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Water: Bioassessment

Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic Macroinvertebrates, and Fish - Second Edition

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Rapid Bioassessment Protocols
For Use in Streams and Wadeable Rivers:
Periphyton, Benthic Macroinvertebrates, and Fish
Second Edition

Michael T. Barbour
Jeroen Gerritsen
Blaine D. Snyder
James B. Stribling


EPA 841-B-99-002

On this page:


This document has been reviewed and approved in accordance with U.S. Environmental Protection Agency policy. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

Appropriate Citation:

Barbour, M.T., J. Gerritsen, B.D. Snyder, and J.B. Stribling. 1999. Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic Macroinvertebrates and Fish, Second Edition. EPA 841-B-99-002. U.S. Environmental Protection Agency; Office of Water; Washington, D.C.

This entire document, including data forms and other appendices, can be downloaded from the website of the USEPA Office of Wetlands, Oceans, and Watersheds:

Download the RBP Chapters

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In December 1986, U.S. EPA's Assistant Administrator for Water initiated a major study of the Agency's surface water monitoring activities. The resulting report, entitled "Surface Water Monitoring: A Framework for Change" (U.S. EPA 1987), emphasizes the restructuring of existing monitoring programs to better address the Agency's current priorities, e.g., toxics, nonpoint source impacts, and documentation of "environmental results." The study also provides specific recommendations on effecting the necessary changes. Principal among these are:

  1. To issue guidance on cost-effective approaches to problem identification and trend assessment.
  2. To accelerate the development and application of promising biological monitoring techniques.

In response to these recommendations, the Assessment and Watershed Protection Division developed the rapid bioassessment protocols (RBPs) designed to provide basic aquatic life data for water quality management purposes such as problem screening, site ranking, and trend monitoring, and produced a document in 1989 (Plafkin et al. 1989). Although none of the protocols were meant to provide the rigor of fully comprehensive studies, each was designed to supply pertinent, cost-effective information when applied in the appropriate context.

As the technical guidance for biocriteria has been developed by EPA, states have found these protocols useful as a framework for their monitoring programs. This document was meant to have a self-corrective process as the science advances; the implementation by state water resource agencies has contributed to refinement of the original RBPs for regional specificity. This revision reflects the advancement in bioassessment methods since 1989 and provides an updated compilation of the most cost-effective and scientifically valid approaches.

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All of us who have dealt with the evaluation and diagnosis of perturbation to our aquatic resources owe an immeasurable debt of gratitude to Dr. James L. Plafkin. In addition to developing the precursor to this document in 1989, Jim was a driving force within EPA to increase the use of biology in the water pollution control program until his untimely death on February 6, 1990. Throughout his decade-long career with EPA, his expertise in ecological assessment, his dedication, and his vision were instrumental in changing commonly held views of what constitutes pollution and the basis for pollution control programs. Jim will be remembered for his love of life, his enthusiasm, and his wit. As a small token of our esteem, we dedicate this revised edition of the RBPs to his memory.

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Dr. James L. Plafkin of the Assessment and Watershed Protection Division (AWPD) in USEPA's Office of Water, served as principal editor and coauthor of the original Rapid Bioassessment Protocols document in 1989. Other coauthors of the original RBPs were consultants to the AWPD, Michael T. Barbour, Kimberly D. Porter, Sharon Gross, and Robert M. Hughes. Principal authors of this revision are Michael T. Barbour, James (Sam) Stribling, Jeroen Gerritsen, and Blaine D. Snyder. Many others also contributed to the development of the original RBP document. Special thanks goes to the original Rapid Bioassessment Workgroup. The Workgroup, composed of both State and USEPA Regional biologists (listed in Chapter 1), was instrumental in providing a framework for the basic approach and served as primary reviewers of various drafts. Dr. Kenneth Cummins and Dr. William Hilsenhoff provided invaluable advice on formulating certain assessment metrics in the original RBP approach. Dr. Vincent Resh also provided a critical review that helped strengthen the RBP approach. While not directly involved with the development of the RBPs, Dr. James Karr provided the framework (Index of Biotic Integrity) and theoretical underpinnings for "re-inventing" bioassessment for water resource investigations. Since 1989, extensive use and application of the IBI and RBP concept has helped to refine specific elements and strengthen the overall approach. The insights and consultation provided by these numerous biologists have provided the basis for the improvements presented in this current document.

This revision of the RBPs could not have been accomplished without the support and oversight of Chris Faulkner of the USEPA Office of Water. Special thanks go to Ellen McCarron and Russell Frydenborg of Florida DEP, Kurt King of Wyoming DEQ, John Maxted of Delaware DNREC, Dr. Robert Haynes of Massachusetts DEP, and Elaine Major of University of Alaska, who provided the opportunity to test and evaluate various technical issues and regional specificity of the protocols in unique stream systems throughout the United States. Editorial and production support, report design, and HTML formatting were provided by a team of Tetra Tech staff -- Brenda Fowler, Michael Bowman, Erik W. Leppo, James Kwon, Amanda Richardson, Christiana Daley, and Abby Markowitz. Technical assistance and critical review was provided by Dr. Jerry Diamond of Tetra Tech.

