004

Printed on recycled paper

Introduction

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

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

primary objectives of the surface waters component of EMAPWest were to (1) develop the monitoring tools (biological 

indicators, stream survey design, 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. Although not specifically defined 

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

help to establish a baseline for comparisons with data obtained 

from future monitoring efforts and could document changing 

biological conditions resulting from changing land-use or landmanagement practices associated with regulatory or restorative 

efforts.

EMAP-West is a partnership between USEPA, States, 

Tribes, and other inter­ested parties in USEPA Regions 8, 9, and 

10. In South Dakota, the principle EMAP-West cooperators 

include the USEPA, South Dakota Department of Game, Fish 

and Parks (GF&P), and the U.S. Geological Survey (USGS). 

Other agencies such as the Natural Resource Conservation 

Service, the South Dakota Department of Environment and 

Natural Resources (SDDENR), State Conservation Dis­tricts, 

and various Tribal departments also have provided valuable 

expertise and assistance.

This fact sheet summarizes the activities and accomplishments associated with EMAP-West in South Dakota during 

2000–2004. Efforts were focused on perennial streams that 

usually can be waded. Large rivers also were assessed during 

EMAP-West under the auspices of USEPA using boats and 

similar techniques, but are not included in the activities discussed here. Data-collection activities for wadeable streams 

were conducted under the auspices of USEPA in South Dakota 

during 2000 and by the USGS during 2001–2004. A more 

detailed description of EMAP-West activities and assessments 

in South Dakota is available in Heakin and others (in press).

Background

Historically, most of the data collected for the USEPA to 

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

consisted of physical and chemical data, which were 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 evaluate environmental trends 

and identify potential problems in their infancy (U.S. Environmental Protection Agency, 1987). This type of ecological “risk 

assess­ment” required development of a core set of indicators 

of ecological condition that could be incorporated into the 

bioassessment process. 

Bioassessments largely consist of surveys involving the 

collection, identification, and enumer­ation of aquatic biota 

(algae, invertebrates, and vertebrates) inhabiting a waterbody. 

Bioassessments also often include enumeration and identification 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 waterbody 

is enhanced, thereby providing more validity and use­fulness to 

water-resources assessments.

Physical changes occurring in a waterbody such as fluctuations in temperature and sediment concentrations, or chemical 

changes such as fluctuations in concentrations of nutrients or 

trace metals, can result from both natural and anthropogenic 

sources. Even subtle changes in physical or chemical conditions 

may stress more sensitive members of the aquatic community, 

causing 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 lowering species diversity. 

Generally speak­ing, a waterbody 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.

In 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 currently used by EMAP-West (U.S. 

Environmental Protection Agency, 2000). However, for EMAPWest, some novel tools still had to be developed, primarily 

to address the large environ­mental variability encountered 

throughout western States (U.S. Environmental Protection 

Agency, 1998). 
USEPA recognized that for the bioassessment information 

to be most useful, the data had to be collected in a consistent 

manner using similar techniques developed specifically to 

provide information for a core set of indicators. Subsequently, 

the USEPA developed a detailed Field Operations Manual for 

Wadeable Streams for EMAP-West (D.V. Peck and others, U.S. 

Environmental Protection Agency, written commun., 2000) 

along with training courses to ensure that EMAP-West data 

would be collected using a similar set of techniques and protocols that focus on a specific core set of indica­tors.

Overview of the Study

The target population for EMAP-West is all wadeable 

perennial streams in USEPA Regions 8, 9, and 10 excluding the 

“Great Rivers” (the Columbia, Snake, Colorado, and Missouri 

Rivers). Because it was neither economically feasible nor practical to sample all perennial streams within those regions, USEPA 

developed a probability design that randomly selected stream 

assessment sites that would be statistically representative of the 

surface waters in the West. This would allow for extrapolation 

of results for streams within each State and for streams in all 

regions that share similar ecological characteristics. EMAPWest also incorporated a systematic grid, which provides uniform spatial coverage, that ensures that each ecological resource 

is sampled in proportion to its geographical presence. 

In South Dakota, bioassessments were conducted at two 

different site categories—randomly selected sites and candidate reference sites (fig. 1). A complete set of core ecological 

indicators established by USEPA were measured at each stream 

assessment site when­ever possible. The ecological indicators 

measured include (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) (fig. 2), (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.

Field data were recorded on standardized field data sheets 

developed by USEPA’s Western Ecology Division (WED) in 

Corvallis, Oregon (fig. 3). The completed data sheets were 

returned to WED where they were optically scanned to facilitate 

quick entry of the data into the database and to reduce data entry 

errors. The WED also was responsible for tabulating, reviewing, 

and verifying the large volume of stream assessment data 

generated by field crews participating in EMAP-West Study. 

Following verification, the data will be made available to the 

public on the EMAP-West Web site at http:/www.epa.gov/emap/

html/dataI/index.html and archived in the USEPA’s Storage 

Figure 1.  Locations of randomly selected sites and candidate reference sites visited during 2000–2004.

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James 

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Little

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Cheyenne

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MISSOURI

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L. Minnesota R

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EXPLANATION 

Randomly selected site 

Candidate reference site 

0 20 40 60 MILES

0 20 40 60 KILOMETERS Omernik level III ecoregions (Omernik, 1987) 

Northwestern Glaciated Plains 

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, 1979–1994

Universal Transverse Mercator projection zones 13 and 14
Once coordinates for latitude and longitude had been 

obtained from the USEPA, the locations of the sites were plotted 

on topographic maps. Sites were then field visited to confirm 

that streams were representative of the target population and 

to determine the precise coordinates on the stream banks using 

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

crew returned to each site to establish the length of the stream 

reach (40 times the wetted width of the stream or a minimum 

length of 150 meters) and to conduct the assessment (fig. 4). 

