SEPA
United States
Environmental Protection
Agency
Office of Research and Development

Washington, DC 20460
 February 2006

EPA/620/R-06/001
 Mid-Atlantic Integrated Assessment (MAIA)

    State of the Flowing Waters Report

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 MID-ATLANTIC INTEGRATED ASSESSMENT (MAIA)
    STATE OF THE FLOWING WATERS REPORT
    Stoddard, J.L.1, A.T. Herlihy2, B. H. Hill3, R.M. Hughes2, P.R. Kaufmann1, DJ. Klemm4,
  J.M. Lazorchak4, F.H. McCormick5, D.V. Peck1, S.G. Paulsen1, A.R. Olsen1, D.P. Larsen1, J.
                          Van Sickle1, T.R. Whittier5

1 U.S. Environmental Protection Agency
 Western Ecology Division
 National Health and Environmental Effects Laboratory
 Office of Research and Development
 200 SW 3 5th Street
 Corvallis, OR  97333

2 Department of Fish and Wildlife
 Oregon State University
 c/o U.S. Environmental Protection Agency
 200 SW 3 5th Street
 Corvallis, OR 97333
3 U.S. Environmental Protection Agency
 Mid-Continent Division
 National Health and Environmental Effects Laboratory
 Office of Research and Development
 6201 Congdon Boulevard
 Duluth, Minnesota 55804-2595

4 U.S. Environmental Protection Agency
 Environmental Research Center
 National Exposure Research Laboratory
 Office of Research and Development
 26 West Martin Luther King Drive
 Cincinnati, OH 45268

5 Dynamac Corp.
 c/o U.S. Environmental Protection Agency
 200 SW 3 5th Street
 Corvallis, OR 97333

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                                 NOTICE
   The  information  in this  document has been funded wholly or in  part by the U.  S.
Environmental Protection Agency. It has been subjected to review by the National Health and
Environmental Effects Research Laboratory and approved for publication. Approval does not
signify that the contents reflect the views of the Agency,  nor does mention of trade names  or
commercial products constitute endorsement or recommendation for use.
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TABLE  OF CONTENTS
   Executive Summary	v
   Foreword	1
   Introduction	3
     Purpose	3
     Stream and River Condition	3
     Regional Statistical Surveys	5
   The Mid-Atlantic Region	7
     Background	7
     Ecological Regions	9
     Stream Size	13
   Ecological Condition	16
     Fish Assemblages	17
     Macroinvertebrate Assemblages	20
     Algal Assemblages	23
     Comparison of Fish, Macroinvertebrate, and Algal Scores	23
   Stressors in MAIA Flowing Waters	25
     Acidification	27
     Other Mining Effects	31
     Nutrient Enrichment	31
     In-Stream Habitat	33
     Riparian Habitat	36
     Non-Native Fish	37
     Summary Ranking of Potential Stressors	43
   Geographic Targeting	48
     Coastal Plain	49
     Piedmont	50
     Valleys	51
     Ridges	52
     North and Central Appalachians	53
     Western Appalachians	54
   Conclusions and Further Directions	55
   Appendix A:  Thresholds	A-l
     Macroinvertebrate Index of Biotic Integrity	A-3
     Algal Index of Biotic Integrity	A-3
     Fish Index of Biotic Integrity	A-4
     Mine Drainage	A-5
     Acid Mine Drainage	A-5
     Acid Deposition	A-6
     Phosphorus	A-6
     Nitrogen	A-6
     Excess Sediment	A-7
     Large Woody Material	A-8
     Riparian Habitat Condition	A-9
   Appendix B:  Calculating Relative Risk	B-l

   MID-ATLANTIC FLOWING WATERS ASSESSMENT                            Page iii

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  Definition and example calculation	B-l
  Confidence intervals for Relative Risk	B-2
Appendix C: Further Reading	C-l
  Environmental Monitoring and Assessment Program	C-l
  Sample Survey Design	C-l
  Ecological Regions	C-2
  Biotic Integrity	C-2
  Stressors	C-3
  Relative Risk	C-4
  Other Mid-Atlantic Assessments	C-4
  Environmental Report Cards	C-4
MID-ATLANTIC FLOWING WATERS ASSESSMENT                             Page iv

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LIST  OF FIGURES

Figure 1. The MAIA region with sampling sites	viii
Figure 2 The Mid-Atlantic Integrated Assessment (MAIA) region	2
Figure 3. The MAIA region with sampling sites	6
Figure 4. Ecological regions (ecoregions) of the Mid-Atlantic region	10
Figure 5. Strahler orders	13
Figure 6. River Continuum Concept	14
Figure 7. Lengths of streamsin different stream orders	15
Figure 8. Distribution of flowing waters with game and non-game fish	16
Figure 9. Fish IBI scores	19
Figure 10.  Macroinvertebrate IBI scores	21
Figure 11.  Algal IBI scores	22
Figure 12.  Land use and land cover	26
Figure 13.  Extent of acid deposition effects	28
Figure 14.  Extent of acid mine drainage	29
Figure 15.  Extent of all mine drainage effects	30
Figure 16.  Extent of excess phosphorus concentrations	32
Figure 17.  Extent of excess nitrogen concentrations	33
Figure 18.  Extent of excess sedimentation	34
Figure 19.  Extent of large wood in flowing	35
Figure 20.  Extent of problems with riparian condition	37
Figure 21.  Relationship between Large Wood and Riparian Condition	38
Figure 22.  Extent of non-native fish species	39
Figure 23.  Cumulative frequency distribution for the percentage of non-native fish	40
Figure 24.  Extent of mercury concentrations	41
Figure 25.  Extent of organic contaminants	42
Figure 26.  Relative extent of major stressors	43
Figure 27.  Relative risk values	45
Figure 28.  Comparison of relative extent and relative risk to fish	47
Figure 29.  Comparison of relative extent and relative risk to macroinvertebrates	47
Figure 30.  Comparison of relative extent and relative risk to algae	48
Figure 31.  Summary of Coastal Plain ecoregion condition	49
Figure 32.  Summary of Piedmont ecoregion condition	50
Figure 33.  Summary of Valley ecoregion condition	51
Figure 34.  Summary of Ridge ecoregion condition	52
Figure 35.  Summary of North and Central Appalachian ecoregion condition	53
Figure 36.  Summary of Western Appalachian ecoregion condition	54
Figure 37.  Two subregions that could be targeted for protection efforts—The Ridge and
    North/Central Appalachian ecoregions	56
Figure 38.  Two subregions that could be targeted for restoration efforts—the Coastal Plain and
    Western Appalachian ecoregions	57
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     Ml
                                                               0   40  80  120  160.
                                                               |^^^^^^^E=^^^^^B K Icmeters
                   The Mid-Atlantic Integrated Assessment (MAIA) region
MID-ATLANTIC FLOWING WATERS ASSESSMENT
Page vi

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EXECUTIVE SUMMARY
   This assessment serves the purpose of a report card on the state of streams and rivers in the
Mid-Atlantic region. It combines data from two sample surveys of flowing waters conducted in
the region by the U.S. Environmental Protection Agency during the period 1993-98 (Figure 1).
Two unique aspects of this assessment are very important:  (1) it focuses first on the biological
status of streams  and rivers (to assess their ecological  condition), and then on the stressors
having both the greatest extent and  the greatest effects  on biological assemblages; and (2) it
results from a sample survey design that allow us to present the results as though every stream
and river in the region had been sampled. It provides the first statistically unbiased assessment of
the health of the region's flowing waters.

   Many will conclude from reading this report that the Mid-Atlantic region is getting a failing
grade. The report  relies on newly created Indices of Biotic Integrity (IBIs) to assess ecological
condition. Biotic integrity  can be  described as "the capacity of an ecosystem to support and
maintain a biota that is comparable to that found in natural  conditions." The IBIs developed for
three key biological assemblages in Mid-Atlantic streams and rivers—fish, macroinvertebrates
and algae—all reach similar conclusions, and they are not encouraging. Roughly one-third of the
region's  stream length exhibits IBI scores that are classified as 'poor,' and forty  percent are
classified as 'marginal,'  regardless of which assemblage is used to draw conclusions. Overall,
only one-quarter to one-third of the  stream resource of the Mid-Atlantic region exhibits good
biotic integrity.
     Biological Assemblage:
Proportion of Stream Resource
      in Poor Condition
 Primary Stressors *
              Fish


       Macroinvertebrates


             Algae
            31%


            41%


            33%
   Non-native fish
 Lack of large wood

Excess fine sediments
      Acidity

     Nutrients
Excess fine sediments
        * based on combination of high relative extent and high relative risk to assemblage

   What kinds of environmental  stressors are associated with poor biotic integrity in the Mid-
Atlantic? The most important stressors are those that share two characteristics: they are relatively
widespread (occurring in a high proportion of stream length) and represent high relative risks to
the biological  assemblages (i.e., they are more likely to be found in streams with poor biotic
integrity).  When both characteristics are considered, each biological assemblage presents its
own list of key stressors.
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                   Ecoregions
                   n Ridge
                   CD Valley
                   (HI Western Appalachians
                   CH North - Central Appalachians
                   I  I Piedmont
                   d! Coastal Plain
       Figure 1.  The Mid-Atlantic Integrated Assessment (MAIA) region, and the sampled streams
       and rivers used in this report. Shaded background colors illustrate the aggregated ecological
       regions used for reporting results in this report.

•  For fish: the introduction of non-native fish species (occurring in 47% of the Mid-Atlantic
   stream resource) and lack of large woody material (necessary to maintain habitat complexity,
   and lacking in 26% of stream length) are both common stressors with high relative risks.

•  For macroinvertebrates: the presence of excess fine sediments (occurring in 28% of the Mid-
   Atlantic stream resource) is the most common stressor with demonstrable effects on biotic
   integrity. Acidity,  from either acid rain or  acid mine drainage, appears to have significant
   deleterious effects  on macroinvertebrate integrity when  it occurs, but is  relatively uncommon
   (<5% of stream length in the region).

•  For algae: two  nutrients, phosphorus and nitrogen, exhibit the  highest relative risks of any
   stressors on  any biological assemblage—both are relatively common in the region (14% to
   18% of total  stream  length). As  with macroinvertebrates,  poor  algal  condition  is  also
   associated with excess fine sediments—the relative risk from excess sediments is lower than
   for nutrients, but they occur in a larger proportion of the stream resource (28%).
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   Not surprisingly, neither ecological condition nor the relative importance of aquatic stressors
is  uniform across the Mid-Atlantic region. When monitoring data are analyzed  according
ecological regions (ecoregions), two  subregions  (the Ridge and North/Central  Appalachian
ecoregions) are clearly in better overall condition than the others, with more than 40% of the
stream resource in good condition for at least one biological assemblage. Two ecoregions are
clearly more degraded than the others (the Coastal Plain and Western Appalachian ecoregions),
with more than 40% of their  total stream length in poor condition for two or more biological
assemblages—in both of these  subregions, the assemblage in poorest condition indicates that
more than 50%  of the stream  resource exhibits poor biotic integrity.  In between these two
extremes of ecoregional condition are two subregions in intermediate  condition—the Piedmont
and Valley ecoregions; both have more than 40% of their stream resource in poor condition for
one of the biological assemblages.
Ecological Region:
Coastal Plain
Piedmont
Valleys
Ridges
North and Central
Appalachians
Western
Appalachians
Summary of
Condition
Relatively Poor
Intermediate
Intermediate
Relatively Good
Relatively Good
Relatively Poor
Biological Assemblage
Most at Risk
(% of stream length in
poor condition)
Macroinvertebrates
(88%)
Macroinvertebrates
(42%)
Macroinvertebrates
(45%)
Fish
(26%)
Fish
(40%)
Algae
(51%)
Primary Stressors*
Excess sediments
Non-native fish
Non-native fish
Nutrients
Non-native fish
Nutrients
Non-native fish
Lack of large wood
Non-native fish
Lack of large wood
Excess sediment
Lack of large wood
    * based on relative extent ofstressor in ecoregion

    We cannot assess relative risk to these assemblages at the ecoregion scale, due to insufficient
numbers of sites, but we can determine which environmental stressors are most common in each
ecoregion. An examination of those stressors found in the greatest extent of the stream resource
should help make decisions about which environmental problems merit the greatest attention in
these subregions:

    •  Ecoregions in relatively poor condition:  The Coastal Plain and Western Appalachian
      ecoregions have a mix of physical and biological habitat indicators as their most common
      stressors. Excess fine sediments are a common stressor in both ecoregions  (54% of
      stream length in the Coastal Plain, 38% in the Western Appalachians); presence of non-
      native fish (Coastal Plain, 55%) and lack of large wood (Western Appalachians, 41%) are
      only slightly less common.
   MID-ATLANTIC FLOWING WATERS ASSESSMENT
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   •   Ecoregions in intermediate condition: The Piedmont and Valley ecoregions share the
       two most common stressors: presence of non-native fish species (69% of the Piedmont
       stream resource,  57% in the Valleys) and nutrients (excessive  phosphorus is found in
       29% of Piedmont stream length, excessive nitrogen is found in 39% of the Valley stream
       resource).

   •   Ecoregions in relatively good condition: The two most common stressors in the Ridge
       and North/Central  Appalachian ecoregions  are  identical:  presence  of non-native fish
       species (47% and 32% of stream length, respectively) and  lack of large woody material
       (25% of the stream resource in both ecoregions).

   An assessment  of the type presented in this Report presents both a  challenge and  an
opportunity to regional managers.  The challenge is to take this report card, examine it in detail,
and decide how best to improve the condition of the region's flowing waters—by focusing on the
assemblages most at risk, the stressors that pose the greatest relative risks to those assemblages,
and the subregions with the greatest problems (or greatest possibilities for protection). The
opportunity is to use this assessment as a  yardstick against which  progress can be measured. If
the regulatory actions, restoration and remediation efforts, and management decisions undertaken
in the  region  are having their intended  effect(s), then  improvements  in ecological condition
should result. It only remains to be seen how effective we can be in improving the condition of
Mid-Atlantic  streams and rivers, given the compass that good data, like those presented in this
Report, can provide.
   MID-ATLANTIC FLOWING WATERS ASSESSMENT                              Page x

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FOREWORD

     This Mid-Atlantic Integrated Assessment (MAIA) "State of the Flowing Waters Report" is
an ecological assessment of non-tidal streams and rivers in the Mid-Atlantic region. It is based
on the combined results of two unique and experimental monitoring  programs implemented
through the U.S. EPA's Environmental Monitoring and Assessment Program  (EMAP) during the
years 1993-98.  We present these results, presented in a way that we hope both environmental
resource managers and the general public find useful, with two major objectives in mind: (1) to
document, in as clear and unbiased  a  manner as possible,  the  overall condition of the  vast
network of flowing waters that drain the Mid-Atlantic region; and (2) to demonstrate the utility
and flexibility of an EMAP-like approach to environmental monitoring at this regional scale.

     The assessment is divided into two major categories.  We  first document the ecological
condition of streams and rivers in the MAIA region, through the use of direct measures of their
resident biological assemblages (fish, macroinvertebrates and algae). We then assess the relative
importance of a long list  of potential stressors on those assemblages, based on direct measures of
their chemical, biological and physical habitat, and human use of the watersheds. We present the
results in this way in order to inform readers about where the major current ecological problems
occur in the region, what the most important threats to the  current ecological condition are, and
how much risk these stressors represent to aquatic ecosystems.

     Our approach in collecting the data for this assessment has two major characteristics. First,
it focuses as much as possible on direct measures of biological indicators, and on the chemical
and physical properties of stream  and rivers that are most likely to have effects on biological
communities.  Second, it uses  an innovative statistical design that insures  that  the results are
representative of the region,  and allows us to extend this statistical certainty in the results to
smaller areas within the  region (e.g., to the major ecological regions within the  MAIA region)
where desired.

     The report is organized into 5 sections and 2 appendices. After a short Introduction to the
assessment, we describe the geographic diversity of the Mid-Atlantic Region and its  streams
and rivers.  In  Section 3 we present the results  of sampling of the Ecological Condition  of
MAIA Flowing Waters,  and  in  Section 4 we expand these results  to include the  relative
importance of Stressors  in MAIA Flowing Waters. Finally, we discuss how stream managers
in the Mid-Atlantic might use the results of this assessment for Geographic Targeting.

     This report is written  for the public, for environmental managers, and for decision-makers.
Much of the technical background for the report has already been published in the scientific
literature, and we include  a list of key  publications in Appendix C at  the back of the report.
Readers who wish to learn more about the design, specific indicators, or other elements of the
assessment are  encouraged to consult this  list and  read the technical papers upon which this
assessment is based.
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     Ml
                                                               0   40   80  120  160.
                                                               |^^^^^^^E=^^^^^B K Icmeters
              Figure 2 The Mid-Atlantic Integrated Assessment (MAIA) region
MID-ATLANTIC FLOWING WATERS ASSESSMENT
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INTRODUCTION

                                      PURPOSE

    The Mid-Atlantic Integrated Assessment (MAIA) Flowing Waters Assessment has a four-
fold purpose:
  1)   Assess and report on the ecological condition of all flowing waters in the Mid-Atlantic
       region.
  2)   Use direct measures of biological assemblages to  describe the ecological condition of
       MAIA streams and rivers.
  3)   Use supplemental measures of chemical, physical and biological habitat to identify and
       rank the relative importance of potential stressors affecting stream and river condition.
  4)   Influence how states design their monitoring programs, how they assess and report on the
       condition of flowing waters.

    Working in partnership with the states (Delaware, Maryland, New Jersey, North Carolina,
Pennsylvania, Virginia, and West Virginia), the U.S. Fish and Wildlife Service (USFWS), U.S.
Geological Survey (USGS), multiple universities, and Environmental Protection Agency (EPA)
Region III, the EPA Environmental Monitoring and Assessment Program (EMAP) assembled
crews in 1993 through 1998 to collect 1050 samples on 850 sites throughout the Mid-Atlantic
region, including both wadeable streams and boatable rivers. All of the crews were trained to use
identical sampling methods to facilitate comparisons across the region. This report explains our
objectives, methods and results.

                      STREAM AND RIVER CONDITION

    Most historic assessments of stream quality have focused on describing the chemical quality
of streams and, occasionally, on sport fisheries impacts. As we have made progress in controlling
chemical problems, it has become obvious that the ultimate concern is actually the health of the
plants and animals that inhabit these streams and rivers.

    In this assessment we have  tried to address this concern not by ignoring physical and
chemical  measurements,  but by  shifting the  focus  to  direct  measurements  of the  biota
themselves. In  this assessment, the  ecological  condition of flowing waters  is defined by
biological  indicators. The biological organisms in a  stream integrate the many physical and
chemical stressors and forces, including other biota (parasites, predators, or competitors), that are
acting  in,  and on,  the stream  ecosystem. Stream and river  condition  can be determined by
assessing appropriate biological indicators (Table 1), or combinations of these indicators called
indices. Information on  the  ecological  condition  of flowing waters  is supplemented by
measurements of  other stream characteristics, especially  those physical, chemical,  or other
biological  factors that might influence or affect stream condition. These stream characteristics
allow us to assess the potential stressors  of stream condition, based on expected signals from
major environmental perturbations (e.g., physical habitat modification, mine drainage, acid rain,
agricultural nutrients, etc.).

   MID-ATLANTIC FLOWING WATERS ASSESSMENT                               Page 3

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                                                Table 1

            Examples of ecological indicators measured in MAIA streams and rivers
  Indicators of Ecological Condition                              Rationale
            Fish assemblages
      Macroinvertebrate assemblages
           Algal assemblages
Important indicators of stream and river condition; respond strongly
to larger-scale disturbances in streams and watersheds, including
channelization and riparian disturbance; middle to upper end of food
web; accumulate contaminants that are then consumed by mammals
and birds. Caution: some smaller streams may naturally lack fish.
Absence offish from small streams cannot be interpreted as an
indicator of poor ecological condition.

Larval stages of macroinvertebrates  (largely aquatic  insects; also
snails and some worms)  are  sensitive to disturbances  to  stream
chemistry and  in-stream  habitat   (particularly  sedimentation).
Because  many  adult  stages  are  mobile,   macroinvertebrate
assemblages are thought to recover rapidly after conditions improve.

