U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2007-1302

Prepared in cooperation with the National Park Service

Methods for Monitoring Fish Communities of Buffalo 

National River and Ozark National Scenic Riverways in the 

Ozark Plateaus of Arkansas and Missouri: Version 1.0
Methods for Monitoring Fish 

Communities of Buffalo National River 

and Ozark National Scenic Riverways 

in the Ozark Plateaus of Arkansas and 

Missouri: Version 1

By James C. Petersen, B.G. Justus, H.R. Dodd, D.E. Bowles, L.W. Morrison, M.H. 

Williams, and G.A. Rowell

Prepared in cooperation with the National Park Service

Open-File Report 2007-1302

U.S. Department of the Interior

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

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

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

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U.S. Government.

Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Suggested citation:

Petersen, J.C., Justus, B.J., Dodd, H.R., Bowles, D.E., Morrison, L.W., Williams, M.H., and Rowell, G.A., 2008, Methods for monitoring fish communities of Buffalo National River and Ozark National Scenic Riverways in the Ozark Plateaus of Arkansas and Missouri: Version 1: U.S. Geological Survey Open-File Report 2007-1302, 94 p.
iii

Contents

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

Introduction.....................................................................................................................................................1

Protocol Narrative .........................................................................................................................................3

Background and Objectives................................................................................................................3

Sampling Design ...................................................................................................................................4

Spatial Design...............................................................................................................................4

Establishing the Sample Frame ........................................................................................4

Selecting the Stretches to be Sampled ..........................................................................5

Mainstem..............................................................................................................................5

Tributaries ............................................................................................................................6

Establishing Sample Reaches ..........................................................................................6

Temporal Design ..........................................................................................................................6

Field Methods and Rationale ..............................................................................................................8

Data Management..............................................................................................................................11

Analysis and Reporting......................................................................................................................11

Analysis .......................................................................................................................................11

Reporting.....................................................................................................................................13

Personnel Requirements and Training............................................................................................13

Operational Requirements ................................................................................................................14

Annual Workload and Field Schedule....................................................................................14

Facility and Equipment Needs .................................................................................................14

Startup Costs and Budget Considerations ............................................................................14

Protocol Revision................................................................................................................................14

Protocol for Monitoring Fish Communities..............................................................................................15

SOP 1: Preparation Version 1.0........................................................................................................16

SOP 2: Training Version 1.0...............................................................................................................17

Sampling Efficiency and Consistency Considerations ........................................................17

Safety Considerations...............................................................................................................17

SOP 3: Reach Selection Version 1.0 ...............................................................................................19

SOP 4: Documenting CORE 5 Water-Quality and Weather Conditions Version 1.0.................20

Discrete CORE 5 Sampling with Hand-Held Meters ............................................................20

Unattended CORE 5 Measurements with Data Logging Sondes .......................................20

Analysis and Reporting.............................................................................................................20

NPSTORET ..................................................................................................................................20

SOP 5: Fish Community Sampling Version 1.0...............................................................................21

Electrofishing Overview............................................................................................................21

Seining Overview.......................................................................................................................22

Sampling Methods for Wadeable Streams ...........................................................................22

Electrofishing.....................................................................................................................22

Seining.................................................................................................................................24

Sampling Methods for Nonwadeable Streams ....................................................................25

Electrofishing.....................................................................................................................25

Seining.................................................................................................................................26

Sample Processing Procedures..............................................................................................26
iv

Quality Assurance/Quality Control Procedures....................................................................27

SOP 6: Physical Habitat Collection Version 1.0.............................................................................29

Habitat Collection ......................................................................................................................29

Instream Habitat Assessment .................................................................................................30

Fish Cover....................................................................................................................................30

Bank Measurements.................................................................................................................30

SOP 7: Measuring Stream Discharge Version 1.0........................................................................33

Background Information...........................................................................................................33

Preparation and Meter Calibration.........................................................................................33

Field Measurements..................................................................................................................34

SOP 8: Equipment Maintenance and Storage Version 1.0..........................................................36

Water-Quality and Current Meters .........................................................................................36

Fish Sampling Equipment .........................................................................................................36

SOP 9: Data Management Version 1.0 ...........................................................................................38

Data Model..................................................................................................................................38

Data Recording ..........................................................................................................................38

Data Entry....................................................................................................................................39

Entering Sampling Occasion Data ..........................................................................................39

Entering Fish Data......................................................................................................................43

Entering Habitat and Discharge Data.....................................................................................43

Entering Water-Quality Data....................................................................................................47

Data Verification ........................................................................................................................47

Data Validation ...........................................................................................................................47

File Organization.........................................................................................................................47

Version Control...........................................................................................................................47

Replication ..................................................................................................................................48

Backups.......................................................................................................................................48

Data Availability .........................................................................................................................48

SOP 10: Data Analysis Version 1.0 ..................................................................................................49

SOP 11: Reporting Version 1.0 .........................................................................................................51

SOP 12: Protocol Revision Version 1.0 ...........................................................................................53

Summary........................................................................................................................................................54

References Cited..........................................................................................................................................54

Appendix 1. Fish species collected within Buffalo National River ..................................................62

Appendix 2. Fish species collected or suspected of occurring within Ozark National

 Scenic Riverways...............................................................................................................64

Appendix 3. Mainstem and tributary sites selected by the Generalized Random

 Tessellation Stratified method for monitoring fish communities at

 Buffalo National Park and Ozark National Scenic Riverways....................................67

Appendix 4. Comparison of selected characteristics of the NAWQA, EMAP, and RBP

 protocols and the Ozark Rivers Fish Community protocol...........................................70

Appendix 5. Fish species known to occur in Buffalo National River and Ozark National

 Scenic Riverways classified by tolerance and by habitat, spawning, substrate,

 and trophic preference .....................................................................................................71

Appendix 6. Metrics used in an index of biotic integrity for midwestern streams........................79

Appendix 7. Metrics modified from the original index of biotic integrity for use on the 

 Current River in southeastern Missouri .........................................................................80
v

Appendix 8. Metrics modified from the original index of biotic integrity for use in Missouri

 streams by the Missouri Department of Conservation ...............................................81

Appendix 9. Metrics selected for an index of biotic integrity for wadeable streams in the

 Ozark Highlands..................................................................................................................82

Appendix 10. Equipment necessary for attended water-quality measurements............................83

Appendix 11. Equipment necessary for unattended water-quality measurements .......................84

Appendix 12. Equipment necessary for conducting fish monitoring at Buffalo National River

 and Ozark National Scenic Riverways ..........................................................................85

Appendix 13. Equipment necessary to collect physical habitat data ...............................................86

Appendix 14. Equipment necessary for collecting discharge data...................................................87

Appendix 15. Fish community field forms for recording environmental conditions and reach

 location................................................................................................................................88

Appendix 16. Fish community field forms for recording individual fish data...................................89

Appendix 17. Data sheet for collecting instream habitat data...........................................................90

Appendix 18. Data sheets for collecting fish cover data ....................................................................92

Appendix 19. Data sheets for collecting bank measurement data ...................................................93

Appendix 20. Data sheet for collecting discharge data......................................................................94

Figures

1. Map showing location of Buffalo National River and Ozark National Scenic Riverways..2

2-11. Diagrams showing:

 2. Hypothetical reach location within a stretch .....................................................................7

 3. Flow diagram for fish and habitat data collection .............................................................8

 4. Single pass zig-zag sampling technique used in electrofishing wadeable

 streams................................................................................................................................23

 5. Double pass zig-zag sampling technique used in boat electrofishing for 

 nonwadeable streams .....................................................................................................25

 6. Transect placement for habitat data collection ...............................................................29

 7. Location of instream habitat and fish cover collection at a transect...........................30

 8. Wentworth substrate codes used for instream habitat assessment ...........................31

 9. Location of banks and flood plain.......................................................................................32

 10. Habitat collection points in a reach with a split channel ...............................................32

 11. Points for measuring discharge at a hypothetical cross section..................................34

12. Computer screen capture of data model for fish communities monitoring ........................39

13. Computer screen capture of river fish database switchboard.............................................40

14. Outline of fish community data forms......................................................................................41

15-18. Computer screen capture of:

 15. Detailed location forms for fish data..............................................................................42

 16. Sampling period forms for fish data...............................................................................44

 17. Sampling event forms for fish data ................................................................................45

 18. Fish community data form................................................................................................46
vi

Tables

1. Revisit plans for monitoring studies proposed at Buffalo National River and Ozark

National Scenic Riverways.........................................................................................................7

2. Estimated annual costs for salaries, equipment, supplies, travel, and other

expenditures................................................................................................................................14

3. Key function summary for the Marsh-McBirney FLO-MATE 2000 velocity meter.......... 34

4. Summary of report types released by National Park Service and review procedures..52
vii

Conversion Factors, Datums, and Selected Abbreviations

Multiply By To obtain

millimeter (mm) 0.03937 inch (in.)

centimeter (cm) 0.3937 inch (in.)

meter (m) 3.281 foot (ft)

kilometer (km) 0.6214 mile (mi)

square kilometer (km2

) 0.3861 square mile (mi2)

cubic meter (m3

) 35.31 cubic foot (ft3))

liter (L) 0.2642 gallon (gal)

meter per second (m/s) 3.281 foot per second (ft/s)

cubic meter per second (m3

/s) 35.31 cubic foot per second (ft3))

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

°F = (1.8 × °C) + 32

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

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

AGFC Arkansas Game and Fish Commission

BUFF Buffalo National River 

EMAP Environmental Monitoring and Assessment 

 Program

EPA U.S. Environmental Protection Agency

GIS Geographic information system

GPS Global Positioning System

GRTS Generalized Random Tesselation Stratified

HTLN Heartland Network

I&M Inventory and Monitoring

IBI Index of Biotic Integrity

MDC Missouri Department of Conservation

MORAP Missouri Resource Assessment Partnership

MWSW Mean wetted stream width

NAWQA National Water-Quality Assessment

NPS National Park Service

NRDT Natural Resource Database Template

OZAR Ozark National Scenic Riverways

QA/QC Quality assurance/quality control

RBP Rapid bioassessment protocol

SOP Standard operating procedure

USFWS U.S. Fish and Wildlife Service

USGS U.S. Geological Survey 
Methods for Monitoring Fish Communities of Buffalo 

National River and Ozark National Scenic Riverways in 

the Ozark Plateaus of Arkansas and Missouri: Version 1.0

By James C. Petersen1, B.G. Justus1, H.R. Dodd2, D.E. Bowles2, L.W. Morrison2, M.H. Williams2, and G.A. 

Rowell2

Introduction

Buffalo National River (BUFF), in north-central Arkansas, and Ozark National Scenic Riverways (OZAR), in southeastern Missouri, are the two largest units of the National Park 

Service in the Ozark Plateaus physiographic province (fig. 1). 

In general the two parks have a similar environmental setting. 

The rich fish communities are important components of the 

ecosystems of the two parks. The environmental setting and 

fish communities of the two parks are described in more detail 

in the “Protocol Narrative” section of the report.

The purpose of this report is to provide a protocol (hereafter called the Ozark Rivers Fish Community Protocol within 

this report) that will be used by the National Park Service to 

sample fish communities and collect related water-quality, 

habitat, and streamflow data in BUFF and OZAR to meet 

inventory and long-term monitoring objectives. This report 

was prepared in cooperation with the Heartland Network 

(HTLN) Inventory and Monitoring (I&M) Program of the 

National Park Service. Although the Ozark Rivers Fish Community Protocol was specifically prepared for use at these two 

parks, the protocol should be helpful for planning of similar 

sampling at other National Park Service units. In addition 

to fish sampling methods, the protocol describes pre- and 

post-sampling activities such as planning, data analysis and 

reporting, and care of equipment. The protocol includes (1) a 

protocol narrative, (2) several standard operating procedures 

(SOPs), and (3) supplemental information helpful for implementation of the protocol.

The protocol narrative provides background information 

about the protocol such as the rationale of why a particular 

resource or resource issue was selected for monitoring, information concerning the resource or resource issue of interest, a 

description of how monitoring results will influence management decisions, and a discussion of the linkages between this 

and other monitoring projects. The narrative also gives an 

overview of the various components of the Ozark Rivers Fish 

Community Protocol, including measurable objectives, sampling design, field methodology, data analysis and reporting, 

Abstract

Buffalo National River located in north-central Arkansas, 

and Ozark National Scenic Riverways, located in southeastern 

Missouri, are the two largest units of the National Park Service 

in the Ozark Plateaus physiographic province. The purpose 

of this report is to provide a protocol that will be used by the 

National Park Service to sample fish communities and collect 

related water-quality, habitat, and stream discharge data of 

Buffalo National River and Ozark National Scenic Riverways 

to meet inventory and long-term monitoring objectives. 

The protocol includes (1) a protocol narrative, (2) several 

standard operating procedures, and (3) supplemental information helpful for implementation of the protocol. The protocol 

narrative provides background information about the protocol 

such as the rationale of why a particular resource or resource 

issue was selected for monitoring, information concerning the 

resource or resource issue of interest, a description of how 

monitoring results will inform management decisions, and a 

discussion of the linkages between this and other monitoring 

projects. The standard operating procedures cover preparation, training, reach selection, water-quality sampling, fish 

community sampling, physical habitat collection, measuring 

stream discharge, equipment maintenance and storage, data 

management and analysis, reporting, and protocol revision 

procedures. Much of the information in the standard operating procedures was gathered from existing protocols of the 

U.S. Geological Survey National Water Quality Assessment 

program or other sources. Supplemental information that 

would be helpful for implementing the protocol is included. 

This information includes information on fish species known 

or suspected to occur in the parks, sample sites, sample design, 

fish species traits, index of biotic integrity metrics, sampling 

equipment, and field forms. 

1 U.S. Geological Survey.

2

 National Park Service.
2 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Figure 1. Location of Buffalo National River and Ozark National Scenic Riverways.

Buffalo

National

River

Ozark

National

Scenic

Riverways

Black River

Current

Black

Big Spring

Meramec

Jacks

Illinois

White

Little

River

River

James

Sac 

 River

North 

Pomme

Richland Mill

 River

South Grand

River

Osage R

Osage 

Niangua

River

Fork

River

River

River

St. Francis River

Fork

de Terre

River

White R

 River

 Cr

 Cr

Buffalo River

Gasconade

RIVER

MISSOURI

River

River

94° 93° 92° 91°

38°

37°

36°

EXPLANATION

Ozark Plateaus Physiographic Province

Boston Mountains

Salem Plateau

Springfield Plateau

Base from U.S. Geological Survey digital data, 1994, 1:100,000

Universal Transverse Mercator projection

Zone 15

0 15 30 60 MILES

0 15 30 60 KILOMETERS

Physiographic division boundaries from

N.M. Fenneman and D.W. Johnson, 1946

Pruitt

Harrison

Van Buren

Springfield

MISSOURI

ARKANSAS

Study

area

ARKANSAS

MISSOURI
Protocol Narrative 3

personnel requirements, training procedures, and operational 

requirements. The narrative also summarizes the history of 

decision-making that accompanied protocol development.

The SOPs cover preparation, training, reach selection, 

water-quality sampling, fish community sampling, physical 

habitat collection, measuring stream discharge, equipment 

maintenance and storage, data management and analysis, 

reporting, and protocol revision procedures. Much of the 

information in the SOPs was gathered from existing protocols 

of the U.S. Geological Survey (USGS) National Water Quality 

Assessment (NAWQA) program or other sources. All of the 

SOPs are written to provide information that can be used to 

maximize the accuracy, representativeness, and completeness 

of the fish community data.

Supplemental information includes information such as 

species lists, sample site lists, comparison of this protocol to 

other fish community sampling protocols, species lists, species characteristics lists, index of biotic integrity metric lists, 

and field forms. The supplemental information is included in 

separate appendixes at the end of the report.

Protocol Narrative 

The protocol narrative provides background information 

about the protocol. The narrative also gives an overview of 

the various components of the protocol and summarizes the 

history of decision making that accompanied protocol development. 

Background and Objectives

The extents of BUFF and OZAR are limited to relatively 

narrow bands along much of the Buffalo River (BUFF) and the 

Jacks Fork and Current River (OZAR) (fig. 1). Consequently, 

these streams and the associated natural and historic characteristics are major, unifying features of each park. 

In general, the two parks have a similar environmental 

setting. Water quality is generally very good, typically exhibiting low nutrient concentrations, small amounts of sediment, 

and low concentrations of trace elements and pesticides (Bell 

and others, 1997; Davis and Bell, 1998; Petersen and others, 

1998; Mott and Luraas, 2004). Both parks are in the Springfield or Salem Plateaus, which are typified by limestone and 

dolomite geologic formations. Karst features, such as sinkholes, caves, springs, and sections of streams that interact with 

ground water by gaining or losing streamflow, are common 

in the Springfield and Salem Plateaus. However, much of 

the drainage area of the upstream part of the Buffalo River 

is within the Boston Mountains physiographic area, which is 

typified by sandstone and shale. While springs are relatively 

common in the Buffalo River Basin, they are not the primary 

contributor to its base flow, and some sections of the Buffalo 

River become dry during the summer because of a lack of 

substantial spring flows (Moix and Galloway, 2005). In comparison, several large springs at OZAR constitute a large part 

of the base flow of the Jacks Fork and Current River and water 

temperatures of the Current River are low enough to support 

a trout population (Panfil and Jacobson, 2001). Some of the 

springs that flow into the Jacks Fork and Current River are 

large with annual mean discharges exceeding 0.3 cubic meter 

per second (m3

/s) (Vineyard and Feder, 1974). At OZAR, Big 

Spring has an annual mean discharge of 12.6 m3/s; the annual 

mean discharge of the Current River upstream from Big 

Spring is about 57 m3/s (Hauck and Nagel, 2004). Because 

a much smaller portion of the base flow of the Buffalo River 

comes from springs, water temperatures typically are warmer 

than in the Jacks Fork and Current River (Panfil and Jacobson, 

2001). 

The fish communities of the Buffalo, Jacks Fork, and 

Current Rivers and their tributaries are important components 

of the river ecosystems of these parks. The Ozark Plateaus is 

one of the richest areas of the United States for fish species. 

More than 175 native and introduced species of fish occur 

in the Ozark Plateaus and adjacent areas (Petersen, 1998). 

Petersen and Justus (2005) and Petersen (2005) reported 74 

species of fish from BUFF, and 112 species of fish have been 

reported to occur in or near OZAR (National Park Service, 

2005) (appendixes 1 and 2). Some of these species are unique 

to the Ozarks. The Buffalo and Current River Basins are 

considered “hot spots” for at-risk fish and mussel species 

(species with a vulnerable or imperiled ranking by The Nature 

Conservancy and the Natural Heritage Network) because of 

the presence of 10 or more at risk species (Master and others, 

1998). Because some fish species, including several darters, 

minnows, and madtoms, are considered intolerant of habitat 

alterations (Robison and Buchanan, 1988; Pflieger, 1997; 

Dauwalter and others, 2003), fish community characteristics 

are useful as a monitoring tool to assess changes in water and 

habitat quality. In addition to their value as environmental 

indicators, direct economic value also can be associated with 

several fish species of the two parks because of money spent 

by anglers fishing for species such as bass, trout, and suckers.

The primary objectives for the monitoring described in 

this protocol are related to temporal changes in fish communities and relations between the fish communities and environmental factors based on sites that were randomly selected in 

a spatially balanced design. Information obtained by meeting 

these objectives can be used by park managers to evaluate the 

effects of past and future activities and management decisions 

(either by park managers or others) on fish communities. The 

specific objectives for fish community monitoring in these two 

parks are: (1) to determine the status and trends in BUFF and 

OZAR fish communities by quantifying metrics such as species richness, percent tolerant individuals, percent invertivores, 

and percent omnivores, and using those metrics to calculate 

multi-metric indices (Karr, 1981; Hoefs, 1989; Dauwalter and 

Pert, 2004) for the mainstem and tributaries in each park, and 

(2) to estimate the spatial and temporal natural variability of 

fish community metric values and indices among collection 

sites, and examine correlations between metric values and 
4 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

associated habitat values such as stream size characteristics, 

habitat availability, riparian characteristics, substrate characteristics, and water quality. 

Sampling Design

A long-term monitoring program needs to specify how 

to efficiently sample numerous environmental factors through 

space and time. An overall sampling design must contain 

multiple components including: (1) a spatial design -- how 

sample sites are located and the area of statistical inference, 

(2) a revisit design -- how frequently sites are sampled, and 

(3) a response design -- how and what data are collected. To 

effectively use limited monitoring resources, information 

derived from a relatively small number of sample sites needs 

to infer changes over a much larger area. For the inference to 

be valid, a probability based sample design within a defined 

reference frame is required.

Spatial Design

Establishing the Sample Frame

An integrated aquatic monitoring plan for both BUFF 

and OZAR was developed to include the co-location and 

co-visitation of multiple vital signs (fish, invertebrates, physical habitat, and water quality) (DeBacker and others, 2005). 

The framework for this plan was conceived in a workshop of 

biologists, statisticians, and administrators held in July 2004 

(McDonald, 2004). This protocol focuses on one of these vital 

signs, the fish communities. Specifically, this monitoring is 

concerned with fish inhabiting the mainstem and tributaries 

located within National Park Service jurisdictional boundaries 

at BUFF and OZAR.

The sample unit has been defined to accommodate the 

field protocols for all vital signs. The common sample unit 

definition is a ‘stretch’ of contiguous stream defined by 

minimum and maximum length criteria. The geomorphology 

of these waterways and the resulting biological processes are 

scale-dependent. For example, as streams become larger, the 

distances associated with pool-riffle sequences increase. A 

key characteristic of this overall design is that all aquatic studies should be capable of producing unbiased estimates that are 

applicable to the entire stretch. While stretches must be long 

enough to accommodate unbiased estimates for all studies, 

they do not have to be the same size. Once defined, sample 

unit boundaries will remain fixed and will be used by all studies under the unified monitoring design. 

Two different categories of stretch size were established. 

In the tributaries and upper mainstem, stretch lengths are 1 to 

2 kilometers (km). In the lower mainstem, stretch lengths are 

3 to 5 km. Within categories, stretch length is not fixed, but 

varies depending upon several factors. Stretches were discontinued at natural features, such as at confluences and spring 

runs. They were also delimited based on changes in Valley 

Segment Type (VST) (see geographic information system 

metadata at: http://science.nature.nps.gov/nrdata/metadata.

cfm?ID=41269 for OZAR and http://science.nature.nps.gov/

nrdata/metadata.cfm?ID=41268 for BUFF), which is based on 

gradient, streamflow, temperature, and other factors. Stretches 

in the tributaries were delimited by the flood-plain boundaries. If initial stretches exceeded the maximum stretch length 

because of a lack of confluences or change in VST the initial 

stretch was divided into two or more stretches.

The sample frames (finite lists of sample units, designated as stretches; statistical inferences can only be made to 

sample units that are part of the frame) for BUFF and OZAR 

were determined based on similar criteria, with the differences reflecting the important biological variations in the 

river systems in each park. For both parks, the initial sample 

frame of stretches was constructed through a cooperative 

agreement with the Missouri Resource Assessment Partnership (MORAP). To determine the sample frame at OZAR, 

MORAP used Missouri Aquatic Gap datasets, the same datasets used by the Missouri Department of Natural Resources 

and Missouri Department of Conservation (MDC). This dataset did not exist for Arkansas; therefore, MORAP developed a 

comparable stream network for BUFF.

MORAP used data from the 1:100,000 National Hydrography Dataset (NHD) that was developed by the USGS and the 

U.S. Environmental Protection Agency (USEPA). The coverage included arcs representing the centerlines of wide streams, 

as well as the segments of single line streams. An Arc/Info 

macro was run on the arc segments to pull select attributes 

from various NHD tables and attach them directly to the arc 

component. These stream segments were classified according 

to a number of variables including temperature, stream size, 

streamflow, geology, soil texture, relative gradient, valley wall 

interaction (a surrogate for potential bluff pool habitat), stream 

size discrepancy, and channel type (see geographic information system metadata website listed above for more detailed 

information). The dataset was restricted to stream segments 

that touched the park jurisdictional boundary or other public 

lands adjacent to the park. Additionally, tributaries to the 

mainstem river were cut where they crossed the flood plain of 

the mainstem river. This allowed these segments to be coded 

as “flood-plain” segments.

For both BUFF and OZAR, the final sample frame consisted of all stretches of the mainstem and tributaries that met 

the inclusion criteria described below. Each stretch in both 

frames has associated with it a large number of characteristics 

based on the geographic information system (GIS) data, which 

could be used in analyses as covariates or domains, that is, 

subpopulations of interest with associated estimates of biological characteristics or metrics. 

To establish the final sample frame for each park, the following inclusion criteria and procedures were used :

(1) All stretches that were not entirely or partially within 

the park boundaries were removed (the MORAP dataset 

included adjacent public lands). 
Protocol Narrative 5

(2) All secondary channels were removed (secondary 

channels occur where a waterway splits and flows around 

an island; secondary channels transport the lesser volume of 

water). 

(3) Stretches were stratified as either mainstems of the 

Buffalo River, Jacks Fork, or Current River, or tributaries of 

these streams.

Selecting the Stretches to be Sampled

It was deemed desirable for sample sites to be spatially balanced. Spatial balance is important because: (1) all 

responses are known to be spatially autocorrelated (units close 

to one another tend to yield correlated responses), and (2) 

parkwide inferences are desired. When responses are correlated in space, spatial balance can greatly improve the precision of the resulting estimates. Thus, the Generalized Random 

Tessellation Stratified (GRTS) method of sample selection 

(Stevens and Olsen, 1999; Stevens and Olsen, 2004) was 

employed. The GRTS method generates a random sample that 

is spatially balanced. It allows multiple studies to maximize 

overlap of selected streams by utilizing a common sample, and 

allows units to be added easily after an initial sample has been 

drawn. Additionally, because GRTS samples are not evenly 

spaced, it is not possible for sample locations to be in phase 

with a cyclic response. 

Perhaps the most desirable characteristic of GRTS is that 

for any sample size, any subset of stretches in the ordered 

GRTS sample constitutes a spatially balanced sample. This 

characteristic is desirable because it allows multiple studies 

to maximize overlap and adds stretches in a way that guarantees spatial balance. It also allows each rotating panel (for 

example, in the case of the tributaries; see below) to represent 

a spatially balanced sample from the entire park.

The S-Draw program developed by Trent McDonald 

(available at www.west-inc.com/computer.php) was used to 

draw the GRTS samples, and mainstem sites were weighted by 

stretch length. S-Draw allows for several options in drawing the sample. The hierarchical structure was randomized 

(Stevens and Olsen, 1999). The reverse hierarchical ordering 

option was employed, which assures that any contiguous set of 

stretches will be spatially balanced (Stevens and Olsen, 2004). 

A random number seed generated from the system clock was 

used (the default option).

All GRTS draws were “oversampled,” in that more 

sites were selected and ordered than would be immediately 

sampled. This allows for increasing the number of sites in 

the future, if budget allows, without decreasing the overall 

degree of spatial balance. This also provides flexibility not 

to sample certain sites if an issue arises and nonsampling is 

deemed appropriate. In such a case, one would simply move 

to the next site in the ordered GRTS lists, thus sacrificing only 

a small degree of spatial balance.

Total annual sample size is limited primarily by budget and personnel. It was determined that 12 sites could 

be sampled in each park per year. This takes into account 

complete processing of all samples, and the number of other 

protocols that will need to be implemented at these sites. At 

BUFF (which has many tributaries) each year six mainstem 

sites will be sampled, and six tributaries will be sampled. At 

OZAR (which has fewer tributaries, but many springs), nine 

mainstem sites and three tributaries will be sampled. Sampling of springs at OZAR will be accomplished as part of a 

separate protocol.

Mainstem 

A greater degree of control was desired at OZAR for the 

mainstem than was possible by selecting all sites from the 

same pool with GRTS, which has a strong random element. 

The Jacks Fork, upper Current River, and lower Current River 

(upstream and downstream, respectively, of the confluence 

with the Jacks Fork) are very different systems, primarily because of the influence of large springs. A total of 130 

stretches comprised the sample frame for these mainstems 

for the Current River and Jacks Fork. Stretches on the Jacks 

Fork (number=39) and upper Current (number=53) were 

approximately 1 to 2 km in length. Stretches in the lower 

Current River above the town of Van Buren, where a break 

in the park’s boundary occurs, were approximately 1 to 2 km 

in length, but stretches below Van Buren were roughly 3 to 5 

km in length. The river below Van Buren has higher flows, 

in large part because of the input of Big Spring (annual mean 

discharge of 12.6 m3

/s). A total of 38 stretches were identified 

on the lower Current River. Because of a preference to have an 

equal number of sample sites on each of these three mainstem 

sections the mainstem of OZAR was divided into three sections (stretches from the Jacks Fork, upper Current River, and 

lower Current River) before selecting the GRTS sample.

The Buffalo River also was divided into lower and upper 

sections prior to drawing the GRTS sample. The Buffalo 

River within the park boundary is 198 km long, and crosses 

three major physiographic areas: the Boston Mountains, the 

Springfield Plateau, and the Salem Plateau. There is a losing 

reach on the Buffalo River (Moix and Galloway, 2005) below 

the confluence with Richland Creek where, during periods 

of low flow, much or all of the water runs underground for 

several kilometers before resurfacing at a spring. Thus, the 

river was divided into an upper section (number=47 stretches) 

above the natural break at the losing reach, and a lower section (number=27 stretches) below the spring. This break also 

approximates a major geologic shift, as the upper section 

includes the Boston Mountains (characterized by sandstone 

and shale), and the lower section primarily includes the 

Springfield and Salem Plateaus (characterized by limestone 

and dolomite). The losing reach was deleted from the frame. 

The length of the river for the two sections is similar (89 

km for the upper, 109 km for the lower); the lower section 

contains fewer stretches because the stretches are longer. 

Stretches above the confluence of Mill Creek near Pruitt were 

approximately 1 to 2 km in length, whereas stretches below 

this point were approximately 3 to 5 km in length. Again, this 
6 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

change in stretch length reflects changing river morphology as 

streamflow increases and the riverbed widens. 

Following these criteria, GRTS was used to oversample 

the number of stretches such that half of the sample frame was 

ordered for OZAR (64 mainstem stretches) and BUFF (37 

mainstem stretches). Only the first nine sites at OZAR and six 

sites at BUFF in the GRTS selection will be sampled (appendix 3); however, this procedure will allow possible increases 

in sample size in the future or integration of other studies with 

a larger sample size and still maintain a spatially balanced 

parkwide sample.

Tributaries

To establish the tributary sample frame, all flood-plain 

stretches were removed. This was done because those portions of the tributaries within the flood plain of the mainstem 

are likely to be more variable because of intermittent backwater inundation. These flood-plain stretches represented a 

relatively short section of most tributaries in both parks. The 

resulting sample frame contained a large number of stretches. 

A number of tributaries, although indicated as perennial on 

7.5-minute topographic USGS maps, drain relatively small 

water basins and, according to park personnel, often have low 

or no flowing water. Thus, the sample frame was revised to 

include only tributaries of second order and above. Some of 

the tributaries had multiple stretches within park boundaries. 

Because all tributaries could not be sampled, and sampling 

multiple stretches of the same tributary would yield relatively 

redundant information, the frame was limited to the most 

downstream stretch of each tributary. The distance between 

the most downstream stretch and the confluence with the 

mainstem may be small enough to allow fish communities of 

the mainstem to affect fish communities in the downstream 

stretches of the tributaries (Petersen, 2004), however in many 

cases the available distance upstream from the mainstem 

is limited by park boundaries. The downstream tributary 

stretches are separated from the mainstem by the width of the 

mainstem flood plain, decreasing the influence of the mainstem on tributary fish communities. Because most of these 

tributaries were relatively small, it was determined that sampling could be accomplished in substantially less than 1 km, 

and the minimum acceptable distance for tributary stretches 

within the park boundary was set at 600 meters (m). Reconnaissance surveys were conducted of selected tributaries that, 

based on a study of maps and consultation with park staff, may 

have been too far in the flood plain of the mainstem, or may 

not have had sufficient flow. 