Samples collected during stream assessments were generally 

shipped overnight to the USEPA for analysis. USEPA has 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 is between June 1 and August 31 

and is the period when most field work was completed during 

the 5-year period 2000–2004.

Figure 2.  Field crew members collected aquatic vertebrate

samples.

and Retrieval (STORET) database at http:/www.epa.gov/storet. 

The EMAP-West Web site provided above also contains a list 

of individuals that should be consulted prior to attempting data 

retrieval and acquisition.

Randomly Selected Sites

During 2000, sampling was completed by USEPA at 22 

randomly selected sites. During 2001–2003, USGS and GF&P 

completed sampling at another 42 randomly selected sites 

bringing the total number of randomly selected sites to 64 

(fig. 1). Eighteen repeat assessments were done at 12 sites to 

provide estimates of important components of variability related 

to determining current status of the target population and trend 

detection (Chaloud and Peck, 1994). Alternate sites were identified and sub­stituted for assigned sites that could not be assessed 

because reconnaissance visits indicated that they were unsafe 

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

permission was denied. 

Figure 3.  Field crew members completed field data sheets during

EMAP stream-assessment activities in South Dakota.

Figure 4.  Field crew members assessed various watershed

characteristics.

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 EMAP-West. In South Dakota, this objective was 

accomplished by establishing a network of ref­erence sites that 

were selected for assessment because, after preliminary field 

reconnaissance, it was determined that they met 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) (fig. 1). 

During 2002–2003, USGS and GF&P were primarily responsible for selecting reference sites for assessment. However, assistance with reference site selection was provided by personnel 

from various State and Federal agencies, Tribal representatives, 
various water-resource professionals, and other interested parties. In 2004, USEPA assigned a list of reference sites to USGS 

for assessment based on a new set of selection cri­teria that they 

recently had developed. 

At the end of the field season in 2004, South Dakota’s 

candidate reference site network included 45 sites. Thus, 109 

stream assessments were completed (excluding repeat visits) 

during EMAP-West in South Dakota. As assessment data 

becomes available from USEPA, the data will be evaluated to 

determine if a site remains a viable candidate for the reference 

site network or if it should be removed.

Benefits of the Study

EMAP-West has and will continue to provide a wealth 

of valuable new bioassessment information for GF&P and for 

other agencies, organizations, and decision makers in South 

Dakota and across the West. Specifically, in South Dakota, 

information relative to the spa­tial distribution of threatened 

and endangered species and invasive or introduced species of 

fish and plants will be available for many streams with little 

or no previous information (fig. 5). The State also will benefit 

by having a new set of environmental monitoring tools and 

techniques available and by having individuals familiar and 

experienced with implementing them to meet future monitoring requirements. Data collected during EMAP-West can serve 

as a baseline for future monitoring efforts and could be used to 

document changing ecological conditions resulting from either 

regu­latory or restorative efforts, or to identify areas where additional or intensified efforts are needed. These data also may be 

useful for assessing trends for some ecological indicators.

Through EMAP-West, USEPA, USGS, and GF&P have 

gained valuable information that can be used to more accurately 

assess the condition of our Nation’s aquatic resources. Furthermore, bioassessment data obtained from EMAP-West could 

be used by SDDENR 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).

The USGS also has benefited from EMAP-West by 

forming new partnerships and strengthening relationships by 

working cooperatively with various State agencies and through 

collaboration with the USEPA. The USGS has provided new 

and timely information concerning the condition of the State’s 

natural resources that can be used in a variety of different ways 

at local, State, or regional levels to advance the science of 

ecological monitoring.

References

Chaloud, D. J., and Peck, D.V., eds., 1994, Environmental Monitoring and Assessment Program: Integrated quality assurance 

project plan for the surface water resource group: Las Vegas, 

Nev., U.S. Environmen­tal Protection Agency 600/X–91/080, 

revision 2.00.

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

(EMAP) activities in South Dakota, 2000–2004: U.S. Geological Survey Scientific Investigations Report 2006–5007.

Omernik, J.M., 1987, Ecoregions of the conterminous United 

States (map supplement): Annals of the Association of 

American Geographers, v. 77, no. 1, p. 118–125, scale 

1:7,500,000.

U.S. Environmental Protection Agency, 1987, Future Risk—

Research strategies for the 1990s: Washington, D.C., U.S. 

Environmental Protection Agency, Science Advisory Board 

SAB–EC–88–040.

U.S. Environmental Protection Agency, 1998, Environmental 

monitoring and assessment pro­gram (EMAP) Research Plan 

1997: Washington, D.C., EPA/620/R–98/002.

U.S. Environmental Protection Agency, 2000, Mid-Atlantic 

Highlands Streams Assessment: EPA–903–R–00–015, 64 p.

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.

For more information, please contact:

Director, South Dakota Water Science Center

U.S. Geological Survey

1608 Mt. View Road

Rapid City, SD 57703

(605) 394-3200

Figure 5.  Field crew members collected Topeka Shiners (Notropis 

topeka) that currently appear on the Federal list of endangered

species. Endangered or protected species were identified,

photographed, and immediately returned to the stream.