vvEPA
United States
Environmental Protection
Agency
Technical Components of State
and Tribal Bioassessment
Programs
NATIONAL PROGRAM SUMMARY
Since 1989 the U.S. EPA has periodically
prepared inventories of state bioassessment
programs for streams and wadeable rivers. This
inventory was recently updated based on 2001
program status and expanded to include tribes,
territories, and basin commissions (Figure 1).
Six technical components are summarized
below from the 2001 inventory:
- Uses of Bioassessment
- Field and Lab Methods
- Monitoring Program Design
- Data Analysis and Interpretation
- Aquatic Life Use Designations and
Decision Making
- Reference Site/Condition Development
This brochure presents highlights of information which
is illustrated in greater detail in the full survey report
entitled Summary of Biological Assessment Programs
and Biocriteria Development for States, Tribes,
Territories, and Interstate Commissions: Streams and
Wadeable Rivers, EPA-822-R-02-048 and can be ordered
from EPA Office of Water's, Water Resource Center at
http://www.epa.gov/OGWDW/resource, or viewed online
at: http://www. epa.gov/bioindicators.
Confederated Tribe of
Colville Reservation
Passamaquoddy
.I In Process (Puerto
II Rico, Nez Perce)
pi \ SeminoleTribe
^^ ifFlorida
Use (All 50 states, DC,Oneida Nation, Pyramid Lake
Tribe, DRBC, ICPRB, ORSANCO, SRBC )
Do Not Use (American Samoa, CNMI, Confederated
Tribe of Colville Reservation, SeminoleTribe of FL,
Passamaquoddy Tribe, U.S. Virgin Islands)
Figure 1. States, tribes, territories and interstate
commissions that have bioassessment programs for
streams and small rivers (2001).
80-
70-
60-
I50'
£: 40-
o
i
-Q 30-
* 20-
10-
0.
65
1-1 Total _ Y _ Under _ N
U Programs Yes U Development No
65 65 65
0
Nonpoint
Source
Assessment
Monitoring Aquatic Life Use Promulgate into Total Maximum
Effectiveness of Determinations/ state quality Daily Load
BestMgmt Ambient standards as Assessment and
Practices Monitoring biocriteria monitoring
Figure 2. Uses of bioassessment for management of
streams and small rivers (2001).
USES OF BIOASSESSMENT
Water quality monitoring, assessment,
and standards programs rely heavily
upon bioassessments (Figure 2). In
1989, only 37 inventoried programs used
bioassessment. Today, all 50 States, DC,
four basin commissions, and two tribes
use bioassessment in their water quality
programs. At least two-thirds of these
programs rely upon bioassessments for
nonpoint source assessments, monitoring
the effectiveness of Best Management
Practices (BMP), aquatic life designated
use assessments, and Total Maximum
Daily Load (TMDL) assessments. Slightly
more than half of these programs also use
bioassessment for promulgating biocriteria
into their water quality standards (narrative
or numeric - see discussion later), but an
additional 10 programs are developing such
standards.
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FIELD AND LAB METHODS
Assessment of only one assemblage of organism
(or type of animal or plant) leads to only
80-85% effectiveness in identifying Aquatic
Life Use (ALU) attainment or non-attainment
(water quality standard effectiveness)1. EPA
encourages the use of two or more organism
groups in biological assessments.
Benthic macroinvertebrates are the
most common type of organism used in
bioassessment, but fish and algae (periphyton)
are also used. All three organism groups
increased in usage in bioassessments between
1995 and 2001; algae use increased the most
(Figure 3). The number of programs using
more than one assemblage increased by about
29% within the original 52 programs with 45
of the 65 total programs using more than one
assemblage (see Figure 3). Twenty-two of the
45 programs use three or more assemblages for
assessment.
In addition to macroinvertebrates
and fish, there are 11 programs that
collect periphyton, nine macrophyte
programs, three that collect amphibians
and reptiles (herpatofauna), three
that use zooplankton and
one that counts waterfowl.