At BUFF, an initial set of 37 tributaries satisfied the 

above criteria. Reconnaissance resulted in adjustment of 

the flood-plain criteria for two tributaries and elimination 

of one tributary because of insufficient flow. Ultimately, a 

total of 32 tributary stretches satisfied the selection criteria 

and constituted the sample frame at BUFF. Thirty of these 

stretches will be sampled on a 5-year rotation (the first 30 as 

ordered by GRTS; appendix 3). If, during the first 5 years, it 

is determined that any of these first 30 tributaries have to be 

deleted from the frame, two alternate tributary stretches can be 

substituted. 

At OZAR, an initial set of 34 tributaries satisfied the 

above criteria. Reconnaissance and consultation with park 

staff, however, resulted in elimination of 18 tributaries that 

were determined to have insufficient flow during the time 

of year selected for sampling (fall). Although many of the 

tributaries at OZAR do contain some water all year, much of 

the flow during the summer and fall is underground through 

the gravel substrate. A total of 16 tributary stretches met the 

selection criteria at OZAR, and constituted the sample frame. 

Fifteen of these stretches will be sampled on a 5-year rotation 

(the first 15 as ordered by GRTS; appendix 3). If, during the 

first 5 years, it is determined that any tributaries need to be 

deleted from the frame, an alternate tributary stretch will be 

substituted.

Establishing Sample Reaches

At each mainstem and tributary stretch, a reach 

will be established for fish monitoring that satisfies specific 

requirements necessary to obtain a representative and unbiased sample (see SOP 3 for details on reach selection). The 

reach length is based on mean wetted stream width (MWSW), 

allowing inclusion of representative macrohabitats (riffle, 

run, and pool habitats) located within the stretch; a length of 

about 20 times the MWSW is used. The downstream end of 

the reach is located at the head of the second riffle upstream 

from the lower stretch boundary (fig. 2). Once located, this 

reach will become a permanent sampling site barring dramatic 

alterations in channel morphology that would require relocation of the sampling reach. 

Temporal Design

At both parks, the revisit design will have an annual 

revisit panel and a set of rotating panels (table 1, appendix 

3). To ensure sufficient representation of monitoring sites 

on the mainstems, the annual revisit panel will consist of 

mainstem stretches (n=6 for BUFF, n=9 for OZAR, or 6 and 

9 sites sampled each year, respectively). The rotating panels 

will consist of tributaries (n=6 for BUFF, n=3 for OZAR, or 

6 and 3 sites sampled each year, respectively), which will be 

sampled every 5 years. At BUFF, 30 total tributary stretches 

will be sampled, while at OZAR (which has fewer tributaries), 

15 total tributary stretches will be sampled. Given the limited 

sample size, this strategy will yield maximum information 

on trends for the mainstems, and maximum spatial coverage 

for the tributaries. If the alternative approach was used for 

the tributaries (maximizing information on trend), we would 

be able to sample only a small fraction of the total number of 

tributaries in each park.
Protocol Narrative 7

Stretch

Fish reach

(20 times the 

mean stream

width)

Head of

second

riffle 

Flow First

riffle

Not to scale

Figure 2. Hypothetical reach location within a stretch.

Table 1. Revisit plans for monitoring studies proposed at Buffalo National River and Ozark National Scenic Riverways.

[An ‘x’ in the year columns indicates all sample units in that panel are to be visited that year]

Year

Study

Revisit

notation1

Panel 

number

 (see 

appendix 

3)

Percent of

 annual

effort 1 2 3 4 5 6 7 8 9 10 11 12

Annual 50 x x x x x x x x x x x x

Buffalo National River

[1-0,1-4]

1 50 x x x

2 x x x

3 x x

4 x x

5 x x

Ozark National Scenic

 Riverways

[1-0,1-4]

Annual 75 x x x x x x x x x x x x

1 25 x x x

2 x x x

3 x x

4 x x

5 x x

1 1-0 indicates an annual panel (1 year of sampling, followed by 0 years of nonsampling). 1-4 indicates a 5-year rotating panel (1 year of sampling, followed 

by 4 years of nonsampling). 
8 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Fish communities at BUFF and OZAR consist of diverse 

assemblages of species in different developmental stages 

with various movement patterns or behaviors. Therefore, it 

is essential that samples are collected within the same timeframe each year to reduce variability in assemblage structure. 

Mass movement of fish is highest during early spring and 

late fall/early winter when fish move between overwintering 

and feeding habitats or make spawning migrations. Because 

this redistribution of species and large numbers of fish can 

cause high variability in assemblage composition and structure within a stream, fish monitoring will be conducted once 

a year during early summer to early fall (May 15 - October 

31) when communities are more stable. Sites at BUFF will 

be sampled in May/June because of the potential drying of the 

upper mainstem and small tributaries in late summer and fall. 

At OZAR, sites will be sampled in October when water levels 

are low to allow for high sampling efficiency. In addition, the 

number of recreational users (for example, canoers, boaters, 

and swimmers) is reduced substantially at OZAR in the fall, 

minimizing disturbance of the sites during sampling. Samples 

at each park should be collected within a short timeframe 

(4-5 weeks) to reduce seasonal effects. If this is not possible 

because of weather conditions, flooding, or other uncontrollable situations, mainstem samples need to be collected within 

one timeframe and tributaries within another timeframe during 

the sampling period for each park (summer at BUFF and early 

fall at OZAR). Following a large, natural disturbance such as 

a flood, at least 2 weeks should be allowed for stabilization of 

fish assemblages prior to sampling.

Field Methods and Rationale

Prior to the field season each year, personnel need to 

review the entire protocol for fish community sampling and 

begin planning for the field activities. Early review of SOP 1 

(preparation) and SOP 2 (training) are particularly important 

because of potential need to address some matters months 

before the fieldwork season begins. Fieldwork must be scheduled in advance so that crews can be assigned. Time spent at a 

sampling site will vary, but 8 or more hours is typical.

Sites generally are sampled in late May through October. Relatively low flows in Ozark streams generally occur in 

June through October (Adamski and others, 1995) and by July 

spawning activities will have declined (if not ceased) for most 

species. Increased leaf fall in late September through October 

can be of some concern because of reduced visibility caused 

by the presence of leaves on the surface of some parts of the 

streams. Sampling location will be determined by random 

selection of sampling stretches, wetted stream width, and 

relation of riffle location to downstream end of the sampling 

stretch (see SOP 3 for details). At each reach, water-quality 

(SOP 4), fish community (SOP 5), habitat data (SOP 6), and 

discharge data (SOP 7) will be collected (fig. 3).

Measure stream width and

calculate reach length

Collect initial CORE 5 water quality

Sample fish within the reach

Locate lower reach boundary

Collect ending CORE 5 water quality

Process fish samples Collect habitat data

Collect discharge data

Locate upper reach boundary

Establish permanent reach

Figure 3. Flow diagram for fish and habitat data collection.
Protocol Narrative 9

Fish communities will be sampled using electrofishing 

and seining methods (SOP 5). Depending on stream width 

and depth, communities will be sampled using backpack, 

towed barge, or boat electrofishing equipment. At sites where 

stream depth requires that boat electrofishing be used, towed 

barge or backpack electrofishing equipment also will be used 

in shallower areas so that benthic species and other small 

species can be sampled adequately. Seines can be used in 

wadeable portions of runs, pools, and backwaters. Riffles will 

be sampled using backpack or towed barge electrofishing gear 

in conjunction with kick seines. 

When monitoring, it is important to note that gear type 

and gear efficiency have been shown to affect fish community data. In a study of multiple-year and multiple-reach fish 

community data from 55 NAWQA sites, Meador and McIntyre 

(2003) found that among electrofishing methods (backpack, 

towed barge, and boat), Jaccard (similarity) index and percent 

similarity index values were significantly greater for backpack electrofishing. Meador and McIntyre (2003) calculated 

the absolute difference between mean species richness for 

multiple-reach and for multiple-year samples and found the 

mean difference for backpack electrofishing, towed barge electrofishing, and boat electrofishing was 0.8 species, 1.7 species, 

and 4.5 species, respectively. These findings indicated relatively high variability in species richness in samples collected 

by boat electrofishing among years. In a comparison of the 

use of backpack electrofishing equipment and a 9.1-m (6-mm 

mesh) minnow seine in Missouri Ozark streams, Rabeni and 

others (1997) found that the minnow seine generally was less 

efficient than the backpack equipment. Efficiencies associated with seining ranged from 0 to approximately 60 percent 

dependent on the fish species, and efficiencies associated 

with backpack equipment ranged from approximately 5 to 65 

percent. They also found that species richness and ShannonWeaver diversity values were consistently lower for samples 

collected with seines than for samples collected with backpack 

electrofishing equipment. However, when data were corrected 

for gear efficiency differences, the richness and diversity 

values were similar. These results (Rabeni and others, 1997; 

Meador and McIntyre, 2003) suggest that data collected using 

different gear, or different combinations of multiple types of 

gear, will be affected by gear type. Therefore, it is imperative 

that gear type used and sampling effort at a site be consistent across years (see appendix 3). It can be important that 

multiple gear types be used at a site to obtain a representative sample because of differences in efficiency for collecting 

certain size fish in specific habitats. For example, large fish in 

deep pools can be more efficiently collected with boat electrofishing equipment and small benthic species in riffles can be 

more efficiently collected with backpack equipment. Where 

appropriate, using multiple types of gear (such as multiple 

types of electrofishing equipment and seines) can increase the 

likelihood of collecting all species present within a reach.

When processing samples and recording data, all sample 

data such as gear used, time spent sampling, electrofishing settings, number of seine hauls, length of stream through which 

the seine was pulled, and species data collected with the gear 

type will be recorded separately for each gear and channel 

type (main channel and backwater/side channel). To the extent 

practical, individual fish will be identified in the field using 

appropriate fish identification keys and other information. 

Specimens that cannot be reliably identified in the field will be 

preserved for identification in the laboratory (see SOP 5). 

There are three alternatives to resolve the problem of analyzing data collected by different gear. First, data can be considered to be affected primarily by the size of the stream when 

gear type usage is based on the stream size and, therefore, data 

are treated as being equivalent across all gear types. Second, 

data can be compared only with other data collected using 

the same gear types. Third, the raw data can be corrected for 

differing gear efficiencies before making comparisons across 

sites associated with different gear types. Analysis for this 

protocol will use the first approach listed above. Because samples collected with electrofishing gear are based on equivalent 

effort (time), all electrofishing samples at a reach will be combined for analysis of fish community trends. However, there 

may be specific monitoring questions where analyzing data by 

channel type or by electrofishing gear is necessary. Therefore, 

in the field, data from different channel type and electrofishing gear will be kept separate. Data collected with seines are 

based on area sampled and will be analyzed separately from 

electrofishing data. 

Habitat data will be collected to establish relations 

between environmental variables and fish communities and to 

determine specific factors affecting community composition 

and structure. A point-transect method will be used to collect 

data on general channel morphology, fish cover, and bank conditions (see SOP 6). Habitat will be sampled in conjunction 

with fish sampling and water-quality measurements. 

Several different sampling approaches or protocols have 

been used by State and Federal agencies to quantify status and 

trends in fish communities. A set of protocols developed by 

the USEPA--the rapid bioassessment protocols (RBPs) (Barbour and others, 1999)--has been adopted by many State agencies and monitoring groups. These RBPs are designed to give 

a quick, broad picture of stream quality and fish assemblages 

throughout a region with minimal field and laboratory efforts. 

Other monitoring groups also use the EPA Environmental 

Monitoring and Assessment Program (EMAP) protocols for 

wadeable (McCormick and Hughes, 1998) and nonwadeable streams (McCormick and Hughes, 2000), and the USGS 

protocols developed for the NAWQA program (Moulton and 

others, 2002). These latter two protocols have more rigorous 

data collection and quantitative methods giving a more complete assessment of fish community composition and structure 

(for example, collection of fish lengths and weights and more 

specific designation of reach length). NAWQA protocols 

or similar methods have been used at several sites at BUFF 

(Petersen, 1998, 2004) and OZAR (Petersen, 1998).

The Ozark Rivers Fish Community Protocol is based on 

the NAWQA approach with selected procedures largely following NAWQA protocols. However, some modifications to 
10 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

the NAWQA protocol were necessary to meet specific requirements of this fish monitoring program (appendix 4). These 

modifications were compiled from EMAP and RBP protocols, 

other literature related to fish community sampling procedures 

and considerations, and from a spatial and temporal sampling 

design for BUFF and OZAR developed during a workshop 

convened by the NPS in July 2004 at Columbia, Missouri 

(McDonald, 2004). 

The Ozark Rivers Fish Community Protocol shares 

many similarities with NAWQA, EMAP, and RBP protocols 

(appendix 4). This protocol is similar to NAWQA protocols 

in terms of length sampled, electrofishing gear used, and data 

collection for fish communities. However, two primary differences between this protocol and the NAWQA protocol relate 

to site selection and electrofishing procedures. In this protocol, 

the locations of the sampling reaches are randomly selected 

and spatially balanced rather than using professional judgment 

or other criteria (see Selecting the Stretches to be Sampled 

section above). NAWQA sampling sites are selected based 

on professional judgment and other criteria such as access, 

presence of streamflow instrumentation, land-use characteristics, and other specific objectives. Objectives of fish community sampling within BUFF and OZAR require that sites 

be selected randomly. The spatially balanced and random site 

selection method used in this protocol allows inferences to 

be made about fish communities in nonsampled areas of the 

parks.

The second primary difference between this protocol 

and the NAWQA protocol is the electrofishing effort used. 

In this protocol, fish communities of wadeable streams are 

sampled using single pass electrofishing, while NAWQA 

protocols specify that two passes be used (appendix 4). Single 

pass electrofishing corresponds with methods described in 

the RBPs (Barbour and others, 1999) and EMAP protocols 

(McCormick and Hughes, 1998, 2000). The advantage of 

single pass electrofishing is that a site can be sampled using 

fewer manhours at reduced cost; however, this approach has 

potential limitations. A study by Meador and others (2003) 

that evaluated 183 NAWQA samples collected at 80 sites 

using backpack electrofishing equipment found that the number of species collected after two passes was greater than the 

number of species collected after a single pass in 50.3 percent 

of the samples. The percentage of the estimated total species 

richness (based on a two-pass removal model) collected during 

the first pass averaged 89.9 percent and ranged from 40 to 100 

percent. However, Meador and others (2003) did not address 

the effects of sampling effort, such as seconds of electrofishing 

time, on the number of species collected and did not specifically address the effects of single-pass or two-pass sampling 

on relative abundance estimates. Pusey and others (1998) 

suggested that data from a single pass alone may compromise 

the ability to relate fish community structure to environmental 

conditions. However, Simonson and Lyons (1995) found that 

catch per effort (catch per unit time in one pass) provided the 

same values for species richness and percent species composition as depletion sampling (three to four passes) and took 

only one-fourth the time required for depletion sampling. 

This study reported an average of 10 species collected with 

three to four passes compared to 9 species with a single pass 

of a towed electrofishing barge (Simonson and Lyons, 1995); 

greater differences in the number of species collected might 

occur in Ozark streams with greater species richness. Meador 

and others (2003) also concluded that multiple pass electrofishing at a large number of sites across a large geographic 

area may not be cost effective. 

Differences between this protocol and the EMAP and 

RBP protocols also are associated with sampling effort 

(appendix 4). For wadeable streams, EMAP sampling efforts 

can be distributed in a specific manner between transects 

within the reach, specific time limits (minimum of 45 minutes, 

maximum of 3 hours) are used, and reach lengths are 40 times 

the wetted channel width. For RBP, reach length criteria considerations are described, but specific length criteria are not 

given. In nonwadeable streams, electrofishing in the EMAP 

protocol is restricted to the area along one bank and use of a 

boat; while the RBP protocols are not designed for nonwadeable streams. Other differences are that, for the EMAP and 

RBP protocols, block nets are sometimes used at the ends of 

the reach and seining is not required. Potential disadvantages 

associated with these methods include the time and effort 

required to establish transects, to monitor the distribution of 

effort (sampling time) between the transects, and to set block 

nets. Using EMAP protocols, restriction of sampling of nonwadeable streams to boat electrofishing of a single bank may 

lead to undersampling of species that are less associated with 

streambanks and more associated with mid-channel pools and 

runs, and undersampling small benthic species such as darters, 

madtoms, and sculpins. Repeatable sampling of mid-channel 

areas in nonwadeable streams can be difficult, however, 

because of the patchiness of habitats and their associated species.

A number of reach length determination methods have 

been recommended for monitoring fish communities. The 

Ozark Rivers Fish Community Protocol follows the NAWQA 

protocol (Fitzpatrick and others, 1998; Moulton and others, 2002), which specifies reach lengths of approximately 

20 MWSW (at low flow) and a reach generally ranges from 

150 to 300 m for wadeable streams and from 500 to 1,000 m 

for nonwadeable streams. The EMAP protocols recommend 

sampling of 40 times MWSW with a minimum reach length 

of 150 m. However, Dauwalter and others (2003) developed 

their Index of Biotic Integrity (IBI) for wadeable Ozark Highlands streams in Arkansas for a reach length of 51 times the 

MWSW. Applying these two multipliers to nonwadeable sections of the lower Buffalo River would result in reach lengths 

of approximately 1,200 to 3,000 m, and reach lengths in lower 

sections of the Current River could exceed 2,000 to 5,000 m. 

Because sampling a reach length of more than about 2,000 m 

is logistically and monetarily impractical, and because metrics 

based on relative abundance data for reaches of 20 MWSWs 

and 80 MWSWs were not significantly different (p<0.05) 

(Dauwalter and Pert, 2004), sampling a reach length of 20 
Protocol Narrative 11

MWSWs should adequately describe most aspects of the fish 

communities of sites. Although Dauwalter and Pert (2004) 

found IBI values calculated from reaches of 20 MWSWs were 

significantly different from IBI values collected from reaches 

that were 50 MWSWs, these values were not substantially 

lower (less than 5 IBI units). An advantage of using similar 

reach lengths at BUFF and OZAR will be direct comparison 

of IBI scores.

Data Management

Data management procedures are an important part of 

any long-term monitoring program in that they provide data 

consistency, data security, and availability over time. Therefore, care must be taken to ensure that adequate time and 

personnel are available for accurate data recording, data entry 

and verification, and analysis. At the core of this data management is the monitoring database organized by primary and 

ancillary data. 

Primary data consist of reach identification and site 

description, sampling personnel, sampling date, sampling 

time, equipment description, sampling duration, and fish 

community data. Examples of ancillary data records include 

identification of various environmental characteristics. 

Data processing typically involves the following steps: 

data entry, data verification, data validation and backups/storage (see SOP 9 for details on each step). Data entry consists 

of transferring field data from field sheets into a monitoring 

database using data-entry forms. Data verification immediately 

follows data entry and involves checking the accuracy of computerized records against the original source, usually paper 

field records. Validation procedures seek to identify generic 

errors, such as missing, mismatched, or duplicate records, as 

well as logical errors specific to particular projects. Spatial 

validation of location coordinates can be accomplished using 

GIS. Global Positioning System (GPS) points are validated 

against DRGs (digital raster graphic files) or DOQQs (digital 

ortho-quarter quadrangles) for their general location.

Frequent backups are critical for preventing loss of longterm data. Full backup copies of the monitoring project are 

stored at an off-site location for safe keeping. Additional digital copies are forwarded to the NPS (WASO) NR-GIS Data 

Store (http://science.nature.nps.gov/nrgis/), NatureBib (http://

www.nature.nps.gov/nrbib/), and NPSpecies Database (http://

science.nature.nps.gov/im/apps/npspp/index.cfm) Systems. 

Analysis and Reporting

Analysis

To provide park staff with information about the natural resources they manage, a long-term monitoring program 

needs a reliable reporting system. The data analysis process, 

however, needs to be flexible enough to allow the use of newly 

developed statistical and analytical techniques and tailoring 

of analyses for a variety of audiences. In determining the 

appropriate statistical approaches for this monitoring protocol, 

it is crucial to consider the primary audience of the various 

reports that will result. This primary audience will consist 

of park resource managers, superintendents, and other staff. 

Park resource managers and staff may not have an indepth 

background in statistical methods, and park superintendents 

may have limited time to devote to such reports. Additionally, 

protocols such as this one may provide much data on many 

different types of variables. Thus, to the extent possible, it 

is important that core data analysis and presentation methods 

are relatively straightforward to interpret, provide a standard 

format for evaluation of numerous variables, can be quickly 

updated whenever additional data become available, and work 

for many different types of indicators, whether univariate or 

multivariate. Additionally, the type and magnitude of variability or uncertainty associated with the results should be somewhat intuitive, and it may be necessary to indicate a threshold 

for potential management action. 

There are four main statistical approaches that can be 

employed with data from long-term monitoring projects: (1) 

testing hypotheses, (2) estimating biological characteristics 

or metrics, (3) multivariate analyses, and (4) applying Bayesian methods. When analyzing ecological data, statisticians 

predominantly employ frequentist methods, and thus many 

resource managers are not familiar with the interpretation of 

Bayesian approaches. Furthermore, Bayesian methods are not 

widely used because they are often difficult to apply, and many 

researchers are not comfortable specifying subjective degrees 

of belief in their hypotheses (Utts, 1988; Hoenig and Heisey, 

2001). Accordingly, the Bayesian approach is not promoted as 

the main method of data analysis in this protocol.

Most hypothesis testing approaches involve a null 

hypothesis of no difference or no change. The problem with 

such approaches is that the hypothesis under test is trivial 

(Cherry, 1998; Johnson, 1999; Anderson and others, 2000, 

2001) because no populations or communities will be exactly 

the same at different times. Thus, the interest of this monitoring program is not whether fish communities are changing, but 

rather in the magnitude of the change, and whether it represents something biologically important. Null hypothesis significance testing relies heavily on P-values, and results primarily in yes/no decisions such as rejecting or failing to reject the 

null hypothesis. P-values are influenced strongly by sample 

size, and with a large enough sample size, one may obtain a 

statistically significant result that is not biologically important. 

Alternatively, with a small sample size, one may determine 

that a biologically important result is not statistically significant (Yoccoz, 1991). Thus, traditional null hypothesis 

testing places the emphasis on the size of the P-value, which is 

dependent on sample size and rejection of the null hypothesis, 

whereas more concern should be placed on whether the data 

support meaningful scientific hypotheses that are biologically 

significant (Kirk, 1996; Hoenig and Heisey, 2001).
12 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Estimation of biological characteristics or metrics 

(hereafter referred to as “metric estimation”) provides more 

information than hypothesis testing, is more straightforward 

to interpret, and easier to compute (Steidl and others, 1997; 

Gerard and others, 1998; Johnson, 1999; Anderson and others, 2000, 2001; Colegrave and Ruxton, 2003; Nakagawa and 

Foster, 2004). Metric estimation emphasizes the magnitude 

of effects and the biological significance of the results, rather 

than making binary decisions (Shaver, 1993; Stoehr, 1999). 

There is no formal classification of error associated with 

metric estimation. One of the primary recommendations from 

a workshop on environmental monitoring organized by the 

Ecological Society of America was that trend studies should 

focus on description of trends and their uncertainty, rather than 

hypothesis testing (Olsen and others, 1997). Thus, most of 

the data analysis suggested in this protocol will take the form 

of metric estimation, rather than null hypothesis significance 

testing. 

Several metrics and analysis techniques have been used 

to detect trends in fish communities and investigate the relations between fish communities and environmental conditions. 

Two common approaches are calculation of individual metrics 

and multiple metric biological indexes (Plafkin and others, 1989; Hughes and Oberdorff, 1998; Barbour and others, 

1999; Simon, 1999), and multivariate statistics (for examples 

applying to Ozark fish communities see Petersen, 1998, 2004). 

Using multiple analytic approaches will provide multiple lines 

of evidence, increasing the validity and confidence of study 

conclusions. A detailed summary of calculated metrics and 

data analysis are given in SOP 10. 

Biological metrics are commonly used by scientists to 

compare the condition of the biological community at multiple 

sites (Simon, 1999) or across time. A metric is a characteristic 

of the biota that changes in a predictable way with increased 

human disturbance (Barbour and others, 1999). Attributes of 

the fish community such as degree of tolerance to disturbance, 

habitat and substrate preferences, spawning preferences, and 

trophic status (appendix 5) are measures frequently reflected 

in metrics making it possible to determine relations between 

biological communities and environmental conditions. 

An extension of the metric approach is to combine multiple metrics into an IBI. This index is used as an indicator 

of overall stream quality, enabling investigators to compare 

conditions at multiple sites (Karr, 1981; Barbour and others, 

1999; Simon, 1999) or at a single site across time. Prior to use 

of fish communities as bioindicators, aquatic invertebrate communities were, and still are, used as indicators of stream quality (Hilsenhoff, 1977). Because of the popularity of fish with 

the general public and stakeholders, fish communities are the 

most commonly used bioindicator for investigating ecological 

relations using the IBI approach (Barbour and others, 1999; 

Simon, 1999). 

One of the first fish IBIs (appendix 6) developed by Karr 

(1981) has been modified for use in many other regions and 

countries (Hughes and Oberdorff, 1998; Simon, 1999). IBI’s 

have been created for three ecoregions in Arkansas (Hlass 

and others, 1998; Dauwalter and others, 2003; Justus, 2003; 

Dauwalter and Jackson, 2004) and for Ozark Highland streams 

(Hoefs, 1989; Dauwalter and others, 2003; and Matt Combes, 

Missouri Department of Conservation, written comm., 2006). 

Hoefs (1989) modified metrics and scoring criteria from 

Karr’s (1981) original index for use in the Current River Basin 

(appendix 7) in southeastern Missouri. Hoefs’ IBI is specific 

to the Current River, and has not been submitted for rigorous peer review. The existing IBI used by the MDC contains 

modified metrics from various IBIs to assess fish communities in the Ozarks (Matt Combes, Missouri Department of 

Conservation, written comm., 2006) (appendix 8). Again, this 

Missouri IBI has not been rigorously peer reviewed and may 

not be applicable to HTLN monitoring data because this IBI 

is based on methods and equipment used specifically in the 

MDC stream assessment program. Within the next 5 years, a 

regionally based IBI for Missouri may be developed through 

joint efforts of MDC and the University of Missouri (Matt 

Combes, Missouri Department of Conservation, oral comm., 

2006). Once developed and peer reviewed, the new Missouri 

IBI will be evaluated for use in the Current River watershed. 

Dauwalter and others (2003) evaluated 38 candidate metrics 

and selected 7 metrics for an IBI applicable to fish communities in wadeable streams of the Ozark Highlands (appendix 

9). Because the IBI by Dauwalter and others (2003) was 

developed for the Ozark Highland region and has been peer 

reviewed, this IBI will be used for assessing fish community 

conditions and stream quality in BUFF and OZAR. 

Multivariate analyses are another commonly used statistical method to explain variability in community data and 

attribute that variability to specific environmental variables or 

gradients (Gauch, 1982; Jongman and others, 1995; Everitt 

and Dunn, 2001; Timm, 2002). Multivariate techniques differ from univariate or bivariate analyses in that the former 

techniques generate a hypothesis from the biological data 

rather than disproving a null hypothesis, and the effectiveness 

improves as the number of variables increase (Williams and 

Gillard, 1971). Two multivariate techniques commonly used 

to analyze community data include ordination and classification (Gauch, 1982; Jongman and others, 1995; Everitt and 

Dunn, 2001; Timm, 2002). 

Control charts also will be employed in data organization and analysis. Control charts, developed for industrial 

applications, indicate when a system is going ‘out of control,’ 

by plotting through time some measure of a stochastic process 

with reference to its expected value (Beauregard and others, 

1992; Gyrna, 2001; Montgomery, 2001; Morrison, in press). 

Control charts may be univariate or multivariate, and can represent many different types of variables. Control charts have 

been applied to ecological data (McBean and Rovers, 1998; 

Manly, 2001), including fish communities (Pettersson, 1998; 

Anderson and Thompson, 2004) and natural resources within 

the NPS’s inventory and monitoring program (Atkinson and 

others, 2003). Control charts contain upper and lower control 

limits specifying thresholds beyond which variability in the 

indicator (estimated metric) reveals a biologically important 
Protocol Narrative 13

change is occurring, and warns that management may need to 

act. Control limits can be set to any desired level.

Although the primary approach to organizing and analyzing data will consist of metric estimation combined with the 

use of control charts, the use of other statistical methods are 

not ruled out at this time. Because of the nature of this longterm monitoring program, other approaches (some which may 

not have even been developed yet) may be appropriate at different points in time, depending upon the needs of the resource 

managers and questions of interest.

A formal power analysis for this protocol was not conducted for three reasons (Morrison, 2007): (1) The primary 

purpose of conducting a prospective power analysis is to determine whether the proposed sample size is adequate. Because 

sample size for this monitoring program is determined 

primarily by budget, an increase in sample size is not possible 

regardless of the result of any power analysis. Furthermore, in 

many analyses sample size will equate with number of years; 

in this case, analyses will simply become more powerful over 

time. (2) Statistical power is dependent upon the hypothesis 

under test and the statistical test used. Over the course of this 

long-term monitoring program, different questions will be of 

interest, and various hypotheses could be evaluated. Thus, 

there is no single “power” relevant to the overall protocol. 

Estimating power at this point in the context of such a longterm, multifaceted monitoring program could be potentially 

misleading, as the test this power is based upon may rarely (or 

never) actually be employed. (3) Most data analyses will take 

the form of metric estimation with control charts, rather than 

null hypothesis significance testing. When estimating metrics, 

there is no associated statistical power. 

Reporting

To distribute findings about the resource in a timely manner, it is necessary to distribute results, including data analysis, 

interpretations, and recommendations from fish community 

monitoring on an annual basis to park managers and State 

agencies. Annual reports will be submitted to the superintendents and resource management staff of each park and to the 

HTLN program. The purpose of annual reports is to update 

general findings and status of the fish community. These 

reports will not deviate substantially from year to year in terms 

of structure or analyses used (see SOP 11). Scientific collection permits are required in Arkansas and Missouri and must 

be renewed annually. As part of the permit process, an annual 

report of the collection activities must be sent to the Arkansas 

Game and Fish Commission (AGFC) and the MDC. 

More extensive summary reports containing trend analysis and detailed explanations of findings will be completed 

every 5 years. The purpose of these reports is to describe 

trends in fish communities and habitat quality, determine 

relations between environmental conditions and fish assemblages, and interpret relations between observed trends and 

park management or land-use changes. Summary reports will 

be sent to park superintendents and resource management staff 

and to HTLN. 

Personnel Requirements and Training 

The personnel required to conduct fish community 

sampling depends on several variables including those related 

to safety, accessibility, and stream size. Safety and time 

considerations largely determine how many personnel are 

necessary for fish sampling, particularly when site access is 

poor (because poor site access may require a larger crew). 

Stream size also dictates the number of personnel needed. For 

example, smaller sites may require only three to four people, 

while larger sites require a minimum of five to six. Therefore, based on the size range of sites sampled in this program 

and the potential difficulties in accessing random sites, fish 

community monitoring will require a minimum crew of five 

each year. The crew will be made up of the fisheries biologist 

(project manager), two aquatic ecologists, and two seasonal 

technicians. The aquatic program leader will also participate 

in fieldwork as their schedule permits, and occasional assistance from park staff or State agencies may be necessary. 

Critical to the success of a monitoring program is a high 

level of consistency in field collection and data analysis from 

year to year. To obtain this consistency, it is necessary to have 

a competently trained staff and, preferably, the same staff 

every year (SOP 2). For the field crew, the fisheries biologist (project manager) and two aquatic ecologists will remain 

relatively consistent from year to year. The project manager 

is responsible for implementing the monitoring protocol, 

leading fish community surveys, and training all crewmembers. Because the aquatic ecologists on the crew will be fairly 

consistent from year to year, they will also help the project 

manager train crewmembers as well as help with fish surveys. 

Training should be done prior to each field season with each 

crewmember reviewing the SOPs outlined in this protocol. 

Training should include discussions with crewmembers on 

safety protocols for fieldwork (SOP 2), demonstrations on 

proper use of water-quality meters (SOP 4), GPS units, and 

electrofishing/seining equipment (SOP 5), and practice of 

proper sampling techniques and fish identification (SOP 5). 

