National Rivers and Streams 

Assessment 2008–2009 

A Collaborative Survey 

DRAFT 

U.S. Environmental Protection Agency

Office of Wetlands, Oceans and Watersheds

Office of Research and Development

Washington, DC 20460

EPA/841/D-13/001 

February 28, 2013
              –  

     

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Table of Contents 

Executive Summary ...........................................................................................xi
�

Key findings...............................................................................................................................xi

Biological quality ............................................................................................................xi

Chemical stressors ........................................................................................................xii

Physical habitat stressors.............................................................................................xiii

Human health indicators..............................................................................................xiii

Change in stream condition .........................................................................................xiii

Implications.............................................................................................................................xiv

Chapter 1. Introduction.......................................................................................1
�

The nation’s rivers and streams................................................................................................ 1

Some facts about large rivers ................................................................................................... 2

Smaller streams and rivers ....................................................................................................... 3

The Wadeable Streams Assessment ......................................................................................... 4

Chapter 2. Design of the National Rivers and Streams Assessment .....................6
�

What area does the NRSA cover?............................................................................................. 6

What regions are used to report NRSA results?....................................................................... 7

How were sampling sites chosen?.......................................................................................... 10

How were waters assessed?................................................................................................... 12

Setting expectations ............................................................................................................... 14

Chapter 3. Condition of the Nation’s Rivers and Streams..................................19
�

Background ............................................................................................................................. 19

Indicators of biological condition ........................................................................................... 19

Macroinvertebrate Multimetric Index.................................................................................... 20

Findings for the Macroinvertebrate Multimetric Index............................................... 23

Macroinvertebrate Observed/Expected Ratio of Taxa Loss................................................... 23

Findings for O/E Taxa Loss ........................................................................................... 24

February 2013 iii

National Rivers and Streams Assessment, 2008 2009
     

              –  

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Table of Contents (Continued) 

Fish Multimetric Index ............................................................................................................ 25

Findings for the Fish Multimetric Index ....................................................................... 25

Periphyton Multimetric Index................................................................................................. 26

Findings for the Periphyton Multimetric Index ........................................................... 27

Aquatic indicators of stress..................................................................................................... 28

Chemical stressors ....................................................................................................... 29

Physical habitat stressors............................................................................................. 35

Ranking stressors: relative extent, relative risk, and attributable risk................................... 40

Relative extent ............................................................................................................. 41

Relative risk .................................................................................................................. 42

Attributable risk ........................................................................................................... 45

Chapter 4. Human Health Considerations in the Nation’s Rivers and Streams...47
�

Background ............................................................................................................................. 47

Mercury in fish tissue.............................................................................................................. 47

Findings for mercury in fish tissue ............................................................................... 49

Pathogen indicators (enterococci).......................................................................................... 50

Findings for enterococci............................................................................................... 52

Chapter 5. Changes in Stream Condition ...........................................................56
�

Findings for changes in stream condition............................................................................... 56

Chapter 6. Ecoregional Results..........................................................................61
�

Introduction ............................................................................................................................ 61

Nationwide comparisons ........................................................................................................ 63

Biological condition — Macroinvertebrate Multimetric Index.................................... 63

Nutrients – total phosphorus and nitrogen ................................................................. 64

Riparian vegetative cover ............................................................................................ 65

Enterococci................................................................................................................... 67

Northern Appalachians ........................................................................................................... 67

iv National Rivers and Streams Assessment, 2008 2009 February 2013 
     

              –  

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Table of Contents (Continued) 

Setting .......................................................................................................................... 68

Summary of NRSA findings, Northern Appalachians ................................................... 68

Southern Appalachians ........................................................................................................... 70

Setting .......................................................................................................................... 70

Summary of NRSA findings, Southern Appalachians ................................................... 71

Coastal Plains .......................................................................................................................... 73

Setting .......................................................................................................................... 73

Summary of NRSA findings, Coastal Plains .................................................................. 74

Upper Midwest ....................................................................................................................... 75

Setting .......................................................................................................................... 75

Summary of NRSA findings, Upper Midwest ............................................................... 76

Temperate Plains .................................................................................................................... 78

Setting .......................................................................................................................... 78

Summary of NRSA findings, Temperate Plains ............................................................ 79

Southern Plains ....................................................................................................................... 80

Setting .......................................................................................................................... 80

Summary of NRSA findings, Southern Plains ............................................................... 81

Northern Plains ....................................................................................................................... 83

Setting .......................................................................................................................... 83

Summary of NRSA findings, Northern Plains ............................................................... 83

Western Mountains ................................................................................................................ 85

Setting .......................................................................................................................... 85

Summary of NRSA findings, Western Mountains ........................................................ 86

Xeric ........................................................................................................................................ 88

Setting .......................................................................................................................... 88

Summary of NRSA findings........................................................................................... 89

February 2013 v

National Rivers and Streams Assessment, 2008 2009
     

              –  

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Table of Contents (Continued) 

Chapter 7. Summary and Next Steps.................................................................91
�

Moving the science forward ................................................................................................... 93

Next steps ............................................................................................................................... 94

Glossary of Terms ...........................................................................................100
�

Sources and References..................................................................................102
�

General references ............................................................................................................... 102

Stream and river sampling and laboratory methods............................................................ 103

Probability designs................................................................................................................ 104

Ecological regions.................................................................................................................. 104

Fish multimetric indices........................................................................................................ 105

Indices of biotic integrity ...................................................................................................... 105

Observed/expected models.................................................................................................. 106

Periphyton............................................................................................................................. 106

Physical habitat ..................................................................................................................... 107

Reference condition.............................................................................................................. 108

Other EMAP assessments ..................................................................................................... 108

Biological condition gradient/quality of reference sites ...................................................... 108

Relative risk........................................................................................................................... 108

Nutrients ............................................................................................................................... 109

List of Abbreviations and Acronyms................................................................110
�

vi National Rivers and Streams Assessment, 2008 2009 February 2013 
     

              –  

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Tables and Figures 

Tables 

Table 1. Length of river and streams represented in the NRSA, by ecoregion ........................... 10

Table 2. Indicators evaluated for the NRSA.................................................................................. 14

Figures 

Figure 1. Biological condition of the nation’s rivers and streams, based on the 

Macroinvertebrate Multimetric Index..........................................................................xii

Figure 2. Average annual precipitation in the U.S.......................................................................... 6

Figure 3. Major NRSA climatic regions............................................................................................ 8

Figure 4. Nine ecoregions surveyed for the NRSA.......................................................................... 8

Figure 5. NRSA sample sites.......................................................................................................... 11

Figure 6. Reach layout used for sampling in the NRSA................................................................. 12

Figure 7. Biological condition of the nation’s rivers and streams based on the -

Macroinvertebrate Multimetric Index......................................................................... 23

Figure 8. Macroinvertebrate taxa loss in the nation’s rivers and streams as measured -

by the Observed/Expected Ratio of Taxa Loss............................................................. 24

Figure 9. Condition of the fish assemblage in the nation’s rivers and streams as -

measured by the Fish Multimetric Index ..................................................................... 26

Figure 10. Condition of periphyton assemblage in the nation’s rivers and streams based -

on the Periphyton Multimetric Index .......................................................................... 28

Figure 11. Total phosphorus concentrations in the nation’s rivers and streams......................... 30

Figure 12. Total nitrogen concentrations in the nation’s rivers and streams .............................. 31

Figure 13. Salinity conditions in the nation’s rivers and streams................................................. 33

Figure 14. Acidification in the nation’s rivers and streams .......................................................... 35

Figure 15. Excess streambed sediment in the nation’s rivers and streams ................................. 37

Figure 16. In-stream habitat in the nation’s rivers and streams .................................................. 38

Figure 17. Riparian vegetative cover in the nation’s rivers and streams ..................................... 39

Figure 18. Riparian disturbance in the nation’s rivers and streams............................................. 40

Figure 19. Relative extent of stressors in the nation’s rivers and streams .................................. 41

Figure 20. Relative extent, relative risk, and attributable risk to macroinvertebrates -

based on the Macroinvertebrate Multimetric Index................................................... 43

February 2013 vii

National Rivers and Streams Assessment, 2008 2009
     

              –  

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Tables and Figures (Continued) 

Figure 21. Relative extent, relative risk, and attributable risk to fish based on the Fish 

Multimetric Index......................................................................................................... 44

Figure 22. Relative extent, relative risk, and attributable risk to periphyton based on -

the Periphyton Multimetric Index ............................................................................... 45

Figure 23. Human health fish tissue assessment for target and sampled populations of -

the nation’s rivers ........................................................................................................ 50

Figure 24. Percent of fish tissue target population sampled for mercury in fish tissue in -

the three major climatic regions of the U.S................................................................. 50

Figure 25. Enterococci human health thresholds exceedance in the nation’s rivers and -

streams......................................................................................................................... 52

Figure 26. Mercury in fish tissue from urban sites ....................................................................... 54

Figure 27. PFOS in fish tissue from urban sites ............................................................................ 55

Figure 28. Change in macroinvertebrate condition and nutrients between 2004 and -

2008–2009, based on percent of length in good condition ........................................ 58

Figure 29. Change in stream fish habitat, riparian vegetation cover, and riparian -

disturbance between 2004 and 2008–2009 ................................................................ 60

Figure 30. Ecoregional surveys for the NRSA................................................................................ 62

Figure 31. Biological condition in rivers and streams based on the Macroinvertebrate -

Multimetric Index across the nine ecoregions............................................................. 63

Figure 32. Total phosphorus levels in rivers and streams across the nine ecoregions ................ 64

Figure 33. Total nitrogen levels in rivers and streams across the nine ecoregions...................... 65

Figure 34. Riparian vegetative cover in rivers and streams across the nine ecoregions ............. 66

Figure 35. Enterococci human health threshold exceedance in rivers and streams -

across the nine ecoregions .......................................................................................... 67

Figure 36. NRSA survey results for the Northern Appalachians ecoregion.................................. 69

Figure 37. NRSA survey results for the Southern Appalachian ecoregion ................................... 72

Figure 38. NRSA survey results for the Coastal Plains ecoregion ................................................. 74

Figure 39. NRSA survey results for the Upper Midwest ecoregion .............................................. 77

Figure 40. NRSA survey results for the Temperate Plains ecoregion ........................................... 79

Figure 41. NRSA survey results for the Southern Plains ecoregion.............................................. 82

Figure 42. NRSA survey results for the Northern Plains ecoregion.............................................. 84

viii National Rivers and Streams Assessment, 2008 2009 February 2013 
     

              –  

 

 

 

 

 

 

 

 

 

 

 

 

 

Tables and Figures (Continued) 

Figure 43. NRSA survey results for the Western Mountains ecoregion....................................... 87

Figure 44. NRSA survey results for the Xeric ecoregions.............................................................. 89

Figure 45. Map of about 1,200 probability sites in California sampled since 2000 using -

compatible EMAP-style survey designs ....................................................................... 96

Figure 46. Biological condition of perennial streams in the six major ecological regions -

of California.................................................................................................................. 97

Figure 47. Percentage of California stream length that exceeds severe and moderate -

threshold values for various chemical and physical habitat stressor variables -

in streams associated with each of three major land cover types .............................. 97

Figure 48. Relative risk of biological impairment associated with a series of habitat and -

chemistry variables in southern California streams .................................................... 98

Figure 49. The combination of probability and reference distributions provides -

objective context for interpreting targeted monitoring data...................................... 98

February 2013 ix

National Rivers and Streams Assessment, 2008 2009

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Executive Summary
�

This National Rivers and Streams Assessment 2008–2009: A Collaborative Survey (NRSA) 

presents the results of an unprecedented sampling effort undertaken by the U.S. Environmental 

Protection Agency and its state and tribal partners. It provides information on the ecological 

condition of the nation’s rivers and streams and the key stressors that affect them, both on a 

national and an ecoregional scale. It also discusses change in water quality conditions in 

streams sampled for an earlier study, the Wadeable Streams Assessment of 2004. 

During the summers of 2008 and 2009, more than 85 field crews sampled 1,924 river and 

stream sites across the country. Using standardized field methods, they sampled waters as 

large as the Mississippi River and as small as mountain headwater streams. Sites were selected 

using a random sampling technique that uses a probability-based design. This design ensures 

that the results of the survey reflect the full variety of river and stream types and sizes across 

the U.S. To determine water quality conditions, sampling results were compared to conditions 

at least-disturbed (or reference) sites in different ecological regions. 

The goals of the NRSA are to determine the extent to which rivers and streams support a 

healthy biological condition and the extent of major stressors that affect them. In addition, the 

survey supports a longer-term goal: to determine whether our rivers and streams are getting 

cleaner and how we might best invest in protecting and restoring them. 