Habitat Assessment
Assessment Type
Total
Visual
Quantitative
Hydrogeomorphology
Combination
# of Programs
57
48
24
12
22
1 Yoder, C.O. and E.T. Rankin. 1995. Biological criteria
program development and implementation in Ohio. In
Biological Assessment and Criteria: Tools for Water
Resource Planning and Decision Making, W.S. Davis and
T.P. Simon (editors), pp. 109-144. Lewis Publishers, Boca
Raton, FL.
1989 1995 2001
combination of 2 or more
In Place
Under Development
Without
Figure 3. Types of assemblages used for bioassessments.
The number of sites sampled each year is dependent upon the
monitoring design and resources available. Many more sample
sites were devoted to benthic macroinvertebrate sampling than
either fish or periphyton. Four invertebrate programs sample
more than 500 sites per year (California, Michigan, Wisconsin,
and West Virginia) while most collect invertebrates from 100-
500 sites. Only one fish program (Wisconsin) collects from
more than 500 sites while the majority collect less than 100
sites per year. Periphyton was collected at less than 100 sites in
14 of 19 programs.
Number of Sites Sampled for Each Assemblage
# sites
sampled/yr
< 100
100-500
>500
Invertebrates
20
32
4
Fish
30
10
1
Periphyton*
14
5
0
* not all programs reported information
Physical characteristics and water quality are basic elements
for assessing habitat quality. Physical characteristics can
include land use, land cover, riparian vegetation, condition
of stream banks and substrate, as well as flow, depth and
width. Habitat quality assessments can be based on visual
observations or detailed measurements of the physical
characteristics. All bioassessment programs (57) depend upon
either a visual habitat assessment comparable to EPA's Rapid
Bioassessment Program (48), a more quantitative physical
habitat assessment similar to EPA's Environmental Monitoring
Assessment Program or EMAP (24), or a hydrogeomorphology
habitat assessment based on Rosgen (12).
Twenty-two programs use a combination of these habitat
assessments.
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Benthic Macroinvertebrates
Sampling
Gear Used
D-Frame
Kicknet
Multiplate
By Hand
Dipnet
Surber
Rock Baskets
# of Programs
Using Gear
31
24
14
14
14
12
7
() = Number of programs
Total of 60programs
Figure 5. Number of benthic
macroinvertebrates subsampled.
Fish
Sampling
Gear Used
Electro-fisher
Seine
Rotenone
Gill nets
# of Programs
Using Gear
backpack- 38
boat- 18
pram- 16
25
1
3
Periphyton is an assemblage
that is becoming more popular
in waterbody assessment.
The most frequent way to
obtain periphyton samples is
through brushing or scraping
rocks or artificial surfaces
to which the periphyton are
attached. Periphyton are found
in a variety of habitats and are
typically classified as diatoms
or down to the species level.
Assessments are conducted in
various ways depending on the
program that a state uses and the
tools accessible to the program.
Different techniques are used for
different types of assemblages.
Macroinvertebrates are mainly
measured using netting techniques
because these animals are benthic
and live within the material at the
bottom of a stream or pond. The
most common technique used
to sample macroinvertebrates
is the D-frame net (Figure 4),
followed by the kick net. Most
macroinvertebrates are found
in and sampled from riffles or
runs because they are considered
the richest and most productive
habitat. On average, about 250
specimens are collected for each
sample. This number ranges for
different programs from 100 to
1200 (Figure 5). When organizing
macroinvertebrates, most
organisms are classified down to
genus and/or species, the lowest
classification is typically used.
Only five states have the lowest
classification as family level.
When fish are sampled most states
use electro-fishers (backpack - see
Figure 6, boat, or pram/tote barges).
Seines and other types of nets are
used as well to capture fish. Fish are
captured in a variety of habitats and
all fish are identified to species.
Periphyton/Algae
Sampling
Gear Used
Brushing/Scraping
By Hand
Periphytometer
Suction
Microslides
# of Programs
Using Gear
16
8
5
5
4
Figure 4. Sampling benthic
invertebrates with D-nets.
Figure 6. Sampling fish with
backpack electro-fisher.
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MONITORING PROGRAM DESIGN
Site selection for assessment and
monitoring can be "targeted", i.e.,
relevant to special studies that focus
on potential or existing problems
and/or "probabilistic", which
provides information on the overall
status or condition of the watershed,
basin, or region (Figure 7).