Attached algae (largely diatoms) grow on surfaces of rocks and fine
substrates (e.g., sand) and are very sensitive to changes in chemistry
(particularly nutrients and pH) and sedimentation; most species are
cosmopolitan (occur throughout the world) and their environmental
tolerances are therefore well known.
        Indicators of Stress

                Acidity
               Nutrients
            In-stream habitat
            Riparian habitat
                        Rationale

Low values of pH and alkalinity result from both acid rain and acid
mine  drainage;  can be  directly  or  indirectly toxic  (e.g.,  by
mobilizing toxic metals) to  fish and macro-invertebrates; leads to
greatly simplified biological assemblages.

Excess amounts of phosphorus  and nitrogen enter streams from
fertilizer  use and  sewage;  stimulate algal growth and simplify
biological assemblages.

Excess supplies of fine  sediments  from watersheds fill  spaces
between gravels, cobbles  and boulders that are normal habitat for
macroinvertebrates  and  spawning   fish;  sediment  movement
downstream disturbs attached algae.  Large wood (formerly Large
Woody Debris) provides in-stream habitat complexity required for
high biodiversity, and helps to stabilize fine sediments.

Stream bank alteration (removal of trees, shrubs, grasses; erosion of
banks; stabilization of banks) affects shading and habitat complexity
of streams.
The combination of biological and stressor indicators listed in Table 1  represents our best current
understanding of the biological, physical and chemical factors that collectively determine stream
and river quality.  Many of the in-stream  stressors listed have a  direct  impact on  biological
assemblages, and are in turn affected by human use and disturbance of the upstream landscape.
    MID-ATLANTIC FLOWING WATERS ASSESSMENT
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    One of the unique aspects of this assessment is that it uses data from two statistical surveys
(see below) of streams and rivers to describe the condition and characteristics of the population
of flowing waters in the Mid-Atlantic region. It is intended to answer, in as direct and unbiased a
way as possible, the question, "What is the condition of Mid-Atlantic streams and rivers?"

                     REGIONAL STATISTICAL SURVEYS

    In  the past, EPA and  the  states  addressed municipal and industrial point sources of
chemicals as major threats to  streams and rivers. This led to focusing monitoring, assessments,
and controls very locally on individual segments of streams above and below known point source
discharges. Monitoring locations were  selected  to  evaluate the effectiveness   of improved
treatment of these municipal and industrial discharges. As these point sources were cleaned up, it
became apparent that additional stressors were threatening our aquatic resources. Some attempts
were made to aggregate existing data and use them in regional assessments, but the limitations of
this approach became apparent because the local sites were not representative of other flowing
waters or areas in  the region, and consistent sampling and analysis methods were rarely used.
Another approach was needed to assess stream quality on a regional basis.

    EPA and the states, working first on small streams in the Mid-Atlantic Highlands, and later
expanding to both  rivers  and  streams throughout the Mid-Atlantic region, wrestled with these
problems and  came up with  a different approach for stream/river monitoring. In addition to
implementing direct measures of the ecological condition of the biota themselves, they devised a
way to  pick monitoring  locations  that do not  focus on known problem areas  (e.g., sewage
outfalls). Instead,  monitoring sites were chosen through  a statistical approach that provides, in
aggregate, a clear and objective view of the condition of all flowing waters. It is hoped that this
approach,  and  this  assessment, can  serve as models for  future  National  Water  Quality
Inventories. These biennial reports (also known as 305[b] reports, after the section of the Act that
mandates them), to Congress  are required by the Clean Water Act, and are often  criticized for
their lack of objectivity.

    During the years 1993 and 1994, EPA researchers used sample survey techniques to identify
representative small streams (1st through 3rd order) throughout the upland portions of the Mid-
Atlantic region. The biological, chemical and physical habitat sampling of those  streams resulted
in the Mid-Atlantic Highlands Streams Assessment (see Appendix C),  the first comprehensive
assessment of the  ecological condition of streams in any region  using both statistical  site
selection and biological indicators. Work in the Highlands (referred to as MAHA) continued in
1995 and 1996, and those  additional data are used in this report.

    In 1997 and 1998, data collection was expanded to all non-tidal streams of the Mid-Atlantic
region (Figures 2 and 3), and for the first time the unique aspects of EMAP sampling (biological
indicators  and statistical design) were extended  to include large (non-tidal) rivers. This larger-
scale project was known  as MAIA. A major emphasis in MAIA was to extend the sampling
methods developed for wadeable streams in MAHA to the large rivers  included in MAIA.  The
result is a set of sampling protocols, all based on identical principles  and producing identical
information, for all sizes of flowing waters (see Lazorchak references in Appendix C).
   MID-ATLANTIC FLOWING WATERS ASSESSMENT                              Page 5

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                    Ecoregions
                    d Ridge
                      alley
                    D Western Appalachians
                    I I North - Central Appalachians
                    C] Piedmont
                    O Coastal Plain
       Figure 3. The MAIA region with sampling sites on small upland streams (open circles,
       sampled as part of the MAHA project), small regional streams (grey circles, sampled as part
       of MAIA) and large rivers (black circles, MAIA).

     Because of the unique statistical properties of the EMAP sample  surveys, we are able to
combine results from both MAHA  and MAIA in this  assessment,  and  produce  unbiased
estimates of the condition of all  flowing waters in the Mid-Atlantic region for the period from
1993 to 1998. In total, the MAHA and MAIA projects collected 1050 samples on 850 sites in the
region. These data are used to estimate such regional characteristics as the proportion of stream
miles that are impaired or degraded biologically, the relative importance of potential stressors
(such as mine  drainage or stream sedimentation) in the region, and the relative risk that these
stressors pose to biological assemblages.

     A statistical survey of flowing waters operates in the same manner as the public opinion
polls used  to project winners and losers of political  elections. A sample  of stream reaches is
selected at random to represent the population of flowing waters in a region, just as the sample of
individuals  in a public opinion  poll is selected to represent the voting population as a whole.
Regional  statistical surveys  have been used for many  years in  forestry and agricultural
monitoring programs to determine the condition of forests and agricultural lands, but their use in
assessments of aquatic ecosystems is just  beginning. Additional  information  on the EMAP
stream design can be found in the references listed in Appendix C.
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    One of the advantages of a regional statistical survey is that, for any estimate of stream and
river condition (e.g., the proportion of stream length in degraded condition), we can also estimate
"confidence intervals"  around  the estimate.  Confidence intervals are measures of uncertainty,
and are exactly analogous to the  "margins of error" that accompany public opinion polls (e.g.,
Candidate A leads Candidate B by 10%, with a margin of error of ± 4%—meaning that the true
lead is somewhere between 6% and 14%). These margins of error are smaller when we use larger
sample sizes (e.g., the number of people taking  part in a poll, or the number of flowing waters
sampled), and are smaller when our population estimates are near one of the extremes (e.g., near
1% or 99%). The greatest uncertainty occurs when the sample size is small (e.g., fewer than 50
sites)  and the population estimate is near 50%—analogous  to a dead heat in a political  poll.
Because the number of sites sampled in MAHA and MAIA varies with different indicators (the
largest number of sites have chemical data; the smallest number of sites have fish data) and the
regions or sub-regions  assessed (e.g., the MAIA region as a whole has the highest number of
sites;  the Coastal Plain ecoregion has the lowest number), the confidence intervals are slightly
different for each estimate of condition that we present. Rather than cluttering the report with
hundreds of confidence intervals, we have chosen to present  a single, general "margin of error"
for each  indicator and each subregion assessed. Each estimated margin of error is the  90%
confidence interval calculated  from  the actual sample size for  each estimate, but assuming a
population estimate of 50%  across the board. Readers of this report may want to keep these
confidence intervals in mind as they contemplate the results (e.g. given a margin of error of plus
or minus 15%, are apparent differences  between subregions significant?).


THE  MID-ATLANTIC REGION
                                  BACKGROUND

    The Mid-Atlantic region  encompasses approximately 180,000 square miles and extends
from the Atlantic Ocean in the east to the Ohio River in the west, and from the headwaters of the
Delaware and Susquehanna drainages in New York in the north to the Neuse River drainage in
North Carolina in the south (Figure 2). It includes all of EPA's Region III, all of the states of
Delaware, Maryland, Pennsylvania, Virginia and West Virginia, and parts of New Jersey, New
York and North Carolina.
                                                 The Mid-Atlantic region is a diverse
                                             place with dramatic changes  in geology,
                                              elevation, climate, vegetation, land cover
                                              and demographics.  These characteristics
                                              work  together  to  create  interesting
                                             patterns  in the landscape. It is helpful to
                                              consider  these patterns,  because  they
                                             provide   a  context  to   discuss   and
                                              understand the health  of the region's
                                              rivers and streams.

                                                  To the east, the low-lying, flat Coastal
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Plain is characterized by many shallow inland bays and meandering tidal rivers.  Chesapeake
Bay, the nation's largest estuary,  dominates the landscape  and provides both commercial and
recreational opportunities to millions of people. Agriculture is the dominant land cover on the
Delmarva peninsula and the eastern shore of Maryland. This area has the smallest amounts of
forested land cover in the region.

     Most of the people in  the Mid-Atlantic region live  in  the urban corridor between the
District of Columbia and Philadelphia, and in the Pittsburgh area. Population growth is highest in
the Coastal Plain, near the ocean and the estuaries; growth is flat or negative in the western areas
of the region.  Historically,  people  have settled where rich farmland and navigable rivers offer
abundant food and easy transportation. Philadelphia is located on the Delaware River; Harrisburg
on the  Susquehanna  River;  Pittsburgh  on the Ohio,  Allegheny and Monongahela  Rivers;
Baltimore on the Patapsco River; Washington,  D.C. on the Potomac River; Richmond on the
James River; and Norfolk directly on the Chesapeake Bay.

     As one travels west across the region, the low, rolling hills of the Piedmont appear. These
hills are like stair steps leading to the Blue Ridge and the Appalachian Mountains farther west.
The  Blue Ridge Mountains form the first barrier to the western  landscape. They  appear as a
sharp, forested ridge.  Once beyond that ridge, the Great Valley of the Shenandoah opens up.
Farmland once again dominates the landscape. These fertile soils have been farmed for centuries.

     Continuing westward, the Appalachian Ridge and Valley province appears,  with sharp-
crested ridges  running from northeast to southwest in clean parallel lines like long waves on an
ocean. These  ridges were  formed by the folding of the landscape,  and the  road cuts offer
excellent opportunities to view the deformed layers of sedimentary rocks. As one might expect,
the ridges of this region  remain largely forested. The slopes are steep, the soils are thin, and they
are not ideal for either  farming or urban development. The valleys of the  Ridge and  Valley
Province are intensively farmed. The landscape is fairly flat in the valleys, and the soil is deep
and fertile.

     Farther to the  west and south, the Allegheny
Escarpment rises abruptly.  At the  top  of this
escarpment, the  layers  of sedimentary  rock  lie
relatively   flat  and  undisturbed.   This  is  the
Allegheny Plateau. Unlike the long, broad, parallel
valleys and ridges to the east, the creeks and rivers
here  dissect the flat plateau to  form deep and
twisting  gorges.  The  valley bottoms  are much
narrower than those to the east.
     The largest tracts of forest  in  the  Region are found  on the Plateau,  to  the  north  in
Pennsylvania, and to the south in West Virginia. Some of these forests are the largest tracts  of
public land in  the  region and offer  significant recreational  opportunities to hikers, hunters,
fisherman, and  others. In the Mid-Atlantic region, many of these forested areas remain forested
because they have  steep slopes  with  poor soils that are unsuitable for agriculture and urban


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development. These characteristics make the areas more susceptible to the effects of acid rain.
Portions of the Allegheny Plateau and Ridges are particularly sensitive to acid rain.

     The Western  Allegheny  Plateau  and Central Appalachians  are  made  up  of  bedrock
containing significant amounts of coal. Bituminous coal fields, where high sulfur coal is found,
are found primarily  in  the  West—western  Maryland, western  Virginia, Pennsylvania  and
northern  West Virginia—and can cause significant acid mine drainage problems when mined.
Lower sulfur, cleaner burning coal is found farther south in southern West Virginia. Much of the
mining activity in recent years  has shifted south to  extract the lower sulfur coal as a result of
tightening clean air regulations. This coal  is often mined by the "valley fill"  process which
removes whole mountain tops to reach the coal-bearing strata, and fills adjacent river valley with
spoils. Nearly all of the anthracite coal  in the United States is found in eastern Pennsylvania.
Anthracite coal is found folded  in discrete layers between layers of sandstone, and results from
the great deformation and movement of rock that produced the Allegheny mountains.

     These regional patterns provide  important context for understanding the health of rivers
and streams at a broad regional scale. Streams in the valleys and on the Delmarva Peninsula,
with  intense  agricultural  land use, might  have  higher  nutrient,  pesticide  and  bacteria
concentrations and problems with sedimentation. Streams and rivers  in the highly urbanized
areas might be impaired by point source and storm water runoff. Streams on the  forested ridges
and in the low-lying southern Piedmont and Coastal Plain areas that have naturally low buffering
capacity  might be impaired by  acid rain. Streams in the coal mining areas of the region might
suffer from acid mine drainage, increased metals and sediment, and larger scale habitat impacts
that result from mining.  These patterns only indicate the  potential  impacts and stressors.  We
must take a step further and consider data on stream ecological health, water quality and physical
habitat quality to determine whether actual impacts exist.

                              ECOLOGICAL REGIONS

    Ecological regions (or ecoregions) are areas that have similar soils, vegetation, climate, and
physical  geography. An ecoregion perspective highlights the differences, for example, between
mountain areas with their steep slopes, shallow soils, and cooler climate, and valley areas that are
relatively flat, have deep  soils, and warmer temperatures; ecoregions permit us to have different
expectations of flowing waters in these very different areas. An ecoregion perspective also helps
us understand why streams  respond  to various  human  disturbances as they  do and which
management  solutions might be  applicable.  Ecoregional  differences play a  major role in
determining  which  flowing waters have been  affected  by, or are susceptible to, different
stressors. Management practices within  an  ecoregion typically are applicable for many of the
flowing waters with similar problems because the characteristics of the streams in the ecoregion
are similar.

    Ecoregions have been developed at many different scales for the entire U.S.,  and for smaller
regions like the Mid-Atlantic. For the purposes of this assessment, we have combined various
levels of ecological  regions into the six ecoregions described in the next section. We feel these
ecoregions do a good job of capturing the intra-regional variability of the Mid-Atlantic. They
include the:  (1) Coastal  Plain;  (2) Piedmont;  (3) Valleys; (4) Ridges; (5) North and Central
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Appalachians;  and  (6) Western Appalachians  (Figure 4).  A more complete  description of
ecoregions can be found in the references of Omernik and Woods in Appendix C.
       Ecoregions
       CH Ridge
       n Valley
       CH Western Appalachians
       CH North - Central Appalachians
       I  I Piedmont
       CH CoastafPlain
       Figure 4. Ecological regions (ecoregions) of the Mid-Atlantic region. Ecoregions are areas
       with similar physical geography, soils, climate and vegetation types. We use six aggregated
       ecoregions to classify and assess stream sites in this report.
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COASTAL PLAIN ECOREGION
                                               For the  purposes  of this assessment, the
                                               "Coastal Plain" comprises both the Middle
                                               Atlantic  Coastal Plain  ecoregion and the
                                               Southeastern Plain ecoregion. It consists of
                                               low  elevation  flat  plains,  with   many
                                               swamps, marshes, and estuaries to the east,
                                               and  a  mosaic   of  cropland,  pasture,
                                               woodland,   and forest  to  the  west.  It
                                               contains many of the urban centers of the
                                               Mid-Atlantic region, including Washington
                                               D.C.,  Baltimore and  Richmond.  Forest
                                               cover  in  the  region   is  predominantly
                                               longleaf and  shortleaf  pine, with smaller
areas of oak, hickory, gum, and cypress near major streams. Poorly drained soils are common.
Elevations and relief are generally less than in much of the Piedmont. Streams in this area are
relatively low-gradient and sandy-bottomed.

PIEDMONT ECOREGION

    The "Piedmont" (for  the  purposes  of this
assessment)   consists  of  both  the Piedmont
ecoregion proper,  and  the Northern Piedmont
ecoregion—physiographers  consider  it the non-
mountainous portion of  the  old  Appalachian
highlands. It comprises a transitional area between
the  mostly  mountainous   ecoregions   of  the
Appalachians to the  northwest and the relatively
flat Coastal Plain to the southeast. It is a complex
mosaic of metamorphic, igneous and  sedimentary
rocks, with  finer-textured  soils  than in  Coastal
Plain. Once  largely cultivated,  much  of  this  region has reverted  to pine and  hardwood
woodlands, and more recently has seen increasing conversion to urban and suburban landuse.

                            VALLEY ECOREGION

                            The Valley  ecoregion,  including  the "Great Valley,"  extends
                            from eastern Pennsylvania southwesterly through southwestern
                            Virginia.  The  valleys  generally  fall  into two types,  those
                            underlain by limestone  and those  with shale. The nutrient rich
                            limestone  valleys  contain  productive  agricultural  land.  By
                            contrast, the shale valleys are  generally less productive, more
                            irregular, and have greater densities of flowing waters. Most of
                            the streams in the limestone valleys are colder and flow all year,
                            whereas  those  in the shale valleys tend to lack  flow  in dry
                            periods. Dense  concentrations of poultry operations can be found
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in many parts of the valleys. Many of the flowing waters in this report are located in the Valley
ecoregion, but drain watersheds that extend  onto  the Ridges. Most ecological classifications
combine the Valleys and Ridges into a single ecoregion.

RIDGE ECOREGION

The Ridge and Blue Ridge ecoregion is a
series of linear mountainous ridges, with
elevations from  approximately 1,000 feet
to  5,700 feet,  running  between  lower
elevation  valleys. This  mostly  forested
ecoregion contains  high gradient,  cool,
clear   streams   occurring   over  mostly
sandstone   and    shale   bottoms.  The
ecoregion has no  major urban areas and
has a  low population density. However,
due in large part to the close proximity of
metropolitan areas in the Coastal Plain and
Piedmont regions to the east, recreational development in the region has increased considerably
in recent years.

NORTH AND CENTRAL APPALACHIAN ECOREGION

                                               The  North  and  Central  Appalachians  in
                                               northern  and  central  Pennsylvania   and
                                               central  West Virginia are a vast elevated
                                               plateau of high hills, open valleys, and low
                                               mountains  with  sandstone,  siltstone,  and
                                               shale   geology,   and   coal  deposits.  The
                                               northern  and  eastern  portions  of  this
                                               ecoregion are the only glaciated areas in this
                                               Report. Much  of the eastern  part  of the
                                               ecoregion is farmed and in pasture, with hay
                                               and grain for dairy cattle being the principal
                                               crops.  There also are large areas in oak and
northern hardwood forests. Land use activities are generally tied to forestry and recreation, but
some coal and gas extraction occurs in the northwestern part of the region.