Key findings 

Biological quality 

Biological condition is the most comprehensive indicator of water body health: when the 

biology of a stream is healthy, the chemical and physical components of the stream are also 

typically in good condition. Twenty-one percent of the nation’s river and stream length is in 

good biological condition, 23% is in fair condition, and 55% is in poor condition, based on a 

robust, commonly used index that combines different measures of the condition of aquatic 

benthic macroinvertebrates (aquatic insects and other creatures such as crayfish). Of the three 

major climatic regions (Eastern Highlands, Plains and Lowlands, and West) discussed in this 

report, the West is in the best biological condition, with 42% of river and stream length in good 

February 2013
 xi

National Rivers and Streams Assessment, 2008 2009
            –

 

 

                         

 

 

 

 

 

 

 

 

 

Executive Summary 

condition. In the Eastern Highlands, 17% of river and stream length is in good condition; in the 

Plains and Lowlands, 16% is rated in good condition (Figure 1). 

Figure 1. Biological condition of the nation's rivers and streams, based on the Macroinvertebrate Multimetric 

Index (EPA/NRSA).

Chemical stressors 

Four chemical stressors were assessed: total phosphorus, total nitrogen, salinity, and 

acidification. Of these, phosphorus and nitrogen are by far the most widespread. Forty percent 

of the nation’s river and stream length has high levels of phosphorus and 28% has high levels of 

nitrogen. Poor biological condition (for macroinvertebrates) is 50% more likely in rivers and 

streams with high levels of phosphorus and 40% more likely in rivers and streams with high 

levels of nitrogen. Acidification, although a problem in less than 1% of U.S. river and stream 

length, has a significant impact on biological condition where it is found: poor biological 

condition is 50% more likely in waters affected by acidification. 

xii National Rivers and Streams Assessment, 2008 2009 February 2013 
            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Executive Summary

Physical habitat stressors 

Four indicators of physical habitat condition were assessed for the NRSA: excess streambed 

sediments, riparian vegetative cover (vegetation in the land corridor surrounding the river or 

stream), riparian disturbance (human activities near the river or stream), and in-stream fish 

habitat. Of these, poor riparian vegetative cover and high levels of riparian disturbance are the 

most widespread stressors, reported in 24% and 20% of the nation’s river and stream length, 

respectively. However, excess levels of streambed sediments, reported in 15% of river and 

stream length, were found to have a somewhat greater impact on biological condition. Poor 

biological condition is 60% more likely in rivers and streams with excessive levels of streambed 

sediments. 

Human health indicators 

Two indicators that provide insight into potential risks to human health were assessed: 

mercury in fish tissue and enterococci (bacteria). Human health screening values for mercury in 

fish tissue are exceeded in 13,144 miles of U.S. river length (streams were not evaluated). In 9% 

of river and stream length, samples exceed an enterococci threshold level for protecting human 

health. 

Change in stream condition 

Compared to the findings of the 2004 WSA, some statistically significant changes are found 

in stream condition. Nationally, the amount of stream length in good quality for 

macroinvertebrate condition dropped from 27.4% in 2004 to 20.5%; this change appears driven 

in large part by a 13.3% decline in streams in good condition in the Plains and Lowlands climatic 

region. In addition, the percent of stream length in good condition for phosphorus dropped 

nationally from 52.8% to 34.2% and declined in all three major climatic regions. However, other 

indicators showed an increase in stream length in good condition: the percent of stream length 

in good condition for nitrogen rose from 46.6% in 2004 to 55.4%; percent of stream length with 

good in-stream fish habitat rose from 51.7% to 68.9%; and percent of stream length in good 

condition for riparian disturbance (i.e., with low levels of disturbance) rose from 22.7% to 

34.8%. It is important to note that these are differences for streams only, between two points 

February 2013 xiii

National Rivers and Streams Assessment, 2008 2009
            –

 

 

 

 

 

 

 

 

Executive Summary 

in time. Future surveys and more data are needed to discern trends and the reasons for those 

trends. 

Implications 

A picture of the condition of the nation’s rivers and streams is emerging from this survey 

and its predecessor streams assessment. Our rivers and streams are under significant stress and 

more than half exhibit poor biological condition. Phosphorus, nitrogen, and streambed 

sediments in particular have widespread and severe impacts; reducing levels of these 

constituents will significantly improve the biological health of rivers and streams. This survey 

suggests the need to address the many sources of these stressors — including runoff from 

urban areas, agricultural practices, and wastewater — in order to ensure healthier waters for 

future generations. 

xiv National Rivers and Streams Assessment, 2008 2009 February 2013 
            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 1. Introduction
�

The nation’s rivers and streams 

This report presents the findings of the National Rivers and Streams Assessment 2008– 

2009: A Collaborative Survey, the first statistically based survey of the condition of the nation’s 

rivers and streams. The survey sampled a stunning range of waters: huge workhorse rivers that 

roll past our largest urban areas, tiny undisturbed creeks tucked away in national parks, and 

everything in between. This report also compares the condition of streams to those of an 

earlier study that focused on small streams (the Wadeable Streams Assessment or WSA) 

conducted by the U.S. Environmental Protection Agency and its partners in 2004. 

Rivers and streams shape our landscape. They supply humans with drinking water, carry 

away our wastes and used water, irrigate our crops, power our cities with hydroelectricity, and 

offer us myriad recreational and commercial opportunities. They support fish and other aquatic 

life and provide shelter, food, and habitat for birds and wildlife of all types. They are the land’s 

vast and interconnected circulatory system, carrying water, sediment, and organic material 

from the mountains to the sea. Clean and healthy rivers and streams greatly enhance the 

quality of our lives. 

Over the centuries, we have radically changed most U.S. rivers and streams by interrupting 

their flows with dams and levees; straightening and modifying their channels for irrigation, 

navigation, or flood control; building our cities and developing our farmland in their watersheds 

and floodplains; withdrawing their water for our use; and discharging our waste materials into 

their flow. Our rivers and streams are also subject to other influences such as seasonal, annual, 

and climate-change-induced variations in precipitation and temperature, as well as changing 

cycles of erosion and deposition (e.g., during flooding or dam releases). To effectively manage, 

restore, and protect these rivers and streams, we must improve the information we need to 

make wise water quality decisions. 

February 2013 1

National Rivers and Streams Assessment, 2008 2009
   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 1. Introduction 

Some facts about large rivers 

The nation’s large rivers — the biggest of which are often referred to as the Great Rivers — 

are familiar to all of us, part of our American history and lore. Their contribution to our nation 

cannot be overestimated. Some examples of their power, breadth, and value: 

� The Mississippi River is the largest in the U.S. by drainage area and discharge; its 

watershed (that is, the area it drains) is one of the largest in the world and covers 1.2 

million square miles. At Lake Itasca, where the Mississippi begins, its average flow rate is 

6 cubic feet per second. At New Orleans the average flow rate is 600,000 cubic feet per 

second. Agriculture is the dominant land use in the Mississippi River basin; 60% of all 

grain exported from the U.S. is shipped on the Mississippi River through the ports at its 

mouth. 

� The Missouri River, known as the “Big Muddy,” is the longest in the U.S., at about 2,540 

miles, and drains one sixth of the country. It begins in the Rocky Mountains in Montana, 

flows east and south, and joins the Mississippi River north of St. Louis, Missouri. It was 

the “highway” used by Lewis and Clark and became an important route for trade and 

westward expansion in the 1800s. The Missouri has been extensively dammed for 

irrigation, hydroelectricity, and flood control, and its river basin is home to ten million 

people from 28 tribes, ten states, and a small part of Canada. 

� The Delaware River is the longest undammed river east of the Mississippi, flowing for 

330 miles from the confluence of the east and west branches in Hancock, New York, 

through Pennsylvania, New Jersey, and Delaware to the Atlantic Ocean. Its 13,539-

square-mile watershed is only about 0.4% of the land area of the continental U.S., but it 

supplies water to 5% of the nation’s population — over 15 million people — including 

residents of New York City and Philadelphia. 

� The Columbia River Basin is the most hydroelectrically developed river system in the 

world. By volume, the Columbia is the fourth-largest river in the U.S., and it has the 

greatest flow of any North American river draining into the Pacific. More than 400 dams, 

including 11 on the Columbia mainstem and hundreds of others on tributaries in the 

watershed, generate more than 21 million kilowatts. 

� The Colorado River flows across 1,450 miles of mountainous and desert terrain from the 

Rocky Mountains to the Gulf of California. It supplies water to over 25 million people in 

seven western states, two Mexican states, and 32 tribal communities; helps irrigate 3.5 

million acres of farmland; and provides electricity for 30 million people. There are ten 

2 National Rivers and Streams Assessment, 2008 2009 February 2013 
   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 1. Introduction

major dams on the Colorado River — among them Hoover Dam — and 80 smaller 

diversions, making it one of the most controlled rivers in the world. 

Smaller streams and rivers 

At the other end of the spectrum from the nation’s large rivers are the small stream and 

river systems often referred to as “wadeable” because they are shallow enough to sample 

without a boat. About 90% of perennial (i.e., continuously flowing) stream and river miles in the 

U.S. are considered wadeable. These smaller streams are the ones we know best: they drain 

our neighborhoods and fields and flow past our campgrounds. They are also a critical part of 

the ecosystem, providing food and shelter to a broad array of aquatic organisms, birds, and 

wildlife. 

Ecologists commonly define stream size according to the “Strahler stream order”; wadeable 

streams usually fall into the first - through fifth-order range. The life of a river begins in its 

headwaters, or first-order streams; as streams of a certain order join one another, their stream 

order increases. 

Stream order affects a stream’s natural characteristics, including the biological communities 

— the plants and animals — that live in it. For example, first- and second-order streams are 

often quite clear and narrow and shaded by grasses, shrubs, and trees growing along their 

banks. The food base of these streams consists of terrestrial insects and leaves from stream 

bank plants, algae that attach to rocks and wood, aquatic insects adapted to shredding leaves 

and scraping algae, and small fish that feed on these organisms. 

In contrast, rivers that are sixth-order and higher typically appear muddy because their 

large flow carries accumulated sediments downstream. They are wide, so the canopy cover 

along their banks shades only the river’s edge. The food base of wide rivers shifts away from 

the stream bank toward in-stream sources such as algae, small organisms that are drifting down 

stream, and eroded matter. The biological communities of mid-sized and large rivers are 

dominated by aquatic insects adapted to filtering and gathering fine organic particles and by 

larger fish that feed on plants, animals, and smaller fish. 

February 2013 3

National Rivers and Streams Assessment, 2008 2009
   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 1. Introduction

Many streams, especially those in the arid West, do not flow year-round. These were not 

included in this survey because well-developed indicators to assess them are not yet available. 

The Wadeable Streams Assessment 

In 2004, EPA and its partners completed sampling for the first statistical survey of the 

condition of the nation’s small, perennial streams. The survey’s purpose was to establish a 

baseline of information on the condition of small streams and the extent of major 

environmental stressors that affect them. Through the efforts of state environmental and 

natural resource agencies, federal agencies, universities, and other organizations, more than 

150 field biologists used standardized methods to collect environmental samples at 1,392 

perennial stream locations. These sites were chosen using a statistical design to ensure that 

results represented the condition of all U.S. streams. The WSA resulted from this groundbreaking collaboration. 

The WSA was implemented to help fill an information need identified over the years by a 

number of independent organizations, including the Government Accountability Office, the 

National Research Council, and the National Academy of Public Administration. In the early 

2000s, these organizations noted that EPA and the states did not have a uniform, consistent 

approach to monitoring that supported water quality decision-making. They called for more 

efficient and cost-effective ways to understand the magnitude and extent of water quality 

problems, the causes of these problems, and practical ways to address them. 

In response, EPA, states, tribes, academics, and other federal agencies began collaborating 

on a series of statistically based surveys called the National Aquatic Resource Surveys (NARS) to 

provide the public and decision-makers with improved, statistically valid environmental 

information. These surveys are nationally consistent and representative, use standardized field 

and laboratory protocols, and follow rigorous quality assurance protocols. The WSA was based 

on 15 years of EPA research and, like other surveys that followed, was designed to begin 

answering such short- and long-term questions as: 

� What is the extent of waters that support a healthy biological condition, recreation, and 

fish consumption? 

4 National Rivers and Streams Assessment, 2008 2009 February 2013 
Chapter 1. Introduction

� How widespread are major stressors that affect water quality? 

� Are we investing wisely in water resource restoration and protection? 

� Are our waters getting cleaner? 

Under the NARS program and since the publication of the WSA in 2006, EPA and its many 

partners have: 

� Completed a survey of the nation’s lakes, ponds, and reservoirs in 2007 (the National 

Lakes Assessment, EPA 841-R-09-001) and conducted field work in the 2012 summer 

sampling season for the next lakes assessment. 

� Completed field work and lab analyses for the next National Coastal Condition Report, 

currently under development. 

� Finished field sampling and embarked on the analysis and reporting stage of the firstever National Wetland Condition Assessment. 

� Developed this National Rivers and Streams Assessment and begun planning for the next 

rivers and streams field season in 2013–2014. 