Most studies conducted by
state water quality agencies for
identification of problems and
sensitive waters are done with a
targeted design. In this case,
sampling site selection is based
on the knowledge of an existing
problem, events that will adversely
affect the waterbody (development
or deforestation), or actions
intended to improve the quality
of the waterbody (installation of
BMPs or habitat restoration). This
method provides assessments of
individual sites or stream reaches.
To meaningfully evaluate biological
condition in a targeted design,
sampling locations must be similar
enough to have similar biological
expectations, which, in turn,
provide a basis for comparison
80
70
60
50
30-
20-
10
D p°ta Din Place D T Without
Programs Development
65
65
65
65
65
Targeted Fixed Station Probabilistic by Probabilistic by Rotating Basin
stream order/ ecoregion or
catchment area statewide
Figure 7. Monitoring designs used by state and tribal bioassessment
programs (2001).
of impairment. If the goal of an
assessment is to evaluate the effects
of water chemistry degradation,
comparable physical habitat
should be sampled at all stations,
otherwise, the differences in the
biology attributable to a degraded
habitat will be difficult to separate
from those resulting from chemical
pollution. Availability of appropriate
| With (Statewide-CA,DE, IN,KS,KY,NE,OR,SC,VA)
Under Development (CT, I A, ID, OK, Wl, ORSANCO)
Without
Figure 8. Implementation status of probabilistic designs for
bioassessment of streams and rivers (2001).
habitat at each sampling location can
be established during preliminary
reconnaissance. In evaluations where
several stations on a waterbody will
be compared, the station with the least
number of productive habitats available
will often determine the type of habitat
to be sampled at all sample stations.
Fixed Station monitoring is a type of
targeted monitoring that samples the
same site on a periodic basis to detect
trends or changes over time.
In a probabilistic or random
sampling regime, stream characteristics
may be highly dissimilar among the
sites, but will provide a more accurate
assessment of biological condition
throughout the area than a targeted
design. Selecting sites randomly
provides an unbiased assessment of
the condition of the waterbody at
a scale above the individual site or
stream. Thus, an agency can address
questions at multiple scales. Studies
conducted for 305(b) status reports on
the conditions of a state's waters and
trend assessments are best done with
a probabilistic design. Probabilistic
sample designs were reported to be
used by 23 programs in 2001, and 15 of
those programs have either adopted or
are developing a probabilistic sample
design in addition to their targeted
design (Figure 8).
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Rotating basin designs ensure that all basins will
be monitored over a period of years determined by the
respective programs. These designs are compatible with
targeted, fixed station, and probabilistic designs and are
used by 39 programs inventoried.
Recently (March 2003), the EPA issued a monitoring
design guideline for all states2. The State monitoring
programs integrate their monitoring designs (e.g.,
fixed station, intensive and screening-level monitoring,
rotating basin, judgmental and probability design) to
meet the full range of decision needs. EPA recommends
that state monitoring design should include probability-
based networks (at the watershed or state-level) that
support statistically valid inferences about the condition
of all State waterbody types, overtime. Studies for ALU
determination and those related to TMDLs can be done
with random (watershed or higher level) or targeted (site-
specific) designs.
USEPA. 2003. Elements of a State Water Monitoring and
Assessment Program. EPA-841-B-03-003. U.S. Environmental
Protection Agency, Office of Wetlands, Oceans and Watershed,
Assessment and Watershed Protection Division, Washington, DC.
DATA ANALYSIS
AND INTERPRETATION
Several methods have been used to analyze
biological community data (Figure 9). The
most common method is the use of biotic
metrics, which are individual measurements
(metrics) of the structure, function, and/or
pollution sensitivity of the aquatic community,
usually combined to create a multi-metric
index. Graphical presentations which create
meaningful visual displays of the data over
time, or stream distance, can provide additional
evidence to support the analysis. Sometimes
the graphical displays of data will yield
important findings that may not be statistically
evident. Multivariate analysis is important
during different phases of the analysis and has
been used to validate multi-metric indices as
well as determining associations of the biotic
response to various stressors. These methods
have been expanding in use, especially the use of
multivariate analysis.