A Technical Experts Panel was convened by the USEPA to provide an in-depth review and recommendations for revisions to this document. This group of esteemed scientists provided not only useful comments, but assisted in revising sections of the document. In particular, Drs. Jan Stevenson and Loren Bahls revised the periphyton chapter; and Dr. Phil Kaufmann provided assistance on the habitat chapter. The Technical Experts Panel included:

Dr. Reese Voshell, Virginia Tech University (Chair)

Dr. Loren Bahls, University of Montana

Dr. David Halliwell, Aquatic Resources Conservation Systems

Dr. James Karr, University of Washington

Dr. Phil Kaufmann, Oregon State University

Dr. Billie Kerans, Montana State University

Dr. Jan Stevenson, University of Louisville

Dr. Charles Hawkins (Utah State University) and Dr. Vincent Resh (University of California, Berkeley) served as outside readers.

Much appreciation is due to the biologists in the field (well over a hundred) who contributed their valuable time to review both the original and current documents and provide constructive input. Their help in this endeavor is sincerely appreciated.

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You will need Adobe Acrobat Reader to view the Adobe PDF files on this page. See EPA's PDF page for more information about getting and using the free Acrobat Reader.








3. ELEMENTS OF BIOMONITORING | PDF Version (17 pp, 378K)



6. PERIPHYTON PROTOCOLS | PDF Version (23 pp, 107K)
By R. Jan Stevenson, University of Louisville, and Loren L. Bahls, University of Montana


8. FISH PROTOCOLS | PDF Version (20 pp, 191K)

9. BIOLOGICAL DATA ANALYSIS | PDF Version (18 pp, 124K)


11. LITERATURE CITED | PDF Version (24 pp, 83K)

Appendix A: SAMPLE DATA FORMS FOR THE PROTOCOLS | PDF Version (40 pp, 214K)




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Figure 3-1 Example of the relationship of data tables in a typical relational database.

Figure 3-2 Example input or lookup form in a typical relational database.

Figure 4-1 Flow chart summarizing the steps necessary to quantify performance characteristics of a bioassessment method (modified from Diamond et al. 1996).

Figure 4-2 Comparison of the discriminatory ability of the SCI between Florida's Peninsula and Panhandle Bioregions.

Figure 8-1 Sequence of activities involved in calculating and interpreting the Index of Biotic Integrity (adapted from Karr et al. 1986).

Figure 9-1 Comparison of the developmental process for the multimetric and multivariate approaches to biological data analysis (patterned after ideas based on Reynoldson, Rosenberg, and Resh, unpublished data).

Figure 9-2 Process for developing assessment thresholds (modified from Paulsen et al. [1991] and Barbour et al. [1995]).

Figure 9-3 Species richness versus stream size (taken from Fausch et al. 1984).

Figure 9-4 Results of multivariate ordination on benthic macroinvertebrate data from "least impaired" streams from Maryland, using nonmetric multidimensional scaling (NMDS) of Bray-Curtis dissimilarity coefficients.

Figure 9-5 An example of a metric that illustrates classification of reference stream sites in Florida into bioregions.

Figure 9-6 Example of discrimination, using the EPT index, between reference and stressed sites in Rocky Mountain streams, Wyoming.

Figure 9-7 Basis of metric scores using the 95th percentile as a standard.

Figure 9-8 Discriminatory power analysis of the Wyoming Benthic Index of Biotic Integrity.

Figure 10-1 Cumulative frequency diagrams (CFD) for the IBI (upper) and the ICI (lower)comparing the pre-1988 and post-1988 status on a statewide basis from Ohio. In each case, estimated attainable level of future performance is indicated. The Warm Water Habitat (WWH) and Exceptional Warm Water Habitat (EWH) biological thresholds are given for each index.

Figure 10-2 Relationship between the condition of the biological community and physical habitat.

Figure 10-3 Data from a study of streams in Florida's Panhandle.

Figure 10-4 Comparison of integrated assessment (habitat, fish, and benthos) among stream sites in Pennsylvania. Station 16 is a reference site. (Taken from Snyder et al. 1998).

Figure 10-5 Use of multidimensional scaling on benthic data to ascertain stream classification. The first and second axes refer to the dimensions of combinations of data used to measure similarity (Taken from Barbour et al. 1996b).

Figure 10-6 Example of a cluster dendrogram, illustrating similarities and clustering of sites (x-axis) using biological data.

Figure 10-7 Results of the benthic assessment of streams in the Mattaponi Creek watershed of southern Prince George's County, Maryland. Percent of streams in each ecological condition category. (Taken from Stribling et al. 1996b).

Figure 10-8 The population of values of the IBI in reference sites within each of the ecoregions of Ohio. Contributed by Ohio EPA.

Figure 10-9 Spatial and temporal trend of Ohio's Invertebrate Community Index. The Scioto River - Columbus to Circleville. Contributed by Ohio EPA.