These accomplishments would not have been possible without collaboration and 

partnership among field biologists, taxonomists, statisticians, data analysts, project managers, 

quality control officers, and reviewers in state, tribal, and federal offices and universities across 

the country. 

Why do we need consistent and statistically valid survey data on rivers and 

streams? 

Under the Clean Water Act, states are expected to monitor and required to assess and report 

on the condition of the nation’s waters, including the extent of waters that support the goals 

of the Act. However, methods of collecting and assessing data vary widely between states 

and change over time, making it difficult to compare this information from state to state, for 

the nation as a whole, or over time. State monitoring programs are generally designed to 

meet state­specific information needs, such as locating impaired waters that require 

additional pollution controls. They are not designed to answer national­level questions such 

as whether or not U.S. water quality is improving — one of the long­term goals of the 

National Aquatic Resource Surveys. These surveys are meant to complement the statespecific information and provide national and regional context to decision­makers. 

February 2013  National Rivers and Streams Assessment, 2008–2009

5
            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

            

Chapter 2. Design of the National Rivers and Streams 

Assessment 

The NRSA is the first nationally consistent survey assessing the ecological condition of the 

full range of flowing waters in the conterminous U.S. (lower 48 states). The target population 

includes the Great Rivers (such as the Mississippi and the Missouri), small perennial streams, 

and urban and non-urban rivers. Run-of-the-river ponds and pools are included, along with 

tidally influenced streams and rivers up to the leading edge of dilute sea water. 

The NRSA was designed to answer basic questions about the extent to which our rivers and 

streams support healthy biological conditions and how widespread their key stressors are. Over 

the longer term, as additional surveys in this series are completed, we will also learn whether 

our waters are getting cleaner over time, and whether our policy decisions to protect and 

restore them are effective or should be changed. 

What area does the NRSA cover? 

This report covers the conterminous U.S. — 3,007,436 square miles. Of this area, 73% is 

state or private land and the rest is federal or tribal land. Initial NRSA projects in Hawaii and 

Alaska are also underway. 

State political boundaries offer few insights into the true nature of the features that affect 

our streams and rivers. The 

most fundamental trait that 

defines our waters is annual 

precipitation (see Figure 2). 

On either side of the 100th 

meridian that runs from west 

Texas through North Dakota, 

a sharp change occurs where 

precipitation falls plentifully 

to the east but sparsely to 

the west. (The high Figure 2. Average annual precipitation in the U.S. (NOAA).

6 National Rivers and Streams Assessment, 2008 2009 February 2013 
                 

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 2. Design of the National Rivers and Streams Assessment 

mountains of the West and the Pacific coast are exceptions to the general scarcity of water in 

the West.) The east–west divide in moisture has shaped not only the character of these waters 

but also how we use them, how we value them, and even the legal system with which we 

manage their allocation. A second divide that defines the nature of our rivers and streams is the 

north–south gradient in temperature. 

This huge area includes a wide diversity of landscapes, from the maple-beech-birch forests 

and coastal plains of the East, to the enormous agricultural plains and grasslands of the midcontinent, to the deserts and shrub lands of the Southwest, and to the giant mountain ranges 

of the Rocky Mountains, Sierra Nevadas, and Cascades in the west. The Appalachian Mountains, 

running from Maine to Alabama, cross state and climatic boundaries and separate the waters 

flowing to the Atlantic from those flowing to the Gulf of Mexico. 

The establishment and spread of European colonies and the industrial revolution of the 18th 

century transformed our natural landscape as more people arrived and modified many of the 

features of our land and waters. Tens of thousands of dams, large and small, have altered the 

flow of virtually every major river and many smaller ones. The current and future condition of 

our waters will continue to be influenced by our population patterns and how we use all 

components of a watershed, including surface water, ground water, and the land itself. 

What regions are used to report NRSA results? 

The broadest scale unit for which results are reported in the NRSA is the continental U.S. 

itself. Next are three climatic regions corresponding to major climate and landform patterns: 

the West, Plains and Lowlands, and Eastern Highlands. The body of this report describes the 

results for these broader-scale reporting units. 

The finest-scale reporting unit included in this report consists of nine ecological regions that 

further divide the climatic regions (Figure 4). The NRSA uses ecoregions to report results 

because the patterns of response to stress, and the stressors themselves, are often best 

understood in the context of these ecological regions. 

February 2013 7

National Rivers and Streams Assessment, 2008 2009
               

            –

   

       

Chapter 2. Design of the National Rivers and Streams Assessment 

Figure 3. Major NRSA climatic regions (EPA/NRSA).

Figure 4. Nine ecoregions surveyed for the NRSA.

8 National Rivers and Streams Assessment, 2008 2009 February 2013 
                 

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 2. Design of the National Rivers and Streams Assessment 

Typically, management practices aimed at preventing degradation or restoring water quality 

may apply to many flowing waters with similar problems throughout an ecoregion. Both the 

climatic regions and ecoregions used in this report are aggregations of ecoregions as described 

by Omernik in 1987. Ecoregion-specific results are included in Chapter 6 of this report. 

� The Eastern Highlands climatic region is composed of the mountainous areas east of the 

Mississippi River. It is further divided into the Northern Appalachians ecoregion 

encompassing New England, New York, and northern Pennsylvania, and the Southern 

Appalachians ecoregion extending from Pennsylvania into Alabama, through the eastern 

portion of the Ohio Valley and including the Ozark Mountains. 

� The Plains and Lowlands climatic region includes five of the NRSA ecoregions. The 

Coastal Plain includes the low gradient areas of the east and southeast. It contains the 

Atlantic and Gulf of Mexico coastal plains and the lowlands of the Mississippi delta, 

which extend from the Gulf northward through Memphis, Tennessee. The Upper 

Midwest is dominated by lakes and has little elevation gradient. The Temperate Plains is 

also known as the Corn Belt. The Northern and Southern Plains are better known as the 

Great Prairies. The Northern Plains includes the Dakotas, Montana, and northeast 

Wyoming. The Southern Plains encompasses Nebraska, Kansas, Colorado, Oklahoma, 

and Texas. 

� The Western climatic region is defined by its Mountainous regions and the arid or Xeric 

region that includes both the true deserts and the arid lands of the Great Basin. 

To get a statistically valid state picture of water quality conditions, some of the states 

participating in the NRSA opted for a finer state-scale resolution than the ecoregion scale by 

increasing the number of sites they sampled within their borders. While their data are included 

in the analyses described in this report, state-scale results are not presented. The states are 

preparing similar analyses that reflect their own water quality standards and regulations. 

It should be noted that NRSA assessments and findings regarding the condition of waters 

nationally and in each ecoregion are not Clean Water Act section 303(d) impaired waters 

determinations. Such determinations are made by states on specific water body segments using 

applicable state water quality standards. 

February 2013 9

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                         

             

   

   

   

   

   

   

Chapter 2. Design of the National Rivers and Streams Assessment 

How were sampling sites chosen? 

NRSA sampling locations were selected using a modern survey design approach. This 

approach, which is based on random selection, has been used in a variety of fields (e.g., health 

surveys, election polls, monthly labor estimates) to determine the status of populations or 

resources of interest using a representative sample of relatively few members or sites. This 

approach is especially cost-effective if the population is so numerous that all components 

cannot be sampled, or if it is not necessary to sample the entire resource in order to reach the 

desired level of precision. 

As consumers of information, we have all become accustomed to seeing survey data 

reported in the news. Results in the NRSA have similar rigor in their ability to estimate the 

percent of stream miles, within a range of certainty, that are in good, fair, and poor condition. 

In order to pick a random sample, one must first know the location of members of the 

population of interest. The NRSA design team used the EPA-USGS National Hydrography 

Dataset Plus (NHD-Plus), a comprehensive set of digital spatial data on surface waters at the 

1:100,000 scale, to identify the locations of perennial streams. They also obtained information 

about stream order from the NHD-Plus. Table 1 shows the length of flowing waters in each of 

the nine ecological regions used for the NRSA. 

Table 1. Length of river and streams represented in the NRSA, by ecoregion

Ecoregion Miles of Rivers and Streams in NRSA

Northern Appalachians 119,094

Southern Appalachians 315,242

Coastal Plains 176,510

Upper Midwest 96,142

Temperate Plains 227,017

Southern Plains 36,594

Northern Plains 27,227

Western Mountains 150,975

Xeric 44,974

10 National Rivers and Streams Assessment, 2008 2009 February 2013 
                 

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

   

Chapter 2. Design of the National Rivers and Streams Assessment 

The 1,924 sites sampled for the NRSA were identified using a particular type of random 

sampling technique called a probability-based sample design. In such a design, every element in 

the population has a known probability of being selected for sampling. This important feature 

ensures that the results of the survey reflect the full range in character and variation among 

flowing waters across the U.S. Site selection rules included weighting to provide balance in the 

number of river and stream sites from each of the size classes. Site selection was also controlled 

for spatial distribution to make sure sample sites were distributed across the U.S. (see Figure 5). 

Among these randomly selected sample sites were 359 of the original 2004 WSA sites. These 

were revisited as part of the NRSA to examine whether conditions have changed. 

When sites were selected for sampling, research teams conducted office evaluations and 

field reconnaissance to determine if the sites were accessible or if a river or stream labeled as 

perennial in NHD-Plus was, in fact, flowing during the sampling season. If a river or stream was 

not flowing or was determined to be inaccessible, it was dropped from the sampling effort and 

replaced with a perennial river or stream from a list of replacement sites within the random 

design. 

Figure 5. NRSA sample sites.

11 February 2013 National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

             

Chapter 2. Design of the National Rivers and Streams Assessment 

How were waters assessed? 

During the summers of 2008 and 

2009, more than 85 trained crews, 

composed primarily of state/tribal 

environmental agency, EPA, and 

contract staff, sampled river and 

stream sites across the U.S. using 

standardized field protocols. The field 

protocols were designed to collect data 

relevant to the ecological condition of 

stream resources and the key stressors 

affecting them. Each site was sampled 

by a three- or four-person field crew. 

During each site visit, crews laid out 

the sample reach (i.e., stretch of river or stream) and the numerous transects to guide data 

collection (see Figure 6). Field crews collected water samples which were sent to a lab for basic 

chemical analysis, and collected biological samples from 11 transects or fixed paths along each 

stream reach which were sent to taxonomists for identification. Crews recorded extensive data 

on field forms and documented information about the physical characteristics of each stream 

and the riparian area adjacent to its banks. Each crew was audited and 10% of the sites were 

revisited as part of the quality assurance plan for the survey. 

The use of standardized field and laboratory protocols for sampling across all 48 states 

included in the NRSA (including the pilots in Alaska and Hawaii) is a key feature of the survey. It 

allows the data to be combined to produce a nationally consistent assessment. This 

standardization is necessary: states, tribes, academics, and federal agencies use a wide range of 

methods to sample streams and rivers, and inconsistent results might have arisen if different 

methods were used in this survey. In fact, this nationwide sampling effort provided an 

opportunity to examine the comparability of different sample protocols by applying both the 

Figure 6. Reach layout used for sampling in the NRSA.

12 National Rivers and Streams Assessment, 2008 2009 February 2013 
                 

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 2. Design of the National Rivers and Streams Assessment 

NRSA method and various state or USGS methods to a subset of the sites. Crews collected 

physical, chemical, and biological data at all NRSA sites. 

The NRSA uses fish, benthic macroinvertebrates (insects and other small animals such as 

snails and crayfish) and algae as biological indicators of ecological condition. It focuses on these 

three groups of organisms because they are each sensitive to different disturbances that result 

from human activities and therefore give us a measurement of the biological integrity of rivers 

and streams. Biological integrity has been defined as “the capability of supporting and 

maintaining a balanced, integrated, adaptive community of organisms having a species 

composition, diversity, and functional organization comparable to that of the natural habitat of 

the region” (Karr and Dudley, 1981). Macroinvertebrates are included in almost every state and 

federal program monitoring rivers and streams, and are increasingly evaluated by volunteer 

water quality monitoring organizations. Water quality monitoring and management programs 

are also enhancing their understanding of biological integrity by adding other biological 

assemblages, including fish and algae. 

The NRSA supplements information on the ecological condition of streams with 

measurements of key stressors that might negatively influence or affect stream condition. 

Stressors are the chemical, physical, and biological components of the ecosystem that have the 

potential to degrade biological integrity. Some of these are naturally occurring, some result 

only from human activities, but most come from both sources. The challenge is in 

understanding and effectively minimizing the pressures humans exert on aquatic systems 

through their use of the surrounding environment. 

Examples of chemical stressors are excess nutrients (nitrogen and phosphorus), salinity, and 

acidification from acid deposition or mining. Most physical stressors — such as excess 

sedimentation, bank erosion, and loss of streamside trees and vegetation — are created when 

the physical habitat within the watershed of a stream network is altered. One of the key 

components of an ecological assessment is a measure of how common each stressor is in a 

region, and how severely it affects biotic integrity. 