    The southern part of the ecoregion  in  West Virginia is  primarily a forested plateau
composed of sandstone  and shale  geology  and coal deposits.  Due to the rugged terrain, cool
climate, and infertile soils, this area is more forested and contains much less agriculture than the
Valley and Western Appalachian ecoregions. Coal mining is a major industry in this part of the
region. Acid mine drainage and stream sedimentation associated with coal mining are possible
stream impacts.
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WESTERN APPALACHIAN ECOREGION
     The Western Appalachian ecoregion runs
from western Pennsylvania into western West
Virginia. The hilly and wooded terrain of this
ecoregion is less rugged and not as forested as
the ecoregions to the east (North and Central
Appalachians). Much of this region has been
mined for bituminous coal. Once covered by a
maple-beech-birch forest,  this region is  now
largely  in  farms,  many of which are dairy
operations. This  ecoregion is characterized by
low rounded hills, low gradient  streams and
extensive areas of wetlands.
                                    STREAM SIZE

    Along with ecoregional differences, and differing amounts of human disturbance, potential
stream condition is strongly affected by stream size. In order to standardize the concept of stream
size when comparing streams across large areas, stream sizes are often broken up into Strahler
orders (Figure 5). This is a convenient, and consistent, approach to classifying streams according
to size, with headwater streams (throughout the world) being classified as first order, and larger
orders referring to larger  streams. For the EMAP data collection effort In the Mid-Atlantic,
where 1:100,000 scale U.S.G.S. maps were used to specify the stream network, the largest rivers
are eighth order.
       Figure 5. Stream sizes  are  categorized by Strahler orders, demonstrated here  for a
       hypothetical watershed in the Mid-Atlantic. The  confluence (joining) of two 1s*  order
       streams forms a 2nd order stream; the confluence of two 2nd order streams forms a 3rd order
       stream, etc.
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     The  size  (or order) of a stream not  only affects its natural  characteristics, but also its
capacity to handle both point source and non-point  source pollutants (Figure 6). Stream size
frequently affects the size and type of biotic community present, particularly for fish, and may
control the relative importance of factors to which the biota respond. Very small streams (first-
order,  headwater streams) are often  quite  clear and shaded by trees;  they are likely to be
dominated by aquatic insects in the stream bottom and with small fish that feed on these bottom
organisms. Large streams (sixth-  to seventh-order rivers)  are often muddy with canopy cover
only along the banks, and are dominated by larger fish that are  omnivorous (feeding on plants
and animals) and/or piscivorous (feeding on smaller fish).
                                                           shredders
                      1 I-
                         wZ. IM^K.     w~x}
                         ^^^ ^^^^^t^    ^r i  *
                                   peri phy ton  I
                                  •     .»•- i.4"
                     10
                     11
                     12
collectors
                          smallmouth
                          bass
                                                                       shredders
                                                                      predators
                               vascular
                               hydrophytes
                        _ catfish
       *» J&{
    b^.;. -/  V
   -^ • p-  predators

   L     /
                                    Relative Channel Width
       Figure 6. Stream characteristics change as the size or order of the stream increases. Smaller
       streams (1s* through 3rd order) dominate in the region. This "State of the Flowing Waters
       Assessment" includes sites throughout the range of stream orders illustrated.
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     Small, first-order streams are the dominant stream class in the Mid-Atlantic region and
throughout the world; over 125,000 stream kilometers (i.e., almost 60% of the total length) are
classified as first-order streams (Figure 7). Second-order streams are larger and start at the point
where two first-order streams come together. Over 35,000  kilometers of streams in the Mid-
Atlantic (i.e., 17%) are second-order streams. Almost 90% (199,000 km) of flowing waters in the
region are small first- through third-order streams. Because small streams contribute most of the
stream length, their condition has a dominant effect on any assessment that presents its results on
the basis of stream length (like this one, and the National Water Quality Inventories required by
the Clean Water Act).

     Historically, management practices have focused on large streams, which are best known to
the public  due to their use  in navigation and boating, and their  visibility  from major road
crossings. Small streams, on the other hand, dominate the total stream  length in the region,
contribute  to  the  quality  and condition of larger streams and rivers, and are  critical  to
determining the condition of all flowing waters in the Mid-Atlantic.

     The stream network used for selecting sampling sites in this assessment, and for estimating
the total length of flowing waters in the region, was the EPA River Reach File, Version 3. This
digital database includes all flowing waters that are represented on USGS maps at a scale of
1:100,000.  The map  scale used is important because it affects the estimate of stream length and
stream order.  The stream  network shown on 1:100,000  scale  maps was  considered  a good
representation of the population of Mid-Atlantic flowing waters—official estimates  of stream
length (e.g., in each state) by EPA's Office of Water are based on this map  scale.

                                    Total Stream Length (km)
                        0      25000    50000    75000    100000   125000
                                10      20      30      40      50
                                    Percent of Stream Length
       Figure 7. Lengths of streams (both in km and as a percentage of the total) in different stream
       orders in the Mid-Atlantic region. Almost 90% of the region's stream length is in small first-
       through third-order streams. Large rivers (fifth- through eighth-order) make up about 5%
       of the total length of flowing waters.
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ECOLOGICAL CONDITION
    To assess the overall condition of MAIA flowing waters, we looked at multiple biological,
chemical  and physical habitat indicators.  To answer  the  specific  question "What  is the
ecological condition of Mid-Atlantic streams and rivers? " we rely on direct measures of the
biological communities that inhabit the streams and  rivers. Throughout this report, ecological
condition—good, marginal, or poor—is determined by biological indicator or index scores. The
fish, algae, aquatic insects, and other animals and plants in a stream serve as "integrators" of the
multiple stressors to which they are  exposed. The biota respond to the cumulative effects  of
chemical  contaminants, modification  of their physical habitat, and changes in both the amount
and the timing of the flow of water.
                       Game and Non-Game Fish
Non-Game
 Fish Only
 No
Fish
                      0    20000  40000  60000   80000  100000  120000
                                 Total Stream Length (km)

       Figure 8. Distribution of flowing waters with game and non-game fish, non-game fish alone,
       and no fish, across the range of stream orders in the Mid-Atlantic. Small streams, especially
       first-order streams, are a very important resource for both game and non-game fish species.

    Historically, game fish have been the primary biotic component of interest to the public, and
an emphasis has been placed on the condition of game fisheries in larger rivers. This emphasis
on game fish and large rivers has resulted in a narrow, incomplete view of the status  of Mid-
Atlantic flowing waters, where  large rivers make up only about 5% of the total stream length.
Some people have defended this large river/game fish perspective by claiming that small streams
do not support fish.  While it is true that a much larger proportion of small streams lack fish than
larger streams, small streams are nonetheless an important resource for fish (Figure 8). There are
more  than  120,000 kilometers  of  streams in the Mid-Atlantic with  game fish, roughly half
(58,000 km) are first-order streams, while only 9% (10,600 km) are fifth-order and larger rivers.
If both game fish and non-game fish are considered, 54% of the stream length with fish present is
in first-order streams, and 6% in fifth-order and larger rivers (of course, a conclusion based on
water volume would be much different).
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    By  sampling  multiple  biological  assemblages (fish,  macroinvertebrates  and  algae)
throughout the Mid-Atlantic, we have the opportunity to move beyond a narrow, game fisheries
focus,  and look instead at the biological integrity of stream and river  ecosystems.   Biotic
integrity has been defined by Jim Karr (a leading proponent of the concept) as, "the ability to
support and maintain a balanced, integrated, and adaptive community of organisms having a
species composition,  diversity  and functional  organization comparable  to  those  of natural
habitats within a region." Most people would  agree that maintaining the biotic  integrity of
flowing waters—also a stipulation of the Clean Water Act—is a laudable goal.  This assessment
is one of the first steps toward achieving that goal.

                               FISH ASSEMBLAGES

    Streams and rivers must meet a number of requirements if they are to support healthy fish
assemblages—providing a sufficient variety of foods and  spawning areas, and a habitat with
diverse forms offish cover, among others. The fish data collected in MAHA and MAIA include
a list of the species found at each site, and a measure of their relative abundances. These  data
allow us  to calculate a  number of characteristics, or metrics, for the fish assemblages—for
example,  the total number of species, the number of native species, the number and proportion of
pollution tolerant and intolerant species, etc. The best  of these metrics (i.e., those that are
repeatable, responsive to human  disturbance), and that contain the most information about the
health  of the fish assemblages) have been combined into an overall Index of Biotic Integrity
(IBI), whose values range from 0 to 100 (more information on the fish IBI is listed in Appendix
A). Our assessments of ecological condition (i.e., for fish, macroinvertebrates  and algae) are all
based on similarly constructed IBIs.

    The  critical step in the process of developing a  fish IBI is the setting of expectations for
each metric used (e.g., How  many  native species do we expect to find? How many benthic
species? How many intolerant species?), and for the  final IBI. When dealing with  a region as
large and diverse as the  Mid-Atlantic, the setting of expectations takes on  a critical role in
determining the validity of our assessment. We need to know if the expected  number of native
species, for example, changes as we move from one ecoregion to another (it does), or from small
streams to large streams (as it also does). In order to set expectations, EMAP relies on estimates
of reference condition (see box). Conceptually, the idea of a reference condition  for flowing
waters  is simple—it is the condition of streams  (and  particularly their biota) in the absence of
significant human  alteration or  degradation. In  practice, the concept of reference  condition
becomes  much more muddy—how much human alteration is "significant", is it equivalent to
"pristine"  condition, what do we do in areas where  all  streams have been degraded to some
degree—and numerous methods  have been developed to estimate it. For this assessment, we
have chosen to use  a reference site approach, where the  least disturbed sites in each  ecoregion
(and across a range of stream sizes) were sampled and their data used as estimates of reference
condition. Alternative approaches include the use of historical  data  (where available),  best
professional judgment, and models.
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                                       What is Reference Condition?

    The concept of establishing reference conditions is relatively simple—we want to know what sorts of conditions
we would find in  streams and rivers in the absence of any significant human disturbance.  In practice, reference
condition is much  more complicated. There exist multiple definitions of the term "reference  condition" - each has
merit and each  has  some historical precedent.  For example, each  of following  categories (and definitions)  of
reference condition are being used in various monitoring and assessment programs today:

    Minimally Disturbed Condition  (MDC) - this  term describes the condition of streams  in the  absence  of
significant human disturbance, and is probably the best approximation or estimate of biotic integrity. One important
aspect of MDC is the recognition that some natural variability in indicators will always occur, and this needs to  be
taken into account when describing MDC. Long-term  climatic, geologic and ecological fluctuations will inevitably
change the characteristics of individual sites,  but the  regional range of MDC should be nearly invariant, and  its
distribution can serve as an anchor by which to judge current condition. It may serve as a benchmark against which
all other definitions of reference condition can be compared.
    Least Disturbed Condition (LDC) - this condition is found in conjunction with the best available physical,
chemical and biological habitat conditions given today's state of the landscape. It is ideally defined by a set of explicit
criteria to which all reference sites must adhere. These criteria will vary from region to region, and are developed
iteratively with the goal of establishing the minimum amount of ambient human disturbance in the region under study.
The specifics of these criteria will vary across ecoregions, as ecological characteristics of the landscape, and human use
of the landscape, vary. Because the condition of the environment changes over time, as either degradation or restoration
proceeds, LDC may vary with time. As the ecological condition of the very best available sites changes through time, so
will our measure of LDC.
    Best Attainable Condition BAG) - this is equivalent to the expected ecological condition of least disturbed sites if
the best possible management practices were in use for  some period of time. Sites in BAG would be places where the
impact on biota of inevitable land use is minimized. This is a somewhat theoretical condition predicted by the
convergence of management goals, best available technology, prevailing use of the landscape, and public commitment
to achieving environmental goals. The upper and lower limits on BAG are set by the definitions of MDC and LDC
respectively (Figure 2). It is unlikely that it will ever be "better" than MDC, nor "worse" than LDC, but may be
equivalent to either, depending on the prevailing level of human disturbance in a region. As is the case with LDC, BAG
is not invariant, because all of the factors influencing it  (e.g., available technology, public commitment) will vary over
time.
    Ideally, we would like to know how our estimates of stream condition would change if we were to adopt each of
these  alternative views  of reference  condition, but  this is often not  possible.  The lack of historical data for any
biological assemblage other than fish makes the estimation of historical condition, and therefore any estimation  of
Minimally Disturbed Condition, very  difficult. Estimates of Best Attainable Condition cannot currently be made with
real data—they rely  on best professional judgment—and are therefore open to criticisms  about their validity and
potential for bias.
    The Environmental Monitoring and Assessment  Program (EMAP) approach to reference condition (used in this
assessment) is to rely on the "Least Disturbed  Condition" definition, and to  use data from sites that meet the least-
disturbed criteria to estimate  reference condition. As we adopt  this definition, we need also to recognize that the
"Least Disturbed Condition," in today's world, may be considerably disturbed.
    One important aspect of  the EMAP  approach is that the reference state (i.e., whether an individual  site is  in
reference condition)  is defined by the  condition of the physical,  chemical  and biological habitat, and not by the
biological assemblages themselves. This avoids some of the circularity (e.g., using biological data to define reference
sites for  use in  interpreting  those same biological data) that can permeate the  process  of estimating reference
condition. Once the sub-population of sites that meet pre-identified criteria is identified, then the biological metric or
ecological index scores measured at those  sites can be  used  to define the  distribution of biological reference
conditions for the region (see "Setting Expectations" box, and Appendix A).
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     In the Mid-Atlantic region as a whole, 21% of the total stream length would be considered
to have fish assemblages in good condition  (Figure 9) that is, their IBI scores indicate biotic
integrity similar to the upper 75% of reference sites. A larger proportion of stream length, 31%,
has  fish assemblages in poor condition,  and  the  largest proportion, 42%, are in  marginal
condition.   Importantly, we could  not calculate IBI scores for about  6%  of the Mid-Atlantic
stream length, because all of these streams drain very small watersheds (i.e., less than two square
kilometers) and contained too few fish when sampled. Because of their small size, we are unable
to determine whether the low numbers offish is due to anthropogenic or natural causes, and they
are left out of the estimates of stream condition based on fish (Figure 9).
  MAIA  Region Overall
     margin of error ± 5%
                                            ....?•	-&--<,
                                                                                Nortii-Convat
                                                                                Appalachians
                                                                                 Piedmont

                                                                              margin of err or ±
    Fish Biotic  Integrity
    • Good
    O Marginal
    • Poor
    O Insufficient data
       Figure 9. Fish IBI scores in Mid-Atlantic flowing waters, and the proportion of the total
       stream length in good, marginal and poor condition. Red, yellow and green markers on the
       map indicate the locations of individual sites that contribute to the estimates  of stream
       length in each condition. About 31% of the Mid-Atlantic stream length has fish assemblages
       in poor  condition. Roughly 6%  of stream sites had  few or no fish, but were  located in
       watersheds too small for us to determine reliably whether they should be expected to have
       fish. Of the six ecological regions, the Coastal Plain ecoregion has the highest proportions of
       stream length in poor condition (44%).
    MID-ATLANTIC FLOWING WATERS ASSESSMENT
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     Not surprisingly, sites with poor biotic integrity for fish are not evenly distributed in the six
ecoregions of the Mid-Atlantic (Figure 9). The Coastal Plain has the highest proportion in poor
condition (44%),  followed  by the North and Central Appalachians  (40%)  and the Valley
ecoregion (33%). The Piedmont ecoregion has a relatively small proportion of stream length in
poor condition (20%), and almost 80% in either good or marginal condition. The ecoregion with
the largest proportion in good condition is the Ridge ecoregion—more than two-thirds (67%) of
stream length in the Ridge ecoregion has fish assemblages in either good or marginal condition.
The two coal mining regions (North and Central Appalachians, and Western Appalachians) had
the smallest proportion of stream  length in the combined good/marginal classes (53% and 58%,
respectively).


                         Setting Expectations for Ecological Condition

      How do we use reference sites (once they are identified) to help set our expectations for biology?
   To help explain this process, it is useful to employ a familiar analogy. Suppose that you wanted to use
   human body temperature as an indicator of human health (as is commonly done). One of the first
   things you would need is information on the normal range of temperatures. In order to estimate this
   range, or distribution, you might draw a subsample of the human population that is considered
   'healthy.' The range of temperatures measured in this subsample is an estimate of reference condition
   for this indicator. Next, we'd want to know how far away from this distribution (or how extreme) a
   temperature needs to be before we'd consider it to be unhealthy. In the case of body temperature, we
   might have very high confidence that we've  correctly identified a healthy subpopulation, and the
   range  of temperatures might be fairly small. In this case, we could use something like the ends or
   extreme  values from the reference distribution (e.g., the lowest  1% or the highest 1% of body
   temperatures  measured  from a large  group of people),  as thresholds beyond which we identify a
   temperature as unhealthy.
      We use a similar approach  for the biological data we report for the Mid-Atlantic region—
   identifying a healthy subsample of sites (i.e., reference sites), collecting indicator information on each
   one, and describing a distribution of reference condition values. But we have less confidence that all
   of the sites we identify as 'healthy' truly are. We can't know to what extent we've missed unknown
   or unobserved stressors to ecological condition, or the degree to which small amounts of degradation
   at our reference sites influence the distribution of metric and index scores.
      For this reason, we use more  conservative thresholds than we  used in the body temperature
   example. Commonly, the 25th percentile value (of the reference distribution) is used as a threshold
                                                                                        st
   between sites  in good condition, and those in fair or marginal condition. We also adopt the 1
   percentile as the threshold between sites in marginal condition and those in poor condition. For these
   sites, we can  be  99% confident that their biotic  integrity is lower than  anything found in our
   subsample of  sites in least disturbed condition (more information on setting expectations can be
   found in Appendix A).

                   MACROEVVERTEBRATE ASSEMBLAGES

     An additional  picture of stream and river condition can be derived from examining the
macroinvertebrates  (aquatic insects,  snails, worms and other benthic invertebrates) in  streams
and rivers. These animals provide food for fish and other wildlife, and serve as a link between
the algae and higher levels of the ecological food web. Macroinvertebrates are considered to be
very good indicators of chemical stresses (e.g., acidity) as well as excess inputs of fine sediment
from local landuse.

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     We use an approach  identical to that for fish to develop an Index of Biotic Integrity for
macroinvertebrates—finding metrics  or characteristics (e.g., the number of mayfly species, the
number of caddis fly species, the pollution tolerance of the species) of the assemblages that are
repeatable, responsive to human disturbance), and that contain the most information about the
health of the assemblage, and combining them into a single IBI score. And as with fish, we use
reference sites to set expectations for the  individual metrics and the IBI  itself (more information
in Appendix A).
  MAIA Region  Overall
     margin of error ± 5%
44% i     Bailey

    margin of error ± 8%
                                                                               North-Central
                                                                               Appalachians
                       h«r V *.  "
                       iS0*. /°  V.
                                                                                Pi&dmont

                                                                             margin of error ± 14%
    Macromvertebrate
     Biotic  Integrity
        • Good
        O Marginal
        • Poor
       Figure 10. Macromvertebrate IBI scores in Mid-Atlantic flowing waters, and the proportion
       of the total stream length in good, marginal and poor condition. Red, yellow and green
       markers on the map indicate the locations of individual sites that contribute to the estimates
       of stream  length  in each condition. About  41%  of the  Mid-Atlantic stream length has
       macroinvertebrate assemblages in poor condition. The Coastal Plain ecoregion  has the
       highest proportion of stream length in poor condition for  macroinvertebrates (88%), while
       the Ridge ecoregion has the highest proportion in good condition (49%).

    For the Mid-Atlantic region as a whole, 26% of the stream length was in good condition
with respect to macroinvertebrate assemblages (Figure 10).  More than 41% of the stream length
had poor macroinvertebrate integrity, and 33% of the stream length was in marginal condition.
    MID-ATLANTIC FLOWING WATERS ASSESSMENT
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     There is  a more uneven distribution of macroinvertebrate IBI  scores across Mid-Atlantic
ecoregions than was the case for fish (Figure 10).  Both the Coastal Plain (88%) and  Western
Appalachian (46%) ecoregions  have relatively  large  proportions  of stream  length  in  poor
condition (and only 0% and 13% in good condition,  respectively). The ecoregions with the
highest biotic integrity for macroinvertebrates are the Ridge ecoregion (nearly 80% in good or
marginal  condition) and the North  and  Central Appalachians  (more than  72% in  good or
marginal condition).
                                                                                  Ridge

                                                                             margin of err or ± 11%
  MAIA Region  Overall
     margin of error ± 6%
                                                         Valley

                                                    margin of error ± 14%
                                cfco  %    •_••	.£-/
                                                                               North-Central
                                                                               Appalachians
                                                                                 Western
                                                                               Appalachians
V.  .V  ».°   *   \J  '
/v*v* „:        -iM
                                                                                Piedmont

                                                                             margin of error ± 3^%
          Algal
     Biotic  Integrity
        • Good
        O Marginal
          Poor
       Figure 11. Algal IBI scores in Mid-Atlantic flowing waters, and the proportion of the total
       stream length in good, marginal and poor condition. Red, yellow and green markers on the
       map indicate the  locations of individual sites that contribute to the estimates of stream
       length in each condition. About  30% of the Mid-Atlantic stream length has  algal
       assemblages in poor  condition. The  Western  Appalachian ecoregion has  the highest
       proportion of stream length in poor condition for attached algae (51%), while the North and
       Central Appalachians have the highest proportion in good condition (45%).
   MID-ATLANTIC FLOWING WATERS ASSESSMENT
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                             ALGAL ASSEMBLAGES

    Attached algae in streams grow on surfaces such as rocks, submerged wood, and  on
individual grains of sand and gravel. We include them as an indicator of biotic integrity in
EMAP because  they yield additional information and a different perspective on the ecological
condition of streams and rivers. Algae are known ecologically as primary producers, meaning
that they produce biomass solely through the process of photosynthesis. They are more directly
affected by excess nutrients, like phosphorus and nitrogen (needed for algal growth), than either
fish or  macroinvertebrates. Like macroinvertebrates,  algae  have strong responses to other
chemical stresses (like acidity) and disturbances to stream substrates (i.e., sedimentation).