Multimetric Index:
An index that combines indicators, or
metrics, into a single index value. Each
metric is tested and calibrated to a
scale aggregated into a multimetric
index. Both the index and metrics
are useful in
assessing and
diagnosing
ecological Statistical methods (e.g.
condition. ordination or discriminant
analysis) for analyzing
physical and biological
community data using
multiple variables.
80-
70-
60-
50-
40-
30-
20-
10-
0-
!°lal D In Place D " , Without
Programs Development
65
n
65
I
65
I
65
65
Summary tables, Parametric Multivariate Biological Disturbance
illustrative ANOVAs Analysis Metrics Gradients
graphs
Figure 9. Biological data analysis tools and methods.
Multivariate Analysis:
The multi-metric index for biological assessment has
become widely used since it first appeared in Karr's
Index3 of Biotic Integrity (IBI). By using a combination
of metrics that have been calibrated and validated using
natural classifications of waterbodies, IBIs characterize
and assess the overall biological condition of streams.
IBIs also provide an index that changes in a predictable
manner across a gradient of human influence. The
multi-metric approach is the basis for the EPA's Rapid
Bioassessment Protocols (http://www.epa.gov/owow/
monitoring/rbp). Biometrics and multivariate analysis
are data analysis tools used to reduce raw data into
workable indicators. This approach is more objective
and systematic, reducing the chance for conflicting
findings among different investigators. Some states use
multivariate analysis to provide additional insight and
to calibrate their multimetric reference conditions. All
programs with bioassessment programs also assess the
physical habitat quality at their sample sites, usually
employing visual based methods in combination with
other measurements.
3 Karr, J.R. 1981. "Assessments of biotic integrity using fish
communities." Fisheries, 66:21-27.
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Assessment of
Aquatic Resources
Cause & Effect
Determinations
Effectiveness of
Corrective Action
Permitted Discharges
Watershed based
management
Restoration of
aquatic resources
D In Place
Under
Development
Without
Figure 10. Uses of bioassessment data in
integrated assessments for decision-making.
ALUs help to describe the overall quality of
water based on levels of support provided for
the aquatic life by the water quality (rated
as fully supporting verses partially/non
supporting). Waterbodies not fully supporting
aquatic life must be listed by the states and
tribes on the 303(d) list, a summary of all the
impaired waters in a state. States and tribes
must develop and adopt criteria or water quality
standards necessary to protect designated
ALUs. Because chemical water quality
standards alone may not ensure a healthy
biological condition, most states are working
to integrate a greater amount of biological
information, including biocriteria (Figure 11),
into their water quality standards.
AQUATIC LIFE USE
DESIGNATIONS AND DECISION MAKING
Narrative biocriteria are written expressions of
desired biointegrity in an aquatic community.
Numeric biocriteria on the other hand, achieve the
same objective, but through a numeric expression
of the biological condition. Many states utilize a
variety of bioassessment information to develop
biological criteria for streams and rivers. Biocriteria,
when developed and adopted in water quality
standards (WQS), are very effective tools to
protect aquatic life. The goals for the preservation
and restoration of aquatic life are referred to as
designated aquatic life uses (ALUs). Designated
uses to support aquatic life can cover a broad range
of biological conditions to support both intact
communities as well as establishing restoration goals
for compromised ecosystems. Bioassessments can
aid in the development of ALUs.
Biocriteria are an effective tool for addressing water
quality problems by providing mechanisms to assess
and help protect the biological resources at risk from
chemical, physical or biological impacts (Figure 10).
Narrative Biocriteria in WQS
Yes
Under Development
No
Numeric Biocriteria in WQS
Figure 11. Number of bioassessment
programs using narrative biocriteria vs.
those using numeric.
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REFERENCE SITE/REFERENCE
CONDITION DEVELOPMENT
One of the key elements in bioassessment
programs is the establishment of reference
conditions to help discern human impacts
from natural variation. A reference
condition is essentially the benchmark
against which changes in water quality are
measured.
EPA recommends using a regional
reference condition (USEPA 2002) and
the most common method for basin-wide
use is based on ecoregions, whereas paired
watersheds are used at a local scale.