In addition to implementing the monitoring, the project 

manager, in collaboration with the data manager, is responsible for managing the collected data. The project manager 

will be responsible for data collection and entry, data verification and validation, and data analysis and reporting. The data 

manager is responsible for database design and modification, 

archiving and securing the data, and dissemination of the data. 

The data manager also is responsible for constructing adequate 

quality assurance/quality control (QA/QC) procedures and 

automating report generation based on the project manager’s 

analysis needs. 
14 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Operational Requirements 

Annual Workload and Field Schedule

Twelve sites will be sampled annually in each park. 

Sampling will begin in early summer at BUFF and early fall 

at OZAR. A minimum of 12 to 14 days will be necessary to 

complete fish monitoring at each park. However, the amount 

of field-person days will depend primarily on site location, 

logistics, and weather. Because of crew safety and protection 

of field equipment, fish monitoring will not be conducted in 

inclement weather, such as thunderstorms. Thus, specific dates 

will not be designated for fieldwork, but a month-long period 

will be scheduled for sampling each park. 

Facility and Equipment Needs

Fish community monitoring will require a laboratory 

to process preserved specimens, in addition to office space 

and storage needs for equipment. The laboratory, presently 

stationed at Missouri State University (Springfield, Missouri), must contain a sink; a flame proof, hazardous materials 

cabinet for storage of preservatives; a work bench; a dissecting 

microscope for identifying small specimens; and shelves for 

storing specimens. Electronic equipment that is temperature 

sensitive, such as data loggers and meters, should be stored in 

the laboratory or office. Equipment not sensitive to temperature fluctuations, such as generators, boat motors, and nets, 

should be stored in a small shed. A summary of field equipment is located in appendixes 10-14. 

Startup Costs and Budget Considerations

Startup costs and annual budgets are important considerations for any monitoring program. Annual costs (in 2007 

dollars) for conducting monitoring are summarized in table 

2. Many network staff including the program coordinator, 

quantitative ecologist, and project leader play a role in this 

monitoring effort and their contributions are accounted for 

in the salary line item. Expenses for fieldwork are based on 

a minimum crew of five people (table 2). Occasional assistance from park staff and State agencies may be necessary to 

complete fish sampling and will offset salary and travel costs 

for the monitoring program. Field costs will vary from year 

to year based on participation of park staff and State agencies, skill level of crew, and size of crew. Startup cost for field 

equipment includes the purchase of a boat electrofishing unit, 

two backpack electrofishing units, a towed barge unit, boat 

motor, and various field equipment (such as waders, nets, and 

gloves) (appendix 12). A majority of the items included under 

field equipment are for long-term use and will only need to 

be purchased during the startup phase of the program (such as 

boat electrofishing unit, and boat motor). Supplies include: 

(1) items that need to be replaced or replenished every year, 

such as jars and preservative for specimens, and waterproof 

paper for recording data, (2) items used for maintenance of 

field equipment, such as oil for boat motors, and (3) equipment shared among projects (such as GPS units and cameras). 

Table 2. Estimated annual costs for salaries, equipment, supplies, 

travel, and other expenditures.

Expense categories

Estimated

cost

 (2007)

Salary $99,553

Field/office equipment $1,710

Supplies $1,140

Computer hardware and software $950

Fieldwork travel $3,610

Vehicle lease $2,280

Overhead to Missouri State University $625

Administrative support to Wilson’s Creek National 

Battlefield $1,470

Laboratory fees $2,500

Total $113,838

Protocol Revision

Revisions to this protocol may be necessary for several reasons, including the development of new statistical 

approaches or more informative metrics and the improvement 

of data-collection methodology. Therefore, documentation of 

protocol revisions is mandatory for maintaining consistency in 

data collection and analysis between the earlier and the revised 

version. The purpose for dividing the protocol into the Protocol Narrative and supporting SOPs is to organize the protocol 

such that minor changes do not require a revision of the entire 

protocol. The Protocol Narrative is a general overview on the 

background and justification for the monitoring project and an 

overview of sampling design and methodology. In contrast, 

SOPs contain more detailed information on completing tasks 

required for monitoring. SOPs may need to be revised more 

frequently than the Protocol Narrative, and changes to SOPs 

do not require revision of the Protocol Narrative section unless 

major changes are made. All versions of the Protocol Narrative and SOPs must be archived in a protocol library, and a 

history log must be filed. Detailed steps on how to change the 

protocol and document these revisions are located in SOP 12. 
Protocol for Monitoring Fish Communities 15

Protocol for Monitoring Fish 

Communities

The protocol for monitoring fish communities of BUFF 

and OZAR, as part of activities of the NPS HTLN, is provided 

in the following SOPs. These SOPs provide information on 

preparation, training, site selection, fish community sampling, 

equipment maintenance and storage, data management, data 

analysis, reporting, and protocol revisions. 

The Ozark Rivers Fish Community Protocol (Protocol 

Version 1.0 and version 1.0 of each SOP) has been developed 

to incorporate sound methods for collecting and analyzing 

fish community data at BUFF and OZAR. However, revisions 

may be necessary as new and improved sampling methods or 

statistical techniques are developed. A Revision History Log 

is included at the beginning of each SOP; SOP 12 describes 

protocol revision procedures. 

 
16 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

SOP 1: Preparation Version 1.0

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At least 2 months prior to fish community sampling, a 

plan needs to be developed that includes details for personnel, equipment, time requirements, and the sample schedule 

necessary to complete sampling. As an initial step in the planning process, unfamiliar sites need to be visited by the project 

manager or the aquatic ecologist stationed at the park and 

equipment needs and accessibility details noted. This process 

will help determine the time and number of personnel needed 

for sampling at a site. As a general rule, small stream sites can 

be sampled within a half day; however, larger and inaccessible 

sites require 8 hours or more to sample. 

Fish community monitoring will be completed at 12 sites 

during late spring for BUFF (May – June) and during early fall 

for OZAR (October). Twelve field days should be planned for 

OZAR. At least fourteen days should be scheduled at BUFF, 

because access to sample sites in the lower Buffalo River 

requires a minimum 2 days to complete with overnight camping. Based on the number of sample sites and the potential for 

inclement weather, a month should be scheduled to complete 

fish sampling in each park. 

Initial selection of the appropriate sampling equipment is 

necessary before reliable, representative fish community data 

can be collected. Equipment that is needed for fish sampling 

and assessment of habitat and water-quality conditions is listed 

in appendixes 10 through 14. When selecting equipment for 

sampling, equipment should be matched to stream size for 

optimal and, perhaps more importantly, consistent sampling 

efficiency. Boat electrofishing units with large generators may 

be necessary for thorough sampling of large streams, while 

backpack electrofishing units or towed electrofishing barges 

are suitable for sampling small streams. If distance to the 

stream and bank slope are not excessive (for example, a distance less than 500 m from vehicle access) and enough personnel are available, sampling equipment such as small boats and 

electrofishing generators can be carried to the stream. 

Some State and Federal agencies are permitting authorities for the natural resources that they manage and oversee. 

To ensure that the equipment planned for sampling meets the 

requirements of permitting authorities and is best suited for the 

conditions that will be encountered, the project manager needs 

to determine if special regulations exist for any water body 

where sampling is planned. If threatened or endangered species are known or suspected to occur at any sampling site, the 

U.S. Fish and Wildlife Service (USFWS) must be contacted 

to determine specific stipulations associated with sampling 

within the species’ respective range, regardless of the specific 

location of the sampling sites. Once general sampling information is known, the AGFC or the MDC should be contacted 

(depending on the location of the sampling sites) and the 

procedures for obtaining collection permits and submitting 

sample results should be determined. Although all sampling 

sites will be on NPS property, it may be necessary to cross 

private property to reach some sites, and permission from 

landowners needs to be acquired where appropriate. 

All equipment should be gathered at least 1 month prior 

to the field season and checked to ensure that equipment 

is in working condition and that supplies such as paper for 

data sheets and preservative for specimens are available. All 

sampling gear should be inspected, particularly nets that tear 

frequently and electronic equipment such as backpack shockers, flow meters, and water-quality meters, to ensure there is 

no damage. A field notebook for the sampling season should 

be prepared with pages for entry of sampling schedules, 

crewmember names, sites visited, field hours per day, and any 

conditions or circumstances that may influence how data are 

reported. Trip reports, which are linked to the fish community database, are based on information recorded in the field 

notebook; therefore, it is important that notebooks are clearly 

organized for ease of data entry.
Protocol for Monitoring Fish Communities 17

Training requirements generally fall into two categories: 

sampling and safety. Sampling crews need to be able to work 

in the field in a manner that will maximize the quality of the 

information collected and ensure their safety. Prior to field 

season, the fisheries biologist and aquatic ecologists should 

review this protocol and operation manuals for water quality 

(for example, dissolved oxygen meter), habitat (for example, 

flow meter), and electrofishing equipment (for example, backpack shocking unit). In the field, additional crewmembers 

will be instructed on procedures and use of equipment by the 

fisheries biologist or the aquatic ecologists. 

Sampling Efficiency and Consistency 

Considerations

An experienced sampling team will result in optimized 

efficiency and consistency of the sampling effort. The fisheries biologist (project manager) should have extensive experience in boat operation and electrofishing procedures and 

have completed the USFWS electrofishing course (Principles 

and Techniques of Electrofishing); at least one person onsite 

with an electrofishing crew is required to have completed the 

course. The aquatic ecologists on the crew also should be 

familiar with boat and electrofishing gear operation prior to 

the field season and will be trained on these techniques by the 

fisheries biologist, if necessary. 

One important consideration is that the team conducting the fish sampling and habitat data collection remain intact 

when possible, or if different teams or team members are 

utilized, they sufficiently understand the importance of consistent sampling. When team members alternate or change, the 

fisheries biologist (with assistance from the aquatic ecologists) 

will explain the importance of consistent sampling, provide an 

overview of sampling equipment, and demonstrate electrofishing and habitat data collection techniques.

Another consideration specific to fish sampling personnel is that the fisheries biologist have taxonomic expertise and 

the fisheries biologist and aquatic ecologists be familiar with 

the local fish fauna. Prior to the field season, the fisheries 

biologist and aquatic ecologists need to re-familiarize themselves with the fish fauna by examining preserved specimens 

located in the reference collection (see SOP 5 for collection of 

reference specimens). The fisheries biologist will train other 

crewmembers in coarse identification of specimens, separating 

them into groups such as sunfish, sculpins, minnows, and darters to aid in initial sorting and processing of fish. 

One last consideration for consistency in data collection is that at least one person on the crew have competent 

data recording abilities. If possible two people should have 

competent abilities, one for fish processing and one for habitat 

collection. This will ensure that the numerous fish measurements and counts will be recorded accurately and habitat data 

will be recorded on the correct form for each transect. Prior to 

recording data, the fisheries biologist or aquatic ecologist will 

explain and demonstrate to the crewmember how to record 

data on the field forms. 

Safety Considerations

Safety qualifications of the sampling crew are an important consideration prior to conducting field sampling. In 

particular, some field-sampling activities carry a real potential 

for personal injury or death. Safety considerations include 

elements of planning, equipment use and maintenance, and 

behavior of crewmembers. Before the field season, all crewmembers are required to read the Heartland Network Safety 

Plan and Procedures (Cribbs, 2006) that describes potential 

dangers and abatement actions for field and laboratory/office 

work. This document includes safety on boating/canoeing, 

fishery/stream surveys, electrofishing, dehydration, camping, 

office work, general/winter driving, and hazardous materials. 

Each crewmember must sign and date an annual review form 

stating that they have read and understand the safety plan. 

Two Department of the Interior (DOI) training courses 

are required for some crewmembers. All DOI employees 

that operate a motorboat are required to have completed the 

DOI motorboat operator course. At least one member of an 

electrofishing crew is required to have completed the USFWS 

electrofishing course.

Sampling teams must always have at least two crewmembers; no one should sample alone. NPS employees must wear 

properly fitting U.S. Coast Guard approved personal floatation devices (PFDs) when in canoes or other boats and should 

wear PFDs when wading in fast current. Each sampling team 

SOP 2: Training Version 1.0

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18 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

needs a first aid kit, a cellular or satellite telephone, and an 

emergency contact list (including medical facilities closest to 

each sampling site) in the boat or in each field vehicle. Safety 

requirements stipulate that prior to sampling at least two crewmembers must be adequately trained in first aid and cardiopulmonary resuscitation (CPR) techniques. Prior to sampling 

with new team members, the electrofishing team coordinators 

(the fisheries biologist and aquatic ecologists) need to explain 

basic safety rules and be sure that new personnel understand 

all safety signals and know the location of all safety switches 

on the electrofishing equipment. 
Protocol for Monitoring Fish Communities 19

A detailed description of stretch designation and selection was discussed in the protocol narrative. Briefly, sampling 

stretches were selected randomly using a method known as 

Generalized Random Tessellation Stratified (GRTS) sampling 

(Stevens and Olson, 2004). Within each stretch, a sampling 

reach will be designated for fish community monitoring.

The reach is the representative portion of the stretch 

that is sampled. Sampling reaches will be established using 

a combination of geomorphic characteristics, such as stream 

width, stream depth (wadeable or nonwadeable), geomorphology (distribution of riffles, runs, and pools), and local habitat 

disturbance. In accordance with NAWQA protocols (Fitzpatrick and others, 1998), reach lengths should be approximately 

equal to 20 times the MWSW at low flow with a minimum 

length of 150 m in small wadeable streams (those less than 1.5 

m deep in most of the channel) and a maximum of 1,000 m in 

large nonwadeable streams. 

In general, the downstream boundary of the mainstem 

and tributary sampling reaches will be placed at the head of 

the second riffle located upstream from the downstream stretch 

boundary (fig. 2). This is to ensure that mainstem reaches are 

not present in the confluence zone of the tributary or spring 

run that may designate the lower stretch boundary, and to 

ensure that the tributary reaches are out of the flood-plain area 

of the mainstem. 

The upstream boundary of the reach will be located at a 

distance approximately 20 MWSWs upstream from the downstream boundary. However, the reach must include portions 

of all available geomorphic channel units (riffles, runs, pools) 

typical of the stretch to ensure a representative sample. Thus, 

reach length (and, therefore, the upper boundary placement) 

may need to be extended to guarantee all typical channel units 

are included in the sample. The upstream boundary of the 

reach also needs to be determined such that the reach avoids 

features such as bridges, dams, waterfalls, and major tributaries by at least 10 MWSWs. If the upstream boundary falls too 

close to a feature, then the location of the reach can be moved 

upstream or downstream to avoid the feature. Preferably, the 

downstream boundary of the relocated reach should be at the 

head of a riffle. Also, if the reach is near a bridge, it is preferable to move the reach upstream from the bridge, but be aware 

that “low-water bridges” can act as low-head dams with differing effects during periods of low and high streamflow.

Upstream and downstream boundaries will be temporarily marked with flagging tape during fish sampling. During 

initial establishment of the permanent reach, boundaries will 

be documented using a GPS unit. Proper use of GPS units for 

collecting location data can be found at the following website:

http://www1.nature.nps.gov/im/units/htln/datamanagement.

cfm. 

Reach descriptions, GPS locations, and reach identification code are recorded on the field sheets (appendixes 15 

through 20). Each reach has a unique identification code that 

begins with the first four letters of the river (BUFF = Buffalo, 

CURR = Current, JACK = Jacks Fork), followed by a letter 

designating the reach as a mainstem site (M) or tributary (T), 

and a number designating that particular reach (see appendix 

3 for list of reach identification codes). Both mainstem sites 

and tributaries in the selected sampling frame are numbered 

consecutively downstream, starting at the upstream-most site 

or tributary as 01. For example, CURRM01 is the first (or 

most upstream site) on the mainstem of the Current River and 

CURRT05 is the fifth tributary that will be sampled on the 

Current River (that is, four tributaries in the sampling frame 

are located upstream from this tributary). 

SOP 3: Reach Selection Version 1.0

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20 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

SOP 4: Documenting CORE 5 Water-Quality and Weather Conditions Version 1.0

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This SOP addresses the equipment (see appendixes 10 

and 11) and methods required to measure CORE 5 water-quality variables (temperature, dissolved oxygen, specific conductance, pH, and turbidity) and weather conditions in association 

with fish monitoring in HTLN parks. Detailed guidance for 

measuring CORE 5 variables, including training, calibration, 

QA/QC, data archiving, meter specifications, field measurements, and trouble shooting, can be found in the Documenting 

CORE 5 Water Quality Variables SOP located at: http://www1.

nature.nps.gov/im/units/htln/fish.cfm. This SOP was prepared 

using guidance and language from National Park Service/

Water Resources Division (2007a) and Wagner and others 

(2006). The methods described in this SOP are specific to this 

protocol and do not conform completely to USGS methods for 

collection of water-quality data. 

For each reach, a crewmember will record their initials 

and the reach identification (ID) code, date, reach location and 

description, stretch number, general weather conditions, and 

water-quality variable values on the field form (appendix 15). 

Water-quality variables and air temperature will be measured 

at the site prior to and following fish sampling to obtain data 

on the range of water-quality conditions during sample collection (using discrete sampling – see next section). 

Two approaches to recording CORE 5 data will be used 

in this protocol: (1) Discrete measurements using hand-held 

instruments, and (2) Unattended measurements using data loggers or sondes.

Discrete CORE 5 Sampling with Hand-Held 

Meters

Discrete CORE 5 measurements using hand-held meters 

do not reflect changes in water quality, such as diurnal fluctuations or those associated with a hydrologic event, that are 

likely to have occurred in the stream. However, these measurements serve two general purposes: (1) they represent the 

natural condition of the surface water at the time of sampling, 

although they are not intended to be a precise measure of 

water-quality condition in the stream, and (2) they serve as 

a cross-check for CORE 5 measurements using unattended 

CORE 5 data sondes (see next section).

Unattended CORE 5 Measurements with Data 

Logging Sondes

CORE 5 water-quality variables measured with small 

intervals (generally minutes to hours) between repeated 

measurements are considered continuous because few if any 

substantial water-quality changes are likely to go unrecorded. 

When the goal is to characterize events of short duration, but 

such events are difficult to capture manually using discrete 

measurements (see above), continuous monitoring is appropriate. Continuous monitoring of CORE 5 variables helps 

address questions concerning daily or seasonal variability, 

or short-term changes (such as precipitation related events) 

that might not be apparent or prevent accurate understanding 

of long-term data. Continuous monitoring also provides the 

most comprehensive temporal dataset upon which to evaluate variability through time. Such information is necessary to 

document correlations, possible cause and effect relations, and 

differentiate natural variability from anthropogenic-induced 

change to an aquatic system. 

Analysis and Reporting 

CORE 5 data will be analyzed using summary statistics 

(mean, median, range, standard deviation, standard error) for 

each site and date. This information will be presented in summary and synthesis reports to support fish collection data. 

NPSTORET 

Collected water-quality data that has been successfully 

subjected to QA/QC will be exported to NPSTORET (SOP 9). 

Only summary data for a site and collection period, in addition 

to pertinent metadata, will be submitted. Instructions for preparing and exporting water-quality data to this archival facility 

can be found at the following website: http://www.nature.nps.

gov/water/infoanddata/index.cfm

 
Protocol Narrative 21

This SOP presents methods for collecting representative samples of stream fish communities that closely follow 

in methodology, wording, and scope the NAWQA protocols described in Moulton and others (2002) and Walsh and 

Meador (1998). The methods have been modified where 

appropriate to meet the specific objectives of the NPS to collect representative samples and measure changes in fish communities from streams in BUFF and OZAR. A representative 

sample contains most, if not all, species in the stream at the 

time of sampling in numbers proportional to their actual abundance. Each reach contains various instream habitats (riffles, 

runs, glides, and pools), substrates, and hydrologic conditions. 

Many fish species are specialized for specific habitat conditions and their occurrence in the stream is determined largely 

by the relative abundance of aquatic habitats. 

 Electrofishing Overview

Electrofishing is viewed as the single most effective 

method for sampling stream fish communities (Bagenal, 1978; 

Barbour and others, 1999) and involves the use of electricity 

to capture fish. A high-voltage potential is applied between 

two or more electrodes that are placed in the water. The voltage potential can be created with either direct current (DC) or 

alternating current (AC) using a pulsator; however, because of 

less harm to fish from the use of DC, only DC will be used for 

this fish monitoring program. DC produces a unidirectional, 

constant electrical current. Pulsed DC is a modified direct current that utilizes a sequence of cyclic impulses to immobilize 

fish. The frequency of the pulses produced when using pulsed 

direct current can be adjusted by the operator and usually 

ranges from 15 to 120 pulses per second (pps; or Hertz, Hz). 

Some fish are more susceptible to electrofishing injury, 

and injury rate can vary by fish species, environmental conditions, and electrofishing techniques. Salmonids (Dalbey and 

others, 1996; Kocovsky and others, 1997; Ainslie and others, 

1998) and larger fish (McMichael and others, 1998) are more 

susceptible to injury than other fish. Pulse frequencies greater 

than 30 pps have proven to be more effective in collecting fish 

but appear to cause spinal injuries, particularly in trout and 

salmon species (Coffelt Manufacturing, Incorporated, cited in 

Meador and others, 1993). Pulse rates of less than 30 pps have 

caused low incidence of injury, but are generally ineffective 

in collecting fish. Therefore, a pulse-frequency range from 

30 to 60 pps is generally used to optimize collection effectiveness with a minimum potential for damage to fish. However, 

Dolan and Miranda (2004) suggested that electrofishing with 

intermediate to high duty cycles (pulse frequency X pulse 

duration X 100, as percent) could reduce injury and mortality to warmwater fish. These intermediate to high (36 to 100 

percent) duty cycles tested by Dolan and Miranda (2004) 

had pulse frequencies of 60 to 100 pps and pulse durations 

of 6 milliseconds or were non-pulsed DC. While fishing, the 

operator should note the behavior of the fish so that adjustments can be made to the output of the electrofishing unit. To 

minimize mortality rates, Dolan and Miranda (2004) recommended that the power output and electrode system should 

be managed to induce narcosis (a state of induced immobility 

with slack muscles) and prevent tetany (immobility with rigid 

muscles) of large individuals. 

Water conductance also affects the response of the fish 

to the electrical field and is the single most important limiting 

abiotic factor in electrofishing effectiveness. Low-conductance 

water is highly resistant to the flow of electrical current and 

the electrical field is limited to the immediate area of the electrode. High-conductance water produces the opposite effect by 

concentrating a narrow electrical field between the anode and 

cathode (Meador and others, 1993). Water in most streams of 

BUFF and OZAR has moderate values of specific conductance 

(typically about 150 to 400 microsiemens per centimeter at 

25 degrees Celsius, μS/cm) (Hauck and others, 1996; Mott 

and Luraas, 2004). Water in the upper mainstem and some 

tributaries of the Buffalo River, however, has lower specific 

conductance (typically about 50 to 150 μS/cm) than water 

from other areas of the two parks. In low-conductance water, 

higher voltage is needed to immobilize fish, while in high-conductance water, lower voltage is needed to achieve the same 

result and to minimize potential damage to the fish. However, 

conductance will vary from site to site and from year to year; 

therefore, some pre-sampling experimentation is necessary.

Water clarity also affects electrofishing success and 

determines which techniques will be used. In clear streams, 

fish can see the electrofishing crew or boat. Evasion will be 

the response to both the electrical field and the presence of 

SOP 5: Fish Community Sampling Version 1.0

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22 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

the crewmembers. In turbid streams, immobilized fish may 

be difficult to see resulting in low capture efficiency. At both 

BUFF and OZAR, water clarity is high and therefore, specific 

ambush or herding techniques (described within this SOP) will 

be used to increase capture rate. 

Seining Overview 

Although electrofishing is the most effective fish sampling method, it is biased toward collection of large-sized fish 

(Wiley and Tsai, 1983; Dolan and Miranda, 2003), and seining 

is a common collection method often used to complement 

electrofishing (Bagenal, 1978; Nielsen and Johnson, 1983). 

Seining is a highly effective method for sampling small-sized 

individuals that are less than about 10 cm total length (Bayley 

and Herendeen, 2000). 

Wadeable streams and shallower parts of nonwadeable 

streams are sampled using a “common sense” seine (about 3 

x 1.2 m with a 6.44-mm mesh size) or a bag seine, depending 

on the size of the stream. Use and effectiveness of a particular seine depend on the channel units (for example, riffles, 

runs, pools), channel size and features, and instream habitats 

present in the sampling reach. The presence of submerged 

objects such as woody snags, large cobble, or boulders in 

a sampling area makes it difficult to collect representative 

samples. Therefore, the potential for collecting a representative and repeatable sample should be evaluated before seining 

an area. Seines are most commonly used in wadeable streams 

with smaller substrates such as gravel or sand with little or no 

woody debris. In nonwadeable streams, seines are generally 

used to collect smaller fish along banks or in shallow backwater areas. 

A second method of seining is known as kick seining. 

This method involves shortening the length of a common 

sense seine by rolling the seine onto the brails. The seine then 

is placed within a riffle, and the substrate is kicked to dislodge 

benthic fish species that then are carried by the current into 

the seine. This technique also is used in combination with 

backpack or towed barge equipment, whereby the crewmember holding the anode will shock down into the seine while 

kicking the substrate. However, using electrofishing equipment 

with a seine is an electrofishing method and not strictly a seining technique.

Sampling Methods for Wadeable Streams 

Electrofishing 

Wadeable streams generally are less than 1.5 m deep, but 

may contain some areas that are substantially deeper. Backpack and towed electrofishing gears are used for sampling fish 

in wadeable streams. Backpack electrofishing with a single 

anode is usually most effective in shallow (less than 1 m), 

narrow (less than 5 m wide) streams. Towed barge electrofishing gear (multiple anodes) is usually more effective in wide 

(greater than 5 m) wadeable streams with pools deeper than 

1 m. Channel width, depth, and access need to be considered 

before choosing between backpack and towed electrofishing 

gear. In some situations, it may be desirable to use a combination of backpack and towed electrofishing gear; for example, 

the backpack might be used in long, shallow riffles (or in conjunction with riffle kicking) and the towed gear in the deeper 

sections of the stream. 

Electrofishing techniques for wadeable streams require 

an electrofishing crew consisting of three to six individuals. 

When using backpack electrofishing gear, one crewmember is 

designated as the operator; with towed gear, three crewmembers are designated as operators (two operate the anodes and 

one operates the barge and generator). Regardless of the gear 

used, two crewmembers (or netters) are assigned to collect 

stunned fish with dip nets and place fish in buckets. One additional crewmember is sometimes needed to assist in netting 

fish and to transfer netted fish into buckets or into a flowthrough holding container (or live cage) if dissolved oxygen 

concentrations are low and water temperatures are high within 

the buckets. For safety reasons, all crewmembers must wear 

non-breathable waders and low-voltage rubber gloves, and 

they also should wear polarized sunglasses to enhance their 

ability to see fish that have been immobilized by the electrical 

field. 

Techniques for collecting samples using either backpack 

or towed electrofishing gear are generally similar in riffle-pool 

streams. To obtain a representative sample using single-pass 

electrofishing, thorough sampling along both banks of the 

stream and in mid-channel areas will be completed at each 

reach. All types of instream habitat features such as woody 

snags, undercut banks, macrophyte beds, or large boulders, 

and geomorphic channel units (riffles, pools, runs) should be 

sampled. This technique requires electrofishing from one edge 

of the water to the other in a “zig-zag” pattern, while attempting to sample all types of habitat features and channel units 

within the reach in proportion to their occurrence (fig. 4). In 

reaches that have substantial and diverse habitat features along 

the banks (such as woody snags/tree roots, and boulder fields), 

it may be necessary for the crew to sample along one bank for 

a distance and then move back downstream and sample critical 

habitat along the opposite bank. 

The electrofishing crew should begin electrofishing at 

the downstream boundary of the sampling reach and proceed 

upstream. Sampling in an upstream direction in wadeable 

streams is preferred over sampling in a downstream direction 

for several reasons (Hendricks and others, 1980). Disturbance 

caused by electrofishing crews walking in the stream increases 

turbidity, thereby greatly reducing visibility and sampling efficiency. Also, sampling in an upstream direction allows stunned 

fish to drift downstream, thus facilitating their capture by the 

netters. Generally, the distance that the net is held downstream 

from the anode increases with current velocity and turbidity. 

It is also important to have one netter near the anode to collect 

fish stunned by the anode and an additional netter downstream 
Protocol for Monitoring Fish Communities 23

from the cathode to collect fish that are stunned near the cathode or that float down from the anode. 

Different fish species have different adaptations and 

several different electrofishing techniques may be necessary 

for efficient sampling. In some situations, applying a continuous electrical current to the water is effective. In other 

situations, it is more effective to apply current intermittently. 

Using a continuous electrical current, schooling species 

can be “herded” into confined spaces where they are more 

susceptible to capture. Fish generally respond to continuously 

applied electrical current by attempting to avoid exposure to 

the electrical field. Thus, continuous application of electricity 

can result in fish moving just ahead and away from the operator. The operator needs to be aware of this response and take 

advantage of natural barriers where fish can be herded (such 

as banks, bars, or shallow riffles) to facilitate their capture by 

the netters. Upon reaching a barrier, fish will turn and attempt 

to evade the approaching electrical current. Therefore, netters 

should be alert when approaching barriers so that fleeing fish 

can be captured. 

Another technique that can be used for capturing fish 

species that flee the weak edge of the electrical field is for the 

crew to herd the fish toward the operator while the electrofishing equipment is turned off and to begin electrofishing once 

fish have come within the electrical field. This approach 

works well in runs or long pools where a crewmember (or 

two) moves upstream from the fish by getting out of the 

stream and walking up the bank. Once ahead of the fish, the 

crewmember returns to the stream and creates a disturbance in 

the water that drives the fish downstream toward the operator. 

The electricity is turned off as the crewmember herds the fish 

back downstream. When the fish are visible and close to the 

anode, the electricity is turned on to stun them. Use of a small 

seine as an additional barrier improves the efficiency of this 

technique.

A third technique, referred to as the ambush technique, 

can be used for capturing fish species such as black bass 

and other members of the sunfish family that have affinities 

for cover, including submerged woody debris, boulders, and 

bedrock ledges. These species can be captured by approaching the cover with the electricity turned off and thrusting the 

anode into the cover while turning on the electricity.

Shallow riffles, cascades, and torrents often are very swift 

and require different electrofishing techniques than run and 

pool areas. A useful technique for sampling shallow riffles is 

to have the operator stand beside the habitat to be sampled and 

sweep the anode across the riffle from upstream to downstream. Stunned fish will be carried downstream and into dip 

nets or a seine. This technique minimizes escape and avoidance of the electrical field by benthic fish species such as darters and sculpins, which commonly inhabit riffles. Sculpins and 

darters do not have swim bladders and, therefore, do not float 

when stunned, but rather roll along the bottom with the water 

current. Because they lack a swim bladder and have cryptic 

coloration, these species may not be seen until the net is examined. Swift riffles, cascades, and torrents with large cobble 

or boulder substrate can be sampled with similar techniques. 

For these habitats the operator works the anode downstream 

through the swift current between rocks and through small 

plunge pools while a dip net or seine is maintained on the bottom and about a meter downstream.

While electrofishing riffles, it may also be necessary for 

the operator to kick the substrate in shallow or slower riffle 

areas to dislodge benthic species into a seine (Hendricks and 

Figure 4. Single pass zig-zag sampling technique used in electrofishing wadeable streams.

Lower reach 

boundary

Upper reach 

boundary

Macrophyte bed

Fallen trees and

woody snags 

Flow

Riffle

Electrofishing

path 
24 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

others, 1980; Matthews, 1986; Bramblett and Fausch, 1991). 

Kicking the stream bottom while electrofishing is an effective technique for collecting these species because it involves 

disturbing the substrate and allowing the water current to carry 

fish into a common sense seine. Two crewmembers enter the 

stream below a riffle and hold the seine in a vertical position 

above the water and perpendicular to the flow at the downstream edge of a riffle. If the riffle is large (wide and long), the 

crewmembers may enter the riffle at some intermediate point 

in the riffle and hold the seine somewhere upstream from the 

downstream edge of the riffle. The crewmembers then thrust 

the brails and lead line of the seine to the stream bottom. The 

brails are slightly angled downstream so that the flow forms a 

slight pocket in the seine. It is important that the lead line be 

on the stream bottom. It may be necessary to remove some 

rocks from beneath the lead line so that there are no gaps 

between the seine and the stream bottom. It may also be necessary for the crewmembers that are holding the seine to reach 

around the front of the brail with one leg and place a foot on 

the lead line to keep it in close contact with the stream bottom. 