    The same approach to building an Index of Biotic Integrity was used for attached algae as
we used for fish and macroinvertebrates.  For the Mid-Atlantic region as a whole, 30%  of the
stream length was in good condition with respect to algal assemblages (Figure 11). A similar
proportion of stream length had poor algal integrity (33%), and 37% of the stream length was in
marginal condition.

    On an ecoregional basis, algae suggest that the Western Appalachians have the poorest
biotic integrity (51% of stream length in poor condition), followed by the Coastal Plain (35% in
poor condition)  and Piedmont (37% in poor condition) ecoregions (Figure  11). The algal IBI
suggests that the mostly forested, upland  ecoregions (the North and Central Appalachian,  and
Ridge ecoregions)  have the best biotic integrity (81% and 79% in either  good or marginal
condition,  respectively. These results are consistent with the types of human disturbance to
which we expect algal  assemblages to respond; both upland ecoregions have relatively small
amounts of agricultural landuse, which helps to keep stream nutrient levels low, and relatively
little human uses  of the land that contribute fine sediments to  streams (e.g.,  agriculture  and
mining).

            COMPARISON OF FISH, MACROINVERTEBRATE,

                             AND ALGAL SCORES

    Differences among estimates of ecological condition based on fish, macroinvertebrates and
algae are expected, because these three groups of organisms respond to different disturbances in
the  environment. For  the region as a whole, macroinvertebrates suggest  the poorest  biotic
integrity, with  41% of Mid-Atlantic stream length  in  poor condition  according  to  the
macroinvertebrate  Index of Biotic Integrity (Table 2). At the level of individual ecoregions, the
fish IBI tends to suggest the fewest miles of stream in good condition. The  only exceptions to
this general pattern are the  Coastal Plain  and Western Appalachians, two highly modified
ecoregions   with   substantial  urban  (Coastal  Plain)  and  agricultural/mining  (Western
Appalachians) land use. None of the streams sampled in the Coastal  Plain  exhibited good
macroinvertebrate integrity, and only 8% of stream length in the Western Appalachians had good
algal integrity.

    Such  differences  can be attributed  to  a number of factors. As  already  stated, fish  and
macroinvertebrates are  expected to  respond differently  to stresses, and the  differences  in the
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relative scores of the fish  and aquatic insect scores in different  ecoregions (where different
stresses are known to dominate) may be indicative of this.
Table 2
Comparison of fish, macro-invertebrate and algal IBI results for Mid- Atlantic flowing
waters, and the six ecological regions.
Region
Mid-Atlantic
Region
Coastal Plain
Piedmont
Valleys
Ridges
North/ Central
Appalachians
Western
Appalachians
% in Good Condition
TT u Macro- A1
Fish . , Algae
invertebrates
21 26 31
20 0 35
20 20 27
19 26 25
26 49 42
23 40 45
19 13 8
% in Poor Condition
„. , Macro- A1
Fish • . . ^ Algae
invertebrates
31 41 33
43 88 41
20 42 37
33 45 34
26 20 21
40 28 19
28 46 51
    Even if the condition estimates for the three biotic assemblages are fairly similar (e.g., 21-
30% of stream length in good condition; 31-33% in poor condition), one might wonder whether
the three IBIs are classifying the same streams as either good or poor. And the answer to this is
"sometimes." Of the stream length classified as in good condition with respect to fish, about 70%
would also be classified as good using the macroinvertebrate IBI. Likewise, about 71% of stream
length in good condition with respect to macroinvertebrates  also exhibits good algal condition.
Not surprisingly, the poorest association in IBI scores is between fish and algae;  about 52% of
stream length with good fish IBI scores also have good algal IBI scores. Assemblages that utilize
habitat at different scales (like fish and algae) are expected  to have more distinct responses to
stressors.

    Of the roughly 220,000  km  of streams in  the Mid-Atlantic region, roughly 107,000 km
(48%) has one or more of the biotic assemblages  in good condition, but only about 7,850 km
(3.5%) would be classified as good by all three IBIs. There are 129,000 km of Mid-Atlantic
   MID-ATLANTIC FLOWING WATERS ASSESSMENT
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streams (58% of the total) that are classified as poor using one or more of the assemblages; fewer
than 4,350 km (2.0%) would be scored as poor using data from all three assemblages. The vast
majority of stream length in the region exists in a middle ground, where one assemblage may be
in good condition and the others in marginal or poor condition. In this middle ground, streams
and rivers are experiencing different sorts of stress; those stressors that are present are affecting
only one or two  of  the  assemblages, and the different responses  of the biotic assemblages
produce differences in how we might view the ecological condition of the sites. Only by looking
further into the relative extent of these stressors, and into how they differentially affect the biotic
assemblages we use  to assess ecological condition, can we begin to understand the different
stories told by fish, macroinvertebrates and algae, and assess the overall condition of flowing
waters in the Mid-Atlantic region.


STRESSORS IN MAIA FLOWING WATERS

     In the  previous section, the ecological condition of the flowing waters in the Mid-Atlantic
region was  described based on direct measurements of stream and river biota.  Here we present
our findings on the stressors to the streams/rivers of the Mid-Atlantic. These are based on direct
measures of physical, chemical or biological characteristics of streams and their watersheds.
They are stream and river attributes that can be directly or indirectly altered as a result of human
activity or intervention in the stream system, and that have been known to have harmful effects
on  stream  and river biota.   We  present this  information in the belief that comparisons of
stressors, like the ones we present here, will be useful to regional managers in determining where
best to focus their limited resources for stream and river protection  and restoration. Additional
technical information on the potential  stressors and  their measurement  can be found in the
references listed in Appendix A.

     We have two primary goals in assessing stressors in the flowing waters of the Mid-Atlantic.
We hope to:
    1.  Estimate the relative extent of each stressor (i.e., the percentages of stream length having
       "poor" stressor condition), demonstrating which stressors are most common. Relative
       extent is one measure of each stressor's relative importance.
    2.  Calculate each stressor's relative risk to the biological assemblages we've used to assess
       ecological  condition. Relative risk measures the association seen in our data between
       poor biological condition and poor stressor condition. It  answers the question, "How
       much  more likely is  a  given  biological  measure (e.g., a fish IBI) to  indicate  poor
       condition if a given stressor (e.g., riparian habitat) is  also in poor condition?" We use
       relative risk as an indicator of the severity of stressor effects on biological assemblages.

     For  each stressor,  a brief description of the nature of the measurements is provided,
followed by the results. Wherever possible, we have  used  a similar strategy  for assessing
stressors  as we have  for biological  measures—the distribution of values in a set of relatively
undisturbed sites (reference sites) is used as a measure of what constitutes acceptable values for
these stressors.  This  distribution of reference site scores is used to determine whether, and to
what extent, the scores  of other sites fall outside this  distribution (more information  on the
reference site approach is given in Appendix A).

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     At the end of this section, we present the relative extent and relative risks of the stressors for
the Mid-Atlantic as a whole, so that the reader can develop some  appreciation of both the extent
and the severity  of individual  stressors. As with the indicators of ecological condition, we also
present the relative extent of stressors for each of the six ecological regions. Unfortunately (due
to the  constraints of small sample  sizes) we  cannot calculate  relative risk on the  scale  of
individual ecoregions.
        Landtover
        I  I Open water
        I  I Low Intensity Residential
        I  I High Intensity Residential
        • Commercial/lndustrial/Transportation
        I  I Bare Rock/Sand/Clay
        I  I Quarry/Strip Wine/Gravel Pit
        C! Transitional
        • Deciduious Forest
        • Coniferous-Forest
        • Mixed Forest
        I  I Pasture/Hay
        • Row Crop
        HH Urban/Recreational Grass
        • Woody Wetland
        I  I Emergent'Herbaceous Wetland
        Figure 12. Land use and land cover in the Mid-Atlantic region, as determined from satellite
        imagery.
    MID-ATLANTIC FLOWING WATERS ASSESSMENT
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     The heterogeneous nature of the land use and land cover in the Mid-Atlantic region is
evident from  satellite  imagery (Figure 12). Agricultural areas, urban and suburban clusters,
forests, mining sites, and other features are interwoven on the landscape, with many of these
features indicating human activity. These human activities have the potential to alter stream and
river quality and affect aquatic biota. The characteristics or stressors in Mid-Atlantic streams and
their watersheds included in this report are:
   (1) Stream/river acidification (from acid rain and mining),
   (2) Other mining impacts,
   (3) Nutrient runoff,
   (4) In-stream habitat alteration (e.g., sedimentation, wood removal),
   (5) Riparian habitat alteration,
   (6) Non-native fish introductions.

                                   ACIDIFICATION

     Streams and rivers can become acidic through the effects of acid deposition (acid rain) or
due to  mine  drainage (particularly from  coal mining). The Mid-Atlantic region is unusual
because it receives some of the  highest rates of acid rain in the U.S., has geology that makes
large  areas within the region susceptible  to acidification, and has a high incidence of coal
mining.

     Acid rain forms when the emissions from smokestacks and automobiles (particularly sulfur
dioxide and nitrogen oxides) combine with moisture in the air, forming  dilute solutions of
sulfuric and nitric acid. Acid deposition can also occur in dry forms, like the particles that make
up soot. When wet and  dry  deposition fall on sensitive watersheds, like those  in the upland
portions of the Mid-Atlantic, they can have deleterious effects on  soils, vegetation and streams
and rivers. In assessing acid rain's effects on flowing waters, we rely on a measure of the water's
ability to buffer inputs of acids, called acid neutralizing capacity or ANC. When ANC values fall
below zero, the water is  considered acidic, and can be either directly or indirectly (e.g.,  by
mobilizing toxic metals like aluminum) toxic to biota.

     Acid mine drainage forms when water moves through mines and mine tailings, combining
with sulfur-bearing minerals to form strong solutions of sulfuric acid, and mobilizing many toxic
metals. As in the case of acid rain, we can  assess the acidity of waters in mining areas by using
their ANC values. Mine drainage also produces extremely high concentrations of sulfate—much
higher than those found in acid rain. While sulfate is not directly toxic to  biota, we use it as an
indicator of mining's influence on streams and rivers.  When ANC and sulfate  are low, we can
attribute acidity to acid rain. When ANC is low and sulfate is high, we can attribute  acidity to
acid mine drainage.
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           3% 2%
                             "•—•"T
      MAIA Region Overall
        margin of error ± 5%
        Acid Deposition
          • None
          O Episodic
          • Chronic
                                                                                Ridge
                                                                            margin of error ± 3%
    Valley

margin of error ± 8%
                                                                              Nofth-Cenlfal
                                                                              Appalachians
                                                                            margin of error ± 7%
                                                                                Western
                                                                              Appalachians
                                                                            margin of error ±
                                                                               Piedmoni
                                                                           ' margin of error *
    Coastal
    Plain
                                                                            margin of error ± 24%
       Figure 13. Extent of acid deposition effects on flowing waters of the Mid-Atlantic, and the
       proportion of the total stream length in unacidified, episodically acidified and chronically
       acidified  categories.  Roughly 5% of the region's stream length  exhibits effects of acid
       deposition. Nearly all of the stream length affected by acid deposition in the Mid-Atlantic is
       in the North and Central Appalachian (14%) and Ridge (8%) ecoregions.

     Streams and rivers may be acidic throughout the year (chronically acidic) or only for short
periods (episodically acidic),  such as when flows are high during storms  or  snowmelt. Both
forms of acidity have deleterious effects  on biota, including all of the biological assemblages we
are using in this assessment. Data from streams sampled during spring and summer, like those in
this Mid-Atlantic  assessment,  can  be  used  to   assess  directly  the  incidence  of chronic
acidification. Across the region as a whole, just over 2% of the total stream length is chronically
acidic (ANCXO) due to acid rain. In order to estimate how  this number would change if we
considered both chronic and episodic acidity, we change the  ANC threshold to 50 jieq/L—the
National Acid Precipitation Assessment Program  concluded  in 1990  that  streams with ANC
values lower than 50  jieq/L are susceptible to episodic acidification,  and may  experience  fish
kills and changes to their macroinvertebrate communities during short-term pulses of acid  rain
runoff.  When both chronic and episodic acidity are considered, we conclude that about 5% of
the total stream  length in the region is affected by acid rain (Figure 13).
    MID-ATLANTIC FLOWING WATERS ASSESSMENT
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            1%1%
                             "•—•"T
      MAIA Region  Overall
        margin of error ± 5%
                                                               I
                       * *  if ^"y.-**    i*c>
                       °rffc>^V*ft f  ••/
      Acid Mine  Drainage
           • None
           O Moderate
           • Severe
                                                                     4% 1%
3% 1%
                                                                                 Ridge
                                                                             margin of error ± 3%
            Valley

        margin of error ± 8%
                                                                              North-Centra!
                                                                              Appalachians
                                                                             margin of error ± 7%
                                                                                Western
                                                                              Appalachians
                                                                            margin of error ± 12%
                                                                                Piedmont
                                                                            margin of error ±
           Coastal
            Plain
                                                                            marginof error ± 24%
       Figure 14. Extent of acid mine drainage in flowing waters of the Mid-Atlantic, and the
       proportion  of the total stream length  in unaffected, moderately affected, and  severely
       affected categories. Acid mine drainage is not as common in the Mid-Atlantic as acid
       deposition effects, with about 2% of stream miles affected. All of the stream length affected
       by acid mine drainage  in the Mid-Atlantic region is in the North and Central Appalachian
       (5%) and Western Appalachian (4%) ecoregions.

     For problems  such  as acid  rain and acid mine drainage,  an  ecoregion  perspective is
particularly  appropriate.  Ecoregion  designations  integrate  similar geology,  soils,  watershed
topography,  climate and vegetation characteristics that help explain stream responses to certain
types of stressors  or pollution. Some ecoregions  have streams that are much more susceptible to
acid rain because they lack the limestone and  other well-buffered bedrocks that  help protect
streams from acidic inputs.  Due to these ecoregional differences, nearly all of the streams in the
Mid-Atlantic affected by  acid rain are in two  ecoregions (Figure 13).  About 8% of the stream
length in the North and  Central Appalachians  is chronically acidic, and an additional  6% is
affected by episodic acidification. Fewer streams are chronically acidic in the  Ridge ecoregion
(less than 1% of total  stream length), but combined episodic and chronic acidification affect 7%
of the total length. None of the other ecoregions has more than 0.5% of stream length affected by
acid rain.
    MID-ATLANTIC FLOWING WATERS ASSESSMENT
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     The extent of acid mine drainage is substantially less than acid deposition—only 2% of the
stream length in the Mid-Atlantic is acidic due to mine drainage (Figure 14), with more than half
of these streams  exhibiting chronic acidity. All of the acid mine drainage streams are located  in
the  Appalachian  ecoregions  where coal  mining is  common. In  the North  and Central
Appalachians, just under 5%  of stream length is affected by acid mine drainage; 4%  of the
stream length is severely and chronically acidic (Figure 14). The Western Appalachian ecoregion
has acid mine effects in roughly 4% of its stream length.
      MAIA Region  Overall
        margin of error ± 5%
         Mine Drainage
           • None
           O Moderate
           • Severe
                                                                      7%
                                                                                  Ridge

                                                                             margin of error ± 8%
    Valley

margin of error:
                                                                               North-Centra!
                                                                               Appalachians
                                                                             margin of error ± 7%
                                                                         43% 1    Western
                                                                               Appalachians

                                                                             margin of error ± 12%
                                                                                Piedmont

                                                                             margin of error ± 13%
    Coastal
    Plain
                                                                             margin of error ±24%
       Figure 15. Extent of all mine drainage effects on flowing waters of the Mid-Atlantic, and the
       proportion of the total stream length in good, marginal and poor condition with respect to
       mining indicators.  Roughly 17% of the region's stream length exhibits effects of mine
       drainage. Nearly all of the stream length affected by mine drainage in the Mid-Atlantic is in
       the North and Central Appalachian (27%) and Western Appalachian (57%) ecoregions.

     In total, there are some 9,600 kilometers of Mid-Atlantic flowing waters that are acidic due
to acid rain or susceptible to  acid rain, and about 4,100  kilometers that are acidic due to mine
drainage.
    MID-ATLANTIC FLOWING WATERS ASSESSMENT
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    OTHER MINING EFFECTS

     Streams  that are acidic  due to mine
drainage are less common  in  the  Mid-
Atlantic than  streams acidified by acid rain,
but mine drainage effects extend far beyond
acidification.  Downstream  effects of mines
include  export of fine sediments and toxic
metal    contamination   (metals   reside
primarily in  stream  bottom  sediments  in
non-acidic streams); these  less well-known
stresses  can  have pronounced  effects  on
bottom-living  organisms.  Although only
about 2% of stream miles in the Mid-Atlantic are acidic because of mine drainage, an additional
15% of the stream length is non-acidic, but degraded by mine drainage (Figure 15). About 10%
of Mid-Atlantic stream miles  would be  considered severely affected by mine drainage (either
acidic, or with  extremely  elevated  concentrations of sulfate indicating a dominant source of
water from mines).

     Only small amounts of mine drainage effects are exhibited outside of the two coal-mining
ecoregions (Figure 15). In the Piedmont and Ridge ecoregions, roughly 1-2% of stream length is
affected by non-acidic mine drainage, due to having mines in the headwaters (the headwaters of
several rivers in the Piedmont  and Ridge ecoregions are in the coal-bearing regions to the East).
In the Western Appalachians, where coal deposits are common, the majority of streams have at
least moderate indicators of mine drainage  effects (57% of total length);  28% of the stream
length in this  region  would be considered  severely  affected.  In  the North  and Central
Appalachians, 27% of the  total  stream length  has some signs of mining effects, with 20% of
stream length having indicators of severe mine drainage affects.

                            NUTRIENT  ENRICHMENT

     The introduction of excessive nutrients (e.g., phosphorus and nitrogen) can affect streams
directly,  for example  by  increasing algal growth, or indirectly,  by  altering the  quality  and
quantity of food for higher trophic levels like macroinvertebrates and fish. In extreme  cases,
nutrients can lead to levels  of algal growth that deplete the oxygen in the water, choke out other
forms of biota,  and  significantly alter the assemblages present.  Common sources  of nutrients
include  municipal sewage, runoff from  septic  fields, and agricultural  fertilizers. Atmospheric
deposition is  an additional  source of nitrogen (but a minor source of phosphorus), and may be
important in areas that are otherwise unaffected  by urban and agricultural land uses.

     The growth of algae in fresh waters (lakes  and streams) in the U.S. are considered to be
primarily limited by the amounts of phosphorus present, and  elevated phosphorus levels are
therefore of special concern. In the  Mid-Atlantic as a whole, phosphorus concentrations would
be considered severely elevated  in about 14% of stream length (Figure  16); more than 44% of
stream length in the region has phosphorus levels we would classify as good.
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     Because of its direct link to agricultural land use, phosphorus is most commonly elevated in
the ecoregions with higher percentages of agriculture—the Piedmont (29% of stream length with
severely elevated phosphorus), Western Appalachian (16%) and Valley  ecoregions (12%). The
primarily forested  areas of the Mid-Atlantic, the North  and Central Appalachian and Ridge
ecoregions, have a majority of their  stream length  (66% and  60%,  respectively)  in  good
condition with respect to phosphorus.
                             "•—"I"
       Total  Phosphorus
              Good
           O Marginal
           • Poor
                                                                                Ridge

                                                                            margin of error ± i
                                                                                Valley

                                                                            margin of error •
                                                                     4%
                                                                   r30% ^    \  North-Central
                                                                        66% J  Appalachians

                                                                            margin of error ± 7%
                                                                               Western
                                                                          ° / Appalachians

                                                                            margin of error* 12%
                                                                        56% 1    Piedmont

                                                                   \y  ^X margin of error ±
Coastal
 Plain
                                                                           margin of error ±24%
       Figure 16. Extent of excess phosphorus concentrations in flowing waters of the Mid-Atlantic,
       and the proportion of the total stream length in good, marginal and poor condition with
       respect to this nutrient.  Roughly 14% of the region's stream  length exhibits excessive
       phosphorus concentrations. The Piedmont ecoregion has the highest proportion of streams
       (29%) with poor phosphorus concentrations.