February 2013 13

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

             

             

   

   

   

     

     

   

       

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 2. Design of the National Rivers and Streams Assessment 

In addition to these stressors, the NRSA investigated human health indicators, specifically 

mercury levels in fish tissue and the fecal indicator enterococci. 

Table 2 shows the key indicators evaluated for this report. NRSA scientists sampled for a 

number of other indicators as well; future reports will discuss these, but they are not included 

here due to technical and time considerations. 

Table 2. Indicators evaluated for the NRSA

Biological Indicators Chemical Indicators Physical Indicators Human Health Indicators

� Benthic � Phosphorus

� Nitrogen

� Salinity

� Acidity

� Streambed sediments

� In­stream fish habitat

� Riparian vegetative cover

� Riparian disturbance

� Enterococci (fecal

indicator)

� Mercury in fish tissue

macroinvertebrates

� Periphyton (algae)

� Fish community

Setting expectations 

In order to interpret the data collected by the NRSA field crews and to assess current 

ecological condition, scientists need to compare the collected data to a benchmark — an 

estimate of what we would expect to find in a natural condition. Setting reasonable 

expectations for each of the indicators is one of the greatest challenges to an assessment of 

ecological condition. Should we take a historical perspective and try to compare current 

conditions to an estimate of pre-Columbian conditions, or to pre-industrial conditions, or to 

conditions at some other point in history? Or should we accept that some level of 

anthropogenic disturbance is a given, and simply use the best of today’s conditions as the 

yardstick against which we compare everything else? These questions, and their answers, all 

relate to the concept of reference condition: what do we use as a reference, or yardstick, to 

assess today’s condition? 

Because it is difficult to estimate historical conditions for many indicators, the NRSA’s 

benchmark is “least-disturbed condition”: the best available physical, chemical, and biological 

habitat conditions given today’s state of the landscape. Least-disturbed condition is defined 

based on data from sites selected according to a set of explicit screening criteria, used to define 

what is least-disturbed by human activities. These criteria vary from region to region to reflect 

the natural variability across the American landscape; for the NRSA, separate criteria were 

14 National Rivers and Streams Assessment, 2008 2009 February 2013 
                 

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 2. Design of the National Rivers and Streams Assessment 

defined for each of the nine ecoregions. The screening criteria were developed with the goal of 

identifying the least amount of ambient human disturbance in each ecoregion. Reference 

criteria, in essence, describe the sites whose condition is “the best of what’s left” in the U.S. 

The NRSA compares a subset of the chemical and physical data collected at each site to the 

screening criteria to determine whether any given site is in least-disturbed condition for its 

ecoregion. The NRSA does not use data on the biological assemblages as a screening factor to 

select reference sites because that would have pre-judged expectations for biological condition. 

For each of the stressor indicators, the NRSA used a similar process (i.e., identifying leastdisturbed sites according to specific criteria, but excluding the specific stressors themselves 

from the criteria identifying the sites). 

The reference site approach is then used to set expectations. The range of conditions found 

in the reference sites for an ecoregion describes a distribution of values expected for leastdisturbed condition. The benchmarks used to define distinct condition classes (e.g., good, fair, 

poor) based on the degree of disturbance are drawn from this reference condition. 

The NRSA approach was to examine the range of values for an indicator in all of the 

reference sites in a region, and to use the fifth percentile of the reference distribution to 

separate the most disturbed sites from moderately disturbed sites. This means that stream 

miles in the most disturbed category are worse than 95% of the best sites used to define 

reference condition. Similarly, the 25th percentile was used to distinguish between moderately 

disturbed sites and least-disturbed sites: stream miles reported as least-disturbed are as good 

as 75% of the sites used to define reference condition. 

Within the reference site population, there are two sources of variability: 

� Natural variability — the wide range of habitat types naturally found within each 

ecoregion — creates a spread of reference sites representing those different habitats. 

Capturing natural variability in reference sites helps establish reference conditions that 

represent the range of natural environments in the ecoregions. 

� Human activities have changed many areas in the U.S., with natural landscapes 

transformed by cities, suburban sprawl, agricultural development, and resource 

extraction. The extent of those disturbances varies across regions. Some regions have 

February 2013 15

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 2. Design of the National Rivers and Streams Assessment 

reference sites in watersheds with little to no evidence of human impact, such as 

mountain streams or rivers in areas with very low population densities. Other regions 

have few sites that have not been influenced by human activities. The least-disturbed 

reference sites in these widely influenced regions display more variability in quality than 

those in areas with little human disturbance. 

Variation within the reference distribution due to disturbance was addressed before 

benchmarks were set for the condition classes of good, fair, and poor. For regions where the 

reference sites exhibited a disturbance signal, the data analysis team accounted for this 

disturbance by shifting the mean of the distribution toward the less-disturbed reference sites. 

NRSA partners supported this reference-condition-based approach, which is consistent with 

EPA guidance and state practice. Interested readers can find more detailed information about 

determining reference condition in the NRSA technical report, published online at 

www.epa.gov/aquaticsurveys. 

16 National Rivers and Streams Assessment, 2008 2009 February 2013 
Chapter 2. Design of the National Rivers and Streams Assessment

Understanding biological condition 

The objective of the Clean Water Act is to restore and maintain the chemical, physical, and 

biological integrity of the nation’s waters. It establishes many national goals to control 

pollution, including that water quality support healthy aquatic communities and provide for 

recreational uses like swimming and fishing wherever attainable. A primary goal of the NRSA is 

to develop a baseline understanding of the biological condition of our nation’s streams.  

One of the most meaningful ways to answer basic questions about water quality is to directly 

observe the communities of plants and animals that live in water bodies. Aquatic plants and 

animals are constantly exposed to various stressors. Therefore, they reflect not only current 

conditions, but also the cumulative impacts of stressors and changes in conditions over time. 

Benthic macroinvertebrates (aquatic insects, crustaceans, worms, and mollusks that live in river 

and stream beds and in vegetation) are widely used to determine biological condition. These 

organisms can be found in all rivers and streams, even in the smallest streams that cannot 

support fish. Because they are relatively stationary and cannot escape pollution, 

macroinvertebrate communities integrate the effects of stressors over time (i.e., pollutiontolerant species will survive in degraded conditions, and pollution­intolerant species will die). 

These communities are also critically important to fish because most game and non­game 

species require a good supply of benthic macroinvertebrates as food. Biologists have been 

studying the health and composition of benthic macroinvertebrate communities in streams for 

decades. Biological condition is the most comprehensive indicator of water body health; when 

the biology of a stream is healthy, the chemical and physical components of the stream are 

also typically in good condition. In fact, several states have found that biological data 

frequently detect stream impairment where chemistry data do not. 

Data on biological condition are invaluable for managing the nation’s aquatic resources and 

ecosystems. Water quality managers can use these data to set protection and restoration goals, 

decide which indicators to monitor and how to interpret monitoring results, identify stresses to 

the water body and decide how they should be controlled, and assess and report on the 

effectiveness of management actions. Many specific state responsibilities under the Clean 

Water Act—such as determining the extent to which waters support aquatic life uses, 

evaluating cumulative impacts from polluted runoff, and determining the effectiveness of 

discharger permit controls—are tied directly to an understanding of biological condition.

February 2013  National Rivers and Streams Assessment, 2008–2009

17
Chapter 2. Design of the National Rivers and Streams Assessment

Using multiple biological assemblages to determine biological condition 

EPA’s guidance on developing biological assessment and criteria programs recommends the 

use of multiple biological assemblages to determine biological condition. The term “multiple 

biological assemblages” simply refers to the three main categories of life found in a water 

body: plants (e.g., algae), macroinvertebrates, and vertebrates (e.g., fish). The purpose of 

examining multiple biological assemblages is to generate a broader perspective of the 

condition of the aquatic resource of interest.  

Each assemblage plays a different role in the way that rivers and streams function. Algae and 

macroinvertebrates occur throughout all types and sizes of rivers and streams, whereas very 

small streams may be naturally devoid of fish. Algae are the base of the food chain and capture 

light and nutrients to generate energy. They are sensitive to changes in shading, turbidity, and 

increases or decreases in nutrient levels. Macroinvertebrates feed on algae and other organic 

material that enters the aquatic system from the surrounding watershed. Macroinvertebrates 

are also an important food source for many aquatic vertebrates such as fish, which in turn serve 

as an important food source for people and wildlife. Each of these groups of aquatic organisms 

is sensitive in its own way to different human­induced disturbances. 

The NRSA uses benthic macroinvertebrates, fish, and algae as biological indicators of 

ecological condition. This is the first time three different biological assemblages have been 

evaluated for one national survey. For each of these assemblages, scientists calculated a series 

of metrics or individual measures and combined them into index scores. Results for each of 

these assemblages are presented in this report.  

However, research is still underway to determine how the different assemblage indices can be 

accurately combined into one overall index. Therefore, the macroinvertebrate assemblage — 

and specifically the Macroinvertebrate Multimetric Index, or MMI — was selected to represent 

overall biological condition for purposes of this report. The Macroinvertebrate MMI integrates 

a broad variety of informative macroinvertebrate metrics into one overall result and provides a 

particularly strong picture of biological condition that is widely used by state water quality 

agencies to assess and report on their rivers and streams. It was also used as the primary 

indicator of biological condition in the 2004 WSA. Work is ongoing to explore methods for 

integrating different assemblage indices into one overall index for future reports in this series. 

National Rivers and Streams Assessment, 2008–2009 February 2013  18 
            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 3. Condition of the Nation’s Rivers and Streams
�

Background 

The goal of the Clean Water Act is to restore and maintain the “chemical, physical, and 

biological integrity” of the nation’s waters. The NRSA examines these three aspects of water 

quality through a set of commonly used and widely accepted indicators. It does not include all 

aspects of aquatic ecosystem integrity or review all possible chemical, physical, or biological 

stressors known to affect water quality. 

This chapter discusses the indicators of biological condition that were measured and 

analyzed for the NRSA, the chemical and physical aquatic indicators of stress, and a ranking of 

the relative importance of the stressors in affecting biological condition. Results for each 

indicator are shown for the nation’s rivers and streams and for the three major climatic regions 

(Eastern Highlands, Plains and Lowlands, and West). Chapter 4 presents the findings of the 

human health indicators, and Chapter 6 presents indicator results for each of the nine NRSA 

ecoregions. An analysis of the changes between this study and the 2004 WSA is presented in 

Chapter 5. It is important to keep in mind that the overall NRSA findings should not be 

compared directly to those of the WSA because of the difference in overall population surveyed 

(rivers and streams versus streams only). 

Indicators of biological condition 

Ecologists evaluate the biological condition of rivers and streams by analyzing key 

characteristics of the communities of organisms that live in them. These characteristics include 

the composition and relative abundance of related groups of organisms that represent a 

portion of the overall biological community. The NRSA focuses on three such key groups, known 

as assemblages: benthic macroinvertebrates (aquatic insects, crustaceans, worms, and mollusks 

that live at the bottom of rivers and streams); periphyton (algae that attach themselves to 

stream and river beds, plants, rocks, and woody debris); and fish. This is the first time three 

different biological assemblages were evaluated for one national statistical survey. The reason 

for evaluating three distinct groups is to secure as robust an understanding of the biological 

condition of rivers and streams as possible. This is because each assemblage plays a different 

February 2013 19

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 3. Condition of the Nation's River and Streams 

role in the way that rivers and streams function. For example, algae are the base of the food 

chain and capture light and nutrients to generate energy. They are sensitive to changes in 

shade, turbidity, and nutrient levels. Macroinvertebrates feed on algae and other organic 

material and are also an important food source for many other aquatic animals, such as fish; in 

turn, fish serve as an important source of food for people and wildlife. Each of these groups of 

aquatic organisms is sensitive in its own way to human disturbances. 

NRSA researchers collected samples of these organisms and sent them to laboratories for 

analysis, yielding data sets that provided the types and number of taxa (i.e., classifications or 

groupings of organisms) found at each site. These were then analyzed to assess the condition of 

each group of organisms, using well-established and tested indices. As a final step in 

interpreting this information, analysts developed a ranking system for the stressors that affect 

each of these biological assemblages. 

Macroinvertebrate Multimetric Index 

Macroinvertebrates are widely used as indicators of biological condition because they 

respond to human disturbance in known and predictable ways. Given their broad geographic 

distribution, abundance, ease of collection, and connection to fish and other aquatic animals 

(i.e., as a source of food), these organisms serve as excellent indicators of the biological quality 

of rivers and streams and of the human stressors that affect them. 