Upstream from the seine, one or two crewmembers vigorously 

disturb (or kick) the substrate and electrofishes by moving the 

anode back and forth while moving toward the seine. After 

reaching the seine, crewmembers lift the seine out of the water 

by grabbing the lead line of the seine. For safety reasons, it 

is important for crewmembers to coordinate turning off the 

power to the electrofishing equipment before reaching for the 

lead line of the seine. 

In the field, samples collected with different electrofishing gear and in different channel types (main channel and 

backwater/side channel) will be processed separately. For 

each gear used in each channel type at a reach (for example, 

backpack in main channel, towed barge in main channel, 

seine in backwater, or backpack in backwater), fish data will 

be entered on separate field forms and gear type and time 

sampled will be recorded (appendix 16). Riffle samples that 

are collected by kicking into a seine while electrofishing are 

considered to be electrofishing samples and, therefore, can be 

combined in the field with samples collected in the same channel type using the same gear. For example, if backpack electrofishing was used in run and pool channel units in the main 

channel of a stream and backpack electrofishing with kicking 

into a seine was used in the riffles, then samples from all three 

channel units are considered to be from the same channel type 

(main channel) and, therefore, combined. However, if a towed 

barge was used in run and pool channel units and a backpack 

with kicking into a seine was used in riffles, then samples 

from the towed barge must be recorded separately from 

those collected with the backpack. In the field, samples from 

backwater areas and isolated side pools will always be kept 

separate even when sampled with the same gear type used on 

the main channel of the stream. Electrofishing will be the predominate method used in the main channel, while electrofishing and seining will be used in the backwater/side channels. 

For analysis, all electrofishing data will be combined for the 

entire reach (main channel and backwater/side channel). However, there may be specific monitoring questions that would 

require analyzing the data by gear or channel type; therefore, it 

is important to process the data separately in the field. 

Seining

Runs and pools of streams can be sampled using a common sense seine or a bag seine, depending on the size (channel 

width and depth) of the stream. Generally, a common sense 

seine would be used in reaches where backpack electrofishing 

gear was used and a bag seine would be used in reaches where 

towed barge or boat electrofishing gear was used. Within the 

reach, specific sites to be seined will most commonly consist 

of backwaters or side channels with smaller substrates and few 

instream obstacles (woody debris and boulders, for example) 

and will be based on professional judgment of the fisheries 

biologist and aquatic ecologists. 

Seining efficiency can be improved by observing several 

guidelines. First, submerged objects (woody snags, large 

cobble, and boulders) make seining difficult, and these areas 

should be avoided when seining. Electrofishing gear should 

be used to draw fish out from submerged objects. Second, 

seining should be completed in a downstream direction, 

which has been demonstrated to be the most effective seining 

technique (Hendricks and others, 1980); however, seining in 

a downstream direction may not be effective in swift currents. 

Third, seining speed should be slightly faster than the stream 

current; faster seining speeds will push water in front of the 

seine and force fish away from the seine. Fourth, maintaining 

contact between the lead line and the bottom of the stream and 

angling the brails back to keep the net bottom well forward 

of the float line will minimize the potential for escaping fish. 

Lastly, when the seine haul is finished, the seine is beached by 

pivoting the seine and dragging it onto the shore. 

Riffle dwelling species (such as darters and sculpins) can 

be sampled using kick seining without the use of electrofishing gear. This technique can be used when electrofishing gear 

is not available or when it is restricted because of presence of 

threatened or endangered species. Similar to the technique of 

electrofishing while kicking into a seine, kick seining requires 

two crewmembers to stand at the downstream end of the riffle 

with a common sense seine while one or two crewmembers 

kick into the net. Dislodged fish are carried by the swift current into the net. 

The approximate time (effort), number, and length 

(meters) of seine hauls should be recorded on the field sheets 

(appendix 16). During field processing and analysis, fish collected by seining should be kept separate from fish collected 

using electrofishing methods. For example, if backpack electrofishing and seining are used to sample backwaters within 

a reach, then these samples must be kept separate because of 

differences in efficiencies of the gear types. Seining methods 

will be predominately used in backwaters. However, if seining is used in both main channel and backwaters, all samples 

collected by this method will be combined for analysis of fish 

community composition. 
Protocol for Monitoring Fish Communities 25

Sampling Methods for Nonwadeable Streams

The following sections describe electrofishing and seining methods for sampling nonwadeable streams. Nonwadeable streams generally are greater than 1.5 m deep through 

most of their areas, although wadeable sections can be somewhat common.

Electrofishing

Nonwadeable streams are sampled using electrofishing 

boats or using boats in addition to towed barge or backpack 

electrofishing gear in shallow riffle areas. The basic components of the boat electrofishing unit include a generator, 

pulsator (control box), cathode (usually the boat), boom (aluminum or polyvinyl chloride tubing used to support electrical 

cables in front of the boat bow), and anodes (cable droppers 

attached to the end of the boom in front of the boat bow). The 

boat should be large enough to hold all the equipment and 

provide safe and adequate work space for the crew. Generally, flat-bottomed aluminum hull boats are preferred, because 

metal hulled boats are easy to ground. A boat electrofishing 

crew should consist of one boat operator and one or two net 

handlers who collect the fish with long-handled (greater than 

3 m) dip nets. Each crewmember will have access to a safety 

switch which will stop electrical current flow in the event of 

an emergency. Special training is required to operate this system. The driver should be skilled at maneuvering the boat as 

effectively as possible to allow crewmembers the best opportunity to capture stunned fish. As with wadeable electrofishing 

methods, all crewmembers must wear waders and low-voltage 

rubber gloves and should wear polarized sunglasses. 

Sampling with an electrofishing boat begins at the 

upstream boundary of the sampling reach and proceeds 

downstream by maneuvering the boat along one shoreline and 

mid-channel areas in a zig-zag pattern (the opposite shoreline 

and mid-channel areas will be sampled in a second pass, again 

proceeding upstream to downstream; fig. 5). Position the 

boat so the bow is angled downstream and toward the bank. 

This allows the boat operator to reverse direction (generally 

upstream and away from the banks) and not pass over stunned 

fish. The electrofishing boat is operated at a speed equal to or 

slightly greater than the current velocity. Periodically, the boat 

should be slowed to less than current speed so that fish drifting 

with the current may be more easily observed. Sampling is 

conducted in a downstream direction because fish are usually 

oriented upstream (into the current) and will either swim into 

the approaching electrical field or turn to escape downstream. 

Figure 5. Double pass zig-zag sampling technique used in boat electrofishing for nonwadeable streams.

Lower reach 

boundary

Upper reach 

boundary

Macrophyte bed

Fallen trees and

woody snags 

Flow

Riffle

Electrofishing

path 
26 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

In turning to escape downstream, fish orient themselves perpendicular to the electrical field, thereby exposing a greater 

surface area of the fish to the electrical field that renders them 

more susceptible to capture. Also, when fish are stunned they 

are carried downstream by the flow, providing greater opportunity for capture. 

Intermittent application of electrical current while drifting 

downstream generally should be used for large, nonwadeable 

streams. In areas with clear or shallow water and submerged 

structure, intermittent application of current may be more 

effective than continuous application. Fish are approached 

with the current off. When the anodes are in position near the 

fish, the current is applied. Instream habitat features, such as 

woody snags and fallen trees, are sampled by maneuvering 

the boat close to the habitat feature with the electrical current off. As the anode is placed near the habitat feature, the 

electrical field is generated and the boat is backed away from 

the habitat feature. This will cause the fish to be pulled away 

from the habitat feature to facilitate their capture. When boat 

electrofishing, the duration for applying electrical current 

should be increased at submerged structures. Fish located in 

deeper water (2 to 3 m) may require 5 to 10 seconds of current 

before a response is observed. This duration increases as water 

temperature decreases. Captured fish are placed into containers on the boat and processed after completion of the first 

electrofishing pass, if necessary. Fish data collected by boat 

electrofishing in the main channel will be kept separate on the 

field forms from data collected in backwater/side channel. 

Nonwadeable streams of the Ozark Plateaus often are 

wadeable in large parts of the sampling reach. For example, 

a stream may be nonwadeable in some areas because of large, 

long pools but wadeable in riffles, runs, and along pool margins. In such situations, a towed barge or a backpack electrofisher should be used in the wadeable parts of the stream. 

In wadeable riffles, electrofishing while kicking into a seine 

is the most effective technique for collecting benthic riffle 

species. This technique for nonwadeable streams is similar to 

that described above for wadeable streams. For nonwadeable 

streams, electrofishing will be the predominate method used 

in the main channel. In situations where samples are collected using multiple types of electrofishing gear, samples are 

processed separately with crewmember initials, electrofishing 

effort, and fish data (lengths, weights, and counts) recorded 

on separate field forms (appendix 16). Similar to wadeable 

streams, samples collected from backwater/side channel 

habitat are processed separately regardless of gear type used. 

For analysis, all data collected with electrofishing gear will be 

combined for the entire reach.

Seining

Nonwadeable streams of the Ozark Plateaus often have 

wadeable riffles, runs, margins of pools, and backwaters 

that can be sampled using a bag seine (or, less frequently, a 

common sense seine). Seining techniques for run and pool 

habitats are the same as those described in the section of this 

SOP describing wadeable streams. However, with nonwadeable streams, excessive water depth and flow can be additional 

factors (in addition to substrate) that adversely affect the use 

of the seine. In some reaches, it may be that only electrofishing techniques can be used effectively in main channel areas 

because of swift current in run and riffle habitats and depths 

in pools. Therefore, seining methods will be used primarily in 

backwater areas. Location of seining sites will be based on: 

(1) the fisheries biologist’s judgment on effectiveness of this 

gear type to collect a representative sample, and (2) safety to 

the crewmembers. Fish from seine hauls should be processed 

and analyzed separately from those collected with electrofishing gear. If seines are used in the main channel, fish collected 

in backwaters/side channels will be processed separately in 

the field. However, for analysis, data collected using seining methods (regardless of channel type) will be combined to 

examine trends in fish communities at each reach.

Sample Processing Procedures 

The goal of processing fish samples in the field is to 

collect information on taxonomic identification, abundance, 

and size structure with minimal harm to specimens that will 

be released alive back into the stream. All captured fish are 

placed in a live cage, aerated buckets, a boat live well, or other 

suitable containers for subsequent processing and an effort 

is made to minimize stress or death to specimens. It may be 

beneficial to use multiple, portable aerated containers for holding and separating each species. Regardless of the effort made 

to minimize handling and stress to fish, some mortality will 

occur. However, minimizing mortality involves recognizing 

which species are sensitive to handling and prolonged confinement and processing them first. Any fish that are released 

before the reach is completely sampled should be released 

downstream from the sampling area to minimize the potential 

for resampling and sample bias.

Crewmembers should be thoroughly familiar with the 

fish species in their study area. Identifications are made by a 

crewmember (fisheries biologist) that is familiar with the fish 

species commonly found in the study area. The primary references used for identification will be Fishes of Arkansas (Robison and Buchanan, 1988) and Fishes of Missouri (Pflieger, 

1997). Taxonomic nomenclature and common names follow 

that established by the American Fisheries Society’s Committee on Names of Fishes (Nelson and others, 2004). An attempt 

is made in the field to identify all fish to the species level. 

Walsh and Meador (1998) can be consulted for additional 

guidance regarding taxonomic identification.

Some species of fish (such as minnow genera Notropis

and Cyprinella, and stonerollers Campostoma anomalum, 

C. oligolepis) are similar and confirmatory characteristics 

are either internal (such as pharyngeal teeth) or require exact 

counts of meristic characteristics (such as the number of 

lateral line scales or anal fin rays). These species cannot be 

accurately identified in the field. Accordingly, specimens 

that cannot be positively identified in the field are preserved, 
Protocol for Monitoring Fish Communities 27

labeled, and identified in the laboratory, and a specimen of 

each species deposited in a reference collection. Because 

of the potentially large number of problematic Campostoma 

individuals occurring at some sites, these two species will only 

be identified to the genus level. 

Some identifiable specimens also will be preserved and 

deposited in a reference collection to aid in instructing crewmembers in fish identification prior to the field season and to 

provide some future assurances about field identifications. In 

general, some individuals of all non-game species should be 

preserved, at the discretion of the fisheries biologist. Federally listed threatened and endangered species should not be 

preserved; other species of concern may be protected by State 

guidelines or regulations. Walsh and Meador (1998) provide 

guidance and criteria for the selection of specimens for a reference collection. All preserved specimens will be added to the 

data sheets once identified.

When processing fish specimens whether in the field 

or laboratory, a group of 30 individuals of each species will 

be measured (total length) and weighed. Individuals will 

be selected using a “blind grab” technique. This technique 

uses a dip net to make a pass through the entire bucket or 

holding tank to ensure that fish of various sizes are captured 

with each “grab.” Some species have a large size range with 

different sizes being collect by specific gears (for example, 

large sunfish collected with boat and small sunfish collected 

with backpack). For these species, a blind grab will be taken 

from samples collected by each gear type and a representative 

subsample will be measured, keeping data from the gear types 

separate. For smaller species (those typically smaller than 100 

mm; minnows, darters, sculpins, and madtoms, for example), 

lengths of individuals will be measured and a batch weight 

will be measured. For species that obtain large sizes (for 

example, bass, sunfish, catfish, and suckers), each specimen 

will be measured and weighed individually.

The major steps in processing collections of fish from 

electrofishing and seining include the following: 

1. Sort fish into identifiable and unidentifiable groups, 

keeping fish collected from different gear types (boat, backpack, barge, seine) and channel types (main channel or backwater/side channel) separate. Process species of concern (for 

example, sensitive species or rare species) and game species 

before other identifiable species. 

2. Hold fish in a manner consistent with minimizing 

stress or death. Do not keep fish out of the water longer than 

necessary to process them. 

3. Identify all species (those that can be identified in the 

field) and measure total length and weight of 30 individuals 

for each species. Once 30 fish from a species has been measured, the remaining specimens are counted.

4. Record data on the fish field data sheet (appendix 16). 

 a. Record the Reach ID (see appendix 3 for list of 

 reaches). 

 b. Record the date, gear type used, habitat sampled 

 (main channel, backwater/side channel, or other), 

 sampling effort (time), number of seine hauls and 

 total length of stream seined. 

 c. Record the initials of all crewmembers. Record the

 person identifying/measuring fish, the person record

 ing the data, and those who operated the electrofish

 ing equipment/seine and netted fish. 

 d. For each individual of a species, record the total 

 length (TL), weight (WT), and any anomalies (AL)

 (deformities, eroded fins, lesions, tumors, and black

 spot) (Smith and others, 2002). For larger fish, 

 record individual weights. For smaller fish, batch 

 weigh 30 specimens. Record the additional number 

 of fish collected for each species under “Species 

 Count.” For example, if 46 white suckers were col-

 lected at a reach, 30 fish would be measured and 

 weighed and the remaining 16 would be counted 

 (Species Count = 16). 

5. Preserve selected specimens (those too small or difficult to identify in the field) for identification in the laboratory or for a reference collection. Specimens will be preserved 

in 10 percent buffered formalin. For specimens larger than 

100 mm, a small incision along the side of the body should 

be made to allow the formalin to penetrate the body cavity. 

For each reach, all unidentified specimens collected from the 

same gear type and channel type (main channel or backwater/

side channel) can be preserved in a single jar with a label that 

contains the reach sampled, date, gear type, habitat type, and 

sampling effort. All preserved specimens will be identified 

and kept at the HTLN Aquatic Program Laboratory at Missouri State University in Springfield, Missouri. Specimens 

preserved for laboratory identification (or for a reference 

collection) should be noted on the fish community field form 

(appendix 16) by putting a check mark in the “vouchered column” (Vchrd). Any comments should be noted in the “comments column” (Cmts).

Quality Assurance/Quality Control Procedures 

A number of procedures can be implemented to ensure 

the representativeness and accuracy of data used to describe 

fish communities of BUFF and OZAR. These procedures 

must be considered in relation to the objectives of the sampling. They include procedures related to collection of fish 

specimens and accurate taxonomic identification.

Fish samples should be collected as consistently as possible from year to year. To the extent possible, consistency can 

be maximized by using the same crew from year to year and 

at all sites sampled within a single field season. The use of 

inexperienced crewmembers will decrease the efficiency and 

consistency of the sampling effort (Hardin and Connor, 1992). 

Ideally, all sites will be sampled during similar biologic and 

hydrologic conditions (during base-flow conditions) because 

doing so will reduce variability associated with fish movements (for example, those related to spawning) and lowered 

sampling efficiency (because of higher stages, higher velocities, and higher turbidity). To the extent possible, sample gear 
28 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

used and sampling effort (generally, sampling time) should 

remain consistent at each site from year to year (appendix 3). 

However, site specific conditions and safety considerations 

dictate sampling period and equipment used; therefore, implementation of all desired practices may not always be feasible 

at a reach.

Because it is not desirable to remove all fish specimens 

from the field to the laboratory for identification, it is important that the person (fisheries biologist) selected for this 

task have adequate experience in taxonomic identification 

and be familiar with fish species expected to be collected at 

BUFF and OZAR. A list of species known or expected to 

occur within BUFF (appendix 1) and OZAR (appendix 2), 

or expected to occur in the area, should be consulted prior to 

sampling. Unidentified specimens, representative individuals 

of taxa that are not positively identified, and other specimens 

of special taxonomic value should be preserved in buffered 10 

percent formalin and labeled appropriately. Problematic specimens should be verified by an independent taxonomist. 
Protocol for Monitoring Fish Communities 29

Habitat composition within a stream is an important component in shaping fish communities. The type and abundance 

of specific habitats (for example, riffles, woody debris, and 

pools) will influence species presence and relative abundance, 

as well as size structure of the populations. Because of its 

importance to fish, physical habitat data will be collected as 

part of the fish community monitoring to examine relations 

between environmental conditions and fish communities. 

The methods described in this SOP have been modified from 

NAWQA protocols (Fitzpatrick and others, 1998) to meet the 

objective of the NPS. 

Habitat Collection 

Once fish sampling is completed, a crew of two to three 

persons will collect physical habitat data within that same 

reach. Equipment necessary to complete habitat sampling is 

found in appendix 13. Eleven equally spaced transects will be 

placed perpendicular to flow to collect instream habitat, fish 

cover, bank stability, and bank vegetation data (fig. 6). For 

example, a reach of 1,000 m length would have 11 transects 

placed at 100 m intervals. Crewmembers can either establish 

all 11 transects prior to data collection by temporarily flagging 

them, or transects can be located as the crew moves upstream 

during data collection. 

For very wide or deep reaches, it may be necessary to 

take measurements from a boat or canoe. In this situation, 

a rope or tagline may be used to stretch across the channel 

allowing crewmembers to stay on the transect while taking 

measurements. In some channels with deep and fast flow, it 

may be difficult or impossible to get a measurement along the 

transect because of safety considerations. Some reaches may 

SOP 6: Physical Habitat Collection Version 1.0

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T1

T3 T2

T6

T10

T11

T8 T7

T5

T4

T9

Lower reach 

boundary Upper reach 

boundary

Macrophyte bed Fallen trees and

woody snags 

Flow

Riffle Riffle

Second riffle 

upstream from

the lower

stretch boundary

Figure 6. Transect placement for habitat data collection.
30 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Flow

Transect

1 meter

1-meter

belt

10-centimeter

circle

Right side Left side

Figure 7. Location of instream habitat and fish cover collection at 

a transect.

also have backwater areas that will need to be recorded separately from the main channel. In backwaters, habitat data are 

collected at three relatively equally spaced transects and length 

of the backwater is recorded. When collecting data (in both 

main channel and backwaters), streambanks are referred to in 

a downstream perspective. Therefore, if the crew is collecting 

data in an upstream direction, river right is on the workers’ 

left, and river left is on the right. 

Instream Habitat Assessment 

At each transect channel morphometry, velocity, substrate, and canopy cover are described. At each transect, 

wetted width, channel unit type, and pool form (if applicable) 

are recorded. Definitions of channel unit types can be found in 

appendix 17. Along the transect, instream habitat is collected 

at three points (center channel and half the distance between 

center and the left and right banks, fig. 7). At each point, depth 

and velocity are measured. A single current velocity reading 

(see SOP 7) will be measured at 60 percent of the depth from 

the surface of the water. Dominant substrate size and substrate 

embeddedness are visually observed within a 10-cm diameter 

circle around each point (fig. 7). Dominate substrate size is 

defined as the average substrate size within the circle using 

the Wentworth scale (fig. 8). For substrate codes 1-3, there are 

no boxes shown in figure 8 by which to estimate their respective sizes because these substrates are so small. However, the 

general rule is that code 1 (silt or clay) feels slick between 

thumb and finger with no evidence of grit. Code 2 (very fine 

sand) has a barely perceptible gritty feel, and code 3 (fine 

sand) has a distinct gritty texture. For these three substrate 

codes, it is necessary to grab a sample from the 10 cm circle 

for assessment of dominate substrate. Canopy cover also is 

visually observed by looking directly overhead at each point 

and categorizing the percentage cover within 1 m upstream 

and downstream from the transect. If a bridge or other manmade structure is producing the canopy, this should be clearly 

indicated in the comments section.

Fish Cover 

It is important to document the presence of fish cover in 

a stream because different species have affinities for various 

cover types. For example, sunfish species typically inhabit 

woody structure or boulder fields along the banks and in pools. 

Therefore, a reach with several snags or large boulders will 

likely have a large number of sunfish. 

To assess fish cover within a reach, all cover types present will be documented along each transect (appendix 18). 

Filamentous algae, hydrophytes, boulders (size 21 to 23 on 

the Wentworth substrate sheet, see fig. 8), and any artificial 

cover are assessed within a 10-cm diameter circle around 

each point. If artificial cover (cinder blocks and car tires, for 

example) is present, the type of cover should be noted in the 

comments section. Small and large woody debris are assessed 

in a 1-m belt along the transect, dividing the belt into left and 

right side of center (fig. 7). Small woody debris is defined as 

being less than or equal to 10 cm in diameter at its largest end, 

and large woody debris is greater than 10 cm in diameter at its 

largest end. Fish cover along the banks is assessed within 1 m 

upstream and downstream from the transect. Cover along the 

banks include trees, roots, overhanging vegetation, undercut 

banks, and bluffs within 5 m of wetted edge.

Bank Measurements 

Characteristics of the bank and riparian areas can affect 

instream processes and fish habitat. For example, banks that 

are mostly bare with steep angles are likely to erode during high flow events, increasing the amount of fine sediment 

entering the stream. This, in turn, degrades habitat for benthic 

species (both fish and invertebrates) by burying large gravel/

cobble substrates. Therefore, collection of bank stability and 

vegetation data may help explain fish community composition 

and abundance.

Before discussing data collection for bank/riparian areas, 

it is necessary to describe what is meant by the term “bank” 

(fig. 9). The bank is defined as the area of steep sloping 

ground bordering the stream that confines the water within 

the channel at normal water levels and is located between the 

channel and the flood plain (Fitzpatrick and others, 1998). 

The flood plain is defined as a flat or gently sloping depositional area adjacent to the stream. At low flows, it may be 

difficult to determine the location of the bank because of the 

presence of bars. Bars are defined as areas usually devoid of 

woody vegetation, such as small trees and shrubs, and contain 

coarse materials such as sand, gravel, or cobble. These areas 
Protocol for Monitoring Fish Communities 31

Figure 8. Wentworth substrate codes used for instream habitat assessment.

Wentworth Substrate Codes

1 = less than 0.062 millimeter (silt/clay)

2 = 0.062 to 0.125 millimeter (very fine sand)

3 = 0.125 to 0.250 millimeter (fine sand)

4 = 0.25 to 0.50 millimeter (medium sand)

5 = 0.5 to 1.0 millimeter (coarse sand)

6 = 1.0 to 2.0 millimeters (coarse sand)

7 = 2.0 to 4.0 millimeters (fine gravel)

8 = 4.0 to 5.7 millimeters (medium gravel)

9 = 5.7 to 8.0 millimeters (medium gravel)

10 = 8.0 to 11.3 millimeters (coarse gravel)

11 = 11.3 to 16.0 millimeters (coarse gravel)

12 = 16.0 to 22.6 millimeters (small pebble)

13 = 22.6 to 32.0 millimeters (small pebble)

14 = 32.0 to 45.0 millimeters (large pebble)

15 = 45.0 to 64.0 millimeters (large pebble)

16 = 64.0 to 90.0 millimeters (small cobble)

17 = 90 to 128 millimeters (small cobble)

18 = 128 to 180 millimeters (large cobble)

19 = 180 to 256 millimeters (large cobble)

20 = 256 to 362 millimeters (boulder)

21 = 362 to 512 millimeters (boulder)

22 = 512 to 1,024 millimeters (boulder)

23 = greater than 1,024 millimeters (boulder)

24 = Bedrock

6 7 8 9

10

11

12

13

14

15

16

17

Note: Box sizes are approximate and may be affected by printer settings.
32 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Figure 9. Location of banks and flood plain.

will be covered by water during normal flow (that is, at flows 

slightly higher than low flow) and therefore, are not considered part of the bank. Each bank measurement begins at the 

“true” bank (that is, the area of steep slope). In some instances, 

the bank will begin at the wetted edge. However, if gravel or 

sand bars are present at a transect, these will not be included 

in the bank assessment, but will be noted in the comments 

section by recording the width of the bar from water’s edge to 

the bank. 

Islands (stable areas with woody vegetation and mature 

trees that split or divide the channel) are treated as banks. For 

reaches with islands, width of the island will be measured at 

each transect as well as the length of the island that is located 

within the reach (recorded in the comments section). At 

transect locations where the channel is split, data will be collected at three points on either side of the island, and the island 

will be considered the “bank” for measuring bank stability/

vegetation because of its stability and role in structuring the 

channel (fig. 10). This will require recording data on two copies of each data sheet (appendixes 17-19)

Bank characteristics are observed at each transect. Bank 

stability is visually observed at the transect, and each bank 

characteristic is categorized (appendix 19). Bank angle and 

substrate are observed from the bottom of the bank (at wetted edge or at the top base of the bar, if one is present), and 

the category code is recorded. To assess the bank substrate, 

the Wentworth scale is used to define the substrate type (silt 

= code 1, sand = codes 2 – 6, gravel = codes 7 – 16, cobble 

= codes 17 – 20, boulder = codes 21 – 23; fig. 8), but the 

category code on the data sheet (and not the Wentworth code 

is recorded. Percent vegetative cover, bank height, and bank 

cover are assessed from the bank bottom to 10 m into thebank. 

For bank cover, more than one cover type may be recorded 

if two cover types are relatively equal in abundance. Bank 

Island

Low flow

water line

Flood plain

Flood plain

Bank

Bank

Gravel

B bar ank angle

Bank angle

cover categories include large trees, small trees/shrubs, grass/

forbs, bare rock/sediment, and artificial cover. If artificial 

cover is present on the bank (for example, rip-rap or concrete 

structures), the type of cover should be noted in the comments 

section. 

Figure 10. Habitat collection points in a reach with a split channel.

Island

Flow

Transect 1

Transect 2

Transect 10

Transect 11

Points of

collection 

Transect 9

Transect 3

Length
Protocol Narrative 33

SOP 7: Measuring Stream Discharge Version 1.0

Revision History Log:

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This SOP is guidance for measuring discharge in rivers 

and streams, specifically at BUFF and OZAR. The methods 

described in this SOP are specific to this protocol and do not 

conform to USGS methods for measurement and computation of streamflow. This guidance is applicable to any meter 

commonly used to measure current velocity, such as MarshMcBirney, Price AA, and Price pygmy meters. This SOP, however, gives specific guidance for using the FLO-MATE 2000 

(Marsh-McBirney) meter because that is the meter currently 

(2007) used within the HTLN by several parks. The SOP 

briefly describes conceptual information about how current 

meters work and describes sampling procedures, calibration 

processes, general maintenance procedures, and equipment 

needed for these procedures. Also, guidance will be provided 

for use of the FLO-MATE meter in the field. If other meters 

are used, field personnel should review the instruction manual 

for instrument specific guidance on how to calibrate and operate those particular meters.

Background Information

Stream discharge (Q) is the volume of water passing a 

cross-section per unit of time and is generally expressed in 

cubic feet per second (ft3/s) or cubic meters per second (m3/s). 

Discharge is the velocity multiplied by the cross-sectional 

area. Cross-sectional area is determined by first measuring the 

width of the stream channel. The cross section is then divided 

into smaller increments (usually 15 to 20 intervals) and depth 

and velocity are measured at each increment. The depth and 

width of the interval are multiplied to get an area for each 

interval and then each interval area and velocity are multiplied 

to produce a discharge for each interval. These discharges are 

summed to produce a total discharge for that cross section of 

the stream. 

Velocity and depth are measured concurrently at each 

interval using a current meter attached to a wading rod. The 

rod allows for quick and easy measurements of depth with 

incremental markings and an adjustable arm that places the 

current meter at the proper depth for measuring velocity (60 

percent of the depth from the surface of the water). Some 

current meters have rotating cups (AA and pygmy models) 

while others have a pair of electronic contacts on a small head 

(FLO-MATE 2000) to measure velocity. The sensor in the 

FLO-MATE 2000 is equipped with an electromagnetic coil 

that produces a magnetic field. A pair of carbon electrodes 

measure the voltage produced by the velocity of the conductor, which in this case is the flowing water. Internal electronics process the measured voltages and output them as linear 

measurements of velocity. Velocity is displayed as either feet 

per second or meters per second. 

Preparation and Meter Calibration 

Prior to using the current meter, inspect the meter, cable, 

probe, and standard wading rod for obvious defects or damage. 

If the meter has been stored for more than a couple of weeks 

the batteries should have been removed, and they should be reinstalled according to the battery compartment’s instructions. 

Batteries should be tested by turning the unit on and checking 

for the low battery display. 

The FLO-MATE 2000 should be zero-adjusted 

before measurements are taken. One calibration per day is 

needed if the meter is not turned off for a period of several 

hours. Turning the meter off for short periods of time will not 

affect the meter’s zero calibration as this is stored internally 

by the meter. For other meters, instruction manuals should be 

referenced for calibration or zero adjustment procedures. To 

ensure there is no film on the sensor, clean the sensor before 

calibration (SOP 8). For zero-adjustment, the meter is turned 

on and the sensor is attached to the wading rod and placed 

in a 20-L bucket of water. A zero reading is taken after 10 to 

15 minutes to ensure the water is not moving, and the filter 

value is set at 5 seconds (table 3). To zero the instrument, the 

STO and RCL keys should be pressed at the same time and 

the value displayed (“3”) should be decremented to zero using 

the DOWN ARROW key. The number 32 will be displayed 

and will decrement itself to zero and turn off, showing that the 

meter is calibrated. Prior to fieldwork, it may be necessary to 

change default functions, such as measurement units (table 3).
34 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

One-key functions

ON/C—Turns unit on. Clears the display and restarts the 

meter.

OFF—Turns unit off.

UP ARROW—Decrements FPA, rC and memory location.

DOWN ARROW—Decrements FPA, rC and memory location.

RCL—Alternates between recall and real-time operating modes.

STO—Stores values in memory.

Two-key functions

ON/C—OFF—Alternates between units of measurement. Also 

turns beeper on and off.

UP ARROW—DOWN ARROW—Alternates between FPA and 

rC filtering

ON/C—STO—Clears memory

RCL—STO—Initiates zero adjust sequence.

Field Measurements

Discharge measurements should be made after other 

measurements such as temperature, dissolved oxygen, pH, and 

specific conductance are complete. Discharge measurements 

require wading across the stream and may cause sediments to 

stir up, disrupting accurate measurement of other water-quality 

characteristics. Prior to taking any measurements, the location where discharge will be measured must be determined. 

An ideal cross section will have the following qualities: (1) 

the stream channel directly above and below the cross section 

are straight, (2) there is measurable streamflow, with a stream 

depth preferably greater than 0.15 m and velocities generally greater than 0.15 m/s, (3) the streambed is a uniform “U” 

shape, free of large boulders, woody debris, and dense aquatic 

vegetation, and (4) the streamflow is laminar and relatively 

uniform with no eddies, backwaters, or excessive turbulence. 