     Nitrogen is another nutrient that can stimulate plant growth, especially in the presence of
high phosphorus concentrations. Like phosphorus, nitrogen is commonly found in agricultural
fertilizers, but may also originate in acid rain (nitrogen deposition), animal manure, and sewage
discharges.   Overall,  17% of Mid-Atlantic stream length  would be considered to be in poor
condition with respect to nitrogen (Figure  17); more than 40% has good nitrogen levels.

     Although both phosphorus and nitrogen result from fertilizer runoff, and other agricultural
practices, additional sources of nitrogen lead to a different ecoregion distribution for this nutrient
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(Figure 17). Nitrogen (either as nitrate or ammonium) can be a major component of atmospheric
deposition, and results both from the combustion of fossil fuels (especially in vehicles) and the
release  of gaseous forms of nitrogen from confined animal feedlots. The Valley (39%) and
Coastal Plain (25%) ecoregions exhibit the highest proportions of stream length with severely
elevated nitrogen, while the forested ecoregions again have the highest proportions of streams
with low nitrogen concentrations (Ridge ecoregion 63%, North and Central Appalachians 48%).
      MAIA Region Overal
        margin of error ± 5%
         Total  Nitrogen
           • Good
           O Marginal
           • Poor
                                                                   7%
                                                                              Ridge

                                                                          margin of error ± 8%
    Valley

margin of error ± 8%
                                                                           Nofth-Centra!
                                                                           Appalachians
                                                                          margin of error ± 7%
                                                                             Western
                                                                           Appalachians
                                                                          margin of error ± 12%
                                                                             Piedmont

                                                                          margin of error ± 13%
    Coastal
    Plain
                                                                          margin of error ± 24%
       Figure 17. Extent of excess nitrogen concentrations in flowing waters of the Mid-Atlantic,
       and the proportion of the total stream length in good, marginal and poor condition with
       respect to this  nutrient. Roughly 17% of the region's  stream length  exhibits excessive
       nitrogen. The Valley ecoregion has the highest proportion of streams  (39%) with  poor
       nitrogen concentrations.

                               IN-STREAM HABITAT

     High  quality habitat  is an important and  often overlooked ingredient  for good stream
condition.  In the  course  of EMAP  sampling,  data were collected  on  many aspects of both
riparian (near-stream) and  in-stream habitat known to be important to biota. These  quantitative
measures of habit  can be used to diagnose the possible causes of habitat degradation. We focus
in this assessment on two characteristics of in-stream habitat (sedimentation  and large woody
    MID-ATLANTIC FLOWING WATERS ASSESSMENT
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material) that play  important roles in  establishing high quality habitat structure  for fish,
macroinvertebrates and algae.
     MAIA Region Overall
        margin of error ± 6%
            s
       Excess Sediments
            • Good
            O Marginal
            • Poor
                                                                        41% i    Ridga
                                                                            margin of error ±
     Valley

margin of error ± 14%



  North-Central
  Appalachians
margin of error * 10%


    Western
  Appalachians
margin of error ± 13%



   Pi&clmom
margin of error ± 13%
    Coastal
     Plain
                                                                            margin of error ± 25%
       Figure 18. Extent of excess sedimentation in flowing waters of the Mid-Atlantic, and the
       proportion of the total stream length in good, marginal and poor condition with respect to
       fine sediments. Roughly 28% of the region's stream length exhibits amounts of fine sediment
       far in excess of expectations. The Coastal Plain ecoregion has the highest proportion of
       streams (54%) with excess fine sediments.

                                 In  order  to  assess  stream  sedimentation,  we compared
                                 measurements of the amount of fine sediments on the bottom
                                 of each stream  (sands  and fines) with  expectations based on
                                 each stream's ability to transport fine sediments  downstream
                                 (a function of the slope, depth and complexity of the  stream).
                                 Fine  sediments  in  excess of expectations  suggest  that the
                                 supply  of  sediments from the watershed to the  stream  is
                                 greater than what the stream  can naturally process.   For the
purposes  of this assessment, we calculated the ratio of observed to expected sediment sizes for
all streams, including  reference sites, and used the distribution of ratios in the reference sites to
define the ratio's natural variability. This is the same approach used for biological measures and
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the other stressors in this assessment—using a set of reference streams to define expectations for
the least disturbed sites in each ecoregion (see Appendix A).

     About 28% of the total stream length in the Mid-Atlantic has fine sediments far in excess of
expectations (Figure 18), but more than half (53%) were within the expected range and would be
considered to be  in  good condition.  The Coastal Plain (54% in  poor condition), Western
Appalachian (38%) and Valley (36%) ecoregions had the highest proportions of stream length
with excessive sediments (Figure 18). Somewhat surprisingly, the  Piedmont ecoregion has the
highest proportion  of stream length (76%) with no excess sediment problems. Note that this does
not mean that the Piedmont region had the lowest levels of fine sediment, only that the amount of
fine sediments in most of these streams are within expectations.
      MAI A Region  Overall
         margin of error ± 6%
                                                                           Appalachians

                                                                         margin of error ± 10%
               ft o   ••      ^ J   • •
               J  *    1   • 7 .   *
               V*    •     **  *
                                                                             Piedmont

                                                                         margin of error ± 13%
            • Good
            O Marginal
            • Poor
       Figure 19. Extent of large wood in flowing waters of the Mid-Atlantic, and the proportion of
       the total stream length in good, marginal and poor condition with respect to in-stream wood.
       Roughly 26% of the region's stream length is completely devoid of large wood.

     Another aspect of in-stream habitat that creates high quality habitat space for biota is the
amount of large woody material.  Downed  and dead trees, falling into streams from  nearby
riparian areas, are widely recognized as crucial components of the complex habitats that typify
streams with high biodiversity. The amounts of wood found in Mid-Atlantic streams are quite
low  compared to many other forested areas of the U.S.,  and may have historically been much
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higher. In assessing large wood, we compare present values only to those of the least disturbed
sites in the region, and not to historical estimates. If historical amounts of wood were higher as is
suspected, then an assessment using historical reference condition might well paint a different
picture.

     For the Mid-Atlantic as a whole, 26% of stream length was completely devoid of large
wood (our definition of poor condition;  see Appendix A), while 47%  had amounts of wood
similar to reference sites (Figure 19). The Coastal Plain ecoregion presents the best picture, with
67% of stream length in good condition, and only 14% in poor condition for wood (Figure  19).
The  Western  Appalachian  (41%  of  stream  length  in  poor  condition)  and Valley (30%)
ecoregions had the  highest proportions of stream length with no large wood.

                                RIPARIAN HABITAT

     Riparian (or  streamside) vegetation provides shade  to flowing waters (particularly small
streams), maintaining cool water temperatures required by many fish species  for reproduction,
growth and survival. Riparian vegetation that washes or falls into the  stream can be a source of
food for stream organisms,  especially macroinvertebrates. It  also  strengthens and stabilizes
stream banks and helps to prevent silt and associated contaminants from entering the stream. In-
stream large wood  derived from riparian trees creates complex habitat and pools for stream fish
and aquatic insects. Human beings alter riparian habitat in a variety of ways: clearing vegetation
from the banks and riparian areas, logging or farming up to the stream edge,  dumping litter or
other wastes in riparian areas, building roads along  and across streams, adding stabilizing
structures (e.g., rip-rap) along banks, and building dams or other diversion structures in or near
the stream channel.
                                             We incorporated aspects of riparian vegetation
                                             cover, structural complexity, and the intensity
                                             of  human  disturbances  into  an  index  of
                                             Riparian   Habitat  Quality  for  use  in  this
                                             assessment.   The index ranges from zero to
                                             one, with a value of one resulting from the
                                             combination of: (1) a multi-storied corridor of
                                             woody vegetation; (2) canopies that are closed
                                             (or nearly closed; and (3) riparian areas free of
                                             visible human disturbance  (trash, roads fences,
                                             etc.).  We calculated this index for all sites, and
                                             compared each  site's score to the  distribution
                                             found in reference sites.
    Riparian habitat results for the Mid-Atlantic as a whole indicate that 23% of the total stream
length had riparian areas in poor condition, while 57% had riparian habitat similar to that of
reference  sites (Figure 20).  The Coastal Plain (26% of stream length in poor condition) and
Western Appalachian (26%) ecoregions have the poorest riparian habitat (Figure 20). As was the
case with  excess sediments, the Piedmont ecoregion has somewhat surprisingly large proportion
of stream  length in good condition (77%). It may not be a coincidence that this region scored
well for both in-stream and riparian habitat, as the two are closely linked. Good riparian habitat
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provides protection from  excess sediment  that might otherwise enter the stream, as well as
supplying large woody material to streams  (Figure 21). Upland areas of the Mid-Atlantic, the
North and Central Appalachian and Ridge ecoregions, also have large proportions of stream
length with good riparian condition (56% and 70%, respectively).
     MAIA Region Overall
        manjiboferror±
       Riparian Condition
            • Good
            O Marginal
            • Poor
                                                                                Ridge

                                                                           margin of error ± 10%
     Vall&y

margin of erf or ± 14%
                                                                             North-Central
                                                                             Appalachians
                                                                           margin of error ± 10%
                                                                               Western
                                                                             Appalachians
                                                                           margin of error ± 13%
                                                                              Piedmont
                                                                           margin of error ± 13%
    Coastal
     Plain
                                                                           margin of error ± 25%
       Figure 20. Extent of problems with riparian condition along flowing waters of the Mid-
       Atlantic, and the proportion of the total stream length in good, marginal and poor condition
       with respect to riparian areas. Roughly 23% of the region's stream length exhibits poor
       riparian condition. The Valley ecoregion has the highest proportion of stream length (37%)
       with poor riparian condition.
                                  NON-NATIVE FISH

     To some people a thriving rainbow trout stream indicates a successful fisheries management
program.  To others it  suggests  the introduction of a  non-native,  and potentially  invasive,
species—and a potential loss of biotic integrity and native biodiversity.
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                          0.2          0.4          0.6          0.8
                           Index of Riparian Habitat Quality
1.0
       Figure 21. Relationship between Large Wood (an areal estimate of wood in stream) and
       Riparian Condition for 592 streams in the Mid-Atlantic. High riparian habitat quality can
       confer many benefits to  streams and rivers, including the supply of wood to maintain
       complex in-stream habitat for biota.

     Some states specifically  recognize trout-stocked fisheries as a "designated use" for certain
streams, yet many consider fish  stocking of non-native species to be a potential stressor in the
stream. Non-native fish do not necessarily imply poor stream condition, but non-native species
have been known to replace native fish by direct predation or  by out-competing  them for
available habitat, food, or both. In the Mid-Atlantic as a whole, 47% of the stream length has at
least some non-native individuals (Figure 22). We don't attempt to identify classes of stream
condition for non-native species (e.g., good, marginal or poor condition based on non-native fish
species), because of the difficulty of setting expectations.  The procedure we've used for all
previous indicators (biology  and  stressors)  involves deciding what  an appropriate  group  of
reference sites might  be  for that indicator, but this creates difficulties for a non-native species
indicator. Many of the reference  sites (nearly 65%) that we might use for a chemical or physical
habitat indicator have at  least  some individuals of introduced species present. If we were using
historical condition as a reference, then it might be reasonable to expect all streams to be free of
non-native species, and any introduced species would be enough to classify a site as poor. But
the difference between historical expectations  (no non-natives) and current conditions (where
65% of reference  sites have non-natives) is so great as to make setting expectations nearly
impossible, especially given the differences in opinion about whether the presence of non-natives
really represents a stress at all.
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                                                                            Piedmont
                                                                         margin of error ± 13%
        Non-Native Fish
        • None
        O0-10%
       Figure 22. Percentage of Mid-Atlantic stream length with non-native fish species present.
       Approximately 47% of total stream length had non-native individuals present, while 46%
       did not. Roughly 7% of stream length is fishless. The Piedmont ecoregion has the highest
       proportion of stream length with introduced fish species (76%).

     One convenient way to display information when  thresholds  between good, marginal and
poor  condition  cannot be  identified,  is  with a  graph known  as a  cumulative frequency
distribution  or CDF. Figure 23 presents a CDF of the  percentages of stream length that have
different proportions of non-native individuals. At any point on the horizontal axis, one can read
the proportion  of stream length (or,  more  correctly in this case, the proportion of stream
kilometers that have at least some fish) that meet or exceed that level. For example, we can
estimate the proportion of stream length with 10% (or more) non-native individuals by reading
the value on the vertical axis that corresponds to the 10% value on the horizontal axis. Similarly,
the proportion of stream length dominated by non-natives (e.g., where more than half of the
individuals are non-native species) would be about 3% (i.e.,  the difference between 100% and
97%, read from the graph). We include these values not as suggestions for identifying classes  of
impairment, but to demonstrate that the reader  can form his  or her  own  opinions of what
constitutes a "non-native fish stressor" and estimate how much of the stream  resource fits these
criteria.
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    O)
    C
    CD
    -"•o
    l~
    CO  O
    CD _O>

    ffi  o
    M— ^-^
    o jz
    sJD  tf)
            100
90
80
70
    E

    O
              ~r\j

                  0     10    20   30   40    50   60   70    80   90   100

                           Percent of Non-Native Individuals

      Figure 23.  Cumulative frequency distribution  for the percentage of non-native fish in
      flowing waters of the Mid-Atlantic. Approximately 50% of the stream miles where fish are
      found had no non-natives present. 18% had 10% (or more) non-natives, while about 3% of
      stream miles were dominated by non-natives (more than 50% of individuals).

    Individual ecoregions exhibit large difference in the presence and absence of non-native fish
species (Figure 22). The Piedmont (76% of stream  length), Valley  (69%) and Coastal Plain
(68%) ecoregions have the highest proportions of stream length with non-native fish present. The
Western  Appalachian  and North  and  Central  Appalachian ecoregions have the  highest
proportions of streams where only native species were found (65% and 53% of stream length,
respectively).

                      CONTAMINANTS IN FISH TISSUE

    EPA has established criteria to protect both  human beings and fish-eating wildlife from
chemical  contaminants that can be concentrated in fish tissue. For the MAIA study, fish tissue
samples were collected and analyzed (whenever a sufficient number of fish were caught) for
selected organic and metal  contaminants. We report here on results for mercury and a combined
index of organic contaminants. In general, these results are intended to indicate the exposure to
wildlife from these chemicals, rather than the risks of human  consumption. We analyzed whole
fish, rather than fillets, and  so our analyses included portions offish not commonly consumed by
human beings.
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     In order to place stream sites in condition classes, we used a wildlife criterion, based on
American river otter (Lontra canadensis), of 0.1 micrograms per gram - a site where any fish
species  exceeded  this concentration was  considered to be in  poor condition with respect to
mercury  (additional information on the mercury criterion can be found in Appendix A. For the
MAIA region as a whole,  19% of the stream and river length had fish exceeding this criterion
(Figure 24). An important caveat in interpreting this statistic is that 36% of the MAIA stream
length either had no fish,  or did not have sufficient fish to allow  contaminant measurements.
While it seems likely that some proportion of this 36% of stream length would also have had fish
with elevated mercury, the exact proportion is not known. The highest proportions of stream
length with elevated mercury in fish were found in the Piedmont (31%) and  Coastal Plain (29%)
ecoregions. The ecoregion with  the fewest  streams with elevated  mercury was the Valley
ecoregion (10% of stream length).
      MAIA  Region Overall
         margin of error ± 6%
                        '•  • a   -	••"" °'
                           *—T-  «
                               !   /-^   K
                               i -*    !•'•'•
                          ->Q   '  » »° /
                  Joi * •  t   f  V F'   '
                     °;^°  T/-..
              -v-  •*  '-y~  *
                  -  *  °  •^•:;*'.':*   *  ^ •>
                         -/I*"* *  *   »o  •
                             i  y     °
                                • •  V-    *  -^
      Mercury in  Fish
       • Good
       • Poor
       O Insufficient data
                                                                   10%
    Ridge

margin of error ± 13%



    Valley

margin ot en of ± 13%


  North-Central
  Appalachians

margin of error ±10%


    Western
  Appalachians

margin of error ± 12%


   Piedmont

margin of emt~± 13%
    Coastal
     Plain
                                                                          margin of error ± 12%
       Figure 24. Percentage of Mid-Atlantic stream length with mercury concentrations in fish
       tissue that exceeded the  criterion for American river otter. Approximately 19% of total
       stream length had elevated mercury concentrations present, while 46% did not. About 36%
       of the stream length either had no fish, or insufficient fish to allow contaminant analysis. The
       Piedmont and  Coastal Plain ecoregions exhibited the highest proportions of stream length
       with fish mercury concentrations exceeding the 0.1 microgram per gram criterion (31% and
       29%, respectively).
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     Fish tissue samples were also  analyzed for  several  organic contaminants,  including
Chlordane, DDT and its  metabolites, Dieldrin  and Polychlorinated Biphenyls (PCBs). Most of
these contaminants (with the exception of PCBs) are primarily from agricultural chemicals, and
might be expected to be  higher in ecoregions dominated by agriculture. We placed all streams
where any fish species exceeded  the American river otter criterion for  any of these organic
contaminants in the poor condition category (see Appendix A for additional information on the
wildlife  criteria used for these contaminants).  Only 4% of the total  stream and river length in
MAIA contained fish that exceeded any of the  organic contaminant criteria (Figure 25). As was
the case for mercury, these results  need to  placed in context—about one-third (34%) of the
MAIA stream length either contained no fish, or did not have sufficient fish to allow contaminant
analysis, so the 4% estimate should probably  be  considered a lower bound on the true value.
Unlike mercury, where the Valley ecoregion had a low proportion of stream length with elevated
concentrations, organic contaminants are more likely to be found  in the Valley (8% of stream
length) than any other ecoregion.  This most likely reflects the different sources for these two
categories   of contaminants—while  the  organic  contaminants  are  primarily  agricultural
chemicals, mercury is thought to derive mostly from atmospheric precipitation.
MAIA Region Overall
   margin of error ± 6%
      Organic Contaminants
              in Fish
           Good
         • Poor
         O Insufficient data
                                                                    6%
                                                                                Ridge

                                                                           margin of error ± 14%
                                                                                Valley

                                                                           margin of eror± 13%
                                                                             North Central
                                                                             Appalachians
                                                                           margin of envr± 11%
                                                                               Wostorn
                                                                             Appalachians
                                                                           margin ofeimi'± 12%
                                                                              Piedmont
                                                                           margin of error ± 12%
                                                                         Coastal
                                                                          Plain
                                                                           manpn of ero/"± 22%
       Figure  25.  Percentage  of Mid-Atlantic  stream  length  with  organic  contaminant
       concentrations  in  fish tissue that exceeded the criterion for American  river otter.
       Approximately 4% of total stream length had elevated concentrations of either Chlordane,
       DDT, Dieldrin or PCBs in fish. The Valley ecoregion exhibited the highest proportions of
       stream length with elevated organic contaminant concentrations (8%).
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           SUMMARY RANKING OF POTENTIAL STRESSORS

    An  important  prerequisite to  making  wise  policy  and management  decisions  is
understanding the relative magnitude or importance of current stressors. There are multiple ways
that we might choose to define "relative importance" with stressors. One aspect to consider is
how common each stressor is—i.e., what is the extent, in kilometers of stream, of each stressor
and how does it compare to the other stressors? We might also want to consider the severity of
each stressor—i.e., how much effect does each stressor have on biotic integrity, and is its effect
greater or smaller than the  effect of the other stressors? Ideally, we'd like to combine these two
factors (extent and severity) into a single measure of relative importance. Currently we have no
good method for producing this combined measure. For this reason we present separate rankings
of the relative extent and the relative severity of stressors to flowing waters in the Mid-Atlantic.
         Introduced Fish
          Sedimentation
    Lack of Large Wood
        Riparian Habitat
         Mercury in Fish
                 Nitrogen
            Phosphorus
          Mine Drainage
       Acidic Deposition
 Organic Contaminants
    Acid Mine Drainage
                         0%      10%      20%      30%      40%

                                          % of Stream Length
50%
      Figure 26. Relative extent of major stressors on stream condition in the Mid-Atlantic. Each
      bar represents the proportion of stream length in poor condition for that stressor, with 90%
      confidence intervals around  each estimate. If introduced fish species are considered a
      stressor, then they are the most common stressor in the Mid-Atlantic. All of the physical
      habitat indicators also rank high in relative importance based on extent.