The Macroinvertebrate Multimetric Index (MMI) is similar in concept to the Leading 

Economic Index in that the total index score is the sum of scores for a variety of individual 

measures (also known as metrics). To develop the Leading Economic Index, economists select 

metrics such as manufacturers’ new orders for consumer goods, building permits, money 

supply, and other aspects of the economy that reflect economic growth. Similarly, to determine 

the Macroinvertebrate MMI, ecologists selected six metrics indicative of different aspects of 

macroinvertebrate community structure: 

� Taxonomic richness — the number of distinct taxa (family or genus) within different 

taxonomic groups of organisms, within a sample. A sample with many different families 

or genera, particularly within those groups that are sensitive to pollution, indicates 

20 National Rivers and Streams Assessment, 2008 2009 February 2013 
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 3. Condition of the Nation's River and Streams 

least-disturbed physical habitat and water quality and an environment that is not 

stressed. 

� Taxonomic composition — the proportional abundance of certain taxonomic groups 

within a sample. Certain taxonomic groups are indicative of either highly disturbed or 

least-disturbed conditions, so their proportions within a sample serve as good indicators 

of condition. 

� Taxonomic diversity — the distribution of the number of taxa and the number of 

organisms among all the taxa groups. Healthy rivers and streams have many organisms 

from many different taxa groups; unhealthy streams are often dominated by a high 

abundance of organisms in a small number of taxa. 

� Feeding groups — the distribution of macroinvertebrates by the strategies they use to 

capture and process food from their aquatic environment, such as filtering, scraping, 

grazing, or predation. As a river or stream degrades from its natural condition, the 

distribution of animals among the different feeding groups will change, reflecting 

changes in available food sources. 

� Habits/habitats — the distribution of macroinvertebrates by how they move and where 

they live. A stream with a diversity of habitat types will support animals with diverse 

habits, such as burrowing under streambed sediments, clinging to rocks, swimming, and 

crawling. Unhealthy systems, such as those laden with silt, will have fewer habitat types 

and macroinvertebrate taxa with less diverse habits (e.g., will be dominated by 

burrowers). 

� Pollution tolerance — the distribution of macroinvertebrates by the specific range of 

contamination they can tolerate. Highly sensitive taxa, or those with a low tolerance to 

pollution, are found only in rivers and streams with good water quality. Waters with 

poor quality will support more pollution-tolerant species. 

The specific metrics chosen for each of these characteristics varied among the nine 

ecoregions used in the analysis. Each metric was scored and then combined to create an overall 

Macroinvertebrate MMI for each ecoregion. Analysts calculated a Macroinvertebrate MMI for 

each site, factored in the river or stream length represented by the site, and then generated an 

estimate of the river and stream length in a region, and nationally, with a given 

Macroinvertebrate MMI score. 

February 2013 21

National Rivers and Streams Assessment, 2008 2009
Chapter 3. Condition of the Nation's River and Streams

Because it integrates a broad variety of informative macroinvertebrate metrics into one 

overall result, the Macroinvertebrate MMI provides a particularly strong picture of biological 

condition that is widely used by state water quality agencies to assess and report on their rivers 

and streams. It was also used as the primary indicator of biological condition in the 2004 WSA. 

For these reasons, and because it is not yet possible to integrate the indices for the three 

different biological assemblages (macroinvertebrates, fish, and periphyton) into one overall 

result, the Macroinvertebrate MMI serves as the key indicator of biological condition for the 

NRSA as well. Work is ongoing to explore methods for integrating different assemblage indices 

into one overall index for future reports in this series. 

What are confidence intervals? 

Confidence intervals (the small lines at the end of the bars in this report’s 

charts) convey the level of certainty or confidence in the condition 

estimates presented in this report. For example, for the Macroinvertebrate 

MMI, the NRSA finds that 20.7% of the nation’s river and stream length is in 

good condition, with a confidence interval of +/­ 2.8 %; this means that 

there is a 95% certainty that the real value is between 17.9 % and 23.5 %. 

The confidence interval depends primarily on the number of sites sampled. 

As more rivers and streams are sampled, the confidence interval becomes 

narrower, meaning there is more confidence in the findings. When fewer 

rivers and streams are sampled, the confidence interval become broader, 

meaning there is less certainty. Figure 7 shows an example of this pattern, 

in which the confidence interval for the national results (the largest sample 

size) is narrowest, whereas the confidence intervals for the major regions, 

where a smaller number of streams were sampled, are generally broader. 

Ultimately the breadth of the confidence interval is a tradeoff between the 

need for increased certainty to support decisions and the money and 

resources dedicated to monitoring. 

National Rivers and Streams Assessment, 2008–2009 February 2013  22 
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

             

         

                   

       

Chapter 3. Condition of the Nation's River and Streams 

Findings for the 

Macroinvertebrate Multimetric 

Index 

As illustrated in Figure 7, the 

Macroinvertebrate MMI results 

show that 21% of the nation’s river 

and stream length (247,558 miles) is 

in good condition, 23% (276,796 

miles) is in fair condition, and 55% 

(659,788 miles) is in poor condition 

compared to least-disturbed 

reference conditions. Of the three 

major climatic regions, the Eastern 

Highlands has the highest 

percentage of river and stream 

length in poor condition (63%, or 

272,171 miles), followed by the 

Plains and Lowlands (58%, or 

328,821 miles) and the West (30%, 

or 58,796 miles). 

Macroinvertebrate Observed/Expected Ratio of Taxa Loss 

The Macroinvertebrate Observed/Expected Ratio of Taxa Loss (or O/E Taxa Loss) measures 

taxa that have been lost at a site. The taxa expected at individual sites (E) are predicted from a 

model developed from data collected at least-disturbed sites. By comparing the list of taxa 

observed (O) at a site with those expected to occur, the proportion of expected taxa that have 

been lost can be quantified as the ratio of O/E. O/E taxa loss models are calibrated for the 

specific natural conditions in each area for which they are used. For the NRSA, analysts 

developed three O/E taxa loss models to predict the extent of taxa loss in rivers and streams in 

the Eastern Highlands, Plains and Lowlands, and West. 

Figure 7. Biological condition of the nation’s rivers and streams

based on the Macroinvertebrate Multimetric Index. This index

combines metrics of benthic community structure and function into a

single index for each region.

February 2013 23

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

               

                 

                   

       

Chapter 3. Condition of the Nation's River and Streams 

O/E Taxa Loss values range from 0 (none of the expected taxa are present) to slightly 

greater than 1 (more taxa are present than expected). Each tenth of a point less than 1 

represents a 10% loss of taxa at a site, so a score of 0.9 indicates that 90% of the expected taxa 

are present and 10% are missing. The quality of reference sites available for a region sets the 

bar for what is expected, so regions with lower-quality reference sites will have a lower bar. It is 

important to keep in mind that this indicator examines only one specific aspect of biological 

condition (biodiversity loss), while the Macroinvertebrate MMI discussed above combines 

multiple characteristics. Therefore, results are not expected to be the same. 

Findings for O/E Taxa Loss 

Findings for O/E Taxa Loss are presented in four categories: (1) less than 10% taxa loss, (2) 

10%–20% taxa loss, (3) 20%–50% 

taxa loss, and (4) more than 50% 

taxa loss. As shown in Figure 8, 40% 

of U.S. stream length lost less than 

10% of taxa; 14% lost 10%–20% of 

taxa; 29% lost 20%–50% of taxa; and 

17% lost more than 50% of expected 

taxa. 

Of the three major regions, the 

West had the highest percentage of 

stream length with 10% or less taxa 

loss (57%) and the smallest 

percentage with more than 50% 

taxa loss (8%). The Plains and 

Lowlands and the Eastern Highlands 

had similar percentages of stream 

length with more than 50% taxa loss 

(19% and 17% respectively), 

although the Plains and Lowlands 

Figure 8. Macroinvertebrate taxa loss in the nation's rivers and

streams as measured by the Observed/Expected Ratio of Taxa

Loss. This indicator displays the loss of taxa compared to the

reference sites for each region.

24 National Rivers and Streams Assessment, 2008 2009 February 2013 
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 3. Condition of the Nation's River and Streams 

had a greater percentage of stream length in the good range with less than 10% taxa loss (41% 

versus 29% for the Eastern Highlands). 

Fish Multimetric Index 

Evaluating the variety and abundance of fish species (the fish assemblage) in streams and 

rivers has been integral to water monitoring and water quality management programs for many 

years. Fish are sensitive indicators of physical and chemical habitat degradation, environmental 

contamination, migration barriers, and overall ecosystem productivity. They need plants, 

insects, and small aquatic creatures to feed on; in-stream and streambank cover to shelter in; 

appropriate streambed substrate conditions for spawning; and overhanging vegetation to 

shade the water in which they live. They are affected by changes in temperature, dissolved 

oxygen, pH, and myriad other physical and chemical constituents in water. They are also longlived, will move (if they can) to avoid pollutants or other stresses, and are economically, 

culturally, and recreationally valuable. Determining the health and wellbeing of the fish 

assemblage helps us evaluate the extent to which our waters are meeting the goals of the Clean 

Water Act. 

For the NRSA, scientists developed a Fish MMI using an approach that estimates expected 

condition at individual sites. Separate indices were developed for each of the three major 

climatic regions. These indices were based on a variety of metrics including taxa richness, 

taxonomic composition, pollution tolerance, habitat and feeding groups, spawning habits 

(specifically, the percent of individuals that deposit eggs on or within the substrate in shallow 

waters), the number and percent of taxa that are migratory, and the percent of taxa that are 

native. Fish were collected using standard electrofishing methods, tallied, and identified in the 

field; except for those used for tissue analysis and as voucher specimens, they were then 

released alive. 

Findings for the Fish Multimetric Index 

As shown in Figure 9, the NRSA Fish MMI indicates that 37% of the nation’s river and stream 

length (or 440,129 miles) is in good condition for this indicator, 15% (174,676 miles) is in fair 

condition, and 36% (425,688 miles) is in poor condition compared to least-disturbed conditions. 

February 2013 25

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                   

             

               

               

Chapter 3. Condition of the Nation's River and Streams 

The remaining 13% of river and 

stream length either is not 

assessed or, for various reasons, 

has insufficient data. Reasons why 

this percentage is relatively large 

include denials of fish collection 

permits by state, federal, or local 

authorities (often because of the 

possible presence of threatened or 

endangered species) and 

conditions and sites that were 

deemed to be unsafe or unsuitable 

for fish sampling. 

Results for the Eastern 

Highlands and Plains and Lowlands 

are similar for this index. The 

Plains and Lowlands region has the 

highest percentage of stream 

length in poor condition (41%, or 

228,331 miles) and an almost 

equal percentage in good 

condition (40%, or 226,169 miles). For the Eastern Highlands, 35% of river and stream length 

(148,002 miles) ranks in poor condition and 38% (165,949 miles) ranks in good condition. In the 

West, on the other hand, good, fair, and poor rankings each apply to about 25% of river and 

stream length. Note that the West has the largest percentage of stream length that was either 

not assessed or had insufficient data. 

Periphyton Multimetric Index 

Periphyton, which are bottom-dwelling algae that attach themselves to stream and river 

beds, plants, rocks, and woody debris, are an important foundation of many river and stream 

Figure 9. Condition of the fish assemblage in the nation's rivers

and streams as measured by the Fish Multimetric Index

(EPA/NRSA). The index combines metrics of fish assemblage structure

and function into a single index for each region.

26 National Rivers and Streams Assessment, 2008 2009 February 2013 
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 3. Condition of the Nation's River and Streams 

food webs. They also stabilize substrates and serve as habitat for many other organisms. 

Because they are attached, they are affected by physical, chemical, and biological disturbances 

in the water body. 

The most common types of periphyton, diatoms, are particularly useful ecological indicators 

because they are found in abundance in most river and stream ecosystems. Diatoms are algae 

with inorganic cell walls composed of silica. They grow as single cells but also form filaments or 

colonies. The great numbers of diatom species in rivers and streams provide multiple, sensitive 

indicators of environmental change and of the specific conditions of their habitat. 

Analysts developed the Periphyton MMI for the NRSA using diatoms. Samples from the 

NRSA sample sites were identified and counted in the laboratory. The Periphyton MMI was 

developed based on 12 metrics related to sensitive-tolerant species, functional composition, 

and diversity composition: 

� The proportion of sensitive-tolerant (diatom) taxa, which are metrics based on 

proportion of sensitive and tolerant taxa from specific families of diatoms relative to all 

taxa. These metrics included the proportion of all sensitive diatom taxa, the proportion 

of several individual sensitive taxa, as well as the proportion of two tolerant taxa. 

� Functional metrics include the proportion of highly motile diatom individuals, stalked 

diatom individuals, and planktonic diatom, relative to all diatom taxa. 

� Diversity metrics include the proportion of diatom taxa relative to the number of 

individual diatoms counted, Shannon diversity of diatoms, and number of diatom 

families per individual diatoms counted. 

Findings for the Periphyton Multimetric Index 

Based on the Periphyton MMI, 42% of the nation’s river and stream length, or 497,738 

miles, is rated in good condition compared to least-disturbed conditions, 14% (169,392miles) is 

rated in fair condition, and 43% (507,007 miles) is rated in poor condition (Figure 10). Of the 

three major climatic regions, the Eastern Highlands has by far the largest percentage of river 

and stream miles in poor condition for this index (64%, or 277,761 miles). The West follows 

with 39% (75,875 miles); for the Plains and Lowlands, 27% (153,371 miles) are rated poor 

compared to least-disturbed condition. 