The cross section will not likely meet all these qualifications but the best location should be selected based on these 

standards. Any discrepancies with the cross section should be 

recorded or sketched on the data sheet (appendix 20). Once 

the cross section is established, the width of the stream is measured with a tape measure to the nearest 0.1 m and the tape 

is secured across the stream for the duration of the discharge 

measurement. The cross section is divided into equal intervals, usually 15 to 20 with a minimum of 10 intervals recommended. The number of intervals will be based on stream 

width; larger reaches will have more intervals. A velocity and 

depth measurement is recorded for each interval across the 

stream at the center of each interval (see appendix 20). For 

Table 3. Key function summary for the Marsh-McBirney FLOMATE 2000 velocity meter.

example, if the stream is 10 m wide, 20 velocity and depth 

measurements will be made at 0.5-m intervals and the first 

measurement will be made at 0.25 m from the water’s edge, as 

shown in figure 11. 

Figure 11. Points for measuring discharge at a hypothetical cross 

section.

To take a velocity reading, the current meter must be 

turned on and the sensor securely attached to the wading rod, 

facing upright. For FLO-MATE 2000, the meter should be set 

to FPA with 20-second intervals for data collection. During 

measurement, one person should be measuring discharge and 

one person should remain on the bank recording data. Measurements start near the water’s edge and move to the center 

of the first interval. With the wading rod as level as possible 

and perpendicular to the water level, depth is read from the 

wading rod to the nearest tenth of a centimeter. Once depth 

has been read, the arm of the rod with the attached sensor 

should be adjusted to the water depth which will place the 

sensor at 60 percent of the depth from the surface of the water, 

a standard depth for measuring velocity in streams. During 

velocity measurement, the person taking the reading should 

stand behind the sensor and make sure there is no disturbance 

(including the sensor cord) around the sensor that interferes 

with the measurement. It may be necessary for the meter to be 

adjusted slightly upstream or downstream to avoid boulders 

or other interferences. Precautions also should be taken to 

face the sensor directly into the flow of the water, which may 

not always be directly parallel with the water’s edge. In this 

instance, the rod and sensor may need to be turned slightly 

with each measurement. If something happens during the 

measurement, such as movement of the wading rod, the meter 

5-meter wide cross section, 10 intervals

5 meters

0.5-meter interval

Velocity and 

depth point
Protocol Narrative 35

.

can be cleared and the reading started again. Once the time bar 

completes two cycles, the crewmember calls out the distance 

from the water’s edge, the depth, and then the velocity to the 

person recording data (appendix 20). The crewmember will 

continue moving across the stream until measurements have 

been made at all intervals. When finished, the sensor should 

be detached from the wading rod and placed back in the mesh 

side pocket for transportation. If the meter will not be used 

for several days, the meter should be turned off and the sensor 

cleaned and stored properly.

 
36 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

SOP 8: Equipment Maintenance and Storage Version 1.0

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Some equipment maintenance will be necessary to maximize the life of water-quality and fish sampling equipment. 

Poorly maintained equipment will adversely affect equipment 

performance, which will decrease accuracy of water-quality 

readings and sampling efficiency of fish sampling equipment. This will introduce variability into the dataset. After all 

fieldwork for a field season is completed, some effort to store 

sampling equipment properly will result in fewer equipment 

problems at the beginning of the next field season. This SOP 

describes general maintenance of water-quality and electrofishing equipment. 

Water-Quality and Current Meters

Many maintenance and storage functions for waterquality and current meters are instrument specific so it is 

important to consult the manual (see appendixes 10 and 11 for 

location of manuals). Cleaning and occasional replacement 

of membranes (for the dissolved-oxygen meter), sensors, and 

electrodes is required after extended use or whenever deposits 

or contaminants appear on the probe. Changing the membrane 

also includes changing electrolyte fluid within the probe. 

Generally a clean, lint-free cloth and distilled water can be 

used to clean deposits from the membrane or sensor. If rinsing the probe in deionized water does not get a sensor clean, 

soaking the probe in water and dishwashing liquid can be used 

to remove dirt or debris from the probe. For the current meter, 

600 grit sandpaper also can be used to remove debris from the 

sensor. 

Generally, for long-term storage, meters should be protected from dust and excessive heat or cold, and the cable and 

probe should be stored dry and free of dirt, with the probe in 

the calibration chamber. For the pH probe, storage requires 

a moist storage area with proper storage solution. It is never 

recommended to store probes in deionized or distilled water. 

For long-term storage, all batteries should be removed from 

the meters and charged. Meters will be stored in the Aquatic 

Program Laboratory located on the Missouri State University 

campus in Springfield, Missouri.

Fish Sampling Equipment

Equipment for fish sampling generally can be classified 

into one of three categories: mechanical equipment, electronic 

equipment, and manual equipment. Each category involves 

varying degrees of maintenance. 

Mechanical equipment (generators, outboard motors) 

should be maintained according to manufacturer’s instructions 

and stored in a shed at Wilson’s Creek National Battlefield 

near Springfield, Missouri. Maintenance of the generator 

motor is similar to the maintenance required by other small 

gasoline engines. Fuel, oil, spark plugs, and air filters need to 

be changed on a routine basis. Carburetion problems (gumming or poor ignition) can be avoided by using gasoline meeting minimum octane requirements and that has been stored 

for short periods (2 or 3 months maximum). For long-term 

storage, gasoline stabilizer should be used in generators to 

prevent condensation and water contamination over the winter. 

Outboard motors are commercially available as two-stroke and 

four-stroke designs. The manufacturer’s operational manuals 

for the specific motor type should be consulted to determine 

appropriate maintenance procedures and service schedules. 

Gasoline should be drained from boat motors if they will not 

be used for more than a few months. All manuals should be 

kept in the Aquatic Program Laboratory so that all personnel 

responsible for operation can access maintenance information. 

Electronic equipment and associated batteries will 

be stored in a secure, dry location at the Aquatic Program 

Laboratory at Missouri State University in Springfield, Missouri. Electrofishing pulsators are very durable and require 

very little maintenance; however, some pulsators may have 

fuses or circuit breakers for surge protection. Reviewing the 

operating manual and having replacement fuses or circuit 

breakers on hand will reduce downtime in the field. Corrosion or tarnishing of electrodes can reduce electrical conductance from the electrofishing boat, barge, or backpack to the 

water. Electrodes should be inspected prior to each sampling 

event. Stainless-steel electrodes (anodes and cathodes) can be 

reconditioned using emery cloth, steel wool, or fine-grained 

sandpaper. Aluminum anodes on some backpack electrofishing units are better cleaned with sandpaper or a small file. 
Protocol Narrative 37

Over extended time (several years), electrical connections at 

junction boxes and other connections will sometimes begin to 

corrode. This corrosion results in a poor connection and can 

result in a reduction of electrofishing power. Connections 

should be inspected before each electrofishing season and 

serviced when necessary.

Electrofishing batteries for backpack units should be 

charged as soon as possible after sampling is completed. 

Electrofishing battery chargers capable of a trickle charge, 

having an automatic shutoff (once the battery is charged), 

and a voltage tester are preferred and can be purchased from 

manufacturers of electrofishing gear. Battery voltage should be 

tested before each sampling effort to be certain that the battery 

is capable of carrying a full charge. If a battery is not capable 

of carrying a full charge, time spent electrofishing will be 

decreased and the battery may need to be replaced. 

Manual equipment (nets, gloves, waders, buckets, and 

safety equipment, for example) should be stored in the Aquatic 

Program Laboratory or in a storage shed at Wilson’s Creek 

National Battlefield. Nets, seines, waders, and personal floata-

tion devices also require maintenance. Nets and seines should 

be cleaned with water and allowed to dry before extended 

storage to prevent moisture damage. Nets and seines should 

be inspected regularly for tears in the mesh and replaced or 

repaired. The life of waders and personal floatation devices 

also will be prolonged if stored in a cool, dark, dry area. Wad-

ers stored for an extended period are susceptible to dry rot. 

Rubber conditioners can be applied to boots to prevent deterio-

ration. Personal floatation devices used for fish sampling 

should be inspected for rotting or torn sections. Inflatable 

preservers that use carbon dioxide cartridges for inflation must 

have the carbon dioxide cartridges replaced periodically and 

according to manufacturers instructions. 

For electrofishing boats that use the boat hull as the 

cathode and are painted, electrical currents are concentrated in 

areas where the aluminum is exposed (the paint has been acci-

dentally scratched, for example). In this situation, boat hulls 

are susceptible to electrolysis, which can result in aluminum 

pitting and, eventually, leaking. Electrolysis can be controlled 

by using a boat with the bottom of the hull unpainted, attach-

ing a zinc plate to the hull, or by using cathode droppers 

independent of the hull. If leaks do occur, welding compounds 

can be used to patch the boat hull.

 
38 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

SOP 9: Data Management Version 1.0

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This SOP explains procedures for data management 

of BUFF and OZAR river fish sampling data. It includes a 

general description of the data model, and procedures for data 

recording, data entry, data verification and validation, and data 

integrity for the primary fish sampling data. 

Data management can be divided into (1) the initial 

design phase that involves defining the data model, its entities 

and their relations and (2) the procedures necessary to implement the database. Microsoft (MS) Access 2003 is the primary software used for maintaining fish data. Water-quality 

data will be stored in the National Park Service’s NPSTORET 

database. Environmental Systems Research Institute (ESRI) 

ArcInfo 9.x is used for managing spatial data associated with 

field sampling locations. Data products derived from this 

project will be available at the NPS I&M Data Store and EPA 

STORET National Data Warehouse. QA/QC guidelines in this 

document are based on recommendations of Rowell and others 

(2005) and citations therein.

Data Model

The NPS I&M program has designed the Natural 

Resource Database Template (NRDT) to be used as a database 

model for storing vital signs monitoring data in MS Access 

(National Park Service, 2006). The template has a core 

database structure that standardizes location and observation 

data to facilitate the integration of datasets. Developed in 

MS Access, the database allows users to enter, edit, display, 

summarize, and generate reports as well as integrate with other 

NPS Natural Resource data systems such as NPSTORET. 

Distributed databases, or replicas, allow data entry or modifications from remote locations (such as at BUFF or OZAR 

offices) and subsequent synchronization with a master 

database archived on the HTLN server at Missouri State 

University in Springfield, Missouri. NPS Water Resources 

Division (WRD) also has designed the NPSTORET database 

to facilitate archiving NPS data in the EPA STORET database 

(National Park Service/Water Resources Division, 2007b). 

NPSTORET is a series of Microsoft Access-based templates 

patterned after the NRDT and includes data entry templates 

and an import module. It supports the core data management 

objectives of data entry and data verification/validation in 

a referentially constrained environment (related locations, 

events, and primary data elements). 

A generalized NRDT entity relation diagram of the 

fish community database is given in figure 12. The tables 

called sampling events (tbl_SamplingEvents) and locations 

(tbl_Locations) are the two core tables of the database and 

contain general information pertaining to the field sampling 

occasion (the when and where of the sample). This includes 

information such as date and time, river stretch ID and UTM 

coordinates, and park/project codes. The fish community 

sampling table (tbl_FishCommunitySampling) serves as 

the organizing hub for fish data. Other tables include site 

conditions (tbl_SiteConditions, not shown), habitat data 

(tbl_BankMeasurmentInfo and tbl_Discharge, not shown), and 

associated lookup tables (tlu_FishAnomalies, not shown; and 

tlu_Species).

Generally, the database model is developed from the 

appropriate tables based on river fish sampling protocols. 

Prior to table development, the data manager coordinates with 

project staff to determine data types (byte, text, numeric, for 

example), precision, and range of values. Acquiring field data 

forms assists with developing data logic (that is, how data 

components relate) and identifying indexes and primary keys. 

The NRDT data dictionary follows standards identified in the 

NRDT phase 2 and is modified where required. Naming standards follow NPS I&M recommended procedures. 

Data Recording 

QA/QC procedures related to data recording are important components of any project. Sampling data, including 

sample methods, effort, weather, water-quality conditions, species abundance data, and habitat data are recorded on the field 

form (appendixes 15-20) and checked for completeness before 

leaving a site or within 24 hours of data recording. This will 

aid in verification and validation of the data after entry into 

the database. To prevent the complete loss of field form data 

because of unforeseen circumstances (for example, fire or 
Protocol for Monitoring Fish Communities 39

flood in the workplace), all field sheets are photocopied and 

a hard copy located in a separate location from the original. 

Field sheets are scanned into a computer and electronic copies 

of the data sheets stored on the HTLN server located at Missouri State University, Springfield, Missouri. This will ensure 

that at least one copy of the field sheets is available for data 

entry and verification. 

Data Entry

Data entry is accomplished in replica databases using 

a tiered set of forms. Upon opening the replica, the user is 

presented with a switchboard (fig. 13) that can be used to 

access these forms (fig. 14). A preliminary set of forms define 

the sampling occasion and requires the input of location, 

period, and event IDs prior to entry of additional data. The 

other forms address the details of fish occurrence, habitat, and 

observers, for example, and includes data entry instructions. 

Once all fields for the preliminary set of forms have been 

completed, data can be entered for the remaining forms. Additional forms document sampling personnel for each occasion 

and their specific hours related to the project (such as sampling hours and travel hours). The replicas then are synchronized with the master database and any subsequent data entry 

in a new replica.

Several features are “built-in” to form properties that 

enable the user to maximize data entry efforts while minimizing error. These include data input masks for ease of viewing multi-part data (such as park/project codes and date in 

PeriodID, LocationID, or EventID), “fill-in-as-you-type” to 

automatically complete a field, default values to autopopulate 

common values, limiting input values to known ranges (or 

restricting null values) or providing “drop-down boxes”, and 

tab indexes to control the order of data entry. Forms also contain fields that require data input or are constrained to properties and integrity of related tables. The “Prevent Deletes” 

option is enforced in replica databases to ensure data are not 

inadvertently deleted.

Entering Sampling Occasion Data

The sampling occasion location (“site”, see SOP 3 and 

appendix 3) is entered by clicking the “Open Locations Form” 

button on the main switchboard (fig. 13). The user then 

selects the appropriate Park Code, Site Type, and Sub Type 

and enters the Site Number and Stretch Number to develop 

a LocationID (fig. 15). The Stretch Number refers to the 

MORAP classified stream identifier and is transcribed from 

the appropriate MORAP StretchID table (see appendix 3 

for Stretch ID). Clicking the “Generate LocationID” button 

passes the user data to a secondary form where additional 

location data are entered. Note the user data on the first form 

are at the top of the secondary form and a LocationID has been 

generated with an input mask to separate Park Code, Project, 

and LocationID. To exit the location form (as well as all other 

forms) the user clicks the “Close Form” button.

Note: tbl_SamplingEvents and tbl_Locations track stream-reach data while 

tbl_FishCommunitySampling serves as the organizing hub for fish data. 

Figure 12. Data model for fish communities monitoring.
40 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Figure 13. River fish database switchboard.

Note: The three primary data entry buttons at the top (locations, periods, and events). 
Protocol Narrative 41

Figure 14. Outline of fish community data forms.

Open sampling period form

Open sampling events form

Fish community data form

Open habitat forms

Site conditions/

site measurements

Generate location identification

Generate period identification

Generate event identification

Select occasion data

Select occasion data

Site conditions

Select occasion data

Location identification data

Period identification data

Even identification data

Species measurement data

In-stream

Bank measurement

Fish cover

Site measurements

Discharge detail

Discharge observers

Discharge gage observers

Species data

Event observers

Observer hours

Discharge form

Discharge gage

Add species

Observers form

Open observers hours

Main forms Data entry subforms

Open locations form

Note: Forms are selected from the main switchboard and data entered into data entry subforms.

Preliminary forms that define the sampling occasion

Remaining forms that can be completed after the preliminary forms are completed
42 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Figure 15. Detailed location forms for fish data.
Protocol Narrative 43

The sampling occasion period (the entire sampling timeframe for each park; for example, 01-Oct-2007 to 16-Nov2007 for OZAR) is entered on the sampling period form (fig. 

16) by clicking the “Open Sampling Period Form” button (fig. 

13). The user then selects the appropriate Park Code and Project and uses the calendars to select the start and end dates of 

the sampling period timeframe to develop a PeriodID (fig. 16). 

Clicking the “Generate Sampling PeriodID” button passes 

the user data to a secondary form where the user reviews then 

accepts the PeriodID and protocol version by clicking the 

“Verify” button. Note the user data on the first form are at the 

top of the secondary form and a PeriodID has been generated 

with an input mask to separate Park Code, Project Code, and 

beginning date of the sampling period.

The sampling occasion event (the specific date of the 

sample within the sample timeframe; for example, 17-Oct2007 for a sample location at OZAR) is entered on the 

sampling event form (fig. 17) by clicking the “Open Sampling 

Events Form” button (fig. 13). The user then selects the Park 

Code, Project Code, and PeriodID and uses the calendars to 

select the start and end dates of the sampling event to develop 

an EventID (fig. 17). Clicking the “Generate Sampling EventID” button passes the user data to a secondary form where 

the user enters additional event data. Note the user data on the 

first form are at the top of the secondary form and an EventID 

has been generated with an input mask to separate Park Code, 

Project Code, and the date of the event.

Entering Fish Data

After inputting sampling occasion data (locations, period, 

and events), the user can begin to enter additional fish data 

(such as individual fish data and corresponding water-quality 

and habitat data for the sampling location and event). The following paragraphs describe data entry for the additional data 

and can be used in any order.

Fish community data are entered (fig. 18) by clicking the 

“Fish Community Data Form” button (fig. 13). Park Code, 

LocationID, EventID, Gear, and Habitat Sampled are selected 

and Pass Number, Effort, Seine Reach Length and Number of 

Seine Hauls are entered specifically for that sampling occasion. Clicking the “Fish ID Crew” button opens a form used 

to document who identified and recorded the fish data and 

clicking the “Fish Shocking Crew” button opens a form used 

to document specific crewmembers and their field task (for 

example, the person electrofished, seined, or both). Clicking 

the “Continue” button in either form will allow the addition 

of multiple entries and clicking the “Return” button will allow 

the user to exit the form. The user then selects species information by selecting the scientific name (fig. 18) and entering additional data specific to the one species. Species data 

comprise three types: individual fish, batch weighed fish, and 

extra fish. Individual fish data consist of a subsample of 30 

individuals of each species that were measured (total length), 

weighed, and any anomalies noted (Anomaly Description is 

set to default to N, no anomaly). After selecting a scientific 

name, the user enters total length and weight and selects 

Anomaly Description (if required). If the individual was 

retained and preserved the Voucher box is checked. Number 

refers to the number of individuals and defaults to one. The 

additional batch fields are ignored and any comments to that 

individual fish are noted. The user is then returned to the 

Total Length field and continues entering data for that species. 

Batch weighed fish consist of those smaller species that were 

individually measured (total length), but weighed in groups. 

Similar to individual fish data, the user selects a scientific 

name and enters the total length. Weight is left blank and any 

anomaly for that specific individual is documented by selecting the Anomaly Description and, if retained, the Voucher box 

checked. As in the individual fish, Number defaults to one. 

The Batch Weight box is checked, a BatchID is entered (for 

example, entering 1, 2, or 3, depending on if it’s the 1st, 2nd, 

or 3rd batch of fish being weighed) and the weight of those 

batch weighed fish is entered in Batch Weight. For subsequent entry of batch weighed fish the Batch Weight box is left 

unchecked, BatchID is set to that batch number, and Batch 

Weight defaults to zero. Any comments to that individual fish 

are noted and the user is returned to the Total Length field to 

continue entering data for that species. Extra fish are those 

collected and merely counted. The user selects a common 

name and enters the number collected in the Number field and 

any comments for those extra fish (other fields are ignored). 

When all fish species data are entered for that fish community 

the user clicks the “Close Form” button to close the form. 

Entering Habitat and Discharge Data

Habitat data are entered by clicking the “Open Habitat 

Forms” button on the main switchboard (fig. 13) and selecting 

the appropriate Park Code, LocationID, EventID, and Habitat Type from the drop down boxes. The user then chooses 

the appropriate Transect Number from the Instream Habitat 

Assessment, Fish Cover, or Bank Measurements data entry 

section of the form. For the Instream Habitat Assessment 

form, the user enters additional fields such as Channel Unit, 

Pool Form, and Width. Clicking on a habitat form passes the 

selected user data to secondary habitat forms. The user then 

enters channel morphology data (depth, velocity, or substrate), 

selects the appropriate fish cover data for presence/absence 

(for example, hydrophytes, small woody debris, and undercut 

bank), and enters bank stability measurements (bank angle, 

percent vegetation cover) and bank cover types (trees, shrubs, 

grass). Each habitat subform is provided with a “Continue” 

button that allows the user to advance to the next observation 

and the “Return” button to exit the form. When finished entering habitat data the user will be returned to the initial habitat 

form and exits the form by clicking the “Close Form” button.

Discharge data are entered by clicking the “Discharge 

Form” button on the main switchboard (fig. 13) and selecting 

the appropriate Park, LocationID, EventID, and Habitat Type 

from the drop down boxes. The user then enters discharge 

measurement units (for distance, depth, velocity) in either
44 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Figure 16. Sampling period forms for fish data.
Protocol Narrative 45

Figure 17. Sampling event forms for fish data.
46 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Figure 18. Fish community data form.
Protocol Narrative 47

English or metric units. Individual depth and velocity readings 

are then entered in the discharge detail form. The user clicks 

the “Continue” button to enter the next replicate data and the 

“Return” button to exit the form. Summary data collected 

from established gaging stations are entered by clicking the 

“Discharge Gage” button on the main switchboard and selecting the appropriate Park, LocationID, EventID and entering 

the summary Discharge data value.

Entering Water-Quality Data

Water-quality data (CORE 5) collected by hand-held 

meters are entered by clicking the “Site Conditions/Measurements Form” button on the main switchboard (fig. 13) and 

selecting the appropriate LocationID and EventID. Additional 

weather condition data (such as percent cloud cover, precipitation, and wind intensity) and beginning/ending measurements 

for temperature, dissolved oxygen, pH, specific conductance, 

and turbidity are entered. Water-quality data collected by 

unattended CORE 5 data loggers (sondes) are uploaded from 

the logger using the manufacturer’s accompanying software 

program and saved in MS Excel. Data then are edited to correct any missing data because of logger maintenance (downtime) and validated to determine if the data meet the expected 

range requirements or critical limits.

CORE 5 water-quality summary data then are entered 

into NPSTORET by using the direct data entry templates or 

the import module. Coordinate data for logger locations are 

collected in accordance with the current HTLN spatial data 

collection techniques and entered into NPSTORET. Metadata are then entered for each characteristic/parameter. An 

NPSTORET database then is sent to the NPS WRD staff on an 

annual basis for initial QA/QC and subsequent upload into the 

WRD master copy of the EPA STORET. 

Data Verification 

Data verification immediately follows data entry 

and involves checking the accuracy of computerized records 

against the original source, usually paper field records. 

Data tables are queried to produce specific sets of data (for 

example, fish community data and bank measurement data) 

and exported to Excel worksheets (by using the QAQC Data 

button, fig. 13). These worksheets then can be compared to 

the original field data sheets to identify missing, mismatched, 

or redundant records. A design master then is used to correct 

or delete errors through data edit forms. As data are edited, 

built-in table triggers store the original record in a backup 

audit table and can be recovered where necessary (audit tables 

mirror the data table).

Data Validation

Although data may be correctly transcribed from the 

original field forms, they may not be accurate or logical. For 

example, field crews collect data per occasion (location and 

event) and the resident data should reflect this. At any given 

occasion, fish sampling is conducted in each reach during 

the sampling event and can be validated by querying the ID 

number for these values. A query of these data should reflect 

these conditions and confirm the coincident (relational) nature 

of the database. 

As annual data are amassed in the database, validation is 

conducted by query and comparison among years to identify 

gross differences. For example, species A may be recorded 

at a location in a specific year, but not in previous years, thus 

representing a possible new locality. The design master then 

is used to correct or delete errors through data edit forms.

Once verification and validation are complete, the dataset 

is turned over to the HTLN Data Manager for archiving and 

storage. These data then can be used for all subsequent data 

activities.

Spatial validation of sample coordinates can be accomplished using the ArcMap component of ArcGIS (ESRI, 

2007). Coordinate data are maintained in the Access database 

and can be added to an ArcMap project and compared with 

existing features (park boundaries, USGS Digital Ortho Quarter Quadrangles, National Hydrography Dataset hydrography) 

to confirm that coordinate data are valid. 

File Organization

The various databases, reports, and GIS coverages 

used and generated by HTLN create a large number of files 

and folders to manage. Poor file organization can lead to confusion and data corruption. As a standard data-management 

technique, files pertaining to the project are managed in their 

own folder: Analysis (for data analysis), Data (for copies of 

archived data as well as data sheets), Documents (for supporting materials related to the project), and Spatial info (for various spatial data and GIS coverages). The database is managed 

in a Databases folder and contains prior versions and backups 

in subfolders.

Version Control

Prior to any major changes of a dataset, a copy is stored 

with the appropriate dataset version number. This allows for 

the tracking of changes over time. With proper controls and 

communication, versioning ensures that only the most current version is used in any analysis. Versioning of archived 

datasets is handled by adding a floating-point number to the 

file name, with the first version being numbered 1.00. Each 

major version is assigned a sequentially higher whole number. 

Each minor version is assigned a sequentially higher number 

incremented by 0.1. Major version changes include migrations 
48 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

across Access versions and complete rebuilds of front-ends 

and analysis tools. Minor version changes include bug fixes 

in front-end and analysis tools. Frequent users of the data are 

notified of the updates and provided with a copy of the most 

recent archived version. 

Replication

The Aquatics Program relies on distributed databases to 

allow remote users to enter/revise data and is accomplished 

through database replication consisting of a design master and 

replicas. The design master is stored on the server at Missouri 

State University in Springfield, Missouri and can be directly 

accessed for local data entry/revisions or design changes. A 

replica is created for users without access to the server and is 

distributed for data-entry activities. When a user has finished 

data activities with the replica, it is returned and synchronized 

with the design master.

Backups 

Secure data archiving is essential for protecting data 

files from corruption. Once a dataset has passed the QA/QC 

procedures specified in the protocol, a new metadata record is 

created using the NPS Metadata Tools (stand alone or within 

ArcCatalog) or Dataset Catalog. Backup copies of the data 

are maintained at an onsite location in the Aquatic Program 

Laboratory at Missouri State University in Springfield, Missouri and at an offsite location at Wilson’s Creek National 

Battlefield. An additional digital copy is forwarded to the 

NPS I&M Data Store. Tape backups of all data are made at 

regular intervals and will be made minimally, once per week, 

with semi-annual tapes permanently archived.

Data Availability

Currently (2007), data are available for research and 

management applications for those database versions where all 

QA/QC has been completed and the data have been archived. 

Data can be transferred using ftp or by e-mail (where files are 

smaller than a few megabytes). Monitoring data generally will 

become available for download directly from the NPS I&M 

Data Store. Metadata for the fish community database are 

developed using ESRI ArcCatalog 9.x and the NPS Metadata Tools and Editor extension and will be available at the 

NPS I&M GIS server (http://science.nature.nps.gov/nrdata/). 

Water-quality data will be stored at the EPA STORET 

National Data Warehouse and be publicly accessible via the 

internet. Additionally, data requests can be directed to:

Heartland I&M Network

Attn. Database Manager

Wilson’s Creek National Battlefield

6424 W. Farm Road 182

Republic, MO 65738-9514
Protocol Narrative 49

SOP 10: Data Analysis Version 1.0

Revision History Log:

Previous

version

number

Revision

date Author Changes made Reason for change

New 

version 

number

Conclusions of ecological studies based on fish and other 

biological, chemical, and physical data are used by resource 

managers to better comprehend underlying system processes 

and develop environmental and management policies that best 

serve the resource. This, in turn, could have substantial ecological and economical repercussions and should be an important 

consideration for investigators responsible for data interpretation. Therefore, every effort should be made to collect reliable 

data and use statistical analyses that are straightforward and 

will result in confident interpretations. 

Primary approaches to analyzing fish data are metric 

estimation with use of control charts and multivariate statistics. Biological metrics are commonly used by investigators 

at all levels (private, State, tribal, and Federal, for example) to 

compare the condition of the biological community at multiple 

sites (Simon, 1999) or examine trends over time. Barbour and 

others (1999) define a metric as a characteristic of the biota 

that changes in an expected direction with increased anthropogenic disturbance. Using these characteristics (appendix 5) 

allows investigators to determine the importance of environmental conditions, clarify which habitat factors play a large 

role in shaping fish communities, and identify specific sources 

of impairment (Karr, 1981). 

By combining multiple metrics and results for those 

metrics into a single index of biotic integrity (IBI), investigators can determine the overall quality of the fish community. 

An IBI also can be used to compare overall ecological conditions over time and between sites, providing that the selected 

metrics have a relation to variables responsible for impairment 

(Karr, 1981; Barbour and others, 1999; Simon, 1999). To 

assess fish community conditions at BUFF and OZAR, the IBI 

developed for Ozark Highland streams by Dauwalter and others (2003) will be used (appendix 9).

Metrics and estimated variables for analysis of river fish 

communities include:

1. Species richness (number of species) for the entire 

sample reach. 

2. Simpson’s Diversity Index (D) for entire sample reach. 

Simpson’s Diversity Index is preferable to the Shannon diversity index and will be used for data analysis because this index 

is independent of sample size. Simpson’s Diversity Index is 

calculated with the following formula:

 (( ) ( )) 2 2

1

/ s

i D nnN N =

=Σ − − 

where S = number of species,

 n = number of individuals of ith species, and

 N = sum of n. 

3. Catch per unit effort. For electrofishing, catch per 

minute for the entire reach (combining gear types) will be 

calculated for all species combined. For seine data, catch per 

area will be calculated. 

4. Average length and weight for each species in the 

reach (combining gear types). 

5. Percent composition by biomass for each species in 

the reach (combining gear types). To calculate this, average weight of a species will be multiplied by number caught 

to obtain individual species biomass. Individual biomass is 

divided by area of the sample reach to get biomass/area for 

each species. To obtain percent composition, biomass/area for 

each species is divided by total biomass/area.

6. Index of biotic integrity (Dauwalter and others, 2003) 

for the entire sample reach. This IBI consists of seven metrics 

that are calculated and scored. Individual metric scores are 

totaled for an IBI score at that sample reach. The metrics are: 

(1) number of darter, sculpin, and madtom species; (2) percent 

of individuals as green sunfish, bluegill, yellow bullhead, 

and channel catfish; (3) percent of individuals as algivorous/

herbivorous, invertivorous, and piscivorous; (4) percent of 

individuals as invertivores; (5) percent of individuals as top 

carnivores; (6) number of lithophilic spawning species; and (7) 

percent of individuals with black spot or an anomaly. Specifics on calculation of and scoring of metrics can be found in 

Dauwalter and others (2003).

Using several of these estimated variables listed above, 

control charts can be employed to determine trends and 

changes in fish communities (Morrison, in press). The construction and interpretation of control charts is covered in 

many texts focusing on quality control in industry (Beauregard 

and others, 1992; Gyrna, 2001; Montgomery, 2001). The 

application of control charts for ecological purposes, however, 

is relatively straightforward. The use of control charts in environmental monitoring is discussed in the texts by McBean and 

Rovers (1998) and Manly (2001), although not as detailed as 
50 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

the texts referenced above focusing on industrial applications. 

Many different types of control charts could be constructed, 

depending upon the type of information desired. For example, 

control charts can be used to evaluate variables or attributes 

(for example, count data, richness, or number of intolerant 

taxa), to focus on measures of central tendency or dispersion, 

and in univariate or multivariate analyses. 