RELATIVE EXTENT

    In Figure 26, stressors are ranked according  to the proportion of  stream/river length
impaired (or in poor quality) with regard to each stressor indicator. The  potential stressor that
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occurs in the highest proportion of flowing waters is non-native fish (47% of the stream length in
the Mid-Atlantic had at least one non-native fish present).  As discussed earlier in this report,
many would not consider non-native fish (often  game fish) to be a stressor; we list it here to
highlight the broad  extent of non-native fish  in the region—indicating a potentially serious
alteration of biological integrity—and leave it  up to the reader to decide whether it  should be
considered a stressor in the same way as other  stressors. The three next-most common stressors
are elements of stream habitat: excess sediments (28% of stream length), absence of large woody
debris (26%) and low riparian habitat quality (23% of stream miles). In terms of rank, the habitat
stressors are followed by  several chemical  stressors  (mercury,  nutrients, acidity)—these  are
found less extensively in the Mid-Atlantic than habitat stressors. Elevated mercury in fish tissue
(19% of stream  length), excess nitrogen (18%  of stream miles) and phosphorus (14%) are still
very common, as are the effects of mine drainage (10%  of stream  length). The percentage of
stream length affected by acid rain (5%), organic contaminants  offish tissue (4%), and acid mine
drainage (1%) appear minor  when compared to the other stressors, at least at the scale of the
Mid-Atlantic as  a whole. They are clearly of greater relative importance in selected ecoregions
(Figures 13 and 14).

RELATIVE RISK

     In  order to address the question of severity of stressor effects, we borrow the concept of
"relative risk" from medical epidemiology, because of the familiarity of the language it uses. We
have all heard, for example, that we run a greater risk of developing heart disease if we have high
cholesterol levels. Often such results are presented in terms of  a relative risk ratio—e.g., the risk
of developing heart  disease is four times higher  for a person  with total cholesterol of 300  mg
than for a person with 150 mg. total cholesterol.

     In Figure 27 we present relative risk values for the biological  and stressor data on streams in
the Mid-Atlantic. Because different biological  assemblages  are expected to be affected by
different stressors, relative risk is calculated separately for the fish IB I, the macroinvertebrate IBI
and the algal IBI. In our case, relative risk  is  defined as  the proportional increase  in  the
likelihood of encountering a poor IBI score when a stressor's condition in the same stream is also
classified as poor (see Appendix B for details of relative risk  calculation). Not all relative risks
are statistically significant, and so we focus this assessment on those that are.

    In an assessment of relative risk based on  cross-sectional survey data (as  opposed to data
from  a controlled experiment) it is impossible to separate completely the effects of individual
stressors that often occur together. For example, streams with high nitrogen concentrations often
exhibit high phosphorus as well; non-acidic streams with mines in their catchments often have
sediments far in excess of expectations. The analysis presented  in Figure 27 treats the stressors as
if they  occur in  isolation,  even though we know they do  not.  We do not  currently have an
analytical technique  to separate the effects of correlated stressors, other than to point  out in the
discussion  where co-occurrence of stressors should be considered in the interpretation of the
assessment.

    One of the  most important conclusions from the analysis in Figure 27 is that different
biological assemblages appear to be affected by different stressors. We certainly expect this to be
the case (it is  the  primary  justification for  including  multiple  assemblages in monitoring

    MID-ATLANTIC  FLOWING WATERS ASSESSMENT                               Page 44

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programs, and  in  assessments like the current one), but  the  results in Figure  27 are strong
confirmation  of this.  The  presence of non-native fish species is associated with poor fish
assemblage integrity, but does not  appear to affect either  macroinvertebrates or algae.  Excess
sediments present a significantly elevated  risk to both macroinvertebrate and algal assemblages,
but not  to  fish. Acidic deposition and  acid mine drainage  put fish and  macroinvertebrate
assemblages at  risk, but do  not appear to increase  the likelihood of finding algal assemblages in
poor condition.
                            Fish
Macroinvertebrates
Algae
      Introduced Fish
      Sedimentation
  Lack of Large Wood
     Riparian Habitat
      Mercury in Fish
           Nitrogen
        Phosphorus
      Mine Drainage
      Acid Deposition
 Orgainc Contaminants
   Acid Mine Drainage

                 0.0    0.5    1.0     1.5    0.0    0.5     1.0    1.5
                                                Relative Risk
                    0.0  0.5  1.0   1.5   2.0  2.5  3.0
       Figure 27.   Relative risk  values  for  associations between  biotic  integrity  (for each
       assemblage) and stressor condition (for each  assessed stressor). Length of bars is the
       increase in likelihood of encountering a poor ecological condition (based  on biological
       indicators) when the  stressor is also ranked as poor. For example, algal assemblages are
       roughly three times as likely to be in poor condition when phosphorus concentrations are
       also poor.  Lines (with caps)  within bars indicate one-sided lower 95% confidence intervals
       for estimated relative risk. A relative risk of 1.0 denotes "no stressor effect", and stressors
       with confidence intervals lying entirely above 1.0  are statistically significant  (one-sided
       p<=0.05), as represented by  yellow bars. Grey bars represent stressors for which we could
       not detect a significant effect.

     The significant relative risks in Figure 27 give us an  idea both of how severe each stressor's
effect on biotic  integrity  is,  and which stressors we might want to focus on when  a given
assemblage is in poor  ecological  condition.  Both  algae and macroinvertebrates exhibit high
relative risks for a  mix of physical and chemical  habitat indicators. For example, the stressors
with  significant  relative risk values for algae are excess sediments  and the two nutrients,
phosphorus and  nitrogen.  Algal assemblages are  1.5 to  3 times more likely to be  in poor
condition when  one (or more) of these stressors is elevated. As mentioned  earlier, algae  are
expected to be directly effected  by elevated nutrient concentrations, because they are the only
primary producers among the biological indicators in this assessment. In fact, the relative risk of
nutrient effects on algae are the  highest ones observable  in  our data. Sediments, which have an
obvious and deleterious scouring effect on attached algae, also appear to pose a significant risk to
algal  biotic integrity.

     The greatest relative  risks to  macroinvertebrates are excess sedimentation, mine drainage
(either acidic or  non-acidic) and  acidic deposition. Again, these quantitative results demonstrate
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what we expect qualitatively  from macroinvertebrate assemblages—namely,  that disturbances
that alter the micro-habitats within streams, or affect pollution intolerant taxa, have significant
effects on macroinvertebrate integrity. Most macroinvertebrate species occupy either  the small
spaces between coarse  streams  substrates like cobbles and gravels, or  cling to hard surfaces
exposed to  stream  currents—both micro-habitats are buried  when excess fine  sediments  are
present in a stream. Figure 27  illustrates both the direct risk we calculate from excess sediments,
and the associated risk posed by non-acidic mine  drainage, where excess  sediments are likely to
occur.  The direct chemical effects of acidification, whether from acidic deposition or acid mine
drainage, are also associated with elevated risks for macroinvertebrates.

    In the case offish assemblages, the significant stressors are a mix of chemical, physical and
biological habitat indicators. The presence of non-native fish  species,  and  the absence of large
woody  material,  are  both strongly  associated with poor fish biotic  integrity in our dataset.
Acidity, whether from acidic deposition or acid mine drainage, is also strongly associated with
poor fish  assemblages, due to the well documented loss of  sensitive taxa in acidic streams.
Nitrogen and phosphorus are not expected to have direct effects on fish biotic integrity, but  our
data suggest significant relative risk values for these nutrients. We cannot determine from these
data whether nitrogen and phosphorus are simply associated with other factors that have direct
effects on fish  (e.g., the many cumulative effects of agricultural landuse),  or whether the other
biotic alterations that occur in streams with high nutrients (increased algal growth,  increased
occurrence of low oxygen concentrations) have effects that reverberate up the trophic pyramid to
affect fish.

    The results in  Figure 27  also illustrate that almost all of the stressors we measure  have a
significant effect on at least one biotic assemblage. The only exception to this is riparian  habitat
condition. Interestingly, riparian habitat is the only stressor indicator that  does not result from
direct,  in-stream measurements. Previous research has shown that riparian habitat is  related to
many of the other stressors we measure in the streams—for example, good riparian condition is
associated with nutrient removal from agricultural runoff, control of erosion (and therefore
control  of excess sediments) and the provision of dead wood to streams to  support complex in-
stream habitat (see Figure 21). The lack of response in our relative risk analysis may have more
to do with the scale at which we assess riparian habitat (e.g., our measurements include only the
riparian habitat along the study reach where biota  are sampled—measurements made at the scale
of the whole watershed, or along an entire stream network may capture more of the disturbance
signal) than its lack of importance to ecological condition.

COMBINING EXTENT AND RELATIVE RISK

    The most  comprehensive assessment of the effect  of stressors on  biotic integrity  comes
from combining the relative extent (Figure 26) and relative risk  (Figure 27)  results—stressors
that pose the greatest risk to individual biotic assemblages will be those that are both common
(i.e., they  rank high in terms of extent in Figure 26) and whose  effects are  potentially severe (i.e.,
exhibit high relative risk ratios in Figure  27). In  order to evaluate these  combined measures of
stressor importance, we present the relative extent and relative risk results for each assemblage in
a side-by-side comparison, below.
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     A quick examination of the combined fish results (Figure 28) suggests that both non-native
species and the absence of large woody material in streams are highly important stressors to fish
biotic  integrity—both demonstrate  significant relative risks,  and both are found in more than
25%  of Mid-Atlantic  stream  length.  Elevated nutrient concentrations also  appear to  pose
significant risk to fish assemblages, but are  found less extensively (roughly 15%  of stream
length).  And the effects of acidic  deposition and acid mine drainage  are  severe when found
(relative risk > 1.5), but are relatively rare in the Mid-Atlantic (less than 5% of stream length).
                      Relative Extent of Stressors
                                 Relative Risk to Fish
         Introduced Fish
          Sedimentation
     Lack of Large Wood
        Riparian Habitat
         Mercury in Fish
              Nitrogen
           Phosphorus
         Mine Drainage
         Acid Deposition
   Orgainc Contaminants
     Acid Mine Drainage
                     0%
10%   20%   30%   40%

  % of Stream Length
50%
    2.0     2.5

Relative Risk
3.0
       Figure 28. Comparison of relative extent (left panel) and relative risk to fish (right panel).
       All stressors with relative risk values greater than 1.5 are significant (see Figure 27) for fish;
       stressors with relative risk values less than one are not shown. Stressors that represent the
       greatest  risk to fish  assemblages are characterized by high values for both extent and
       relative risk (e.g., non-native fish).
                       Relative Extent of Stressors
                                    Relative Risk to
                                  Macro in vertebrates
         Introduced Fish
          Sedimentation
      Lack of Large Wood
         Riparian Habitat
         Mercury in Fish
               Nitrogen
            Phosphorus
          Mine Drainage
         Acid Deposition
    Orgainc Contaminants
      Acid Mine Drainage
                     0%   10%   20%   30%   40%   50%

                              % of Stream Length
                                       Relative Risk
       Figure 29. Comparison of relative extent (left panel) and relative risk to macroinvertebrate
       biotic integrity (right  panel). All stressors with relative risk values greater than  1.4 are
       significant (see Figure 27) for macroinvertebrates; stressors with relative risk values less
       than one are not shown. Stressors that represent the greatest risk to macroinvertebrate
       assemblages are characterized by high values for both extent and relative risk (e.g., excess
       sediments).
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   In the case of macroinvertebrates (Figure 29), excess sediments are quite clearly the most
important stressor—they  are strongly and  significantly associated with poor macroinvertebrate
integrity, and are relatively common (ca. 28% of Mid-Atlantic stream length). As was the case
with fish, acidic  conditions can have a severe  effect on macroinvertebrates when they occur
(either from acidic deposition or acid mine drainage), but their relative extent is low (<5%) and
are therefore of lower overall importance to regional macroinvertebrate integrity.

    Elevated nutrient concentrations appear to  be of the first importance (Figure 30) to algal
assemblages—they  exhibit the  highest calculated  relative  risk ratios  in  our  data, and are
relatively common (roughly 15% of stream length). Excess sediments might be considered to be
of nearly equivalent importance—the relative risk to algal biotic integrity is lower than that of
nutrients, but they are nearly twice a common  (ca. 28% of Mid-Atlantic stream length). No other
stressor exhibited significant relative risk values for algae.
                    Relative Extent of Stressors      Relative Risk to Algae
        Introduced Fish
         Sedimentation
     Lack of Large Wood
        Riparian Habitat
        Mercury in Fish
             Nitrogen
          Phosphorus
         Mine Drainage
        Acid Deposition
   Orgainc Contaminants
     Acid Mine Drainage
                         10%   20%   30%   40%
                           % of Stream Length
   2.0     2.5
Relative Risk
       Figure 30. Comparison of relative extent (left panel) and relative risk to algal biotic integrity
       (right panel). All stressors with relative risk values greater than 1.6 are significant (see
       Figure 27) for algae. Stressors that  represent the greatest risk to algal assemblages are
       characterized by high values for both extent and relative risk.
GEOGRAPHIC TARGETING
     Throughout this assessment we have observed ecoregional differences in the condition of
MAIA flowing waters—both in ecological condition and in the relative importance of stressors.
It would be reasonable for land managers to ask, "Can we use these results to help guide (target)
how we spend our resources? Are there  sub-regions of the Mid-Atlantic that we should make a
higher priority than others? Should we be tackling different problems in different areas?"

     With the wealth of data collected  by  the  MAHA  and  MAIA  projects, we can begin to
provide answers to some of these questions. Within each ecoregion, the condition of the three
different biological assemblages, and the relative importance of different stressors, can be used
to guide stream protection and restoration goals. In this section, we provide very short summaries
of the condition assessments for each Mid-Atlantic ecoregion, and speculate briefly on what the
results might imply to  managers. This comparative  look  at the  results  of an  ecological
assessment might be termed "geographic targeting."
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                              COASTAL PLAIN
                                      Poor Ecological Condition
                     Fish
      Macro-invertebrates
                   Algae


          Introduced Fish
           Sedimentation
      Lack of Large Wood
         Riparian Habitat
          Mercury in Fish
                 Nitrogen
             Phosphorus
           Mine Drainage
        Acidic Deposition
   Organic Contaminants
      Acid Mine Drainage
Stressors
                          o
                           100
                                      20        40       60        80
                                         Percent of Stream Length
       Figure 31. Summary of Coastal Plain ecoregion condition.

   Perhaps the most striking result for the Coastal  Plain ecoregion is the large proportion of
stream length in poor condition for macroinvertebrates. Although stream managers might be
tempted to focus on macroinvertebrates (or, more specifically, on the stressors that are known to
degrade their condition), it is important to recognize that all three biological assemblages are
more  commonly  found in  poor condition in the Coastal Plain than in the Mid-Atlantic as a
whole—88% vs. 41% for macroinvertebrates, 43% vs. 31% for fish, and 41% vs. 33% for algae.
   This region has the highest proportion (relative to other ecoregions) of stream length with
severe sedimentation, and the relative risk assessment (previous section) suggests strongly that
macroinvertebrates (as well as algae) are strongly  affected by excess fine sediments. If stream
and watershed managers in the Coastal Plain were to focus on the single environmental problem
with the largest probability of improving biotic integrity, then controlling sediment inputs might
be a wise choice.
   The Coastal Plain also exhibits a very large proportion of stream miles with non-native fish
species present. While non-native  fish  species are  difficult  to eradicate once they  become
established,  measures  to limit further introductions and dispersal  might help prevent further
degradation of the biotic integrity offish assemblages in this ecoregion.
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                                  PIEDMONT
                                      Poor Ecological Condition
                     Fish
     Macro-invertebrates
                   Algae


          Introduced Fish
           Sedimentation
     Lack of Large Wood
         Riparian Habitat
          Mercury in Fish
                 Nitrogen
             Phosphorus
           Mine Drainage
        Acidic Deposition
   Organic Contaminants
     Acid Mine Drainage
Stressors
                          0
                  80
100
                                      20        40        60
                                          Percent of Stream Length
       Figure 32. Summary of Piedmont ecoregion condition.

   Like the Coastal Plain, the Piedmont ecoregion has a larger proportion of stream length in
poor condition for macroinvertebrates than for any other biological assemblage. But unlike the
Coastal Plain, the Piedmont does not have an  obvious stressor to focus on—no single stressor
known to affect macroinvertebrates (sedimentation, acidity) is particularly prevalent.
   The Piedmont is  instead characterized  by  a relatively even ranking of the most common
stressors (all of the habitat stressors and both of the nutrient stressors are found in 15% to 30% of
stream length), and the largest proportion of stream length  with non-native fish (nearly 70%).
Excessive concentrations of both nitrogen and phosphorus  are found in a larger proportion of
streams in this ecoregion than in the Mid-Atlantic as a whole, while the habitat stressors are
uncommon relative to the larger region. Even  though nutrients rank relatively low in the Mid-
Atlantic stressor  hierarchy (Figure 26),  a focus on them in the Piedmont might be warranted.
Interestingly, algae are the only assemblage in  the Piedmont where the proportion of streams in
poor condition is substantially higher than in the Mid-Atlantic as a whole. Our relative risk
analysis suggests that high nutrient concentrations pose a significant risk  to algal biotic integrity,
and high proportions  of poor stream condition for both algae and nutrients  in the Piedmont
certainly  suggest  that a focus on nutrients would be beneficial in improving streams  in the
region.
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                                   VALLEYS
                                      Poor Ecological Condition
                     Fish
     Macro-invertebrates
                   Algae


          Introduced Fish
           Sedimentation
     Lack of Large Wood
         Riparian Habitat
          Mercury in Fish
                 Nitrogen
             Phosphorus
           Mine Drainage
        Acidic Deposition
   Organic Contaminants
     Acid Mine Drainage
Stressors
                          o
                            100
                                      20        40        60        80
                                          Percent of Stream Length
       Figure 33. Summary of Valley ecoregion condition.

   In common with both of the other lowland ecoregions (the Coastal Plain and Piedmont) the
Valley  ecoregion  has  a  larger  proportion  of  stream  length  in  poor  condition  for
macroinvertebrates than for any other biological assemblage, although poor condition is found in
all three assemblages in a slightly larger proportion of streams in the Valley ecoregion than in the
Mid-Atlantic as a whole—45% vs. 41% for macroinvertebrates, 33% vs. 31% for fish, and 34 %
vs. 33% for algae.
   Like the Piedmont, the Valley ecoregion is characterized by a relatively even ranking of the
most common stressors (all of the habitat Stressors, as well as nitrogen, are found in 25% to 40%
of stream length),  but all  have greater extents  here  than in  the Piedmont. There  has  been
substantial monitoring and research work to  show that intact  riparian areas can help prevent
nitrogen  runoff (largely from  agricultural fertilizers) from reaching streams. Protecting and
restoring riparian areas in the Valley  ecoregion could well lead to improvements in all of the
most common stressors in the region—controlling sediment and nitrogen inputs, and providing
additional large woody material to streams deficient in wood. Managers might well look at the
summary in Figure 33  and conclude that focusing their restoration and remediation resources on
improving riparian condition could provide the single biggest improvement in stream condition.
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                                       RIDGES
                                         Poor Ecological Condition
                       Fish
        Macro-invertebrates
                      Algae


             Introduced Fish
              Sedimentation
        Lack of Large Wood
            Riparian Habitat
             Mercury in Fish
                   Nitrogen
                Phosphorus
              Mine Drainage
           Acidic Deposition
      Organic Contaminants
        Acid Mine Drainage
Stressors
                                      20       40        60        80
                                         Percent of Stream Length
                            100
       Figure 34. Summary of Ridge ecoregion condition.

   The Ridge  ecoregion might be considered to be in the best condition of any Mid-Atlantic
ecoregion. All  three biological assemblages are found in poor condition in less than 25% of
stream length—well below the region-wide proportion for the Mid-Atlantic as  a whole. It is
easier to  decide what not to focus on in this  ecoregion than to identify an obvious target for
restoration resources. Nutrients, for example, are a  problem in 4-5% of stream length, and are
probably best managed on a site-specific basis,  rather than through a region-wide effort.