February 2013 27

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

           

           

             

     

Chapter 3. Condition of the Nation's River and Streams 

Aquatic indicators of stress 

In the aquatic environment, a 

stressor can be anything that could 

adversely affect the community of 

organisms that resides there. For the 

NRSA, a set of chemical and physical 

stressor indicators were selected 

because they are widespread, of 

potential concern, and can be 

measured. These indicators of stress 

were not intended to be allinclusive. Some important stressors 

were not included in the survey due 

to technical or cost constraints. 

Several others — primarily more 

leading-edge indicators or more 

complex analytes — were sampled 

but are still undergoing analysis and 

are not included in this report. EPA 

and its partners will be reporting on 

these stressors in supplemental technical documents or in peer-reviewed journals. 

NRSA indicators are based on direct measures of stress in the river or stream or in its 

adjacent riparian areas. This report does not track the origins of these stressors, which can 

come from a wide variety of human activities, natural sources, and land uses. A summary of the 

national and regional results for chemical and physical stressors are shown in Figures 11 

through 18. See the “Ranking Stressors” section below for a discussion of the severity of 

impacts from individual stressors and the benefits that would be derived if those stressors were 

reduced or eliminated. The purpose of these NRSA analyses is to help rank the different threats 

Figure 10. Condition of periphyton assemblage in the nation's

rivers and streams based on the Periphyton Multimetric Index

(EPA/NRSA). This index combines metrics of periphyton pollution

sensitivity and taxa diversity.

28 National Rivers and Streams Assessment, 2008 2009 February 2013 
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 3. Condition of the Nation's River and Streams 

posed by stressors to our water resources, and assist in setting priorities for management 

actions. 

Chemical stressors 

Four chemical stressors were assessed as indicators in the NRSA: total phosphorus, total 

nitrogen, salinity, and acidification. These stressors were selected because of national or 

regional concerns about the extent to which they might be affecting the quality of the biological 

communities in rivers and streams, and to allow comparison of findings with the 2004 WSA. 

Scientists developed thresholds for interpreting the data for these indicators from a set of leastdisturbed reference sites for each of the nine NRSA ecoregions, as described in Chapter 2. 

These thresholds are the same as those used for the WSA. 

Total phosphorus 

Phosphorus is an essential nutrient in the environment and a common component of 

fertilizers. Because of the naturally low concentrations of phosphorus in most rivers and 

streams, even small increases can adversely affect water quality and biological condition. High 

concentrations in rivers and streams may be associated with poor agricultural practices, runoff 

from urban areas and lawns, leaking septic systems, or discharges from sewage treatment 

plants. Too much phosphorus can lead to increased growth of algae and large aquatic plants; 

decaying algae and plants reduce dissolved oxygen levels and water clarity, interfere with 

swimming, and reduce aesthetic enjoyment of our waters. High levels of phosphorus can also 

lead to algae blooms that can produce toxins harmful to human and animal health. Natural 

variability in phosphorus concentrations is reflected in the regional thresholds for high, 

medium, and low levels, which are based on least-disturbed reference sites for each of the nine 

NRSA ecoregions. 

February 2013 29

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

         

                 

             

         

Chapter 3. Condition of the Nation's River and Streams 

Findings for total phosphorus 

Approximately 34% (407,225 

miles) of the nation’s river and 

stream miles are in good condition 

for phosphorus compared to leastdisturbed reference conditions, 26% 

(308,177 miles) are in fair condition, 

and 40% (475,598 miles) are in poor 

condition (Figure 11). Of the three 

major climatic regions, the Eastern 

Highlands has the greatest 

proportion of river and stream 

length in poor condition based on 

phosphorus levels (48%, or 208,435 

miles). 

Total nitrogen 

Nitrogen is an essential nutrient 

that, at high concentrations, can 

stimulate excess growth of algae and large aquatic plants when phosphorus levels are also high. 

Common sources of excess nitrogen include fertilizers, wastewater, animal wastes, and 

atmospheric deposition. Low dissolved oxygen levels, algae blooms, and degraded habitat 

conditions for benthic macroinvertebrates and other aquatic life can result from high nitrogen 

concentrations. 

Figure 11. Total phosphorus concentrations in the nation's rivers

and streams (EPA/NRSA). Percent of river and stream length in

good, fair, and poor, condition based on phosphorus concentrations

compared to least­disturbed regional reference sites.

30 National Rivers and Streams Assessment, 2008 2009 February 2013 
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

              

                 

                 

     

Chapter 3. Condition of the Nation's River and Streams 

Findings for total nitrogen 

About 55% (660,168 miles) of the 

nation’s river and stream miles are in 

good condition for nitrogen 

compared to least-disturbed 

reference conditions (Figure 12). 

About 17% (201,517 miles) are rated 

fair for nitrogen, and 28% (329,314 

miles) are rated poor. Unlike the 

findings for phosphorus, however, 

the findings for the Plains and 

Lowlands show the greatest 

proportion of river and stream length 

with high concentrations of nitrogen 

(32%, or 182,824 miles), followed by 

the Eastern Highlands (24%, or 

103,128 miles) and the West (22%, or 

43,362 miles). Figure 12. Total nitrogen concentrations in the nation's rivers

and streams (EPA/NRSA). Percent of river and stream length in

good, fair, or poor condition for nitrogen compared to leastdisturbed regional reference sites.

February 2013 31

National Rivers and Streams Assessment, 2008 2009
Chapter 3. Condition of the Nation's River and Streams

Nutrients and eutrophication in rivers and streams 

Eutrophication is a condition that results from high levels of nutrients in a water body and is 

characterized by excessive plant growth. Although eutrophication is a natural process, human 

activities can accelerate it by increasing the rate at which nutrients and organic substances enter 

waters from surrounding watersheds. Agricultural and urban runoff, leaking septic systems, sewage 

discharges, eroded stream banks, and similar sources can increase the flow of nutrients and organic 

substances into rivers and streams, and subsequently into downstream lakes and estuaries. These 

substances can over­stimulate the growth of algae and aquatic plants, creating eutrophic conditions 

that interfere with recreation and the health and diversity of insects, fish, and other aquatic organisms.  

Nutrient enrichment due to human activities has long been recognized as one of the leading 

problems facing our lakes, reservoirs, and estuaries. It has also been more recently recognized as a 

contributing factor to river and stream degradation. Nutrient over­enrichment of rivers and streams is 

a problem because of the negative impacts on aquatic life, adverse health effects on humans and 

domestic animals, aesthetic and recreational use impairment, and excessive nutrient input into 

downstream water bodies. 

Excess nutrients can lead to excessive growth of phytoplankton (free­floating algae) in slow­moving 

rivers, periphyton (algae attached to the substrate) in shallow streams, and macrophytes (aquatic 

plants large enough to be visible to the naked eye) in all waters. Unsightly filamentous algae can 

impair the aesthetic enjoyment of rivers and streams. In more extreme situations, excessive growth of 

aquatic plants can slow water flow in flat streams and canals, interfere with swimming, snag fishing 

lures, and clog water intake screens. 

Nutrient enrichment in streams has also been demonstrated to affect animal communities. For 

example, declines in invertebrate community structure have been correlated directly with increases in 

phosphorus concentration. High concentrations of nitrogen in the form of ammonia (NH3) are known 

to be toxic to aquatic animals. Excessive levels of algae have also been shown to be damaging to 

invertebrates. Finally, fish and invertebrates will experience growth problems and can even die if either 

oxygen is depleted or pH increases are severe; both of these conditions are symptomatic of 

eutrophication.  

As a river or stream system becomes more enriched by nutrients, different species of algae may 

spread and species composition can shift. However, unless such species shifts cause clearly 

demonstrable symptoms of poor water quality — such as fish kills, toxic algae, or very long streamers 

of filamentous algae — the general public is unlikely to be aware of a potential ecological concern. 

National Rivers and Streams Assessment, 2008–2009 February 2013  32 
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

               

           

             

Chapter 3. Condition of the Nation's River and Streams 

Salinity 

Salts can be toxic to freshwater plants and animals and can make water unsafe for drinking, 

irrigation, and livestock watering. Excess salinity can occur in areas where evaporation is high 

and made worse by repeated use of water for irrigation or water withdrawals; where road deicers are applied; and in mining, oil drilling, and wastewater discharges. Conductivity (a 

measure of water’s ability to pass an electrical current) was used as a measure of salinity for 

this study. 

Findings for salinity 

Salinity is not a problem in 87% of the nation’s river and stream miles (or 1,030,381 miles). 

About 10%, or 117,423 miles, are rated fair for salinity, and 4% (42,336 miles) are rated poor 

compared least-disturbed sites in 

the nine NRSA ecoregions (Figure 

13). All three major climatic regions 

have about 3%–4% of stream length 

rated poor for salinity. However, the 

Eastern Highlands region has a 

higher percentage of waters rated 

fair (14%, or 62,283 miles), 

compared to 7% (41,401 miles) for 

the Plains and Lowlands and 7% 

(13,738 miles) for the West. 

Acidification 

Streams and rivers can become 

acidic because of acid deposition 

(acid rain), or acid mine drainage, 

particularly from coal mining. These 

problems tend to be focused in a 

few geographic areas. Streams and 

Figure 13. Salinity conditions in the nation's rivers and streams

(EPA/NRSA). Thresholds are based on conditions of least­disturbed

regional reference sites. Indicator based on electrical conductivity.

February 2013 33

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 3. Condition of the Nation's River and Streams 

rivers can also be acidic because of natural conditions, such as high levels of dissolved organic 

compounds. Some fish and macroinvertebrates are acid-sensitive and can only tolerate small 

changes in acidity. Acidification can also indirectly affect aquatic life by releasing toxic metals 

such as aluminum from soils into the water. 

The NRSA identifies the extent to which flowing waters are not acidic, are naturally acidic 

(similar to reference conditions), and are acidic because of anthropogenic sources. This last 

category includes rivers and streams that are acidic due to chronic or episodic acid deposition, 

or because of mine drainage. 

Acid deposition forms when smokestack and auto emissions (primarily sulfur dioxide and 

nitrogen oxides) combine with moisture in the air to form dilute solutions of sulfuric acid and 

nitric acid. It can also occur in dry form, such as the particles that make up soot. Acid deposition 

on sensitive watersheds can have damaging effects on soils, vegetation, and aquatic systems. 

To assess the effect of acid deposition on flowing waters, the NRSA relied on a measure of 

water’s ability to buffer inputs of acids, called acid-neutralizing capacity (ANC). When ANC 

values fall below zero, water is considered acidic and can be either directly or indirectly toxic to 

aquatic life. When ANC is between 0 and 25 milliequivalents, the water is considered sensitive 

to episodic acidification during rainfall events. These threshold values were determined based 

on values derived from the National Acid Precipitation Assessment Program. 

Acid mine drainage occurs when water moves through mines and mine tailings, combining 

with sulfur released from certain minerals to form strong solutions of sulfuric acid and 

mobilizing toxic metals. The acidity of waters in mining areas can also be assessed by using ANC 

values. However, since mine drainage also produces very high concentrations of sulfate, sulfate 

serves as an indicator of the influence of mines on streams and rivers. Thus when ANC values 

and sulfate values are low, acidity can be attributed to acid rain; when ANC values are low and 

sulfate values are high, acidity can be attributed to acid mine drainage. 

34 National Rivers and Streams Assessment, 2008 2009 February 2013 
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

             

Chapter 3. Condition of the Nation's River and Streams 

Findings for acidification 

Figure 14 shows that the vast 

majority of U.S. rivers and streams 

(99%, or 1,178,614 miles) are not 

affected by acidification. 

Anthropogenic sources in the 

remaining waters include acid 

deposition (0.1%, or 1,245 miles of 

river and stream length), mine 

drainage (0.2%, or 2,902 miles) and 

episodic acidity due to high runoff 

events (0.2%, or 2,825 miles). About 

0.3% (5,233 miles) of river and 

stream length is affected by acidity 

from natural sources. In the Eastern 

Highlands region, acid mine drainage 

affects 0.6% (2,391 miles) of river 

and stream length and acid 

deposition affects 0.3% (1,425 miles). In the Plains and Lowlands region, 0.5% of river and 

stream length, or 2,825 miles, is affected by episodic acidity. 

Physical habitat stressors 

Many human activities such as construction, agriculture, removal of vegetation near 

streams, land development, and spread of impervious surfaces (such as roads and parking lots) 

stress the physical condition of rivers and streams and, consequently, stress fish and other 

aquatic organisms. The NRSA focuses on four indicators of physical habitat conditions in rivers 

and streams: excess streambed sediments, in-stream fish habitat, riparian (streamside) 

vegetation, and riparian disturbance. 