Although some of the above-mentioned texts discuss 

the use of multivariate control charts (using the Hotelling T2 

statistic), this approach is only practical for a small number of 

variables, and assumes a multivariate normal distribution. In 

general, species abundances are not distributed as multivariate 

normal (Taylor, 1961), and traditional multivariate procedures 

are frequently not robust to violations of this assumption 

(Mardia, 1971; Olson, 1974). A new type of multivariate 

control chart recently has been described for use with complex 

ecological communities (Anderson and Thompson, 2004). A 

software application entitled ControlChart.exe is available for 

constructing these types of multivariate control charts (see 

Anderson and Thompson, 2004). Multivariate temporal autocorrelation will violate the assumption of stochasticity upon 

which this method is based, however, and it is important to test 

for temporal autocorrelation using Mantel correlograms prior 

to using this method.

Multivariate analysis is another frequently used analysis 

technique and involves methods used to explain variability in 

community data and to identify the environmental variables 

that best explain, and have an assumed responsibility for, the 

variability measured (Gauch, 1982; Jongman and others, 1995; 

Everitt and Dunn, 2001; Timm, 2002). Multivariate techniques elicit a hypothesis from the biological data rather than 

disproving a null hypothesis. Two commonly used multivariate 

techniques include: ordination (such as principal components 

analysis, canonical correspondence analysis, and detrended 

correspondence analysis) and classification (such as two-way 

indicator species analysis). Detailed discussion of these methods can be found in several texts (Gauch, 1982; Jongman and 

others, 1995; Everitt and Dunn, 2001; Timm, 2002). 

Rather than requiring a list of specific data analyses, the 

data analysis process should be flexible enough to allow the 

use of newly developed statistical and analytical techniques 

and tailoring of analyses for a variety of audiences with a 

variety of questions about the aquatic resources at the parks. 

This primary audience will consist of park resource managers, 

superintendents, and other staff who may not have an indepth 

background in statistical methods or may have limited time for 

evaluation of these analyses. Thus, to the extent possible, it 

is important that core data analysis and presentation methods 

are relatively straightforward to interpret, provide a standard 

format for evaluation of numerous variables, can be quickly 

updated whenever additional data become available, and work 

for many different types of indicators, whether univariate or 

multivariate. Additionally, the type and magnitude of variability or uncertainty associated with the results should be somewhat intuitive, and it may be necessary to indicate a threshold 

for potential management action. More detailed analysis of 

the data generally will benefit from the use of multiple dataanalysis methods. 

 
Protocol Narrative 51

SOP 11: Reporting Version 1.0

Revision History Log:

Previous

version

number

Revision

date Author Changes made Reason for change

New 

version 

number

Results from the fish monitoring program will be 

reported by the NPS annually to park managers and superintendents of each park (table 4) prior to the start of monitoring 

the following year (BUFF in May and OZAR in October). A 

copy of annual reports also will be kept on file with the HTLN 

office of the National Park Service, Republic, Mo. The content of annual reports will include location of sites, methodology used, and data analysis such as number of species caught, 

diversity, relative abundance, and IBI (see SOP 10 for detailed 

list of variables). Before distribution to park staff, annual 

reports will be internally reviewed by at least two HTLN staff 

to evaluate grammatical soundness and metric calculations. 

Scientific collection permits for Arkansas and Missouri 

are required for collection of fish data. Renewal of the permit 

requires a report be submitted to the AGFC and the MDC 

describing the results of collection activities. This report typically includes a description of sampling locations, sampling 

gear, number and taxa of collected specimens, and specimen 

disposition. Requirements occasionally change, and permit 

requirements need to be consulted each year. Reports for permit renewal are less detailed than annual reports submitted to 

park staff and HTLN.

More comprehensive summary reports containing results 

from multivariate statistics, control chart analysis, and detailed 

explanations and interpretations of findings will be completed 

every 5 years with summary reports replacing annual reports 

in those years (table 4). These reports will be sent to park 

superintendents and resource management staff and will be on 

file at the HTLN office. Comprehensive reports will be sent to 

State agency personnel who have participated in data collection or have expressed interest in the summary data. Prior to 

dispersal of a summary report, an internal review by HTLN 

staff will be completed by the HTLN Quantitative Ecologist 

and a staff member knowledgeable of the monitoring program. 

This internal review provides not only review of the technical 

writing, but also evaluation of statistical methods and interpretations of the results. 

For both annual and comprehensive reports, the template 

for regional natural resource technical reports will be followed (http://www.nature.nps.gov/publications/NRPM/index.

cfm). Natural resource reports are the designated medium for 

disseminating high priority, current natural resource management information with managerial application. The natural 

resource technical report series is used to disseminate results 

of scientific studies in the physical, biological, and social 

sciences for both the advancement of science and the achievement of the NPS’s mission. Standards for scientific writing as 

recommended in the CBE Style Manual (Council of Biological 

Editors Style Manual Committee, 1994) should be used, and 

reports should be direct and concise. Refer to the CBE Style 

Manual (Council of Biological Editors Style Manual Committee, 1994), Writing with Precision, Clarity and Economy 

(Mack 1986), Strunk and White (2000), Day and Gastel 

(2006), and Goldwasser (1999) for writing guidelines. All 

reports will be dispersed through the HTLN website: http://

www1.nature.nps.gov/im/units/htln/reports.cfm. 
52 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Table 4. Summary of report types released by National Park Service and review procedures.

[HTLN is Heartland Network Inventory and Monitoring Program]

Type of report Purpose of report Primary audience Review procedure Frequency

Annual status reports

for specific protocols

Summarize monitoring data

collected during the year 

and provide an update on

the status of selected natural

resources. Document

related data-management

activities and data

summaries.

Park resource

managers and 

external scientists

Internal peer

review by HTLN staff

Annual

Executive summary

of annual reports for

specific protocols

Same as annual status

reports but summarized

to highlight key points

for non-technical 

audiences.

Superintendents, 

interpreters, and the

general public

Internal peer

review by HTLN staff

Simultaneous

with annual

reports

Comprehensive trends,

analysis, and synthesis

reports

Describe and interpret trends 

in individual vital signs.

Describe and interpret 

relations among observed

trends nd factors such as park 

management, known stressors,

and climate. Highlight

resources of concern that

may require management

action.

Park resource

managers and 

external scientists

Internal peer

review by HTLN staff

Every 5 to 7 years
Protocol for Monitoring Fish Communities 53

SOP 12: Protocol Revision Version 1.0

Revision History Log:

Previous

version

number

Revision

date Author Changes made Reason for change

New 

version 

number

The Ozark Rivers Fish Community Protocol (Protocol 

Version 1.0 and version 1.0 of each SOP) has been developed 

to incorporate sound methods for collecting and analyzing 

fish community data at BUFF and OZAR. However, revisions 

may be necessary as new and improved sampling methods or 

statistical techniques are developed. Protocol and SOP versions later than version 1.0 are considered separate documents 

that (although based on Protocol Version 1.0 and version 1.0 

of each SOP) may be authored by a different group of individuals, reviewed by different individuals or entities, and may not 

be USGS publications. All revisions to this protocol should be 

made in a timely manner to allow for review of the new version of the protocol. Minor changes to sampling techniques, 

such as adding additional seine hauls, will require revision 

of relevant SOPs, while major changes to the study design or 

underlying sampling methodology will require revision of the 

Protocol Narrative. Minor changes to the protocol will require 

internal review by HTLN staff. However, major revisions 

to the protocol (for example, changes in study design) will 

require an outside review by regional NPS staff and experts 

from other agencies familiar with fish community monitoring. 

Documenting revisions to this protocol is mandatory 

for maintaining consistency in data collection and analysis 

between versions. All versions of the Protocol Narrative and 

SOPs must be archived in a protocol library. Documentation of changes to the protocol will be filed in the Revision 

History Log located within each SOP. Items recorded in the 

log include: previous version number, revision date, person 

(author) revising the protocol, specific changes made, reason 

for changes, and the new version number. Once changes have 

been made, the version number of the protocol will increase 

by 0.1 (starting with the original protocol at version 1.0). Revisions to the protocol also will be recorded in the fish community database under a field identifying the protocol version 

in use at time of data collection. This will ensure that staff 

managing the data and running analyses are aware of revisions 

in collection techniques that may require changes in database 

design or analytical procedures. Once revisions are complete, 

the new version will be posted on the HTLN website: http://

www1.nature.nps.gov/im/units/htln/fish.htm
54 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Summary

Buffalo National River (BUFF), in north-central Arkansas, and Ozark National Scenic Riverways (OZAR), in southeastern Missouri, are the two largest units of the National Park 

Service in the Ozark Plateaus physiographic province (fig. 1). 

The purpose of this report is to provide a protocol that will be 

used by the National Park Service to sample fish communitiesand collect related water-quality, habitat, and stream discharge 

data of BUFF and OZAR to meet inventory and long-term 

monitoring objectives. 

The protocol includes (1) a protocol narrative, (2) several 

standard operating procedures and (3) supplemental information helpful for implementation of the protocol. The protocol 

narrative provides background information about the protocol 

such as the rationale of why a particular resource or resource 

issue was selected for monitoring, information concerning the 

resource or resource issue of interest, a description of how 

monitoring results will inform management decisions, and 

a discussion of the linkages between this and other monitoring projects. The SOPs cover preparation, training, reach 

selection, water-quality sampling, fish community sampling, 

physical habitat collection, measuring stream discharge, equipment maintenance and storage, data management and analysis, 

reporting, and protocol revision procedures. Much of the 

information in the SOPs was gathered from existing protocols 

of the USGS NAWQA program or other sources.

All of the SOPs are written to provide information that 

can be used to maximize the accuracy, representativeness, and 

completeness of the fish community data. SOP 1 describes 

preparations that should be completed prior to fish community 

sampling. SOP 2 describes training requirements related to 

sampling and safety. SOP 3 describes sampling reach designation. SOP 4 addresses the equipment and methods required 

to measure water-quality variables (temperature, dissolved 

oxygen, specific conductance, pH, and turbidity). The fish 

community sampling SOP (SOP 5) includes methods for sampling fish communities and for processing samples. Methods 

are described for using backpack, towed barge, and boat electrofishing equipment and seines in wadeable and nonwadeable 

streams. Wadeable streams will be sampled using a singlepass method and nonwadeable streams will be sampled using 

a two-pass method. SOP 6 describes methods for collecting 

physical habitat data that will be collected as part of the fish 

community monitoring to examine relations between environmental conditions and fish communities. SOP 7 provides 

guidance for measuring discharge in streams associated with 

the fish community sampling. SOP 8 describes equipment 

maintenance necessary to maximize the life of water-quality 

and fish sampling equipment. SOP 9 explains procedures for 

data management of BUFF and OZAR river fish sampling 

data. SOP 10 describes methods that can be used to analyze 

the fish community, water-quality, and physical habitat data. 

SOP 11 describes the reporting requirements associated with 

the annual monitoring. SOP 12 describes methods for making 

revisions that may be necessary as new and improved sampling methods or statistical techniques are developed.

Supplemental information that would be helpful for 

implementing the protocol is included. This information 

includes information on fish species known or suspected to 

occur at the parks, sample sites, sample design, fish species 

characteristics, index of biotic integrity metrics, sampling 

equipment, and field forms. 

References Cited 

Adamski, J.C., Petersen, J.C., Freiwald, D.A., and Davis, J.V., 

1995, Environmental and hydrologic setting of the Ozark 

Plateaus study unit, Arkansas, Kansas, Missouri, and Oklahoma: U. S. Geological Survey Water-Resources Investigations Report 94-4022, 69 p.

Ainslie, B.J., Post, J.R., and Paul, A.J., 1998, Effects of pulsed 

and continuous DC electrofishing on juvenile rainbow trout: 

North American Journal of Fisheries Management v. 18, p. 

905-918.

Anderson, D. R., Burnham, K. P., and Thompson, W.L., 2000, 

Null hypothesis testing: Problems, prevalence, and an alternative: Journal of Wildlife Management, v. 64, p. 912-923.

Anderson, D. R., Link, W.A., Johnson, D.H., and Burnham, 

K.P., 2001, Suggestions for presenting the results of data 

analyses: Journal of Wildlife Management v. 65, p. 373-378.

Anderson, M. J. and Thompson, A.A., 2004, Multivariate 

control charts for ecological and environmental monitoring: 

Ecological Applications, v. 14, p. 1921-1935.

Atkinson, A. J., Fisher, R.N., Rochester, C.J., and Brown, 

C.W., 2003, Sampling design optimization and establishment of baselines for herpetofauna arrays at the Point Loma 

Ecological Reserve: U.S. Geological Survey, 39 p.

Bagenal, Timothy, 1978, Methods for assessment of fish 

production in fresh waters: Oxford, Blackwell Scientific 

Publications, 365 p.

Barbour, M.T., Gerritsen, J., Snyder, B.D. and Stribling, J.B., 

1999, Rapid bioassessment protocols for use in streams and 

wadeable rivers: periphyton, benthic macroinvertebrates, 

and fish. EPA 841-B-99-002. Office of Water. U.S. Environmental Protection Agency, Washington, D.C. [variously 

paginated].

Bayley, P.B. and Herendeen, R.A., 2000, The efficiency of a 

seine net: Transactions of the American Fisheries Society, v. 

129, p. 901-923. 
Summary 55

Beauregard, M. R., Mikulak, R.J., and Olson, B.A., 1992, A 

practical guide to statistical quality improvement: Opening 

up the statistical toolbox: New York, Van Nostrand Reinhold, 469 p.

Becker, G.C., 1983, Fishes of Wisconsin: Madison, Wisconsin, 

University of Wisconsin Press, 1,052 p.

Bell, R.W., Davis, J.V., Femmer, S.F., and Joseph, R.L., 1997, 

Water-quality assessment of the Ozark Plateaus study unit, 

Arkansas, Kansas, Missouri, and Oklahoma—organic 

compounds in surface water, bed sediment, and biological 

tissue, 1992-95: U.S. Geological Survey Water-Resources 

Investigations Report 97-4031, 30 p.

Bramblett, R.G., and Fausch, K.D., 1991, Fishes, macroinvertebrates, and aquatic habitats of the Purgatoire River in 

Pinon Canyon, Colorado: Southwestern Naturalist, v. 36, p. 

281–294.

Council of Biological Editors Style Manual Committee, 1994, 

Scientific style and format: The CBE manual for authors, 

editors, and publishers. 6th edition.: New York, Cambridge 

University Press, 825 p.

Cherry, S., 1998, Statistical tests in publications of The Wildlife Society: Wildlife Society Bulletin, v. 26, p. 947-953.

Colegrave, N. and Ruxton, G.D., 2003, Confidence intervals 

are a more useful complement to nonsignificant tests than 

are power calculations: Behavioral Ecology, v.14, p. 446-

450.

Cribbs, J. T., 2006, Heartland Network Safety Plan and Procedures: U.S. National Park Service, Heartland I&M Network 

and Prairie Cluster Prototype Monitoring Program, Wilson’s 

Creek National Battlefield, Republic, Mo., 66 p.

Dalbey, S.R., McMahon, T.E., and Fredenberg, W., 1996, 

Effect of electrofishing pulse shape and electrofishinginduced spinal injury to long-term growth and survival of 

wild rainbow trout: North American Journal of Fisheries 

Management, v. 16, p. 560-569

Dauwalter, D.C. and Jackson, J.R., 2004, A provisional fish 

index of biotic integrity for assessing Ouachita Mountain 

Streams in Arkansas, U.S.A.: Environmental Monitoring 

and Assessment, v. 91, p. 27-57.

Dauwalter, D.C., Pert, E.J., and Keith, W.E., 2003, An index 

of biotic integrity for fish assemblages in Ozark Highland 

Streams of Arkansas, Southeastern Naturalist, v. 2, p. 447-

468.

Dauwalter, D.C., and Pert, E.J., 2004, Management briefs--

effect of electrofishing effort on an index of biotic integrity: 

North American Journal of Fisheries Management, v. 23, p. 

1247-1252.

Davis, J.V, and Bell, R.W., 1998, Water-quality assessment of 

the Ozark Plateaus study unit, Arkansas, Kansas, Missouri, 

and Oklahoma—nutrients, bacteria, organic carbon, and 

suspended sediment in surface water, 1993-95, 56 p. 

Day, R.A. and Gastel, B., 2006, How to write and publish a 

scientific paper, 6th edition: Westport, Conn., Greenwood 

Press, 320 p.

DeBacker, M.D., Young, C.C. (editor), Adams P., Morrison 

L., Peitz D., Rowell G.A., Williams M., Bowles D, 2005, 

Heartland Inventory and Monitoring Network and Prairie 

Cluster Prototype monitoring program vital signs monitoring plan: U.S. National Park Service, Heartland I&M 

Network and Prairie Cluster Prototype Monitoring Program, 

Wilson’s Creek National Battlefield, Republic, Mo., 104 p.

Dolan, C.R., and Miranda, L.E., 2003, Immobilization thresholds of electrofishing relative to fish size: Transactions of 

the American Fisheries Society, v. 132, p. 969-976. 

Dolan, C.R., and Miranda, L.E., 2004, Injury and mortality 

of warmwater fishes immobilized by electrofishing: North 

American Journal of Fisheries Management, v. 24, no. 1, p. 

118-127. 

ESRI, 2007, GIS and mapping software: accessed October 17, 

2007 at URL http://www.esri.com/software/arcgis/index.

html

Etnier, D. A. and Starnes, W.C., 1993, The fishes of Tennessee: Knoxville, Tennessee, The University of Tennessee 

Press, 681 p. 

Everitt, B.S., and Dunn, G., 2001, Applied Multivariate Data 

Analysis, 2nd edition, 342 p. 

Fenneman, N.M., and Johnson, D.W., 1946, Physical divisions of the United States (Map): Washington, D.C., U.S. 

Geological Survey.

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

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

characterizing stream habitat in the National Water-Quality 

Assessment Program: U.S. Geological Survey Water-Resources Investigations Report 98-4052, 67 p. 

Gauch, H.G., Jr., 1982, Multivariate analysis in community 

ecology. Cambridge, U.K., Cambridge University Press, 

298 p. 

Gerard, P. D., Smith, D.R., and Weerakkody, G., 1998, Limits 

of retrospective power analysis: Journal of Wildlife Management, v. 62, p. 801-807.

Goldstein R.M., and Meador M.R., 2004, Comparisons of fish 

species traits from small streams to large rivers: Transactions of the American Fisheries Society v. 133, p. 971-983.
56 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Goldwasser, L, 1999, A collection of grammatical points: Bulletin of Ecological Society of America, v. 79, p. 148-150.

Gyrna, F. M., 2001, Quality planning and analysis: From 

product development through use: New York, McGraw-Hill 

Irwin, 752 p.

Hardin, S. and Connor, L.L., 1992, Variability of electrofishing crew efficiency, and sampling requirements for estimating reliable catch rates: North American Journal of Fisheries 

Management, v. 12, p. 612–617

Hauck, H.S., Huber, L.G., and Nagel, C.D., 1996, Water 

resources data—Missouri, water year 1995: U.S. Geological 

Survey Water Data Report MO-95-1, 320 p.

Hauck, H.S., and Nagel, C.D., 2004, Water resources data—

Missouri, water year 2003: U.S. Geological Survey Water 

Data Report MO-03-1, 776 p. 

Hendricks, M.L., Hocutt, C.H., and Stauffer, J.R., Jr., 1980, 

Monitoring of fish in lotic habitats, in Hocutt, C.H., and 

Stauffer, J.R., Jr., eds., Biological monitoring of fish: Lexington, Mass., Lexington Books, p. 205–231.

Hilsenhoff, W.L., 1977, Use of arthropods to evaluate water 

quality of streams: Wisconsin Department of Natural 

Resources Technical Bulletin No. 100, p. 1-15.

Hlass L. J., Fisher, W.L., and Turton, D.J., 1998, Use of the 

index of biotic integrity to assess water quality in forested 

streams of the Ouachita Mountains Ecoregion, Arkansas: 

Journal of Freshwater Biology, v. 13, no. 2, p. 181-192. 

Hoefs, N.J., 1989, Applying the index of biotic integrity to 

resource inventory in the Current River Basin, Missouri: 

unpublished Masters thesis, Colorado State University, Fort 

Collins, Colo., 111 p.

Hoenig, J. M. and Heisey, D.M., 2001, The abuse of power: 

The pervasive fallacy of power calculations for data analysis: The American Statistician, v. 55, p. 19-24.

Hughes, R.M., and Oberdorff, T. 1998. Applications of IBI 

concepts and metrics to waters outside the United States and 

Canada, in Simon, T.P., ed., Assessment and approaches for 

estimating biological integrity using fish assemblages: Boca 

Raton, Florida, Lewis Press, p. 79-93. 

Jenkins, R. E. and Burkhead, N.M., 1994, Freshwater fishes of 

Virginia: Bethesda, Maryland, American Fisheries Society, 

1,080 p.

Johnson, D. H., 1999, The insignificance of statistical significance testing: Journal of Wildlife Management, v. 63, p. 

763-772.

Jongman, R.H.G., ter Braak, C.J.F., and van Tongeren, O.F.R., 

1995, Data analysis in community and landscape ecology: 

Cambridge, Cambridge University Press, 299 p. 

Justus B.G., 2003, An index of ecological integrity for the 

Mississippi Alluvial Plain Ecoregion: Index development 

and relations to selected landscape variables. U.S. Geological Survey Water-Resources Investigations Report 03–4110, 

32 p.

Karr J.R., 1981, Assessment of biotic integrity using fish communities: Fisheries, v. 6, p. 21–27.

Kirk, R. E., 1996, Practical significance: A concept whose 

time has come: Educational and Psychological Measurement, v. 56, p.746-759.

Kocovsky, P.M., Gowan, C.G., Fausch, K.D., and Riley, S.C., 

1997, Spinal injury rates in three wild trout populations in 

Colorado after eight years of backpack electrofishing: North 

American Journal of Fisheries Management, v. 17, p. 308-

313

Mack, R.N., 1986, Writing with precision, clarity, and 

economy: Bulletin of Ecological Society of America, v. 67, 

p. 31-35.

Manly, B. F. J., 2001, Statistics for environmental science and 

management: Boca Raton, Florida, Chapman & Hall/CRC, 

326 p.

Mardia, K. V., 1971, The effect of nonnormality on some multivariate tests and robustness to nonnormality in the linear 

model: Biometrika v. 58, p. 105-121.

Master, L.L, Flack, S.R., and Stein, B.A., eds., 1998, Rivers of 

life: Critical watersheds for protecting freshwater biodiversity: Arlington, Va., The Nature Conservancy, 71 p. 

Matthews, W.J., 1986, Fish faunal structure in an Ozark 

stream—Stability, persistence and a catastrophic flood: 

Copeia, v. 1986, p. 388–397.

McBean, E. A. and Rovers, F.A., 1998, Statistical procedures 

for analysis of environmental monitoring data and risk 

assessment: Upper Saddle River, New Jersey, Prentice Hall 

PTR, 320 p.

McCormick, F.H., and Hughes, R.M., 1998, Aquatic vertebrates in Lazorchak, J.M., Klemm, D.J., and Peck, D.V., 

eds., Environmental Monitoring and Assessment Program—

Surface waters: Field operations and methods for measuring 

the ecological condition of wadeable streams: U.S. Environmental Protection Agency Report, EPA 620–R–94–004F, 

[variously paginated].

McCormick, F.H., and Hughes, R.M., 2000, Aquatic vertebrates in Lazorchak, J.M., Hill, B.H., Averill, D.K., Peck, 

D.V., and Klemm, D.J., eds., Environmental Monitoring and 

Assessment Program—Surface waters: Field operations and 

methods for measuring the ecological condition of nonwadeable streams: U.S. Environmental Protection Agency 

Report, EPA 620–R–00–007, [variously paginated].
References Cited 57

McDonald, Trent, 2004, Ecological survey recommendations 

for the Buffalo National River and Ozark National Scenic 

Riverways Parks: West, Inc. 15 p.

McMichael, G.A., Fritts, A.L., and Pearsons, T.N., 1998, 

Electrofishing injury to stream salmonids; Injury assessment 

at the sample, reach, and stream scales: North American 

Journal of Fisheries Management, v. 18, p. 894–904.

Meador, M.R., Cuffney, T.F., and Gurtz, M.E., 1993, Methods for sampling fish communities as part of the National 

Water-Quality Assessment Program: U.S. Geological Survey Open-File Report 93-104, 40 p.

Meador, M.R, and McIntyre, J.P., 2003, Effects of electrofishing gear type on spatial and temporal variability in fish 

community sampling: Transactions of the American Fisheries Society, v. 132, p. 709-716. 

Meador, M.R, McIntyre, J.P., and Pollock, K.H., 2003, Assessing the efficacy of single-pass backpack electrofishing to 

characterize fish community structure: Transactions of the 

American Fisheries Society, v. 132, p. 39-46. 

Mettee, M.F., O’Neil, P.E., and Pierson, J.M., 1996, Fishes 

of Alabama and the Mobile Basin: Birmingham, Alabama, 

Oxmoor House, Inc., 820 p. 

Moix, M.W., and Galloway, J.M., 2005, Base flow, water 

quality, and streamflow gain and loss of the Buffalo River, 

Arkansas, and selected tributaries, July and August, 2003: 

U.S. Geological Survey Scientific Investigations Report 

2004-5274, 36 p.

Montgomery, D. C., 2001, Introduction to statistical quality 

control: New York, John Wiley & Sons, Inc., 776 p.

Morrison, L.W., 2007, Assessing the reliability of ecological 

monitoring data: Power analysis and alternative approaches: 

Natural Areas Journal, v. 27, p. 83-91. 

Morrison, L.W., in press, The use of control charts to interpret 

environmental monitoring data: Natural Areas Journal.

Mott, D.N., and Luraas, Jessica, 2004, Water resources management plan, Buffalo National River, Arkansas: Buffalo 

National River, Harrison, Arkansas, 144 p. 

Moulton, S.R., II, Kennen, J.G., Goldstein, R.M., and Hambrook, J.A., 2002, Revised protocols for sampling algal, 

invertebrate, and fish communities as part of the National 

Water-Quality Assessment Program: U.S. Geological Survey Open-File Report 02-150, 75 p.

Nakagawa, S. and Foster, T.M., 2004, The case against retrospective power analyses with an introduction to power 

analysis: Acta Ethologica v. 7, p. 103-108.

National Park Service, 2005, Ozark National Scenic Riverways, nature and science, fish: accessed May 10, 2005 at 

URL http://www.nps.gov/ozar/pphtml/subanimals4.html. 

National Park Service, 2006, Inventory and Monitoring Natural Resource Database Template Version 3.1 documentation: 

Fort Collins, Colorado, Natural Resource Program Center, 

Office of Inventory, Monitoring, and Evaluation, 28 p.

National Park Service/Water Resources Division, 2007a, Vital 

signs long-term monitoring projects: Part C draft guidance 

on WRD required and other field parameter measurements, 

general monitoring methods and some design considerations 

in preparation of a detailed study plan, accessed April 27, 

2007 at URL http://www.nature.nps.gov/water/Vital_Signs_

Guidance/Guidance_Documents/wqPartC.pdf

National Park Service, 2007b, Vital signs water-quality data 

management and archiving, accessed on April 27, 2007 at 

URL http://www.nature.nps.gov/water/infoanddata/index.

cfm.

Nelson, J.S., Crossman, E.J., Espinoza-Perez, Hector, Findley, 

L.T., Gilbert, C.R., Lea, R.N., and Williams, J.D., 2004, 

Common and scientific names of fishes from the United 

States, Canada, and Mexico: Bethesda, Md., American Fisheries Society, Special Publication 29, 386 p.

Nielsen, L.A., and Johnson, D.L., 1983, Fisheries techniques: 

Bethesda, Md., American Fisheries Society, 468 p.

Olsen, T., Hayden, B.P., Ellison, A.M., Oehlert, G.W., and 

Esterby, S.R., 1997, Ecological resource monitoring: 

Change and trend detection workshop report: Bulletin of the 

Ecological Society of America v. 78, p. 11-13.

Olson, C. L., 1974, Comparative robustness of six tests in 

multivariate analysis of variance: Journal of the American 

Statistical Association, v. 69, p. 894-908. 

Page, L. M. and Burr, B.M., 1991, A field guide to freshwater 

fishes: North America north of Mexico: Boston, Houghton 

Mifflin Company, 432 p.

Panfil, M.S., and Jacobson, R.B., 2001, Relations among geology, physiography, land use, and stream habitat conditions 

in the Buffalo and Current River Systems, Missouri and 

Arkansas: Biological Science Report 2001-0005, 112 p.

Petersen, J.C., 1998, Water-quality assessment of the Ozark 

Pla¬teaus study unit, Arkansas, Kansas, Missouri, and 

Oklahoma—Fish communities in streams of the Ozark Plateaus and their relations to selected environmental factors: 

U.S. Geological Survey Water-Resources Investigations 

Report 98-4155, 32 p. 
58 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Petersen, J.C., Adamski, J.C., Bell, R.W., Davis, J.V., Femmer, S.R., Freiwald, D.A., and Joseph, R.L., 1998, Water 

quality in the Ozark Plateaus, Arkansas, Kansas, Missouri, 

and Oklahoma, 1992—95: U.S. Geological Survey Circular 

1158, 33 p.

Petersen, J.C., 2004, Fish communities of the Buffalo River 

Basin and nearby basins of Arkansas and their relation to 

selected environmental factors, 2001-2004: U.S. Geological 

Survey Scientific Investigations Report 2004-5119, 93 p.

Petersen, J.C., 2005, Fishes of Buffalo National River: U.S. 

Geological Survey Scientific Investigations Map 2005-

2908, 1 sheet.

Petersen, J.C. and Justus, B.J., 2005, The fishes of Buffalo 

National River, 2001-2003: U.S. Geological Survey Scientific Investigations Report 2005-5130, 37 p.

Pettersson, M., 1998, Monitoring a freshwater fish population: 

Statistical surveillance of biodiversity: Environmetrics, v. 9, 

p. 139-150.

Pflieger, W.L., 1997, The fishes of Missouri: Missouri Department of Conservation, 372 p.

Plafkin, J.L., Barbour, M.T., Porter, K.D., Gross, S.K., 

Hughes, R.M., 1989, Rapid bioassessment protocols for use 

in streams and rivers: Benthic macroinvertebrates and fish: 

Office of Water Regulations and Standards, U.S. Environmental Protection Agency, EPA 440-4-89-001, Washington, 

D.C., [variously paginated].

Pusey, B. J., Kennard, M.J., Arthur, J.M., and Arthington, 

A.H., 1998, Quantitative sampling of stream fish assemblages: Single- vs. multiple-pass electrofishing: Australian 

Journal of Ecology v. 23, p. 365–374.

Rabeni, C.F., Sarver, R.J., Wang, Ning, Wallace, G.S., 

Weiland, Mark, and Peterson, J.T., 1997, Development of 

regionally based biological criteria for streams of Missouri: 

Columbia, Mo., Missouri Cooperative Fish and Wildlife 

Research Unit, a report to the Missouri Department of Natural Resources, 273 p. 

Rohde, F. C., Arndt, R.G., Lindquist, D.G., and Parnel, J.F., 

1994, Freshwater fishes of the Carolinas, Virginia, Maryland, and Delaware: Chapel Hill, North Carolina, University 

of North Carolina Press, 228 p.

Robison, H.W., and Buchanan, T.M., 1988, Fishes of Arkansas: Fayetteville, Arkansas, University of Arkansas Press, 

536 p. 

Ross, S.T., 2001, The inland fishes of Mississippi: Oxford, 

Mississippi, University of Mississippi Press, 736 p. 

Rowell, G. A., Williams, M.H., and DeBacker, M.D., 2005, 

Data management plan: Heartland I&M Network and Prairie Cluster Prototype Monitoring Program: Wilson’s Creek 

National Battlefield, Republic, Mo., 64 p. 

Shaver, J. P., 1993,. What statistical significance testing is, and 

what it is not: Journal of Experimental Education, v. 61, p. 

293-316.

Simon T.P., 1999, Assessing the sustainability and biological 

integrity of water resources using fish communities: Boca 

Raton, Florida., CRC Press, Inc., 671 p.

Simonson, T.D, and Lyons, John, 1995, Comparison of catch 

per effort and removal procedures for sampling stream fish 

assemblages: North American Journal of Fisheries Management, v. 15, no. 2, p. 419-427. 

Scott, W.B. and Crossman, E.J., 1973, Freshwater fishes of 

Canada: Ottawa, Fisheries Research Board of Canada, Bulletin 184, 966 p.