Figure 10-10 Cumulative distribution of macroinvertebrate index scores. 21% of sites scored at or below 60. The median index score is 75, where the cumulative frequency is 50%.

Figure 10-11 Biological assessment of sites in the Middle Rockies, showing mean and standard deviation of repeated measures and the assessment threshold (dashed line).

Figure 10-12 Integration of data from habitat, fish, and benthic assemblages.

Figure 10-13 The response of the benthic macroinvertebrate assemblage (ICI) to various types of impacts. (Provided by Ohio EPA).

Figure 10-14 Guidance for Florida Ecosummary - A one-page bioassessment report. (Contributed by Florida DEP).

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Table 2-1 Chronology of USEPA bioassessment guidance (relevant to streams and rivers).

Table 4-1 Progression of a generic bioassessment field and laboratory method with associated examples of performance characteristics.

Table 4-2 Translation of some performance characteristics, derived for laboratory analytical systems, to biological laboratory systems (taken from Diamond et al. 1996).

Table 4-3 Suggested arithmetic expressions for deriving performance characteristics that can be compared between 2 or more methods. In all cases, x.jpg = mean value, X = test site value, s = standard deviation. Subscripts are as follows: capital letter refers to site class (A or B); numeral refers to method 1 or 2; and lower case letter refers to reference (r) or test site (t) (modified from Diamond et al. 1996).

Table 5-1 Components of EMAP physical habitat protocol.

Table 5-2 Example of habitat metrics that can be calculated from the EMAP physical habitat data.

Table 6-1 Summary of collection techniques for periphyton from wadeable streams (adapted from Kentucky DEP 1993, Bahls 1993).

Table 6-2 Environmental definitions of autecological classification systems for algae (as modified or referenced by Lowe 1974). Definitions for classes are given if no subclass is indicated.

Table 7-1 Definitions of best candidate benthic metrics and predicted direction of metric response to increasing perturbation (compiled from DeShon 1995, Barbour et al. 1996b, Fore et al. 1996, Smith and Voshell 1997).

Table 7-2 Definitions of additional potential benthic metrics and predicted direction of metric response to increasing perturbation.

Table 8-1 Fish IBI metrics used in various regions of North America.

Table 9-1 Some potential metrics for periphyton, benthic macroinvertebrates, and fish that could be considered for streams. Redundancy can be evaluated during the calibration phase to eliminate overlapping metrics.

Table 9-2 Statistics of repeated samples in Wyoming and the detectable difference (effect size) at 0.05 significance level. The index is on a 100 point scale (taken from Stribling et al. 1999).

Table 9-3 Maine's water quality classification system for rivers and streams, with associated biological standards (taken from Davies et al. 1993).

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Acronym Full Name (acronym stands for)
AFDM Ash Free Dry Mass
ANOVA Analysis of Variance
APHA American Public Health Association
ASTM American Society of Testing and Materials
AUSRIVAS Australian River Assessment System
AWPD Assessment and Watershed Protection Division
BEAST Benthic Assessment of Sediment
BMP Best Management Practices
CBWD Chesapeake Bay and Watershed Programs
CWA Clean Water Act
DEC Department of Environmental Conservation
DEM Department of Environmental Management
DEM Division of Environmental Management
DEP Department of Environmental Protection
DEQ Department of Environmental Quality
DHEC Department of Health and Environmental Control
DNR Department of Natural Resources
DNREC Department of Natural Resources and Environmental Control
DQO Data Quality Objectives
EDAS Ecological Data Application System
EMAP Environmental Monitoring and Assessment Program
EPA Environmental Protection Agency
EPT Ephemeroptera, Plecoptera, Trichoptera
GIS Geographic Information System
GPS Global Positioning System
HBI Hilsenhoff Biotic Index
IBI Index of Biotic Integrity
ICI Invertebrate Community Index
ITFM Intergovernmental Task Force on Monitoring
ITIS Integrated Taxonomic Information Service
IWB Index of Well Being
MACS Mid-Atlantic Coastal Systems
MBSS Maryland Biological Stream Survey
MIWB Modified Index of Well Being
NAWQA National Water Quality Assessment Program
NPDES National Pollutant Discharge Elimination System
NPS nonpoint source pollution
PASS Preliminary Assessment Scoresheet
PCE Power Cost Efficiency
POTWS Publicly Owned Treatment Works
PTI Pollution Tolerance Index
QA Quality Assurance
QC Quality Control
QHEI Qualitative Habitat Evaluation Index
RBP Rapid Bioassessment Protocols
RDMS Relational Database Management System
RM River Mile
RPS Rapid Periphyton Survey
SAB Science Advisory Board
SCI Stream Quality Index
SOP Standard Operating Procedures
STORET Data Storage and Retrieval System
SWCB State Water Control Board
TCR Taxonomic Certainty Rating
TMDL Total Maximum Daily Load
TSN Taxonomic Serial Number
USDA United States Department of Agriculture
USEPA United States Environmental Protection Agency
USGS United States Geological Survey
WPA Watershed Protection Approach
WQD Water Quality Division

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