The ecoregion approach recognizes
geographic patterns of similarity among
ecosystems and the subsequent distribution
of biological communities grouped on
the basis of environmental variables
such as climate, soil type, physiography,
and vegetation. Describing a reference
condition from a combination of data
collected from several minimally disturbed
sites is preferable to using data from only a
single reference site to compare biosurvey
results. Regional reference conditions
are developed from data collected from
a combination of specific sites with
similar physical characteristics. Reference
conditions typically represent the healthiest
conditions that can be identified for sites
with the same or similar characteristics.
One of the more impressive improvements
to bioassessment programs found within
the past six years was the increase in
regional reference conditions as a basis
for making comparisons and detecting
use impairment (see Figures 12 and 13).
In 1989, only four states (Arkansas,
Nebraska, North Carolina, and Ohio)
were actively using reference conditions
to establish numeric values for biological
community expectations. Between 1995
and 2001, the number of programs using
regional reference conditions increased by
21, from 15 to 36 programs. Meanwhile,
programs using site-specific reference
conditions decreased by 12.
Reference Condition Determinations
Site-Specific
Paired
Watersheds
Regional
Professional
Judgment
Characterization of Reference Sites within a
Regional Reference Condition Approach
Historical
Conditions
9
Least or Minimally
Disturbed Sites
Gradient
Response
Professional
Judgment
Figure 12. Number of bioassessment programs by method
to determine reference condition and reference sites for
regionalization method.
i-i Total
D Programs
Under
Development
Nn
No
60
50
40 _
"o 30
I
I 20
10 -
1989
1995
2001
50
unknown
Regional
^ference
52 52
26
Regional
Reference
52 52
Regional
Reference
Figure 13. Growth in bioassessment programs
using regional reference sites vs. programs using
site-specific reference conditions.
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3J
\ PRo^
01
CD
EPA Office of Water
Washington DC 20460
EPA-822-F-03-009
January 2004
EPA recommends the following bioassessment program elements4 for the
most effective assessment and management of aquatic life resources:
Index period:
A well-documented seasonal index period(s)
calibrated with data for reference conditions;
Natural Classification of Waterbodies:
True regional approach that transcends
jurisdictional boundaries to strengthen
inter-regional classification and recognizes
zoogeographical aspects of assemblages;
Reference conditions:
Regional reference conditions are established
within the applicable waterbody ecotype;
Indicator Assemblages:
Two or more assemblages with high taxonomic
resolution;
Field and Laboratory Protocols:
Standard operating procedures are well documented
supported by a formal QA/QC program;
Precision of Biological Methods:
High repeatability in assessments and a high level of
confidence in analytical results that can distinguish
between human and natural influences based on a
gradient of stressors/human influence;
Analysis of the Data:
Biological index(es) or model(s) for multiple
assemblages is developed and calibrated throughout
the State or region. Attainment thresholds are based
on discriminant model or distribution of candidate
reference sites
4 USEPA. 2002. Consolidated Assessment and Listing Methodology: Toward a
Compendium of Best Practices. First Edition. Prepared by U.S. Environmental Protection
Agency, Office of Wetlands, Oceans, and Watersheds, Washington, DC July 2002.
(http://www.epa.gov/owow/monitoring/calm.html)
Office of Water
Office of Environmental Information
Office of Science and Technology
Susan Jackson (202) 566-1112
William Swietlik (202) 566-1129
Treda Smith (202) 566-1128
Tom Gardner (202) 566-0386
Kellie Kubena (202) 566-0448
http://www.epa.gov/waterscience/biocriteria
Office of Wetlands, Oceans, and Watersheds
Chris Faulkner (202) 566-1185
Laura Gabanski (202) 566-1179
Susan Holdsworth (202) 566-1187
http://www.epa.gov/owow/monitoring/bioassess.html
ENVIRONMENTAL
INFORMATION
Wayne Davis (410) 305-3030
Elizabeth Jackson (202) 566-0626
http://www.epa.gov/bioindicators
Office of Research and Development
Susan Cormier (513) 569-7995
Sue Norton (202) 564-3246
Steve Paulsen (541) 754-4428
Glenn Suter (513) 569-7808
http ://www. epa. gov/ord
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