Smith, S.B., Donahue, A.P., Lipkin, R.J., Blazer, V.S., Schmitt, 

C.J., and Goede, R.W., 2002, Illustrated field guide for 

assessing external and internal anomalies in fish: U.S. Geological Survey Information and Technology Report 2002-

0007, 46 p.

Steidl, R. J., Hayes, J.P., and E. Schauber, E., 1997, Statistical power analysis in wildlife research: Journal of Wildlife 

Research, v. 61, p. 270-279.

Stevens, D. L., Jr. and Olsen, A.R., 1999, Spatially restricted 

surveys over time for aquatic resources: Journal of Agricultural, Biological, and Environmental Statistics, v. 4, p. 

415-428.

Stevens, D.L, and Olson, A.R., 2004, Spatially balanced sampling of natural resources: Journal of the American Statistical Association, v. 99, p. 262-278

Stoehr, A. M., 1999, Are significance thresholds appropriate 

for the study of animal behaviour? Animal Behaviour, v. 57, 

p. F22-F25.

Strunk, W. Jr., and White, E.B., 2000, The elements of style 

(4th Edition): New York, Macmillan, 43 p.

Taylor, L. R., 1961, Aggregation, variance, and the mean: 

Nature, v. 189, p. 732-735.

Timm, N.H., 2002, Applied multivariate analysis: University 

of Pittsburgh Press, 693 p.

Utts, J., 1988, Successful replication verses statistical significance: The Journal of Parapsychology v. 52, p. 305-320.
References Cited 59

Vineyard, J.D., and Feder, G.L., 1974, Springs of Missouri 

with sections on Fauna and flora, by W.L. Pflieger and R.G. 

Lipscomb: Rolla, Missouri Department of Geology and 

Land Survey Water Resources Report 29, 212 p., (reprinted 

1982).

Wagner, R.J., Boulger, R.W., Jr., Oblinger, C.J., and Smith, 

B.A., 2006, Guidelines and standard procedures for con-

tinuous water-quality monitors—Station operation, record 

computation, and data reporting: U.S. Geological Survey 

Techniques and Methods 1–D3, 51 p. + 8 attachments

Walsh, S.J., and Meador, M.R., 1998, Guidelines for qual-

ity assurance and quality control of fish taxonomic data 

collected as part of the National Water-Quality Assessment 

Program: U.S. Geological Survey Water-Resources Investi-

gations Report 98-4239, 33 p.

Wiley, M.L., and Tsai, Chu-Fa, 1983, The relative efficiencies 

of electrofishing vs. seines in Piedmont streams of Mary-

land: North American Journal of Fisheries Management, v. 

3, p. 243–253.

Williams, W.T., and Gillard, P., 1971, Pattern analysis of a 

grazing experiment: Australian Journal of Agricultural 

Research, v. 22, p. 245-260. 

Yoccoz, N. G., 1991, Use, overuse, and misuse of significance 

tests in evolutionary biology and ecology: Bulletin of the 

Ecological Society of America: v. 72, p. 106-111.

Appendixes 1-20
62 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

 

 

Appendix 1. Fish species collected within Buffalo National River.—Continued

[From Petersen and Justus (2005)]

Common name Scientific name

American brook lamprey Lampetra appendix

American eel Anguilla rostrata

Arkansas saddled darter Etheostoma euzonum

Banded darter Etheostoma zonale

Banded sculpin Cottus carolinae

Bigeye chub Hybopsis amblops

Bigeye shiner Notropis boops

Black bullhead Ameiurus melas

Black crappie Pomoxis nigromaculatus

Black redhorse Moxostoma duquesnei

Blackside darter Percina maculata 

Blackspotted topminnow Fundulus olivaceus

Bluegill Lepomis macrochirus

Bluntnose minnow Pimephales notatus

Brook silverside Labidesthes sicculus

Brown trout Salmo trutta

Carmine shiner Notropis percobromus

Central stoneroller Campostoma anomalum

Channel catfish Ictalurus punctatus

Checkered madtom Noturus flavater

Chestnut lamprey Ichthyomyzon castaneus

Common carp Cyprinus carpio

Creek chub Semotilus atromaculatus

Duskystripe shiner Luxilus pilsbryi

Flathead catfish Pylodictis olivaris

Freshwater drum Aplodinotus grunniens

Gilt darter Percina evides

Gizzard shad Dorosoma cepedianum

Golden redhorse Moxostoma erythrurum

Green sunfish Lepomis cyanellus

Greenside darter Etheostoma blennioides

Highfin carpsucker Carpiodes velifer

Hornyhead chub Nocomis biguttatus

Largemouth bass Micropterus salmoides

Largescale stoneroller Campostoma oligolepus

Least brook lamprey Lampetra aepyptera

Logperch Percina caprodes

Longear sunfish Lepomis megalotis

Longnose gar Lepisosteus platostomus

Northern hog sucker Hypentelium nigricans

Northern studfish Fundulus catenatus
Appendixes 63

Appendix 1. Fish species collected within Buffalo National River.—Continued

[From Petersen and Justus (2005)]

Common name Scientific name

Orangethroat darter Etheostoma spectabile

Ozark bass Ambloplites constellatus

Ozark chub Erimystax harryi

Ozark madtom Noturus albater

Ozark minnow Notropis nubilus

Ozark sculpin Cottus hypselurus

Ozark shiner Notropis ozarcanus

Pealip redhorse1 Moxostoma pisolabrum

Quillback Carpiodes cyprinus

Rainbow darter Etheostoma caeruleum

Rainbow trout Oncorhynchus mykiss

Redear sunfish Lepomis microlophus

Redspotted sunfish Lepomis miniatus

River carpsucker Carpiodes carpio

River redhorse Moxostoma carinatum

Slender madtom Noturus exilis

Smallmouth bass Micropterus dolomieu

Southern redbelly dace Phoxinus erythrogaster

Speckled darter Etheostoma stigmaeum

Spotted bass Micropterus punctulatus

Spotted sucker Minytrema melanops

Steelcolor shiner Cyprinella whipplei

Stippled darter Etheostoma punctulatum

Striped shiner Luxilus chrysocephalus

Telescope shiner Notropis telescopus

Walleye Sander vitreus

Warmouth Lepomis gulosus

Wedgespot shiner Notropis greenei

White bass Morone chrysops

White sucker Catostomus commersoni

Whitetail shiner Cyprinella galactura

Yellow bullhead Ameiurus natalis

Yoke darter Etheostoma juliae

1 Formerly was shorthead redhorse (Moxostoma macrolepidotum) 

 
64 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 2. Fish species collected or suspected of occurring within Ozark National Scenic Riverways.—Continued

[Michael Williams and Victoria Grant, National Park Service, written commun., 2006]

Common name Scientific name

American brook lamprey Lampetra appendix

American eel Anguilla rostrata

Arkansas saddled darter Etheostoma euzonum

Banded darter Etheostoma zonale

Banded sculpin Cottus carolinae

Bigeye chub Hybopsis amblops

Bigeye shiner Notropis boops

Bigmouth buffalo Ictiobus cyprinellus

Black buffalo Ictiobus niger

Black bullhead Ameiurus melas

Black crappie Pomoxis nigromaculatus

Black redhorse Moxostoma duquesnei

Blackside darter Percina maculata

Blackspotted topminnow Fundulus olivaceus

Blacktail shiner Cyprinella venusta

Bleeding shiner Luxilus zonatus

Blue sucker Cycleptus elongatus

Bluegill Lepomis macrochirus

Bluntnose minnow Pimephales notatus

Bowfin Amia calva

Brindled madtom Noturus miurus

Brook silverside Labidesthes sicculus

Brown trout Salmo trutta

Carmine shiner Notropis percobromus

Central stoneroller Campostoma anomalum

Chain pickerel Esox niger

Channel catfish Ictalurus punctatus

Checkered madtom Noturus flavater

Chestnut lamprey Ichthyomyzon castaneus

Common carp Cyprinus carpio

Creek chub Semotilus atromaculatus

Creek chubsucker Erimyzon oblongus

Current darter Etheostoma uniporum

Cypress darter Etheostoma proeliare

Emerald shiner Notropis atherinoides

Fantail darter Etheostoma flabellare

Fathead minnow Pimephales promelas

Flathead catfish Pylodictis olivaris

Flier Centrarchus macropterus

Freckled madtom Noturus nocturnus
Appendixes 65

Appendix 2. Fish species collected or suspected of occurring within Ozark National Scenic Riverways.—Continued

[Michael Williams and Victoria Grant, National Park Service, written commun., 2006]

Common name Scientific name

Freshwater drum Aplodinotus grunniens

Gilt darter Percina evides

Gizzard shad Dorosoma cepedianum

Golden redhorse Moxostoma erythrurum

Golden shiner Notemigonus crysoleucas

Goldeye Hiodon alosoides

Goldfish Carassius auratus

Gravel chub Erimystax x-punctatus

Green sunfish Lepomis cyanellus

Greenside darter Etheostoma blennioides

Highfin carpsucker Carpiodes velifer

Hornyhead chub Nocomis biguttatus

Johnny darter Etheostoma nigrum

Lake chubsucker Erimyzon sucetta

Largemouth bass Micropterus salmoides

Largescale stoneroller Campostoma oligolepis

Least brook lamprey Lampetra aepyptera

Logperch Percina caprodes

Longear sunfish Lepomis megalotis

Longnose gar Lepisosteus osseus

Mississippi silvery minnow Hybognathus nuchalis

Mooneye Hiodon tergisus

Mountain madtom Noturus eleutherus

Mud darter Etheostoma asprigene

Northern hog sucker Hypentelium nigricans

Northern studfish Fundulus catenatus

Orangespotted sunfish Lepomis humilis

Ozark chub Erimystax harryi

Ozark madtom Noturus albater

Ozark minnow Notropis nubilus

Ozark sculpin Cottus hypselurus

Ozark shiner Notropis ozarcanus

Paddlefish Polyodon spathula

Pealip redhorse1 Moxostoma pisolabrum

Pirate perch Aphredoderus sayanus

Pugnose minnow Opsopoeodus emiliae

Rainbow darter Etheostoma caeruleum

Rainbow trout Oncorhynchus mykiss

Redear sunfish Lepomis microlophus

Redfin pickerel Esox americanus
66 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 2. Fish species collected or suspected of occurring within Ozark National Scenic Riverways.—Continued

[Michael Williams and Victoria Grant, National Park Service, written commun., 2006]

Common name Scientific name

Redfin shiner Lythrurus umbratilis

Redspotted sunfish Lepomis miniatus

Ribbon shiner Lythrurus fumeus

River carpsucker Carpiodes carpio

River redhorse Moxostoma carinatum

Sauger Sander canadensis

Shadow bass Ambloplites ariommus

Shortnose gar Lepisosteus platostomus

Shovelnose sturgeon Scaphirhynchus platorynchus

Silver redhorse Moxostoma anisurum

Skipjack herring Alosa chrysochloris

Slender madtom Noturus exilis

Smallmouth bass Micropterus dolomieu

Smallmouth buffalo Ictiobus bubalus

Southern cavefish Typhlichthys subterraneus

Southern redbelly dace Phoxinus erythrogaster

Speckled darter Etheostoma stigmaeum

Spotted bass Micropterus punctulatus

Spotted gar Lepisosteus oculatus

Spotted sucker Minytrema melanops

Stargazing darter Percina uranidea

Steelcolor shiner Cyprinella whipplei

Stippled darter Etheostoma punctulatum

Striped shiner Luxilus chrysocephalus

Suckermouth minnow Phenacobius mirabilis

Tadpole madtom Noturus gyrinus

Telescope shiner Notropis telescopus

Threadfin shad Dorosoma petenense

Walleye Sander vitreus 

Warmouth Lepomis gulosus

Wedgespot shiner Notropis greenei

Weed shiner Notropis texanus

Western mosquitofish Gambusia affinis

White bass Morone chrysops

White crappie Pomoxis annularis

White sucker Catostomus commersoni

Whitetail shiner Cyprinella galactura

Yellow bullhead Ameiurus natalis

Yellow perch Perca flavescens

1

 Formerly was shorthead redhorse (Moxostoma macrolepidotum).

 
Appendixes 67

Appendix 3. Mainstem and tributary sites selected by the Generalized Random Tessellation Stratified method for monitoring fish communities at Buffalo National River and Ozark National Scenic Riverways.—Continued[UTM is Universal Transverse Mercator coordinates (zone 15); horizontal datum is North American Datum of 1983; BT, boat; BP backpack; BA, barge]

Stretch

Reach 

identification code River basin Site type

Site/ 

tributary 

number Tributary name

Panel

 number 

(year ) County UTM easting UTM northing

Electrofishing 

gear used

Percent 

effort by 

gear

Buffalo National River

24 BUFFM01 Buffalo Mainstem 01 Annual Newton 464088.50 3981659.30 BT, BP 70, 3055 BUFFM02 Buffalo Mainstem 02 Annual Newton 490340.90 3987599.90 BT, BP 40, 6059 BUFFM03 Buffalo Mainstem 03 Annual Newton 499985.28 3983483.70 BT, BP 90, 1069 BUFFM04 Buffalo Mainstem 04 Annual Searcy 520484.74 3981679.66 BT, BA 60, 4073 BUFFM05 Buffalo Mainstem 05 Annual Searcy 529619.95 3984878.60 BT, BP 40, 6087 BUFFM06 Buffalo Mainstem 06 Annual Marion 545997.97 3995359.40 BT, BP 60, 40

640 BUFFT03 Buffalo Tributary 03 Whiteley 1 Newton 463933.84 3982976.75 BP 100

420 BUFFT09 Buffalo Tributary 09 Little Buffalo 1 Newton 490340.91 3987600.00 BT, BP 20 ,80

300 BUFFT22 Buffalo Tributary 22 Spring 1 Searcy 536995.44 3986311.00 BP 100

649 BUFFT24 Buffalo Tributary 24 Hickory 1 Marion 540092.81 3992069.50 BP 100

603 BUFFT30 Buffalo Tributary 30 Middle 1 Marion 551428.31 3993556.50 BP 100

623 BUFFT31 Buffalo Tributary 31 Leatherwood 1 Marion 551307.69 3996258.00 BP 100

462 BUFFT05 Buffalo Tributary 05 Cecil 2 Newton 479905.44 3992743.25 BP 100

646 BUFFT07 Buffalo Tributary 07 Mill 2 Newton 487979.09 3990501.25 BA 100

242 BUFFT12 Buffalo Tributary 12 Sheldon Branch 2 Newton 492781.88 3983234.50 BP 100

241 BUFFT21 Buffalo Tributary 21 Brush 2 Searcy 527984.75 3983963.00 BP 100

238 BUFFT25 Buffalo Tributary 25 Little Panther 2 Marion 540006.31 3993475.25 BP 100

390 BUFFT33 Buffalo Tributary 33 Stewart 2 Marion 552646.50 4000976.50 BP 100

441 BUFFT04 Buffalo Tributary 04 Sneeds 3 Newton 472172.12 3990497.25 BP 100

244 BUFFT13 Buffalo Tributary 13 Big 3 Newton 495709.59 3981030.75 BA, BP 80, 20

383 BUFFT15 Buffalo Tributary 15 Davis 3 Newton 504216.16 3984923.25 BA, BP 80, 20

225 BUFFT16 Buffalo Tributary 16 Mill Branch 3 Newton 504310.34 3984978.25 BP 100

378 BUFFT19 Buffalo Tributary 19 Calf 3 Searcy 520463.22 3981045.50 BA, BP 80, 20
68 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways Appendix 3. Mainstem and tributary sites selected by the Generalized Random Tessellation Stratified method for monitoring fish communities at Buffalo National River and Ozark National Scenic Riverways.—Continued [UTM is Universal Transverse Mercator coordinates (zone 15); horizontal datum is North American Datum of 1983; BT, boat; BP backpack; BA, barge] Stretch Reach identifica- tion code River basin Site type Site/ tributary number Tributary name Panel number (year ) County UTM easting UTM northing Electro- fishing gear used Percent effort by gear 484 BUFFT28 Buffalo Tributary 28 Boat 3 Marion 543933.19 3998512.25 BP 100 279 BUFFT01 Buffalo Tributary 01 Smith 4 Newton 464098.72 3978179.75 BP 100 403 BUFFT06 Buffalo Tributary 06 Glade 4 Newton 481332.88 3992648.50 BP 100 638 BUFFT10 Buffalo Tributary 10 Wells 4 Newton 490814.66 3986624.00 BP 100 317 BUFFT11 Buffalo Tributary 11 Rock 4 Newton 492478.22 3984111.00 BP 100 472 BUFFT20 Buffalo Tributary 20 Bear 4 Searcy 526905.38 3983413.50 BT, BA, BP 20, 60, 20 574 BUFFT23 Buffalo Tributary 23 Water 4 Searcy 538186.50 3989492.75 BA, BP 80, 20 229 BUFFT08 Buffalo Tributary 08 Vanishing 5 Newton 489406.03 3989463.00 BP 100 367 BUFFT14 Buffalo Tributary 14 Lick 5 Newton 499899.69 3983426.50 BP 100 304 BUFFT17 Buffalo Tributary 17 Richland 5 Searcy 509734.38 3975988.00 BA, BP 80, 20 476 BUFFT27 Buffalo Tributary 27 Clabber 5 Marion 540925.44 3998147.75 BA, BP 80, 20 366 BUFFT29 Buffalo Tributary 29 Big 5 Marion 547400.69 3992751.25 BA, BP 80, 20 275 BUFFT32 Buffalo Tributary 32 Cow 5 Marion 551138.19 3998892.75 BP 100 232 BUFFT18 Buffalo Tributary 18 Slay Branch Alternate Searcy 514572.59 3979212.00 BP 100 694 BUFFT26 Buffalo Tributary 26 Rush Alternate Marion 540617.75 39978810.50 BP 100 Ozark National Scenic Riverways 14 CURRM01 Current Mainstem 01 Annual Shannon 623336.28 4141730.82 BA 100 35 CURRM02 Current Mainstem 02 Annual Shannon 637468.41 4131822.17 BT, BP 70, 30 42 CURRM03 Current Mainstem 03 Annual Shannon 643252.57 4126300.08 BT, BP 75, 25 67 CURRM04 Current Mainstem 04 Annual Shannon 661785.40 4111783.86 BT, BP 80, 20 71 CURRM05 Current Mainstem 05 Annual Shannon 666195.85 4111128.94 BT, BP 90, 10

97 CURRM06 Current Mainstem 06 Annual Carter 684220.63 4078321.12 BT, BP 90, 10

105 JACKM01 Jacks Fork Mainstem 01 Annual Shannon 619895.88 4101117.92 BT, BP 85, 15114 JACKM02 Jacks Fork Mainstem 02 Annual Shannon 627768.31 4102604.03 BT, BP 80, 15, 5
Appendixes 69

Appendix 3. Mainstem and tributary sites selected by the Generalized Random Tessellation Stratified method for monitoring fish communities at Buffalo National River and Ozark National Scenic Riverways.—Continued[UTM is Universal Transverse Mercator coordinates (zone 15); horizontal datum is North American Datum of 1983; BT, boat; BP backpack; BA, barge]

Stretch

Reach 

identification code River basin Site type

Site/ 

tributary 

number Tributary name

Panel

 number 

(year ) County UTM easting UTM northing

Electrofishing 

gear used

Percent 

effort by 

gear

123 JACKM03 Jacks Fork Mainstem 03 Annual Shannon 633244.58 4108431.69 BA 100907 JACKT01 Jacks Fork Tributary 01 Flat Rock Hollow 1 Shannon 627068.19 4101683.25 BP 100

657 CURRT08 Current Tributary 08 Rocky 1 Shannon 661958.31 4110833.50 BA, BP 90, 10

685 CURRT13 Current Tributary 13 Mill 1 Carter 672241.31 4100790.25 BP 100

542 JACKT02 Jacks Fork Tributary 02 Water Branch 2 Shannon 639856.63 4114033.50 BP 100

850 CURRT02 Current Tributary 02 Sutton 2 Shannon 649132.00 4118740.25 BP 100

930 CURRT11 Current Tributary 11 Chilton 2 Carter 673293.31 4103594.50 BP 100

494 CURRT07 Current Tributary 07 Powder Mill 3 Shannon 662035.12 4116885.50 BP 100

695 CURRT09 Current Tributary 09 Carr 3 Shannon 666007.31 4111876.50 BP 100

711 CURRT10 Current Tributary 10 Thorny 3 Shannon 666068.69 4111169.25 BP 100

699 JACKT03 Jacks Fork Tributary 03 Shawnee 4 Shannon 650824.38 4115207.50 BP 100

819 CURRT01 Current Tributary 01 Shafer Spring 4 Dent 622056.00 4144309.50 BP 100

576 CURRT03 Current Tributary 03 Thompson 4 Shannon 652336.88 4117663.00 BP 100

920 CURRT04 Current Tributary 04 Prairie Hollow 5 Shannon 654127.81 4116782.50 BP 100

917 CURRT06 Current Tributary 06 Blair 5 Shannon 659132.19 4116340.75 BP 100

950 CURRT12 Current Tributary 12 Rogers 5 Carter 672338.69 4102176.50 BP 100

473 CURRT05 Current Tributary 05 Thorny Hollow Alternate Shannon 657045.31 4115739.25 BP 100
70 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 4. Comparison of selected characteristics of the NAWQA, EMAP, and RBP protocols and the Ozark Rivers Fish Community 

protocol.

[NAWQA = National Water-Quality Assessment program; EMAP = Environmental Montoring and Assessment Program; RBP = Rapid Bioassessment Protocol; X = times; GRTS = generalized random tesselation stratified sampling]

Characteristic NAWQA EMAP RBP Ozark Rivers Fish 

Community Protocol

Reach length minimum and 

maximum (meters)

150-1,000 150 (minimum) Variable 150-1,000 

Reach length relative to mean 

wetted channel width

20X 40X (wadeable 

streams), (40 to 

100X for nonwadeable)

Variable 20X 

Time limit (hours) None specified 0.75 to 3 Not specified None specified

Number of electrofishing 

passes

2 1 1 Wadeable, 1; non-wadeable, 2

Electrofishing gear Backpack, barge, or 

boat as appropriate

Backpack or boat 

as appropriate

Backpack or barge as appropriateBackpack, barge, or boat as 

appropriate

Block nets No Optional Optional No

Seining Optional (electrofishing and one or more 

other methods used)

Optional No Standard and kick seine

Length-weight measurements 30 per species 30 per species Optional, not required 30 per species

Recording of anomalies Yes Yes Yes Yes

Selection of reach location 

(general)

Professional judgment Randomized, systematic designProfessional judgment GRTS 

Selection of reach boundary Relative to riffle, run, 

pool1

Randomized, systematic designProfessional judgment Bottom of reach is top of 

second riffle upstream 

from bottom of stream area 

selected by GRTS

Other -- Option to subsample between 

transects (wadeable streams)

Fish less than 20 millimeters total length not 

included

--

Other -- Subsampled between transects 

(non-wadeable 

streams) 

Several potential metrics 

listed

--

1

One-half of mean wetted channel width downstream or upstream from a riffle, run, or pool boundary. Generally selected to include multiple runs, riffles, and 

pools.
Appendixes 71

Appendix 5. Fish species known to occur in Buffalo National River and Ozark National Scenic Riverways classified by tolerance and by 

habitat, spawning, substrate, and trophic preference.—Continued

[modified from Goldsteain and Meader (2004); tolerance values are from Barbour and others (1999); Unk is unknown; I is intolerant, M is moderate tolerance, T 

is tolerant, first tolerance value is greatest consensus]

Habitat preference Spawning preference

Common name Scientific name References

Tolerance Riffle Pool

Run or

main

channel

BackwaterBroadcasterSimple

nester

Complex

nester

Migratory

American brook

 lamprey (ammocoete) 

Lampetra appendix a, g Unk X X

American brook lamprey

 adult 

Lampetra appendix a, b, c, g I X X X

American eel Anguilla rostrata b, g, j M-T X X

Arkansas saddled 

darter 

Etheostoma euzonum g Unk X

Banded darter Etheostoma zonale b, c, d, g I X X

Banded sculpin Cottus carolinae b, d, g M X X

Bigeye chub Hybopsis amblops b, d, g I-M X X X

Bigeye shiner Notropis boops d, g, i I X X

Bigmouth buffalo Ictiobus cyprinellus c, g, h M X X X X

Black buffalo Ictiobus niger c, g, h M-I X X X

Black bullhead Ameiurus melas a, b, c, g M-T X X X

Black crappie Pomoxis nigromaculatus a, b, c, g M X X X

Black redhorse Moxostoma duquesnei b, c, d, g I X X X

Blackside darter Percina maculata a, b, c, g M X X X

Blackspotted 

topminnow 

Fundulus olivaceus d, g, h M X X X

Blacktail shiner Cyprinella venusta d, g, h Unk X X

Bleeding shiner Luxilus zonatus g, j, k Unk

Bluegill Lepomis macrochirus a, b, c, g M-T X X

Blue sucker Cycleptus elongatus c, d, g I X X X

Bluntnose minnow Pimephales notatus b, c, d, g T X X X

Brindled madtom Noturus miurus d, g, h I-M X X

Brook silverside Labidesthes sicculus b, c, g M-I X X

Brown trout Salmo trutta c, g M-I X X X

Carmine shiner (traits

from rosyface shiner)

Notropis percobromus a, c, d, g I X X X

Central stoneroller Campostoma anomalum b, c, d, g M-T X X X X X

Chain pickerel Esox niger b, d, g M X X

Channel catfish Ictalurus punctatus b, c, g M X X X

Checkered madtom Noturus flavater g, j, k Unk

Chestnut lamprey adult Ichthyomyzon castaneus a, c, g, k M X X

Common carp Cyprinus carpio b, c, g T X X

Creek chub Semotilus atromaculatus b, c, d, g T X X
72 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 5. Fish species known to occur in Buffalo National River and Ozark National Scenic Riverways classified by tolerance and by 

habitat, spawning, substrate, and trophic preference.—Continued

[modified from Goldsteain and Meader (2004); tolerance values are from Barbour and others (1999); Unk is unknown; I is intolerant, M is moderate tolerance, T 

is tolerant, first tolerance value is greatest consensus]

Habitat preference Spawning preference

Common name Scientific name References

Tolerance Riffle Pool

Run or

main

channel

BackwaterBroadcasterSimple

nester

Complex

nester

Migratory

Creek chubsucker Erimyzon oblongus b, c, d, g M-T-I X X X

Current darter (traits from 

orangethroat darter)

Etheostoma uniporum d, g, k M X X X

Cypress darter Etheostoma proeliare d, g, h M X X X

Duskystripe shiner Luxilus pilsbryi g, j, k Unk X X

Emerald shiner Notropis atherinoides b, c, d, g M X X X

Fantail darter Etheostoma flabellare b, c, d, g M X X

Fathead minnow Pimephales promelas b, c, g T X X

Flathead catfish Pylodictis olivaris b, c, g M X X

Flier Centrarchus macropterus b, d, g, i M X X X

Freckled madtom Noturus nocturnus d, g, h M-I X X X

Freshwater drum Aplodinotus grunniens b, g M X X X

Goldfish Carassius auratus c, g, i T X X X

Gilt darter Percina evides b, c, g I X X

Gizzard shad Dorosoma cepedianum b, c, d, g M-T X X X

Golden redhorse Moxostoma erythrurum a, b, c, d, g M-I X X X

Golden shiner Notemigonus crysoleucas b, c, d, g T X X X

Goldeye Hiodon alosoides a, c, g I X X X

Gravel chub Erimystax x-punctatus c, g, j M-I X X X

Green sunfish Lepomis cyanellus a, b, c, g T-M X X X

Greenside darter Etheostoma blennioides b, d, g M-I X X

Highfin carpsucker Carpiodes velifer c, d, g I-M X X X X

Horneyhead chub Nocomis biguttatus a, c, g I-M X X X

Johnny darter Etheostoma nigrum b, c, d, g M X X

Lake chubsucker Erimyzon sucetta b, d, g M X X X

Largemouth bass Micropterus salmoides a, b, c, g M-T X X X

Largescale stoneroller Campostoma oligolepis c, g, h, k M X X X X

Least brook lamprey 

adult 

Lampetra aepyptera b, g, j, k M-I X X

Least brook lamprey 

ammocoete 

Lampetra aepyptera g Unk X X

Logperch Percina caprodes b, c, g, j M X

Longear sunfish Lepomis megalotis b, g, h I-M X X

Longnose gar Lepisosteus osseus a, c, g M X X X

Mississippi silvery 

minnow 

Hybognathus nuchalis c, d, g M-I X X X
Appendixes 73

Appendix 5. Fish species known to occur in Buffalo National River and Ozark National Scenic Riverways classified by tolerance and by 

habitat, spawning, substrate, and trophic preference.—Continued

[modified from Goldsteain and Meader (2004); tolerance values are from Barbour and others (1999); Unk is unknown; I is intolerant, M is moderate tolerance, T 

is tolerant, first tolerance value is greatest consensus]

Habitat preference Spawning preference

Common name Scientific name References

Tolerance Riffle Pool

Run or

main

channel

BackwaterBroadcasterSimple

nester

Complex

nester

Migratory

Mooneye Hiodon tergisus c, g, i I X X X

Mountain madtom Noturus eleutherus b, d, g, k I X X X

Mud darter Etheostoma asprigene d, g, i M X X

Northern hog sucker Hypentelium nigricans a, c, d, g I-M X X X

Northern studfish Fundulus catenatus b, d, g, i I X X

Orangespotted sunfish Lepomis humilis c, d, g M X X

Orangethroat darter Etheostoma spectabile d, g, k M X X X

Ozark bass Ambloplites constellatus b, g, l Unk X X

Ozark chub (traits from 

streamline chub)

Erimystax harryi b, d, g I X X X

Ozark madtom Noturus albater g, j, k Unk X X

Ozark minnow Notropis nubilus c, g, j I X X X

Ozark sculpin Cottus hypselurus g, j, k Unk X

Ozark shiner Notropis ozarcanus g, k Unk X X

Paddlefish Polyodon spathula b, g, h I X X X

Pealip redhorse (traits 

from 

shorthead redhorse)

Moxostoma pisolabrum b, c, d, g M X X X X X

Pirate perch Aphredoderus sayanus b, c, d, g M X X X

Pugnose minnow Opsopoeodus emiliae a, d, g, k I X X

Quillback Carpiodes cyprinus b, c, g M-T X X X X

Rainbow darter Etheostoma caeruleum a, b, c, d, g M-I X X X

Rainbow trout Oncorhynchus mykiss a, c, g M-I X X X X

Redear sunfish Lepomis microlophus b, g, h M X X X

Redfin pickerel Esox americanus a, c, g M X X

Redfin shiner Lythrurus umbratilis c, d, g M-T X X

Redspotted sunfish Lepomis miniatus d, g, h Unk X X

Ribbon shiner Lythrurus fumeus not listed M

River carpsucker Carpiodes carpio c, g, h M X X X

River redhorse Moxostoma carinatum b, c, d, g I X X X

Sauger Sander canadensis b, c, g M X X X X X

Shadow bass Ambloplites ariommus b, g, l Unk X X

Shortnose gar Lepisosteus platostomus c, d, g M X X

Shovelnose sturgeon Scaphirhyncus platorynchusc, d, g M X X

Silver redhorse Moxostoma anisurum b, c, d, g M X X X
74 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 5. Fish species known to occur in Buffalo National River and Ozark National Scenic Riverways classified by tolerance and by 

habitat, spawning, substrate, and trophic preference.—Continued

[modified from Goldsteain and Meader (2004); tolerance values are from Barbour and others (1999); Unk is unknown; I is intolerant, M is moderate tolerance, T 

is tolerant, first tolerance value is greatest consensus]