   As one  of the few ecoregions where the proportion of stream length with poor fish
assemblages is higher than the proportion of macroinvertebrate and algal assemblages, focusing
on those stressors that represent the greatest relative  risk to fish would make sense. Reducing the
extent  of non-native fish, for example,  may  be a  cost effective strategy for improving fish
assemblages.

   Alternatively, regional managers might look at the  relatively high biotic integrity in this
ecoregion, and conclude that efforts to conserve remaining areas of  good ecological condition
should focus on this ecoregion.
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              NORTH AND CENTRAL APPALACHIANS
                                     Poor Ecological Condition
                    Fish
     Macro-invertebrates
                  Algae


          Introduced Fish
           Sedimentation
     Lack of Large Wood
         Riparian Habitat
          Mercury in Fish
                Nitrogen
            Phosphorus
          Mine Drainage
        Acidic Deposition
   Organic Contaminants
     Acid Mine Drainage
Stressors
                         o
                          100
                                     20       40       60        80
                                        Percent of Stream Length
      Figure 35. Summary of North and Central Appalachian ecoregion condition.

   The  North  and Central Appalachians,  like the  Ridge ecoregion,  are in relatively good
condition compared to the Mid-Atlantic as a whole (Figure 35). Only fish assemblages are found
in poor condition in a larger proportion of stream length here (40%) than in the entire region
(31%).

   Relatively rare problems with sedimentation and nutrients might well be responsible for the
small  proportion of algal assemblages found in poor condition. But mine drainage and acidic
deposition, both of which put fish and macroinvertebrate assemblages  at risk (Figure 27), are
more extensive in the North and Central Appalachians than in the rest of the Mid-Atlantic (with
the exception of mine drainage in the Western Appalachians, below). The combined effects of
acidification and (non-acidic) mine drainage could well explain the large proportion of stream
length with poor fish IBI scores in the region. These two problems are likely to occur in different
places (acid deposition effects are found in otherwise pristine upland watersheds; non-acidic
mine drainage problems, like the transport of coal fines, are found in lower elevation watersheds
with mines in their headwaters).
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                          WESTERN APPALACHIANS
                                         Poor Ecological Condition
                       Fish
         Macro-invertebrates
                      Algae


             Introduced Fish
              Sedimentation
         Lack of Large Wood
            Riparian Habitat
             Mercury in Fish
                   Nitrogen
                Phosphorus
              Mine Drainage
           Acidic Deposition
      Organic Contaminants
         Acid Mine Drainage
Stressors
                                      20        40        60       80
                                         Percent of Stream Length
                           100
       Figure 36. Summary of Western Appalachian ecoregion condition.

   The Western Appalachian ecoregion has high proportions of stream length in poor condition
for nearly all of the common stressors (Figure 36). But the results here are not all bad news—fish
assemblages in this ecoregion are in poor condition in a smaller proportion of streams than in the
Mid-Atlantic as a whole, and the extent of non-native fish species is lower than for any other
ecoregion. Problems with biotic integrity are more common in the macroinvertebrate and algal
assemblages in the Western Appalachians, and this allows managers to focus on the stressors
likely to affect those assemblages.

   Perhaps the most obvious stressor to focus  on  in this ecoregion is excess  sedimentation.
Because it puts both macroinvertebrate and algal biotic integrity at  risk (Figure 27), and is a
likely side effect  of non-acidic mine drainage, sedimentation may be  a reasonable target for
future stream management actions. The extent of acid mine drainage in this heavily-mined region
is  quite low—perhaps  as a result  of control  measures to control metals and acidity—but
additional measures to control the input and movement of sediments from coal mining operations
in  Western Appalachian streams (e.g., improving riparian areas, also commonly degraded in the
region) could well lead to improved biotic integrity.
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CONCLUSIONS AND FURTHER DIRECTIONS

   For more than a decade, numerous organizations have decried the lack of useful information
available for producing a report card on the nation's environment. There have been two recent
efforts, the Heinz Center's State of the Nation's Ecosystems report and EPA's own Draft Report
on the Environment (see Appendix C) to produce a national report card. Both reports conclude
that, in order to produce a true  assessment of the nation's environment, monitoring efforts must
be focused on  collecting comparable  indicators,  based on consistent field protocols,  and
implement a sample survey design that produces a representative set of sample sites. This MAIA
State of the Flowing Waters Assessment, and the research/monitoring program that produced its
data, provides a regional-scale template for how a national report card might one day be created.

   For a report card to be effective, the information it provides must be used to make decisions
and to set future directions. An  effective  report card should fulfill two objectives. First, it should
describe whether there is a problem, how big the problem is, and whether the  problem  is
geographically localized or widely distributed. Second, it should give some clues  about what
needs  to be changed in  order to improve ecological condition.  Our MAIA  assessment has
discussed both aspects.

   Are there problems in the Mid-Atlantic region? We have used biological indices, based on
fish, macroinvertebrate and algal assemblages, to answer this question. The information can be
viewed from two perspectives: what is going well (i.e., how much of the resource is  in good
condition)  and what is not going well (i.e., how much of the resource is  in poor condition).
Regardless of which assemblage is examined, the Mid-Atlantic region appears to be in  trouble.
For none of the  three assemblages is more than 30% of the stream resource classified  in good
condition, and more than 30% of the resource is consistently assessed as in poor condition:

                                      Percent of Stream Resource in:
       Assemblage                                  .   ,              _,
                         /-   j /->  1-4.-            Marginal              Poor
                         Good Condition         „  ° .             „   ,. .
                                                Condition           Condition

           Fish                 21                  42                  31

    Macroinvertebrates          26                  33                  41

          Algae                30                  37                  33
   Historically, we have focused primarily on  streams in either good or poor condition, but
perhaps a third strategy is to concentrate our attention on the proportion of stream resource in the
marginal category. Following the traditional medical concept of triage, we could focus on trying
to prevent streams and rivers from slipping into the poor category, by focusing our attention on
those that are now considered marginal. As the table above suggests, a large proportion of the
resource falls into this category.


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PROTECTION vs. RESTORATION

    Are  problems  in  the Mid-Atlantic  region  localized  or  widely  distributed? Are there
subregions in good condition that should be targets for protection efforts? Are there subregions
in particularly  poor condition  that would be targets for restoration?  Based on  a protection
strategy, the Ridge ecoregion and the North Central Appalachian  ecoregion would be targets
Figure 37). Each of these regions had over 40% of the flowing waters in good condition for at
least one of the three biological assemblages.
                            Ridge Ecoregion
                              Poor Ecological Condition
                   North/Central Appalachian Ecoregion
                            Poor Ecological Condition
                  Fish
     Macro-invertebrates
                 Algae


          Introduced Fish
           Sedimentation
      Lack of Large Wood
          Riparian Habitat
          Mercury in Fish
               Nitrogen
            Phosphorus
           Mine Drainage
         Acidic Deposition
     Organic Contaminants
       Acid Mine Drainage
Stressors
Stressors
                             20      40      60      80
                             Percent of Stream Length
                           20     40     60     80
                            Percent of Stream Length
                                                                                           100
       Figure  37. Combined results for two subregions that could be targeted for protection
       efforts—The Ridge and North/Central Appalachian ecoregions.

    If one uses a restoration strategy, and focuses on the subregions in the poorest condition, the
Valley, Western Appalachian, Piedmont and Coastal Plain ecoregions could all be targeted. Each
of these ecoregions has over 40% of the stream/river resource in poor condition for at least one
biological assemblage.  Notice that these two  strategies are mutually exclusive—no ecoregion
would be identified for both protection and restoration. Four out of six ecoregions are identified
by the restoration strategy, which is a not particularly helpful finding if our objective is to focus
the restoration effort, but it certainly does reinforce the idea that, overall, Mid-Atlantic flowing
waters are in trouble. If more  stringent criteria are use—at  least two of the three  biological
assemblages must show greater than 40% of the stream resource in poor condition—then only
two subregions emerge as high priorities: the Coastal Plain and Western Appalachian ecoregions
(Figure 38). These more stringent criteria yield a more focused geographic target for restoration
efforts.
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   With what sorts  of stressors are the Mid-Atlantics  problems  associated?  Our analyses
indicate that excess sedimentation, increased nutrients, non-native fish species, and the absence
of large woody material in streams  all pose significant relative risks, and are among the most
prevalent stressors throughout the region. Within the Coastal Plain, one of the two regions on the
potential priority list for restoration,  several stressors should be considered: non-native fish,
excess sedimentation, and increased nutrients all represent significant relative risks and are found
extensively  throughout the ecoregion.  Within the Western Appalachian ecoregion, both excess
sediment and  lack of large wood are  widespread stressors associated with significant relative
risks. Mine drainage, while posing a  somewhat lower relative risk, certainly is widespread within
the Western Appalachian ecoregion.
                          Coastal Plain Ecoregion
                             Poor Ecological Condition
                      Western Appalachians Ecoregion
                            Poor Ecological Condition
                  Fish
       Macro-invertebrates
                 Algae


          Introduced Fish
           Sedimentation
       Lack of Large Wood
          Riparian Habitat
          Mercury in Fish
               Nitrogen
            Phosphorus
           Mine Drainage
         Acidic Deposition
     Organic Contaminants
       Acid Mine Drainage
Stressors
Stressors
                             20     40      60     80
                              Percent of Stream Length
                           20     40     60     80     100
                            Percent of Stream Length
       Figure 38. Combined results for two subregions that could be targeted for restoration
       efforts—the Coastal Plain and Western Appalachian ecoregions.

    The simple  conclusions reached here are based on the kind of unbiased  assessment that
probability monitoring  can  provide. Any environmental protection and  restoration efforts are
likely to use these results as only one factor, among many,  in making decisions on how to move
forward. Other  considerations will include  socio-economic  and political factors, as well as
extensive  public input  on priorities. But all of these other factors  can be more effectively
considered if environmental managers and the public are  well informed about the state of the
environment—educated evaluation, based on unbiased scientific assessment, should  be a key
ingredient in making sound environmental and economic decisions. Because of their importance,
similar environmental reports should become high priority  precursors to the making of effective
environmental policies  and  decisions. We hope that the approach demonstrated here will help
guide the design of such future regional and national assessments.
    MID-ATLANTIC FLOWING WATERS ASSESSMENT
                                                Page 57

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APPENDIX A:  THRESHOLDS
     Perhaps the most critical step in creating the kind of assessment presented in this report is
the setting of thresholds—how do we decide, in the most  scientifically justifiable way, which
sites to place in Good, Marginal and Poor classes? As scientists, our role is to  avoid being
judgmental, and letting our own opinions influence the labels we place on individual sites  or
regions. We need an approach that relies entirely on data, not opinion, and lets the data "answer
the questions" about condition classes.

     Throughout this report we use what is known as the "reference site approach" to identify
criteria. For nearly  every variable (biological index, chemical concentration, or habitat index) we
identify a set of reference sites, and use the distribution of variable values for this set of sites  to
define what "good" looks like. The only departures from this approach are for chemical variables
(like acid neutralizing capacity) whose values have special  meaning—e.g., any ANC value less
than zero defines the class "acidic" chemically, and doesn't require any further classification.

     We feel strongly that circular thinking, a common problem in any discussion  of reference
condition, should be avoided at all costs. The most common way that circularity finds its way  in
to the science or reference condition is through the use of biological data to identify reference
sites that are then used in interpreting the same biological data. This approach essentially asks,
"based on the biology, which are the best sites?",  and then uses data from those "best" sites  to
answer  the  question, "for the  set of reference sites identified,  how would I characterize the
biology?" For this reason, we choose to define "reference" differently for each index or variable
we want to classify, always avoiding the use of the variable  itself (or elements  of  it, if the
variable is an index) to define reference condition. For example, if we want to classify scores for
our fish Index of Biotic Integrity, we need to avoid using any fish data to define which sites are
in reference condition.

     The details of how we  define "reference", as well as how we chose to use the reference
distribution to  set  thresholds, and  how we incorporate  potential ecoregional  differences, are
presented below for each indicator used in this report. For each indicator where a reference site
approach is appropriate, we first  identified  the  independent  criteria that could be used  to
determine reference condition, then examined the range of index or variable values that were
found in all of the   sites meeting those  criteria. Each of these exercises produced a distribution
like the one shown in Figure A-l. Once this distribution was established, we consistently used
the 25th percentile value to set the lower limit on "Good" condition. The 1st  percentile was used
as the threshold below which values were deemed "Poor." Values between the  1st  and 25th
percentiles were classified as "Marginal". In this  hypothetical example, higher scores indicate
better condition—if an indicator worked in reverse (e.g., for phosphorus and nitrogen,  higher
values indicate excess nutrients), we used the 75th and  99th percentile values  in an exactly
analogous way to define the classes.

     There is nothing magical about our choice of the 1st and 25th (or 99th and 75th) percentiles.
EMAP data allow us to set these thresholds anywhere within the distribution .  We chose to be
consistent among all of the indicators we assess, and to use these thresholds because they have
some understandable statistical meaning. Sites we classify as in "Poor" condition for any given

    MID-ATLANTIC FLOWING WATERS ASSESSMENT                               1

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indicator have a greater than 99% probability of being outside of (or more extreme than) our
reference distribution. Sites classified  as "Good" have  a 75% probability of being within the
reference distribution.  Many  other thresholds  are possible, and  are in fact in use in other
programs. The 25th  percentile  is quite commonly used as a line separating "Good" from
"Marginal." Some bioassessments use the 5th, or even the 10th, percentile as a threshold to define
"Poor"  condition,  often invoking the  argument that our  knowledge of  what constitutes
"reference" is imperfect and we are bound to include some sites in the reference distribution that
are not truly the least disturbed in a region. For this reason, it can be argued, it is reasonable for
some of the reference sites to have scores that we would label as "Poor." This is an issue that will
continue to be debated, but thus far there is  no  scientific consensus. We have chosen to use a
conservative estimate of the Marginal/Poor threshold because of its statistical power to define
what we mean by "Poor."

                               Reference Distribution




0)
0
0
CO
X
0
c




1 UU

90

80 -

70 -
60 -

50 -

/in

Percentiles:
o gg*11





" 95th







75*
50th 1
2gth Good
t
cih Ma rq, rial
0 ,
n -si *
1 Poor
     Figure A-l. Example of the range of scores in reference sites (for a hypothetical indicator
or index), and percentile values of the reference distribution. In this assessment, we use the 25th
percentile as threshold between Good and Marginal condition, and the 1st percentile as the line
between Marginal and Poor condition.
   MID-ATLANTIC FLOWING WATERS ASSESSMENT
Page A-2

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        MACROINVERTEBRATE INDEX OF BIOTIC INTEGRITY

IBI construction: We modified an Index of Biotic Integrity developed for the Mid-Atlantic
Highlands by Klemm et al. (2003), for use in  the Mid-Atlantic region as a whole.  We
examined the Klemm et al. metrics for responsiveness across the region, and eliminated one
(Plecoptera richness) because it  does not respond well to human  disturbances  as Mid-
Atlantic streams become very large. The remaining metrics were re-scored and the final IBI
divided  into classes  according to  the reference distribution. As in Klemm et al., different
metric  scoring criteria were  developed for pool-dominated streams and riffle-dominated
streams. One major  concern in developing a Mid-Atlantic IBI for macroinvertebrates was
finding metrics that were responsive both in the uplands  and in the Coastal Plain. Our final
list of metrics is very closely aligned with those of an  IBI developed specifically for the
Coastal Plain by Maxted et al. (1999).

Reference definition: We used the  process described by Waite et al. (2000) for the Mid-
Atlantic Highlands,  to  define reference sites for macroinvertebrates. The  chemical  and
physical variables used to identify  candidate reference included ANC (non-acidic sites only),
sulfate  (sites with no  effects  of mine  drainage),  phosphorus and nitrogen (no excess
nutrients), chloride  (high chloride  sites  excluded—chloride is  an indicator of general
watershed disturbance),  and overall habitat quality (based on Rapid Bioassessment Protocol
[RBP] measures of habitat).

Thresholds: Based on the reference  distribution, the classification thresholds for the MAIA
macroinvertebrate IBI were:
                  Classes
Macroinvertebrate IBI Thresholds
              Good Condition
            Marginal Condition

              Poor Condition
        62.25 <  IBK 100
         4KIBK62.25
           0
-------
reference  included ANC (non-acidic sites only),  sulfate  (sites  with no effects of mine
drainage), phosphorus  and nitrogen (no excess nutrients),  chloride  (high chloride  sites
excluded—chloride is an indicator of general watershed disturbance), and  overall  habitat
quality (based on Rapid Bioassessment Protocol [RBP] measures of habitat).

Thresholds: Based on the reference distribution, the classification thresholds for the MAIA
algal IBI were:
                   Classes
Algal IBI Thresholds
               Good Condition
             Marginal Condition
               Poor Condition
   58
-------
IBI Threshold for:
Good Condition
Marginal Condition
Poor Condition
Upland
Streams
59 < IBI < 100
32 < IBI < 59
0
-------
                               ACID DEPOSITION

Index construction: We used ANC values for sites that had no indicators of mine drainage
(see above) to determine their status with respect to acid rain.

Thresholds: Sites unaffected by mine drainage were further classified by their ANC values:
sites with ANC < 0 were classified as chronically  acidic; those with 0 < ANC < 50 jieq/L
were classified as being episodically acidic.
                                   PHOSPHORUS

Index construction: We used measured values of total phosphorus as indicators of nutrient
enrichment in streams.

Reference definition:  Reference sites were identified as those with less than 10% non-
natural land cover in their watersheds. Sites with more than 10% combined landuse classified
as urban, agricultural or mining were eliminated from the candidate reference list. A total of
317 sites met these criteria, but none were in the Coastal Plain. Because we were unable to
determine whether phosphorus thresholds that were appropriate for  the rest of the Mid-
Atlantic were appropriate  for the Coastal  Plain,  we used  a separate approach for this
ecoregion. We used published EPA criteria (as used for  the Mid-Atlantic Highlands—see
U.S. EPA 2000 report in Appendix C) for phosphorus in the Coastal Plain.
Thresholds (concentrations in |ig/L):
          Phosphorus
         Threshold for:
   Non-Coastal Plain
       Ecoregions
Coastal Plain Ecoregion
        Good Condition

      Marginal Condition

        Poor Condition
0 < Total Phosphorus < 14    0 < Total Phosphorus ^50

14 < Total Phosphorus < 63  50 < Total Phosphorus < 100

  Total Phosphorus > 63       Total Phosphorus > 100
                                    NITROGEN

Index construction: We used measured values of total nitrogen as indicators of nutrient
enrichment in streams.

Reference definition:  Reference sites were identified as  those with less than 10% non-
natural land cover in their watersheds. Sites with more than 10% combined landuse classified
as urban, agricultural or mining were eliminated from the candidate reference list. A total of
   MID-ATLANTIC FLOWING WATERS ASSESSMENT
                                                 Page A-6

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317 sites met these criteria, but none were in the Coastal Plain. Because we were unable to
determine whether nitrogen thresholds that were appropriate for the rest of the Mid-Atlantic
were appropriate  for the Coastal  Plain, we  used  a  separate approach for  this ecoregion.
Criteria developed for the Mid-Atlantic  Highlands Report (see U.S. EPA 2000 in Appendix
C) were used in the Coastal Plain—the thresholds for phosphorus listed above for the Coastal
Plain were multiplied by 15 (the ratio of nitrogen to phosphorus in algae)  to create nitrogen
criteria for this ecoregion.
Nitrogen Thresholds (concentrations in |ig/L):
       Nitrogen Threshold
              for:
    Non-Coastal Plain
        Ecoregions
Coastal Plain Ecoregion
        Good Condition

      Marginal Condition

        Poor Condition
   Total Nitrogen < 425         Total Nitrogen < 750

425 ^Total Nitrogen < 1200   750 ^Total Nitrogen < 1500

   Total Nitrogen > 1200        Total Nitrogen > 1500
                                EXCESS SEDIMENT

Index construction: We used the "Relative Bed Stability Index" of Kaufmann et al. (1999)
as an indicator of excess fine sediments in streams. This index compares the observed mean
substrate size to each stream's  expected substrate size, based on  stream bed  shear stress
during bank-full stage (calculated from stream size, slope, channel complexity, large wood
and bed  armoring). Values of the sediment index range from negative to positive, with
theoretical expectations near values of zero.