Figure 14. Acidification in the nation's rivers and streams

(EPA/NRSA).

February 2013 35

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 3. Condition of the Nation's River and Streams 

Excess streambed sediments 

The size and shape of natural stream and river channels and the size of the particles that 

make up their beds reflect the interplay between sediment inputs and the flow of water. 

Human uses of the landscape, such as agriculture, construction, and urbanization, can increase 

the amount of fine sediments entering streams and rivers. The same types of land uses can also 

change the amount and timing of water runoff into channels, especially when they increase the 

amount of impervious land surfaces. Typically these hydrologic alterations increase the 

frequency of high-magnitude floods, and channels can respond by down-cutting (incising), 

eroding their banks, and washing away important aquatic habitat. The most common response 

to increased fine sediment inputs is a shift to a channel formed of finer, more unstable particles 

as these sediments are transported downstream. These excess fine sediments can fill in the 

habitat spaces between stream cobbles and rocks where many aquatic organisms live or breed. 

For the NRSA, scientists measured the ratio between the particle size of observed 

sediments to the size of sediments each river or stream can move or scour during its flood 

stage, based on measures of the size, slope, and other physical characteristics of the stream 

channel. This ratio, also known as relative bed stability (RBS), differs naturally among regions 

depending on characteristics such as geology, topography, hydrology, natural vegetation, and 

natural disturbance history. Very high RBS, indicating channels with beds that are substantially 

more stable than expected (e.g., evidence of hardening after prolonged scouring or reduced 

fine sediment supply, concrete-lined channels) was not assessed by the NRSA as it is difficult to 

determine the role of human alteration in stream coarsening on a national scale. In this report, 

the NRSA addresses bed sediment conditions at the low end of RBS, indicating lower-thanexpected streambed stability, or higher excess sedimentation, resulting from high inputs of fine 

sediments or increases in stormflows. 

Findings for excess streambed sediments 

About 55% (654,401 miles) of the nation’s river and stream length has streambed sediment 

characteristics in good condition compared to regional reference conditions (Figure 15). 

Streambed sediment characteristics are rated fair in 30% (351,696 miles) of river and stream 

length and poor in 15% (177,493 miles). For this indicator, a slightly higher percentage of rivers 

36 National Rivers and Streams Assessment, 2008 2009 February 2013 
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

             

Chapter 3. Condition of the Nation's River and Streams 

and streams in the West are rated 

in poor condition (18%, or 34,539 

miles) than in the Eastern Highlands 

(15%, or 63,111 miles) or the Plains 

and Lowlands (14%, or 79,844 

miles). 

In-stream fish habitat 

The healthiest and most diverse 

communities of fish and 

macroinvertebrates are found in 

rivers and streams that have 

complex and varied forms of 

habitat, such as boulders, undercut 

banks, tree roots, and logs within 

the stream banks. Human use of 

rivers and streams and their 

adjacent riparian areas often results 

in the removal or loss of much of this habitat, which in turn affects the biological condition of 

the stream. The NRSA uses a habitat complexity measure that sums the amount of in-stream 

fish habitat and concealment features such as undercut banks, boulders, large pieces of wood, 

brush, and cover from overhanging vegetation within the water body and its banks. Because 

this measure differs naturally within and among ecoregions, low in-stream fish habitat 

complexity was assessed by comparison with expected values at least-disturbed sites adjusted 

for factors such as geography and climate within ecoregions. 

Findings for in-stream fish habitat 

Compared to least-disturbed reference condition, 68% (816,510 miles) of the nation’s river 

and stream length is in good condition for in-stream fish habitat, 20% (239,627 miles) is in fair 

condition, and 11% (136,675 miles) is in poor condition (Figure 16). Of the major climatic 

regions, the highest proportion of river and stream length in poor condition for in-stream 

Figure 15. Excess streambed sediment in the nation's rivers and

streams (EPA/NRSA).

February 2013 37

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

             

Chapter 3. Condition of the Nation's River and Streams 

habitat is in the Plains and 

Lowlands, where 15% (84,889 

miles) of river and stream length is 

rated poor. In the West, 10% 

(18,786 miles) of river and stream 

length is rated poor, as is 8% 

(32,999 miles) in the Eastern 

Highlands region. 

Riparian vegetative cover 

A river or stream can be 

buffered from the effects of human 

disturbance in the watershed by 

varied, multi-layered vegetation in 

the land corridor that surrounds it. 

Healthy, intact vegetative cover in 

these riparian areas can help 

reduce nutrient and sediment Figure 16. In­stream habitat in the nation's rivers and streams

(EPA/NRSA).

runoff from the surrounding 

landscape, prevent streambank erosion, provide shade to reduce water temperature, and 

provide leaf litter and large wood (such as branches and logs) to serve as food, shelter, and 

habitat for aquatic organisms. The NRSA uses a measure of riparian vegetative cover that sums 

the amount of cover provided by three layers of riparian vegetation: the ground layer, woody 

shrubs, and canopy trees. Because the amount and complexity of riparian vegetation differs 

naturally within and among ecoregions, lower-than-expected riparian vegetative cover was 

assessed by comparison with expected values at least-disturbed sites estimated within 

ecoregions. 

Findings for riparian vegetative cover 

Over half of the nation’s river and stream length (56%, or 669,687 miles) is in good 

condition for riparian vegetative cover compared to least-disturbed regional reference 

38 National Rivers and Streams Assessment, 2008 2009 February 2013 
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                 

Chapter 3. Condition of the Nation's River and Streams 

conditions. Another 20% (240,376 

miles) is in fair condition, and 24% 

(283,712 miles) is in poor 

condition. The Eastern Highlands 

has the highest proportion of 

rivers and streams with poor 

riparian vegetative cover (27%, or 

116,534 miles), followed by the 

Plains and Lowlands (23%, or 

130,820 miles) and the West 

(19%, or 36,359 miles) (Figure 17). 

Riparian disturbance 

The closer harmful human 

activities are to a river or stream, 

the more impact they will have on 

it. The NRSA uses a direct 

measure of riparian human 

disturbance that tallies 11 specific forms of human activities and their proximity to the river or 

stream in 22 riparian plots along the water body. Examples of human disturbance include 

roads, pavement and cleared lots, buildings, pastures and rangeland, row crops, dams, and 

logging or mining operations. The same disturbance criteria were applied to define high, 

medium, and low riparian disturbance in streams and rivers nationwide. For example, a river or 

stream scored medium if one type of human influence was noted in at least one-third of the 

riparian plots, and scored high if one or more types of disturbance were observed at all of the 

plots. 

Findings for riparian disturbance 

Thirty-four percent (411,035 miles) of the nation’s river and stream length had low levels of 

riparian disturbance and scored as good for this indicator, 46% (543,374 miles) had medium 

levels of disturbance and were rated as fair, and 20% (239,366 miles) had high levels of 

Figure 17. Riparian vegetative cover in the nation's rivers and

streams (EPA/NRSA).

February 2013 39

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

           

Chapter 3. Condition of the Nation's River and Streams 

disturbance and were rated poor 

for this indicator. The most 

widespread types of riparian 

disturbance were roads, pastures 

and rangeland, and buildings. 

Compared to the other physical 

stressors discussed above, a much 

greater proportion of U.S. river and 

stream length was rated as fair 

(with medium levels of riparian 

disturbance) and a significantly 

lower percentage of river and 

stream length was rated as good. 

The three major climatic regions 

had similar proportions of river and 

stream length in the 

good/fair/poor categories, 

although the West had the highest 

proportion of stream length rated as poor for riparian disturbance (24%, or 47,510 miles) and 

the lowest proportion rated as good (29%, or 56,995 miles) (Figure 18). 

Ranking stressors: relative extent, relative risk, and attributable risk 

One of the key roles of the NRSA, and of all assessments in this series, is to provide 

perspective on key stressors affecting the biological condition of our waters. This includes 

estimating the benefits that would be derived if those stressors were reduced or eliminated. 

For the NRSA, analysts use three approaches to assess the influence of stressors on the 

ecological condition of the nation’s rivers and streams. The first, relative extent, looks at how 

extensive any particular stressor is (e.g., how many miles of rivers and streams have excess 

phosphorus concentrations). The stressor discussions earlier in this chapter are based on 

relative extent. The second approach, relative risk, examines the severity of the impact from an 

Figure 18. Riparian disturbance in the nation's rivers and streams

(EPA/NRSA).

40 National Rivers and Streams Assessment, 2008 2009 February 2013 
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                  

Chapter 3. Condition of the Nation's River and Streams 

individual stressor when it is found at high levels (e.g., how much more likely poor biological 

conditions are when phosphorus levels are high). To assess how ecological conditions may 

change when a stressor is reduced or removed requires taking both of these perspectives into 

consideration; this leads to the third approach, attributable risk. Attributable risk is derived by 

combining the first two risk values into a single number that estimates the expected 

improvement in biological conditions if that stressor is eliminated. 

Throughout this section, stressors are assessed and reported on independently and as such 

do not sum to 100%. Most rivers and streams are likely to experience multiple stressors 

simultaneously, which can result in 

cumulative effects not accounted for 

in this analysis. 

Relative extent 

It is important for water resource 

managers to take into account how 

extensive a stressor is when setting 

priority actions at the national, 

regional, and state scale. Stressors 

that can be found in all geographic 

areas but are not pervasive do not 

have high relative extent. 

Nationally, the most widespread 

stressors measured as part of the 

NRSA are phosphorus and nitrogen 

(Figure 19). Phosphorus levels are high 

compared to least-disturbed 

conditions in 40% of river and stream 

length; nitrogen is found at high levels 

Figure 19. Relative extent of stressors in the nation's rivers and in 28% of river and stream length. 

streams (EPA/NRSA).

February 2013 41

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

                                                 

 

 

Chapter 3. Condition of the Nation's River and Streams 

Riparian vegetative cover is rated poor in 24% of river and stream length, and riparian 

disturbance is rated at high levels in 20%. With a few exceptions, the extent of these stressors 

shows a similar pattern across the three major climatic regions. 

Relative risk 

Relative risk is a way to examine the severity of the impact of a stressor when it occurs. 

Relative risk is used frequently in the human health field. For example, a person who smokes is 

15 to 30 times more likely to get lung cancer or die of lung cancer than a person who does not.1 

Similarly, scientists can examine the likelihood of finding poor biological conditions in a river or 

stream when phosphorus concentrations are high, relative to the likelihood of poor biological 

conditions when phosphorus concentrations are low. When these two likelihoods are 

quantified, their ratio is called the relative risk. A relative risk value of 1 means that you are just 

as likely to find poor biological conditions when the stressor is high as when it is low — in 

essence, no demonstrable effect. A relative risk of 1.5, however, means that you are 50% more 

likely to find poor biological conditions when a stressor is high. 

Results of the relative risk analyses for NRSA are presented in the middle panels of Figures 

20 through 22. Relative risk differs for macroinvertebrates, fish, and periphyton. For 

macroinvertebrates nationally, the relative risks are largest for total phosphorus, excess 

sedimentation, and acidification, all in the range of 1.5. In other words, when these stressors 

occur in excess levels, streams and rivers are 50% more likely to have poor macroinvertebrate 

communities than when these stressors are low. The relative risks posed by the various 

stressors differ in the three major climatic regions, with the West showing the most sensitivity 

to all the stressors compared to the other regions. In the West, macroinvertebrate communities 

are 200%–300% more likely to be in poor condition when stressors are at excessive levels 

compared to when they are at normal levels. 

1 Centers for Disease Control. Lung cancer: Risk factors. 

http://www.cdc.gov/cancer/lung/basic_info/risk_factors.htm (accessed November 7, 2012). 

42 National Rivers and Streams Assessment, 2008 2009 February 2013 
               

            –

                       

Chapter 3. Condition of the Nation's River and Streams 

Figure 20. Relative extent, relative risk, and attributable risk to macroinvertebrates based on the

Macroinvertebrate Multimetric Index (EPA/NRSA).

February 2013 43

National Rivers and Streams Assessment, 2008 2009
               

            –

                         

Chapter 3. Condition of the Nation's River and Streams 

Figure 21. Relative extent, relative risk, and attributable risk to fish based on the Fish Multimetric Index

(EPA/NRSA).

44 National Rivers and Streams Assessment, 2008 2009 February 2013 
               

            –

 

 

 

 

 

 

 

 

 

 

                       

Chapter 3. Condition of the Nation's River and Streams 

Figure 22. Relative extent, relative risk, and attributable risk to periphyton based on the Periphyton

Multimetric Index (EPA/NRSA).

Previous studies in the mid-Atlantic Highlands and in the western U.S. provided some 

evidence of very different patterns of relative risk for macroinvertebrates, fish, and periphyton. 

The NRSA results are inconclusive on this. The relative risk values are consistently low for 

macroinvertebrates, both nationally and in the Eastern Highlands and Plains and Lowlands. For 

periphyton, relative risk scores are consistently high for salinity and variable by region for the 

other stressors. The relative risk values for fish are somewhat variable across the three regions. 