Habitat preference Spawning preference

Common name Scientific name References

Tolerance Riffle Pool

Run or

main

channel

BackwaterBroadcasterSimple

nester

Complex

nester

Migratory

Skipjack herring Alosa chrysochloris c, g, h M X X X

Slender madtom Noturus exilis c, d, g, i I X X X X

Smallmouth bass Micropterus dolomieu a, b, c, g M-I X X X

Smallmouth buffalo Ictiobus bubalus c, d, g M-I X X X X

Southern cavefish Typhlichthys subterraneus not listed Unk

Southern redbelly dace Phoxinus erythrogaster c, d, g M-I X X

Speckled darter Etheostoma stigmaeum b, d, g Unk X X X

Spotted bass Micropterus punctulatus b, d, g M X X X

Spotted gar Lepisosteus oculatus d, g, i M X X X

Spotted sucker Minytrema melanops c, d, g M-I X X

Stargarzing darter Percina uranidea b, d, g I X

Steelcolor shiner Cyprinella whipplei b, d, g M-I X X X

Stippled darter Etheostoma punctulatum g, j, k Unk X

Striped shiner Luxilus chrysocephalus b, c, d, g M-T X X X

Suckermouth minnow Phenacobius mirabilis b, c, d, g M X X X X

Tadpole madtom Noturus gyrinus b, c, g, i M-I X X X

Telescope shiner Notropis telescopus b, d, g Unk X X

Threadfin shad Dorosoma petenense b, d, g, h M X

Walleye Sander vitreus b, c, g M X X X X X

Warmouth Lepomis gulosus b, d, g M X X X

Wedgespot shiner Notropis greenei g, j Unk X X

Weed shiner Notropis texanus c, d, g I X X X

Western mosquitofish Gambusia affinis d, g, i M-T X

White bass Morone chrysops b, c, g M-T X X X

White crappie Pomoxis annularis b, c, g M-T X X X

White sucker Catostomus commersoni b, c, d, g T X X X X

Whitetail shiner Cyprinella galuctura b, d, g Unk X X

Yellow bullhead Ameiurus natalis a, b, c, g T-M X X X

Yellow perch Perca flavescens a, b, c, g M X X X

Yoke darter Etheostoma juliae g, j, k Unk X
Appendixes 75

Appendix 5. Fish species known to occur in Buffalo National River and Ozark National Scenic Riverways classified by tolerance and by 

habitat, spawning, substrate, and trophic preference.—Continued

[modified from Goldsteain and Meader (2004); tolerance values are from Barbour and others (1999); Unk is unknown; I is intolerant, M is moderate tolerance, T 

is tolerant, first tolerance value is greatest consensus]

Substrate preference Trophic status

Common name Scientific name

Cobble/

rubble/

(rocky) Gravel Sand

Mud

(silt, clay

detritus)

VegetationHerbivorePlanktivoreDetritivoreInvertivoreCarnivore

American brook

 lamprey (ammocoete) 

Lampetra appendix X X

American brook lamprey

 adult 

Lampetra appendix X X X

American eel Anguilla rostrata X X

Arkansas saddled 

darter 

Etheostoma euzonum X X

Banded darter Etheostoma zonale X X

Banded sculpin Cottus carolinae X X X

Bigeye chub Hybopsis amblops X X X

Bigeye shiner Notropis boops X X

Bigmouth buffalo Ictiobus cyprinellus X X

Black buffalo Ictiobus niger

Black bullhead Ameiurus melas X X X X

Black crappie Pomoxis nigromaculatus X X X X X

Black redhorse Moxostoma duquesnei X X X X

Blackside darter Percina maculata X X X

Blackspotted 

topminnow 

Fundulus olivaceus X X X X

Blacktail shiner Cyprinella venusta X X

Bleeding shiner Luxilus zonatus X X

Bluegill Lepomis macrochirus X X

Blue sucker Cycleptus elongatus X X X X

Bluntnose minnow Pimephales notatus X X X X

Brindled madtom Noturus miurus X X X X

Brook silverside Labidesthes sicculus X X

Brown trout Salmo trutta X X X

Carmine shiner (traits

from rosyface shiner)

Notropis percobromus X X X X X

Central stoneroller Campostoma anomalum X X

Chain pickerel Esox niger X X

Channel catfish Ictalurus punctatus X X X X X

Checkered madtom Noturus flavater

Chestnut lamprey adult Ichthyomyzon castaneus X X X

Common carp Cyprinus carpio X X X

Creek chub Semotilus atromaculatus X X X X
76 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 5. Fish species known to occur in Buffalo National River and Ozark National Scenic Riverways classified by tolerance and by 

habitat, spawning, substrate, and trophic preference.—Continued

[modified from Goldsteain and Meader (2004); tolerance values are from Barbour and others (1999); Unk is unknown; I is intolerant, M is moderate tolerance, T 

is tolerant, first tolerance value is greatest consensus]

Substrate preference Trophic status

Common name Scientific name

Cobble/

rubble/

(rocky) Gravel Sand

Mud

(silt, clay

detritus)

VegetationHerbivorePlanktivoreDetritivoreInvertivoreCarnivore

Creek chubsucker Erimyzon oblongus X X X X

Current darter (traits from 

orangethroat darter)

Etheostoma uniporum X X

Cypress darter Etheostoma proeliare X X X

Duskystripe shiner Luxilus pilsbryi X X

Emerald shiner Notropis atherinoides X X

Fantail darter Etheostoma flabellare X X X

Fathead minnow Pimephales promelas X X X X

Flathead catfish Pylodictis olivaris X X

Flier Centrarchus macropterus X X

Freckled madtom Noturus nocturnus X X X

Freshwater drum Aplodinotus grunniens X X

Goldfish Carassius auratus X X X X

Gilt darter Percina evides X X

Gizzard shad Dorosoma cepedianum X

Golden redhorse Moxostoma erythrurum X

Golden shiner Notemigonus crysoleucas X X

Goldeye Hiodon alosoides X

Gravel chub Erimystax x-punctatus X X

Green sunfish Lepomis cyanellus X X X

Greenside darter Etheostoma blennioides X X

Highfin carpsucker Carpiodes velifer X X X

Horneyhead chub Nocomis biguttatus X X X X

Johnny darter Etheostoma nigrum X X X

Lake chubsucker Erimyzon sucetta X X X X

Largemouth bass Micropterus salmoides X X X X X

Largescale stoneroller Campostoma oligolepis X X

Least brook lamprey adult Lampetra aepyptera X X

Least brook lamprey 

ammocoete 

Lampetra aepyptera X X

Logperch Percina caprodes X X

Longear sunfish Lepomis megalotis X X X X

Longnose gar Lepisosteus osseus X X

Mississippi silvery 

minnow 

Hybognathus nuchalis X X
Appendixes 77

Appendix 5. Fish species known to occur in Buffalo National River and Ozark National Scenic Riverways classified by tolerance and by 

habitat, spawning, substrate, and trophic preference.—Continued

[modified from Goldsteain and Meader (2004); tolerance values are from Barbour and others (1999); Unk is unknown; I is intolerant, M is moderate tolerance, T 

is tolerant, first tolerance value is greatest consensus]

Substrate preference Trophic status

Common name Scientific name

Cobble/

rubble/

(rocky) Gravel Sand

Mud

(silt, clay

detritus)

VegetationHerbivorePlanktivoreDetritivoreInvertivoreCarnivore

Mooneye Hiodon tergisus X

Mountain madtom Noturus eleutherus X X X

Mud darter Etheostoma asprigene X X X

Northern hog sucker Hypentelium nigricans X X X X

Northern studfish Fundulus catenatus X X

Orangespotted sunfish Lepomis humilis X X

Orangethroat darter Etheostoma spectabile X X

Ozark bass Ambloplites constellatus X X X

Ozark chub (traits from 

streamline chub)

Erimystax harryi X X

Ozark madtom Noturus albater X X

Ozark minnow Notropis nubilus X X X

Ozark sculpin Cottus hypselurus X X X

Ozark shiner Notropis ozarcanus X X X

Paddlefish Polyodon spathula X X

Pealip redhorse (traits

from shorthead redhorse)

Moxostoma pisolabrum X X

Pirate perch Aphredoderus sayanus X X X X

Pugnose minnow Opsopoeodus emiliae X X X

Quillback Carpiodes cyprinus X X X X

Rainbow darter Etheostoma caeruleum X X X

Rainbow trout Oncorhynchus mykiss X X X

Redear sunfish Lepomis microlophus X X X

Redfin pickerel Esox americanus X X X

Redfin shiner Lythrurus umbratilis X

Redspotted sunfish Lepomis miniatus X X X

Ribbon shiner Lythrurus fumeus

River carpsucker Carpiodes carpio X X X X

River redhorse Moxostoma carinatum X X X

Sauger Sander canadensis X X X X X

Shadow bass Ambloplites ariommus X X X X X

Shortnose gar Lepisosteus platostomus X

Shovelnose sturgeon Scaphirhyncus platorynchus X X X

Silver redhorse Moxostoma anisurum X
78 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 5. Fish species known to occur in Buffalo National River and Ozark National Scenic Riverways classified by tolerance and by 

habitat, spawning, substrate, and trophic preference.—Continued

[modified from Goldsteain and Meader (2004); tolerance values are from Barbour and others (1999); Unk is unknown; I is intolerant, M is moderate tolerance, T 

is tolerant, first tolerance value is greatest consensus]

Substrate preference Trophic status

Common name Scientific name

Cobble/

rubble/

(rocky) Gravel Sand

Mud

(silt, clay

detritus)

VegetationHerbivorePlanktivoreDetritivoreInvertivoreCarnivore

Skipjack herring Alosa chrysochloris X X X

Slender madtom Noturus exilis X X X

Smallmouth bass Micropterus dolomieu X X X

Smallmouth buffalo Ictiobus bubalus X X

Southern cavefish Typhlichthys subterraneus

Southern redbelly dace Phoxinus erythrogaster X X

Speckled darter Etheostoma stigmaeum X X

Spotted bass Micropterus punctulatus X X X

Spotted gar Lepisosteus oculatus X

Spotted sucker Minytrema melanops X X X

Stargarzing darter Percina uranidea X X

Steelcolor shiner Cyprinella whipplei X X X

Stippled darter Etheostoma punctulatum X X

Striped shiner Luxilus chrysocephalus X X X

Suckermouth minnow Phenacobius mirabilis X X X X

Tadpole madtom Noturus gyrinus X X X X

Telescope shiner Notropis telescopus X X

Threadfin shad Dorosoma petenense X

Walleye Sander vitreus X X

Warmouth Lepomis gulosus X X X X

Wedgespot shiner Notropis greenei X X X

Weed shiner Notropis texanus X X X

Western mosquitofish Gambusia affinis X

White bass Morone chrysops X X

White crappie Pomoxis annularis X X X X

White sucker Catostomus commersoni X X X X

Whitetail shiner Cyprinella galuctura X X

Yellow bullhead Ameiurus natalis X X X X X

Yellow perch Perca flavescens X X X

Yoke darter Etheostoma juliae X X
Appendixes 79

Appendix 6. Metrics used in an index of biotic integrity for midwestern streams.

[From Karr (1981)]

Metric classification Metric description

Richness

Total number of fish species

Number and identity of darter species1

Number and identity of sunfish species

Number and identity of sucker species1

Tolerance

Proportion of individuals as green sunfish

Number and identity of intolerant species

Trophic

Proportion of individuals as omnivores

Proportion of individuals as invertivorous cyprinids1

Proportion of individuals as piscivores

Density

Number of individuals in sample

Incidence of disease/hybridization

Proportion of individuals as hybrids

Proportion of individuals with disease, tumors, fin damage, 

and skeletal anomalies

1

This metric could also be classified under “Tolerance”. In the Ozarks these groups generally represent intolerant species. 

 
80 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 7. Metrics modified from the original index of biotic integrity (Karr, 1981) for use on the Current River 

in southeastern Missouri.

[From Hoefs (1989)]

Metric classification Metric description

Richness

Total number of fish species

Number and identity of sunfish and water-column cyprinid species

Number and identity of sucker and minnow species1

Number and identity of darter, sculpin, and round bodied sucker 

species1

Tolerance

Proportion of individuals as green sunfish

Number and identity of intolerant species

Trophic

Proportion of individuals as omnivores

Proportion of individuals as invertivorous cyprinids1

Proportion of individuals as piscivores

Spawning preference

Proportion of individuals as lithophilic spawners1

1

 This metric could also be classified under “Tolerance.” In the Ozarks these groups generally represent intolerant species.
Appendixes 81

Appendix 8. Metrics modified from the original index of biotic integrity (Karr, 1981) for use in Missouri streams 

by the Missouri Department of Conservation.

[From Matt Combes, Missouri Department of Conservation, written commun., 2004]

Metric classification Metric description

Richness

Number of native taxa

Number of native minnow taxa1

Number of native centarchid taxa 

Number of native watercolumn taxa 

Number of benthic taxa1

Number of native longlived taxa1

Density

Catch per unit effort for native individuals

Tolerance

Percent of tolerant taxa

Trophic

Percent omnivore/herbivore 

Percent carnivore

Percent invertivore

1

This metric could also be classified under “Tolerance”. In the Ozarks these groups generally represent tolerant species.
82 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 9. Metrics selected for an index of biotic integrity for wadeable streams in the Ozark Highlands.

[From Dauwalter and others (2003)]

Metric classification Metric description

Tolerance

Number of darter, sculpin, and madtom species1

Percent green sunfish, bluegill, yellow bullhead, and channel catfish2

Trophic

Percent (of individuals) as algivorous/herbivorous, invertivorous, and 

piscivorous

Percent invertivores3

Percent top carnivores

Spawning preference

Number of lithophilic species3

Incidence of disease/hybridization

Percent of fish with black spot or anomaly

1

 This metric could also be classified under “Taxa Richness.” However, in the Ozarks these groups generally represent intolerant species.

2

This metric could also be classified under “Taxa Richness.” However, in the Ozarks these groups generally represent intolerant species.

3

 This metric could also be classified under “Tolerance.” In the Ozarks these groups generally represent intolerant species.
Appendixes 83

Appendix 10. Equipment necessary for attended water-quality measurements.

[oC, degrees Celsius; FS, full scale; NIST, National Institute of Standards and Technology: μS/cm, microsiemens per centimeter at 25 degrees Celsius; mg/L, 

milligrams per liter; cm, centimeters; mL, milliliters; ≥, greater than or equal to; %, percent; DO, dissolved oxygen]

pH, Specific Conductance, and Water Temperature 

YSI® Model 63 pH, Conductivity, Temperature & Salinity Meter 

Meter requirements for pH and conductivity (preferred)*

Battery powered with automatic temperature compensation (25oC, range -5°C to 45oC) and slope compensation.

Display: to 0.01 pH units, 0.1 μS/cm

Range: 0 to 14 pH units, 0 to 499 μS/cm

Resolution: 0.01 pH units, 0.1 μS/cm

Stabilization Criteria: ±0.1 pH units, ±0.5% FS

(variability/repeatability should be within the value shown)

*these specifications may differ for specific instruments

 but should be close to these values

YSI Model 63, Operations Manual, YSI Incorporated, December 2001**

Factory calibrated thermometer (liquid in glass or digital) traceable to NIST (not 

for field use) with a calibration point at 20°C, instrument accuracy: 0.1oC

pH probe (gel filled probe is recommended for field use) and stand for probe

buffer solutions at pH 4, 7, 10 and pH probe storage solution and cap

Specific conductance standard within range of expected values 

(100-μS/cm to 1,000-μS/cm). 

100-mL graduated cylinder and plastic beakers, assorted sizes

Dissolved Oxygen 

YSI® Model 55 Dissolved Oxygen Meter 

Meter requirements (preferred*):

Temperature readout display, temperature/pressure compensated

Operating range at least -5oC to 45oC

Measure concentrations ≥ 1 to 20-mg/L

Minimum scale readability preferred 0.05-mg/L

Instrument accuracy within 5% of actual value

*these specifications may differ for specific instruments but should 

be close to these values

YSI Model 55 Operations Manual, YSI Incorporated, August 1997 **. 

(contains Oxygen solubility chart)

DO sensor membrane replacement kit (O-rings, membrane, filling solution)

Pocket altimeter-barometer (for Dissolved Oxygen calibration)

Calibration chamber 

Turbidity and Air Temperature

Turbidity tube, 120 cm capacity (available from Wildlife Supply Company, www.wildco.com)

•	 Liquid-in-glass thermometer or digital thermometer for air temperature

General equipment/supplies

•	 Large container or plastic box for water bath, to hold 1 gallon of water

•	 Box filled with packing insulation

•	 Deionized water at room temperature and squeeze bottle

•	 Extra batteries

•	 Small soft brush

•	 Lint-free paper tissues

•	 Log books for recording calibrations, maintenance, and repair

•	 Data sheets on waterproof paper (see Appendix 13)

**All YSI manuals are available on-ling at: http://www.ysi.com
84 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 11. Equipment necessary for unattended water-quality measurements.

YSI 6920

YSI 6600

YSI 650 Display/Logger

YSI 6091 Field cable

YSI 6095B “Y” cable with DB-9 adapter (connects personal computer to field cable)

Specific probes

YSI 6136 Turbidity Probe

YSI 6552 Dissolved-Oxygen Probe

YSI 6560 Conductivity/Temperature Probe

YSI 6561 pH probe

Dissolved-oxygen sensor membrane replacement kit (O-rings, membrane, filling solution)

Extra batteries, membranes, and filling solution

Deionized water

Calibration chamber

Low dissolved-oxygen solution (~ 1 gram of anhydrous sodium sulfite and a few crystals of cobaltous chloride dissolved 

in 1 liter of distilled water (with little or no head space), prepared fresh before each use

Probe guard

Hydrolab

YSI Environmental Operations Manual for YSI 6920 and YSI 6600 data sondes, YSI Incorporated, January 2002 located at

 http://www.ysi.com

Log book for recording repairs, maintenance, and calibrations

Data sheets on waterproof paper
Appendixes 85

Appendix 12. Equipment necessary for conducting fish monitoring at Buffalo National River and Ozark National Scenic Riverways.

General Equipment Seine

Waders Buckets

Rain gear Tub for larger fish

Polarized glasses Aerators (2)

Hats Batteries (rechargeable)

Maps Dip nets

Flagging Electrofishing gloves

Stop watch

Collecting permits Fish Sampling - Deep River

Field guides Electrofishing unit boat w/ long handled dip-nets

Camera generator

Tool box - hammer, wrench, pliers, screwdrivers pulse box and cradle

Volt/ohm meter boom and cords

Electric winch Seine

Flashlight Canoe with paddles

Wader repair kit Outboard motor and gas can

Battery charger for rechargeable batteries Gas can for generator

Park radio and charger Extra motor oil

Cell phone Personal floatation devices

Directions to hospital Large tub or live well

First aide kit Electrofishing gloves

Bug spray

Sun screen Fish Processing Equipment

Flow through tank or instream pen for large fish

Fish Sampling - Tributary and Shallow River Aquarium nets

Backpack electrofishing unit 1 gallon jugs and 5 gallon buckets with lids

 backpack Knives, scalpel, scissors

 anode Clipboard - pens, pencils, waterproof markers

 cathode Waterproof paper

 batteries Data sheets -Fish Sheet 2

 battery charger Measuring board

Towed barge electrofishing unit Hanging scales

 barge Weighing balance

 generator small scales and batteries (rechargeable)

 pulse box large scales and batteries (rechargeable)

 anodes Plastic container for balance

 cathodes 100 percent buffered formalin (37 percent buffered formaldehyde)

 gas can with gas Tags for jars

 oil
86 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 13. Equipment necessary to collect physical habitat data.

Flow meter with wading rod

 Batteries

Digital depth sounder (to collect depth in large pools)

Tape measure (100 meters)

Range finder

 9-volt battery

Survey rod (in meters)

Heavy rope - 50 to 100 meters

Clipboard with data forms

 Instream habitat form

 Fish cover form

 Bank measurement form

Instruction manuals for flow meter, range finder, and depth sounder

Personal floatation devices
Appendixes 87

Appendix 14. Equipment necessary for collecting discharge data.

[°C, degrees Celsius]

FLO-MATE Model 2000 (Marsh-McBirney) velocity meter

 Accuracy of ±2 percent operates in temperatures between 0 °C and 72 °C.

Tape measure (in increments of feet and/or meters)

Stakes for mounting tape measure if necessary

Top-setting wading rod (in increments of feet or meters)*

3-5 gallon bucket

 Extra batteries (D alkaline)

Carrying case

Log book 

Data sheets on waterproof paper

Instruction Manual for the Flo-Mate model 2000 portable flowmeter. 

Marsh-McBirney Inc., Frederick, Maryland 21704-9452

*Standard wading rods come in both metric and English standard units. 

Discharge measurements are generally recorded in English units as cubic feet per second. 

Whatever units are used, ensure that there is consistency between the settings on the velocity meter, the wading rod, and the

 tape measure and that the units are clearly recorded on the data sheet. 
88 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 15. Fish community field forms for recording environmental conditions and reach location. 

Fish Community Field Data Sheet 1 Page ___ of ___

Reach ID:________________ Date:___________ Reach Length(m):_______ Stretch #:_____ 

Recorder:______________ Reach Description: ____________________________________

_______________________________________________________________________________

_______________________________________________________________________________

Weather Conditions: Cloud cover:_______% Wind: Calm Light Moderate Gusty 

Precipitation: None Rain Sleet Snow Intensity: N/A Light Moderate Heavy

Other Weather:______________________________________________________________________

 

Reach Data:

Fish Reach Coordinates: Lower UTM Coordinates ________________ ______________ 

 Upper UTM Coordinates ________________ ______________ 

Discharge (m3

/s):__________ (record points on Discharge datasheet & transfer total discharge here)

Beginning Measurements: Ending Measurements: Time Time

Water Temperature (o

C) Water Temperature (oC)

Air Temperature (o

C) Air Temperature (oC)

pH pH

Specific Conductance (μS/cm) Specific Conductance (μS/cm) 

Conductivity (μS/cm) Conductivity (μS/cm)

Dissolved Oxygen (mg/L) Dissolved Oxygen (mg/L)

Additional Comments:___________________________________________________________

_____________________________________________________________________________

_____________________________________________________________________________

_____________________________________________________________________________

Date Initials

Data Entered

Data Verified
Appendixes 89

Appendix 16. Fish community field forms for recording individual fish data.

 page ___ of ___

Fish Community Data Sheet 2 

Reach ID:____________ Date: ____________ IDed by: ____________ Recorder: ____________

Gear: Backpack Barge Boat Seine Habitat: Main Channel Backwater/Side Channel Other ____________

Effort (sec.): _________ No. Seine Hauls: _________ Seine Reach Length (m): _________ Crew: Shocker(s): _______

 Boat/Barge: _______

Anomalies: D = deformities, E = Eroded fins, L = lesions, T = tumors, B = blacksport Netter(s): _________

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:

Species:

TL (mm) Wt (g) Anom Vchrd Cmts

Species Count:
90 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 17. Data sheet for collecting instream habitat data.

Instream Habitat Assessment Form Page ____ of ____

Reach ID: Stretch No: Date: Crew:

Reach Length: Transect Spacing Interval (reach length / 10): Channel : Main Side Backwater

Trans Channel Pool Width Depth Velocity Dominant ** Embeddedness Canopy

Unit Form (m) (cm) (m/sec) Substrate Cover

1* Lt Lt Lt Lt Lt

Ctr Ctr Ctr Ctr Ctr

Rt Rt Rt Rt Rt

2 Lt Lt Lt Lt Lt

Ctr Ctr Ctr Ctr Ctr

Rt Rt Rt Rt Rt

3 Lt Lt Lt Lt Lt

Ctr Ctr Ctr Ctr Ctr

Rt Rt Rt Rt Rt

4 Lt Lt Lt Lt Lt

Ctr Ctr Ctr Ctr Ctr

Rt Rt Rt Rt Rt

5 Lt Lt Lt Lt Lt

Ctr Ctr Ctr Ctr Ctr

Rt Rt Rt Rt Rt

6 Lt Lt Lt Lt Lt

Ctr Ctr Ctr Ctr Ctr

Rt Rt Rt Rt Rt

7 Lt Lt Lt Lt Lt

Ctr Ctr Ctr Ctr Ctr

Rt Rt Rt Rt Rt

8 Lt Lt Lt Lt Lt

Ctr Ctr Ctr Ctr Ctr

Rt Rt Rt Rt Rt

9 Lt Lt Lt Lt Lt

Ctr Ctr Ctr Ctr Ctr

Rt Rt Rt Rt Rt

10 Lt Lt Lt Lt Lt

Ctr Ctr Ctr Ctr Ctr

Rt Rt Rt Rt Rt

11 Lt Lt Lt Lt Lt

Ctr Ctr Ctr Ctr Ctr

Rt Rt Rt Rt Rt

CHANNEL UNIT CODES POOL FORM CODES Embeddedness & Canopy Cover

GL Glide B Backwater Pool 0 = Absent (0%)

RI Riffle F Bluff Pool 1 = Sparse (<10%)

RU Run/Race I Impoundment 2 = Moderate (10-40%)

PO Pool L Lateral Pool 3 = Heavy (40-75%)

RRX Riffle-Run complex M Mid-Channel Pool 4 = Very Heavy (>75%)

PGX Pool-Glide complex O Obstruction Pool (Canopy within 1m on each side of transect)

Transects are equally spaced as determined by dividing the reach length by 10.

*Transect 1 is located at the downstream end of the reach; Transect 11 is located at the upstream end of the reach

** Dominate substrate is average substrate within a 10 cm diameter circle around the point where depth is taken
Appendixes 91

Appendix 17 Continued.

Embeddedness is assessed within a 10 cm diameter circle around 

point

Channel Unit Types

Riffle An area of the stream with steepest slope and shallowest depth, often rocky substrate, and swift current.

Thalweg is usually poorly defined.

Run Differ from riffles in that depth of flow is typically greater and slope of the bed is less than that of riffles. 

Runs will often have a well defined thalweg. 

Runs sometimes are referred to as races.

Glide Normally located immediately downstream from pools and upstream from riffles. 

The slope of the channel bed through a glide is negative while the slope of the water surface is positive. 

The head of the glide can be difficult to identify. Use these characteristics to help locate the head of the glide:

 - the location of increased flow velocity coming out of the pool

 - the location at which the steeply sloped bed rising out of the pool decreases to a lesser gradient 

 - the location at which the thalweg coming out of the pool becomes less defined and fades completely

 - the location at which elevation is approximately the same elevation as the tail of the run.

Pool. Has a relatively slow current and is usually found at stream channel bends, upstream from riffles, 

or on the downstream side of obstructions such as boulders or fallen trees. 

The stream bottom in a pool is often bowl shaped and represents the deepest locations of the reach. 

Water-surface slope of pools at below bankfull flows is zero.

For pools, indicate the pool form type.

Riffle/Run This code is recorded when a portion of the channel is a riffle habitat (shallow, fast turbulent flow, large

 substrate)

Complex and the other portion is run habitat (deeper and fast but not turbulent flow). 

 This type of habitat unit is typically formed by instream gravel bars.

Pool/Glide This code is recorded when a pool is transitioning into a glide. 

Complex Because the head of a glide is difficult to identify, use this code if unsure about the exact location of the glide. 
92 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 18. Data sheets for collecting fish cover data

Fish Cover Form Page ____ of ____

Reach ID: Stretch No.: Date: Crew:

Reach Length: Transect Spacing Interval: Channel: Main Side Backwater

Fish Cover*

Trans. Circle all cover types present. Comment

1 Lt FA HY BO AR SWD LWD T/R OV UC BL

Ctr FA HY BO AR

Rt FA HY BO AR SWD LWD T/R OV UC BL

2 Lt FA HY BO AR SWD LWD T/R OV UC BL

Ctr FA HY BO AR

Rt FA HY BO AR SWD LWD T/R OV UC BL

3 Lt FA HY BO AR SWD LWD T/R OV UC BL

Ctr FA HY BO AR

Rt FA HY BO AR SWD LWD T/R OV UC BL

4 Lt FA HY BO AR SWD LWD T/R OV UC BL

Ctr FA HY BO AR

Rt FA HY BO AR SWD LWD T/R OV UC BL

5 Lt FA HY BO AR SWD LWD T/R OV UC BL

Ctr FA HY BO AR

Rt FA HY BO AR SWD LWD T/R OV UC BL

6 Lt FA HY BO AR SWD LWD T/R OV UC BL

Ctr FA HY BO AR

Rt FA HY BO AR SWD LWD T/R OV UC BL

7 Lt FA HY BO AR SWD LWD T/R OV UC BL

Ctr FA HY BO AR

Rt FA HY BO AR SWD LWD T/R OV UC BL

8 Lt FA HY BO AR SWD LWD T/R OV UC BL

Ctr FA HY BO AR

Rt FA HY BO AR SWD LWD T/R OV UC BL

9 Lt FA HY BO AR SWD LWD T/R OV UC BL

Ctr FA HY BO AR

Rt FA HY BO AR SWD LWD T/R OV UC BL

10 Lt FA HY BO AR SWD LWD T/R OV UC BL

Ctr FA HY BO AR

Rt FA HY BO AR SWD LWD T/R OV UC BL

11 Lt FA HY BO AR SWD LWD T/R OV UC BL

Ctr FA HY BO AR

Rt FA HY BO AR SWD LWD T/R OV UC BL

Fish Cover Types* Additional comments:

FA = Filamentous Algae

HY = Hydrophytes & Mosses FA, HY, BO, AR are assessed within a 10-cm diameter circle around

BO = Boulders each point on transect

AR = Artificial SWD is < 10 cm in diameter at largest end; LWD is >10 cm at largest end

SWD = Small Woody Debris SWD & LWD assessed on a 1-m belt along transect on left and right side

LWD = Large Woody Debris of center channel

T/R = Trees/Roots T/R, OV, UC, BL are assessed within 1 m on either side of transect along

OV = Overhanging Vegetation bank

UC = Undercut bank

BL = Bluff within 5 m of water 10 cm or 0.1 m
Appendixes 93

Bank Angles

1

2

3

1

2

3

Appendix 19. Data sheets for collecting bank measurement data.

Bank Measurment Form

Reach ID: Stretch No: Date: Crew:

Reach Length: Transect Spacing Interval: Channel: Main Side Backwater

Bank Stability Bank Cover*

Trans. Angle Veg Height Sub Circle Dominant (>50%) Cover Comment

1 Lt TR SH GR BA AR

Rt TR SH GR BA AR

2 Lt TR SH GR BA AR

Rt TR SH GR BA AR

3 Lt TR SH GR BA AR

Rt TR SH GR BA AR

4 Lt TR SH GR BA AR

Rt TR SH GR BA AR

5 Lt TR SH GR BA AR

Rt TR SH GR BA AR

6 Lt TR SH GR BA AR

Rt TR SH GR BA AR

7 Lt TR SH GR BA AR

Rt TR SH GR BA AR

8 Lt TR SH GR BA AR

Rt TR SH GR BA AR

9 Lt TR SH GR BA AR

Rt TR SH GR BA AR

10 Lt TR SH GR BA AR

Rt TR SH GR BA AR

11 Lt TR SH GR BA AR

Rt TR SH GR BA AR

*Bank cover is assessed within 1 m on each side of transect and 10 m up the bank from wetted edge 

Bank Angle, Degrees Vegetative Cover (%) Height (m) Substrate Bank Cover Types*

1 = 0 - 30 1 = >80 1 = 0-1 1 = Bedrock/Artificial TR = Large trees (> 3 in. dbh)

2 = 31-60 2 = 50-80 2 = 1.1-2 2 = Boulder/Cobble SH = Small trees and shrubs

3 = >60 3 = 20-49 3 = 2.1-3 5 = Silt GR = Grass and Forbes

4 = <20 4 = 3.1-4 8 = Sand BA = Bare rock/sediment

5 = >4 10 = Gravel/Sand AR = Artificial
94 Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways

Appendix 20. Data sheet for collecting discharge data.

Discharge

Park: ____________________ Stream name: ____________________ Reach ID ____________________

Date: ____________________ Time: ___________________________ Crew Initials: ________________

Stream width: _____________ ft or m Meter used: _______________________________________

Interval Tap Measure

Reading

Interval Width

ft or meters

Depth

ft or meters

Velocity

ft/s or m/s

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

Notes:
Publishing support provided by:

Lafayette and Rolla Publishing Service Centers

For more information concerning the research described

in the report:

U.S. Geological Survey

Arkansas Water Science Center

401 Hardin Road

Little Rock, AR 72211-3528

(501) 228-3600

http://ar.water.usgs.gov
Petersen and others—Methods for Monitoring Fish Communities —Open-File Report 2007–1302