Reference definition: Reference sites  were identified as those meeting the same chemical
criteria as for the macroinvertebrate and algal indices, in addition  to having good riparian
condition (see below). A total  of 42  sites met these  criteria. Because the Piedmont and
Coastal  Plain ecoregions have  much  lower  gradient streams  than the regions for which
Kaufmann's bed stability index was  developed, we  were particularly  concerned about
defining expectations for these ecoregions. Unfortunately, there were insufficient numbers of
reference sites in the Piedmont or Coastal Plain to determine whether thresholds needed to be
determined separately for these low-gradient ecoregions. Rather than apply an inappropriate
threshold, we chose to use the reference sites to set criteria for higher gradient ecoregions,
and best professional judgment to set criteria for the Piedmont and Coastal Plain.
   MID-ATLANTIC FLOWING WATERS ASSESSMENT
                                                   Page A-7

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Sediment Thresholds:
Sediment Threshold
for:
Good Condition
Marginal Condition
Poor Condition
Non-Piedmont and Non-
Coastal Plain Ecoregions
Index > -0.3
-0.9 <_Index < -0.3
Index < -0.9
Piedmont and Coastal Plain
Ecoregions
Index > -1.5
-2.0<_Index<-1.5
Index < -2.0
                         LARGE WOODY MATERIAL

Index construction: We used areal estimates of wood in streams, collected according to the
EMAP stream and river protocols  (see Lazorchak et al. references in  Appendix C),  as
indicators of large wood in streams. These estimates are calculated as the proportion of the
area of the wetted stream channel covered by wood, and vary from 0 to 1. Details of the
calculation of the index are covered in Kaufmann (1999).

Reference definition:  Reference sites were identified as those with less than 10%  non-
natural land cover in their watersheds, and with excellent riparian habitat (see below—we
used a riparian habitat index value of 0.8 or greater to identify excellent riparian habitat). A
total of 50 sites met these criteria.
Large Wood Thresholds (units are proportion of wetted stream area):


                      Classes
                 Good Condition

                Marginal Condition

                  Poor Condition
Area of Large Wood (ALW)
        Thresholds
   2.2% < ALW < 100%

     0% < ALW < 2.2%

        ALW = 0%
   MID-ATLANTIC FLOWING WATERS ASSESSMENT
                                Page A-8

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                      RIPARIAN HABITAT CONDITION

Index construction: We used the riparian habitat condition index described by Kaufmann et
al. (1999) as an indicator of the riparian condition of Mid-Atlantic flowing waters. This index
combines quantitative measures of the complexity of riparian vegetation (i.e., presence  of
multiple layers of trees and  shrubs), canopy cover, and visible human disturbances in the
riparian area. The index is unit-less and ranges from 0 to 1.

Reference definition:  Reference sites were identified as those meeting the same chemical
criteria as for the macroinvertebrate and algal indices, in addition to expected amounts of fine
sediments (Bed Stability Index >  -1;  see discussion above), and little or no  direct  human
disturbance in the riparian area. A total of 31 sites met these criteria.
Riparian Habitat Index Thresholds:

                     Classes
                  Good Condition

                Marginal Condition

                  Poor Condition
Riparian Habitat Index Thresholds
           Index > 0.61

        0.5 < Index < 0.61

           Index < 0.5
   MID-ATLANTIC FLOWING WATERS ASSESSMENT
                                    Page A-9

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                          CONTAMINANTS IN FISH

Index construction: Composite fish samples collected at each site (where possible); the goal
was to collect common species found throughout the MAIA region, and that are likely to be
abundant in a majority of streams. Crews attempted to collect two contaminant samples from
each stream reach: (1) a primary target species (species whose adults are small, such as
minnows, sculpins and darters); and (2) a secondary target species (species with large adults,
such as suckers, bass, trout, sunfish and carp). Details of sampling and sample handling can
be found in the MAIA field  manual (Lazorchak et al. 1998). Mercury and organic
contaminant concentrations were measured in homogenized whole fish collected by  these
methods.

Reference definition: Reference sites were not used in setting contaminant thresholds. We
instead used published threshold values based on wildlife risk from Lazorchak et al. (2003).
These thresholds were calculated specifically for the Mid-Atlantic region, based on toxicity
studies of commonly occurring wildlife species that rely almost exclusively on fish for their
diets. We chose to use the values for American River  otter (see table below). Stream and
river sites were classified into one of three classes:

   1. No fish collected (or no fish present)
   2. Neither primary nor secondary target species exceeds American River otter criterion
      ("good" condition)
   3. One or both fish samples (primary and secondary) exceeds American River criterion
      for one or more contaminants ("poor" condition)

Thresholds:  Wildlife criteria values  for mercury  and organic contaminants  (reproduced
from Lazorchak et al. (2003); concentrations in |ig/g offish):
Contaminant
Mercury
Chlordane
DDT and metabolites
Dieldrin
PCBs

Detection Limits
0.025
0.002
0.002
0.002
0.002
Wildlife
Otter
0.10
1.14
0.49
0.03
0.18
values (|ig/g
Mink
0.07
0.83
0.36
0.02
0.13
offish)
Kingfisher
0.03
0.005
0.02
0.36
0.44
   MID-ATLANTIC FLOWING WATERS ASSESSMENT                           Page A-10

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APPENDIX B:  CALCULATING RELATIVE RISK

              DEFINITION AND EXAMPLE CALCULATION

   We define relative risk as the ratio of two probabilities:

                     Pr(Poor IBI score, given Poor Stressor Score)
                     Pr(Poor IBI Score, given Good Stressor Score)

   where the numerator and denominator are conditional probabilities of a poor IBI score under
poor (numerator) vs. good (denominator) Stressor conditions.

   As an example we calculate the relative risk of excess sediments for macroinvertebrates. We
begin by collecting together all sample sites having the same combinations of good and poor
condition for macroinvertebrate IBI and for sedimentation.

                                           Sediment Condition
                      Number of Sites
                                           Good      Poor

                , ,    .    . A  .     Good       78         8
                Macromverte orate
                   Condition       „          cn        ,,
                                  Poor       50        55
   Next, we estimate the total number of stream kilometers in each of the table's classes, by
summing the sampling weights for all of the sites in each class.

                                           Sediment Condition
                 Estimated stream length
                         (km)
                                            Good      Poor

                , ,    .    ,  ,  ,    Good     22697.5    3934.1
                Macromverte orate
                   Condition                27446.3    27678.7
   The next step is to express the stream lengths as percentages of the total. The sum of stream
weights across all four classes is 81756.6 km. Only a small percentage of streams have Good IBI
when Sediment is Poor.
   DRAFT MID-ATLANTIC FLOWING WATERS ASSESSMENT                  Page B-1

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                                          Sediment Condition
          % of Stream Length
   Macroinvertebrate
       Condition
Good

Poor

Sum
Good

27.8%

33.5%

61.3%
 Poor

 4.8%

33.9%

38.7%
                                                                     Total: 100%
   Now, we estimate the probability, or "risk", of a poor IB I, for poor sediment sites only, as
being equal to 33.9/38.7 = 0.876.  Likewise, the risk of a poor IBI in streams with good sediment
conditions is given by 33.5/61.3 = 0.546. Comparison of these two risks shows that a poor IBI
has a greater risk of occurring when sediment conditions are poor (risk = 0.876) then when
sediment conditions are good (risk = 0.546).

   The relative risk ratio expresses this relationship in a single number, the ratio of the poor-
stressor IBI risk to the good-stressor IBI risk—that is, the relative risk = 0.876/0.546 = 1.60.

   The way we interpret this number in this assessment is that a poor  IBI is  1.60 times more
likely to occur when sediment conditions are poor than when they are good.

             CONFIDENCE INTERVALS FOR RELATIVE RISK

   We used  large-sample approximations to  construct  confidence intervals  for relative risk
(RR). Large-sample distributions for estimated RR are better approximated using  the  log
transformation to produce symmetry about the null value of 1.0, and to ensure that confidence
bounds remain within the domain of the  estimated parameter (see Lachin reference in Appendix
C). Given an estimate of the standard error for the estimated log(RR), percentiles of the standard
normal distribution were then used to construct a conventional large-sample confidence interval
for log(RR).  Finally, interval endpoints  were back-transformed  to give  the corresponding
confidence interval for RR.

   To  estimate the  standard error of log(RR),  we used a Taylor linearization  method (see
Sarndal et al. reference in Appendix C), which accounts for the unequal inclusion probabilities of
the MAIA sampling design.
   DRAFT MID-ATLANTIC FLOWING WATERS ASSESSMENT
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APPENDIX C: FURTHER READING

         ENVIRONMENTAL MONITORING AND ASSESSMENT

                                 PROGRAM

Environmental Monitoring and Assessment Program website: http://www.epa.gov/emap2/

Stevens  Jr.,  D.L.  1994.  Implementation of a  national  monitoring program.  Journal of
      Environmental Management 42:1-29.

Paulsen, S.G., R.M.  Hughes,  and  D.P. Larsen.  1998. Critical  elements in  describing and
      understanding our nation's aquatic resources. Journal of the American Water Resources
      Association 34:995-1005.

Hughes, R.M., J.L. Stoddard, and S  G. Paulsen. 2000. A national, multiassemblage, probability
      survey of ecological integrity. Hydrobiologia 422/423:429-443.

Landers, D.H., R.M. Hughes, S.G.  Paulsen, D.P.  Larsen, and J.M.  Omernik. 1998. How can
      regionalization  and  survey  sampling make  limnological  research  more relevant?
      Verhandlungen Internationale Vereinigung Limnologie 26:2428-2436.

Lazorchak, J.M.,  B.H. Hill, O.K. Averill, D.V. Peck,  and  D.J. Klemm,  editors.  2000.
      Environmental Monitoring and Assessment Program-Surface Waters: Field Operations
      and Methods for Measuring the Ecological  Condition of Non-Wadeable Rivers and
      Streams. U.S. Environmental Protection Agency, Cincinnati, OH.

Lazorchak, J.M., D.J. Klemm, and D.V. Peck. 1998. Environmental Monitoring and Assessment
      Program-Surf ace Waters:  Field Operations and Methods for Measuring the Ecological
      Condition of Wadeable  Streams.  EPA/620/R-94/004,  U.S.  Environmental  Protection
      Agency, Washington, DC.

                         SAMPLE SURVEY DESIGN

Herlihy, A.T., D.P. Larsen, S.G. Paulsen, N.S. Urquhart, and B.J. Rosenbaum. 2000. Designing a
      spatially balanced, randomised site selection process for regional stream surveys: The
      EMAP Mid-Atlantic Pilot Study. Environmental Monitoring and Assessment 63:95-113.

Olsen, A.R., J. Sedransk, D.Edwards, C.A. Gotway, W. Liggett, S. Rathbun, K.H. Reckhow, and
      L.J. Young. 1999. Statistical issues for monitoring ecological and natural resources in the
      United States. Environmental Monitoring and Assessment 54:1-45.

Stevens Jr., D.L. 1997. Variable density grid-based  sampling designs for continuous spatial
      populations. Environmetrics 8:167-195.

Stevens Jr., D.L., and A.R.  Olsen. 1999. Spatially  restricted  surveys over time for aquatic
      resources. Journal of Agricultural, Biological, and Environmental Statistics 4:415-428.

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Stevens Jr., D.L., and N.S. Urqhart. 2000. Response designs and support regions in sampling
       continuous domains. Environmetrics 11:11-41.

                            ECOLOGICAL REGIONS

Omernik, J.M. 1987. Ecoregions of the conterminous United States. Annals of the Association of
       American Geographers 77:118-125.

Woods, A.J., J.M.  Omernik,  D.D. Brown,  and C.W.  Kiilsgaard.  1996.  Level III and IV
       Ecoregions of Pennsylvania and the Blue Ridge Mountains, the Ridge and Valley, and
       the Central Appalachians of Virginia, West Virginia, and Maryland. EPA/600R-96/077,
       U.S.  Environmental Protection  Agency, National Health and Environmental  Effects
       Research Laboratory, Corvallis, OR.

                               BIOTIC INTEGRITY

Hill, B.H.,  A.T. Herlihy,  P R. Kaufmann, R J.  Stevenson, F.H. McCormick, and C.  Burch
       Johnson. 2000. Use of periphyton assemblage data as  an index of biotic integrity. Journal
       of the North  American Benthological Society 19:50-67.

Hughes, R.M., P.R.  Kaufmann, A T. Herlihy, T.M. Kincaid, L. Reynolds, and D P. Larsen. 1998.
       A process for developing and evaluating indices of fish assemblage integrity. Canadian
       Journal of Fisheries and Aquatic Science  55:1618-1631.

Hughes, R.M.,  D.P. Larsen, and J.M. Omernik. 1986. Regional  reference sites: A method for
       assessing stream potentials. Environmental Management 10:629-635.

Karr, J.R. 1981. Assessment of biotic integrity using fish communities. Fisheries 6:21-27.

Karr,  J.R.,  and E.W.  Chu. 1997.  Biological  monitoring and assessment:  using multimetric
       indexes effectively. EPA/235/R97/001, University of Washingon, Seattle, WA.

Karr, J.R., and D.R. Dudley. 1981. Ecological perspective on water quality goals. Environmental
       Management 5:55-68.

Klemm, D.J., K.A.  Blocksom,  F. A. Fulk, A.T. Herlihy, R.  M. Hughes, P.R. Kaufmann, D.V.
       Peck, J.L.   Stoddard,  and W.T. Thoeny.  2003.  Development  and evaluation  of  a
       macroinvertebrate biotic integrity index (MBII) for regionally assessing  Mid-Atlantic
       Highlands streams. Environmental Management 31:656-669.

Larsen, D.P., and AT.  Herlihy.  1998. The dilemma of sampling streams for macroinvertebrate
       richness. Journal of the North American Benthological Society 17:359-366.

Maxted, J.,  M.T. Barbour, J. Gerritsen, V. Poretti, N. Primrose,  A. Silvia, D. Penrose, and R.
       Renfrow. 1999. Assessment Framework for Mid-Atlantic Coastal Plain Streams Using
       Benthic  Macroinvertebrates. NHEERL-NAR-X-255, U.S. Environmental  Protection
       Agency, Narraganset, RI.

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McCormick, F.H., R.M.  Hughes, P.R. Kaufmann, D.V. Peck, J.L.  Stoddard, and A.T. Herlihy.
       2001. Development of an index of biotic integrity for the Mid-Atlantic Highlands region.
       Transactions of the American Fisheries Society 130:857-877.

Pan, Y.,  RJ. Stevenson, B.H.  Hill, and A.T. Herlihy. 2000. Ecoregions and benthic  diatom
       assemblages in Mid-Atlantic Highlands streams, USA. Journal of the North American
       Benthological Society 19:518-540.

Pan, Y., RJ. Stevenson, B.H. Hill, P.R. Kaufmann, and A.T. Herlihy. 1999. Spatial patterns and
       ecological determinants of benthic algal assemblages in Mid-Atlantic Highlands streams.
       Journal of Phycology 35:460-468.

Plafkin,  J.L.,  M.T.  Barbour,  K.D.  Porter,  S.K.  Gross,  and R.M. Hughes.  1989.  Rapid
       Bioassessment Protocols  for  Use in  Streams and Rivers. EPA/440/4-89/001, U.S.
       Environmental Protection Agency, Washington DC.

Roth, N.E.,  M.T. Southerland, J.C. Chaillou, RJ.  Klauda, P.P. Kazyak,  S.A.  Stranko, S.B.
       Weisberg, L.W. Hall, Jr.,,  and R.P. Morgan II. 1998. Maryland biological stream  survey:
       Development  of a  fish  index  of biotic integrity. Environmental  Monitoring  and
       Assessment 51:89-106.

Waite, I.R., A.T.  Herlihy, D.P. Larsen, and DJ.  Klemm.  2000.  Comparing  strengths of
       geographic and nongeographic classifications of stream benthic macroinvertebrates in the
       Mid-Atlantic Highlands,  USA. Journal of the North American Benthological  Society
       19:429-441.

U.S. Environmental Protection  Agency. 1996a. Biological Criteria:  Technical  Guidance for
       Streams and Small Rivers. EPA/822/B-96/001, U.S. Environmental Protection Agency,
       Washington, DC.

                                     STRESSORS

Baker, L.A., A.T. Herlihy, P.R. Kaufmann, and J.M. Eilers. 1991.  Acidic lakes and streams in
       the United States: The role of acidic deposition. Science 252:1151-1154.

Herlihy, A.T., P R. Kaufmann, M E. Mitch, and D.D. Brown.  1990. Regional estimates of acid
       mine drainage impact on streams in the mid-Atlantic and southeastern United States.
       Water Air and Soil Pollution 50:91-107.

Herlihy,  A  T., J.L.  Stoddard,  and C.B. Johnson.  1998. The relationship between  stream
       chemistry and watershed land  use data in the Mid-Atlantic region, U.S. Water Air and
       Soil Pollution  105:377-386.

Kaufmann, P.R., P. Levine, E.G. Robison, C. Seeliger, and  D. Peck. 1999. Quantifying Physical
       Habitat in Wadeable Streams. EPA/620/R-99/003, U.S. EPA, Washington, D.C.
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Lazorchak, J.M., F.H. McCormick, T.R. Henry, and A.T. Herlihy. 2003. Contamination offish
      in streams of the Mid-Atlantic Region: an approach to regional indicator selection and
      wildlife assessment. Environmental Toxicology and Chemistry 22:545-553.

                                RELATIVE RISK

Lachin, J.M. 2000. Biostatistical Methods: The Assessment of Relative Risk. John Wiley and
      Sons, New York.

Sarndal, C.E., B. Swensson, and J. Wretman. 1992. Model-assisted Survey Sampling. Springer-
      Verlag, New York.

                 OTHER MID-ATLANTIC ASSESSMENTS

Mid-Atlantic Integrated Assessment website: http://www.epa.gov/maia/

Ator, S.W., and MJ.  Ferrari. 1997. Nitrate and selected pesticides in ground water of the Mid-
      Atlantic region. U.S.G.S. Water Resources Investigations Report 97-4139.

Boward, D., P. Kayzak, S. Stranko,  M. Kurd, and A. Prochaska.  1999. From the Mountains to
      the  Sea:  The  State of Maryland's Freshwater  Streams.  EPA/903/R-99/023,  U.S.
      Environmental Protection Agency, Philadelphia, PA.

Bryce, S.A., D.P. Larsen, R.M. Hughes, and P R. Kaufmann. 1999. Assessing the relative risks
      to aquatic ecosystems in the Mid-Appalachian region of the United States. Journal of the
      American Water Resources Association 35:23-36.

Hill, B.H.,  A.T. Herlihy,  P.R. Kaufmann, and R.L.  Sinsabaugh.  1998.  Sediment microbial
      respiration in a synoptic survey of Mid-Atlantic streams. Freshwater Biology 39:493-501.

Jones, K.B., K.H. Riitters, J.D. Wickham, R.D. Tankersley, R. V. O'Neill, D.J.  Chaloud, E.R.
      Smith, and A.C. Neale. 1997. An Ecological  Assessment of the  United States  Mid-
      Atlantic Region: A Landscape Atlas. EPA/600/R-97/130, U.S. Environmental Protection
      Agency, Washington, DC.

U.S. Environmental  Protection Agency.  1998.  Condition  of  the Mid-Atlantic  Estuaries.
      EPA/600/R-98/147 U.S. Environmental Protection Agency, Washington, DC.

U.S. Environmental Protection Agency. 2000. Mid-Atlantic  Highlands Streams Assessment.
      EPA/903/R-00/015, U.S. Environmental Protection Agency, Region 3, Philadelphia, PA.
      (available at: http://www.epa.gov/maia/html/maha.html)

                    ENVIRONMENTAL REPORT CARDS

H. John Heinz III Center for Science, Economics, and the Environment. 2002. The State of the
      Nation's Ecosystems: Measuring the Lands, Waters,  and Living Resources of the United
      States. Cambridge University Press, Cambridge,  UK.

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U.S. Environmental Protection Agency. 2003. Draft Report on the Environment. EPA 260-R-02-
      006, U.S. Environmental Protection Agency, Washington, DC.
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