Attributable risk 

Attributable risk represents the magnitude or importance of a potential stressor and can be 

used to help rank and set priorities for policymakers and managers. Attributable risk is derived 

by combining relative extent and relative risk into a single number for purposes of ranking (see 

February 2013 45

National Rivers and Streams Assessment, 2008 2009
               

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 3. Condition of the Nation's River and Streams 

third panels of Figures 20 through 22). Conceptually, attributable risk provides an estimate of 

the proportion of poor biological conditions that could be reduced if high levels of a particular 

stressor were eliminated. This risk number is presented in terms of the percent of length that 

could be improved. 

For example, as noted above, phosphorus occurs at excess levels in 40% of river and stream 

length. Rivers and streams are 50% more likely to have poor conditions for macroinvertebrates 

when phosphorus is high (relative risk of 1.5). Relative extent and relative risk combined result 

in an attributable risk level of about 17%. That is, if phosphorus levels were reduced, one might 

expect to see 17% of river and stream length improve to good conditions for 

macroinvertebrates. For periphyton, the attributable risk for phosphorus is 18%; for fish, it is 

22%. In the West, where relative risks are large, the amount of improvement in river and 

stream length to good biological condition is correspondingly large. 

Some stressors can have fairly large relative risk but small attributable risk (regardless of 

biological community) because the relative extent of this problem is small. For example, 

national relative risk levels for salinity are between 1.3 (for macroinvertebrates) and 1.7 (for 

fish), yet excess salinity occurs in only 4% of river and stream length nationally. Therefore, the 

resulting attributable risk levels are small. 

46 National Rivers and Streams Assessment, 2008 2009 February 2013 
            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 4. Human Health Considerations in the Nation’s 

Rivers and Streams 

Background 

In addition to physical, chemical, and biological indicators of the condition of the nation’s 

rivers and streams, the NRSA includes two indicators that provide insight into potential risks to 

human health: mercury in fish tissue, and the pathogen indicator enterococci. 

Most human exposure to mercury is through the consumption of fish. When pregnant 

women, nursing mothers, and women who might become pregnant eat fish with mercury 

concentrations above specified thresholds for human protection, this poses a 

neurodevelopmental health risk to fetuses, babies, and young children. States issue 

consumption advisories for specific fish species and water bodies when state or local sampling 

results indicate elevated mercury concentrations. More information on fishing advisories is 

available from local health agencies and 

water.epa.gov/scitech/swguidance/fishshellfish/fishadvisories/index.cfm. 

Enterococci are indicators of the presence of fecal material in water and, therefore, of the 

possible presence of disease-causing bacteria, viruses, and protozoa. These pathogens can 

sicken swimmers and others who use rivers and streams for recreation or eat raw shellfish or 

fish. 

Mercury in fish tissue and enterococci were not evaluated for the 2004 WSA. These results 

are not intended to represent the full range of pollutants in rivers and streams that might 

adversely affect human health. 

Mercury in fish tissue 

Mercury is widely distributed in the environment, due to both natural processes and human 

activities. It enters the atmosphere from the natural degassing of the earth’s crust (e.g., from 

volcanic action) and from some industrial sources such as coal-burning power plants and 

hazardous waste incineration. Once in the atmosphere, it can circulate widely and be deposited 

on land and water through rain and snow. 

February 2013 47

National Rivers and Streams Assessment, 2008 2009
                   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 4. Human Health Considerations in the Nation’s Rivers and Streams 

Microorganisms in water convert inorganic mercury to a toxic form of organic mercury 

called methylmercury. Methylmercury accumulates in fish, primarily in muscle tissue. Nearly all 

fish contain traces of mercury, and the amount of mercury measured in fish tissue usually 

increases with fish age and size. It also varies among fish species — those that prey on other 

fish typically accumulate higher concentrations of mercury than those that eat insects or other 

aquatic organisms. Measuring mercury levels in fish is critical because about 80% of all fish 

consumption advisories currently in effect involve mercury. Human health effects can include 

damage to the immune and nervous systems; developing embryos are particularly at risk. 

For the NRSA, field sampling teams applied consistent methods to collect fish from 542 

randomly selected river segments (fifth-order or larger) distributed across the lower 48 states. 

These 542 sites are a subset of the total sites sampled for the NRSA. The teams also collected 

additional fish at about 10% of the sites to evaluate field sampling variability. Each sample was 

a composite, consisting of multiple adult fish of the same species and similar size. Field teams 

selected fish species that people commonly eat, including largemouth and smallmouth bass, 

walleye, and various trout and catfish species. Fish fillet contaminant levels were then 

compared to EPA’s human health screening values. 

EPA analyzed the NRSA fish tissue samples for total mercury in addition to other 

contaminants. Following EPA guidance, scientists made the conservative assumption that all 

mercury is present in fish tissue as methylmercury. The human health screening value used to 

interpret mercury concentrations in fillet tissue is 0.3 milligrams of methylmercury per kilogram 

of tissue (wet weight) or 300 parts per billion, which is EPA’s tissue-based water quality 

criterion for methylmercury. This threshold represents the concentration that, if exceeded, can 

be harmful to human health. 

For a wide variety of additional chemicals (including selenium, pesticides, polychlorinated 

biphenyls (PCBs), and other contaminants of emerging concern), analyses are still underway 

and will be presented in future publications. 

48 National Rivers and Streams Assessment, 2008 2009 February 2013 
                   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 4. Human Health Considerations in the Nation's Rivers and Streams 

Findings for mercury in fish tissue 

The human health fish tissue indicator focused on fifth-order and larger rivers. This subpopulation contains 106,247 river miles, which represents 9% of the total NRSA river and 

stream miles associated with all flowing waters (1,193,755 miles). The NRSA limited the target 

population to fifth-order and larger rivers both because of resource constraints and the need to 

focus the assessment on waters that would likely support a population of fish of the size that 

are typically sought for human consumption. Given that levels of mercury in fish tissue vary but 

tend to increase with size and trophic level, this focus was intended to address both fish taken 

for subsistence and for sportfishing and produce assessment results that could be comparable 

across all the waters sampled. The sampled population is the portion of the target subpopulation for which we can determine whether mercury levels were above or below the 

human-health-based screening value. The sampled population, 49% of the target subpopulation, consists of 51,544 river miles. Mercury levels in the other 51% of the target subpopulation (54,703 river miles) cannot be assessed because sites could not be sampled due to a 

variety of factors, including inability to obtain permits, lack of suitable fish, insufficient time to 

collect fish samples, and denial of access to sites. 

All fillet samples analyzed for the NRSA contain quantifiable levels of mercury. Fish tissue 

results indicate that 13,144 river miles have concentrations above the 300 parts per billion 

human-health-based water quality criterion for mercury; 38,400 river miles do not. Figure 23 

summarizes the target and sampled populations for the fish tissue indicator. 

In the Eastern Highlands, 3,419 river miles exceed the human health screening value for 

mercury in fish tissue and 11,200 miles do not. In the Plains and Lowlands, the screening value 

is exceeded in 7,424 river miles and not exceeded in 22,315 miles. In the West, 2,301 miles 

exceed the screening value and 4,885 miles do not exceed it. Particularly in the West and the 

Plains and Lowlands, a high percentage of river length was not sampled for mercury in fish 

tissue. Results from the sampled sites cannot be extrapolated to these unassessed waters. 

Figure 24 shows the percent of rivers and streams in each of the three ecoregions that were 

sampled for mercury in fish tissue. 

February 2013 49

National Rivers and Streams Assessment, 2008 2009
                   

            –

                           

                               

                                           

                                 

                             

                                   

                   

                   

Chapter 4. Human Health Considerations in the Nation’s Rivers and Streams 

Figure 23. Human health fish tissue assessment for target (middle graphic) and sampled populations (right

graphic) of the nation's rivers (EPA/NRSA). The fish tissue target population (106,247 miles of fifth order and larger

rivers) is a subset of the overall NRSA population for all other indictors. No assessment can be made for the 54,703 miles

of the target population that were not sampled, and the fish tissue target population assessment cannot be extrapolated

to the entire rivers and streams target population. The fish tissue sampled population assessment (right graphic, 51,544

miles) cannot be extrapolated to either the entire rivers and streams target population, or the fish tissue target

population.

Figure 24. Percent of fish tissue target population sampled for mercury in

fish tissue in the three major climatic regions of the U.S. (EPA/NRSA).

50 National Rivers and Streams Assessment, 2008 2009 February 2013 
                   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 4. Human Health Considerations in the Nation's Rivers and Streams 

Pathogen indicators (enterococci) 

Enterococci are bacteria that live in the intestinal tracts of warm-blooded animals, including 

humans, and therefore indicate possible contamination of streams and rivers by fecal waste. 

Enterococci are typically not considered harmful to humans, but their presence in the 

environment may indicate that other disease-causing agents such as viruses, bacteria, and 

protozoa may also be present. Epidemiological studies conducted at beaches affected by 

human sources of fecal contamination have established a relationship between the density of 

enterococci in ambient waters and the elevated incidence of gastrointestinal illness in 

swimmers. Other potential health effects can include diseases of the skin, eyes, ears, and 

respiratory tract. Eating fish or shellfish harvested from waters with fecal contamination can 

also result in human illness. Significant economic losses can occur due to beach closures, 

swimming and boating bans, and closures of fishing and shellfishing areas due to fecal 

contamination. 

Sources of fecal indicator bacteria such as enterococci include wastewater treatment plant 

effluent, leaking septic systems, stormwater runoff, sewage discharged or dumped from 

recreational boats, domestic animal and wildlife waste, improper land application of manure or 

sewage, and runoff from manure storage areas, pastures, rangelands, and feedlots. There are 

also natural, non-fecal sources of fecal indicator bacteria, including plants, sand, soil, and 

sediments, that contribute to a certain background level in ambient waters and vary based on 

local environmental and meteorological conditions. In some situations, background levels of 

fecal indicator bacteria can be high and not necessarily related to the occurrence of fecal 

contamination or human health risks. Watershed-scale sanitary investigations can provide 

important context to fecal bacteria monitoring results. 

For the NRSA, water samples were analyzed using a process known as quantitative 

polymerase chain reaction, or qPCR, a methodology that facilitates the detection of DNA 

sequences unique to these bacteria. Analysts compared the NRSA results to a new EPA qPCR 

threshold for protecting human health in ambient waters designated for swimming (1,280 

calibrator cell equivalents per 100 milliliter). 

February 2013 51

National Rivers and Streams Assessment, 2008 2009
                   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

       

               

                   

     

Chapter 4. Human Health Considerations in the Nation’s Rivers and Streams 

Findings for enterococci 

About 85% (1,009,897 miles) of the 

nation’s river and stream length are in 

good condition for enterococci (i.e., 

samples do not exceed the threshold 

level). About 9% (105,970 miles) are in 

poor condition, with samples that 

exceed the threshold level. Nearly 7% of 

river and stream length is not assessed 

for enterococci or has no data. Of the 

three major climatic regions, the 

Eastern Highlands has the highest 

percentage of stream length exceeding 

the threshold (12%, or 49,836 miles), 

followed by the Plains and Lowlands 

(9%, or 51,013 miles). In the West, only 

3% (8,121 miles) of stream length 

exceed the threshold for enterococci 

(Figure 25). 

Figure 25. Enterococci human health thresholds exceedance

in the nation's rivers and streams (EPA/NRSA). Percent of

rivers and streams length exceeding or not exceeding EPA human

health thresholds for enterococci.

52 National Rivers and Streams Assessment, 2008 2009 February 2013 
Chapter 4. Human Health Considerations in the Nation's Rivers and Streams

Urban rivers

Cities share one key characteristic: they are comparatively small areas full of people, buildings, and 

businesses. The urban rivers that flow through and near them can serve as vital economic resources, 

often providing drinking water and recreational opportunities, boosting tourism, and improving the 

quality of city life. However, urban rivers also take on large, concentrated amounts of pollution from a 

variety of sources, including industrial discharges, mobile sources (e.g., cars/trucks), residential and 

commercial wastewater, trash, and polluted stormwater runoff from urban landscapes. As urban 

populations often share centralized water sources, this pollution creates public and environmental 

health hazards like lowered drinking water quality, water bodies that are not safe to swim in, and fish 

that aren’t safe to eat. NRSA fish tissue sampling offered an opportunity to target these important 

waters to determine if a wide range of toxic substances were of concern. 

To assist researchers in evaluating urban water quality, EPA identified each site selected for NRSA as 

either urban or non­urban. Urban waters were defined by intersecting a modified version of the Census 

Bureau national urban boundary geographic information system (GIS) coverage with the NHD­Plus. 

This essentially gave EPA a way to identify whether selected river and stream sites were within areas 

identified as contiguous census block groups and urban clusters meeting Census Bureau minimum 

population density requirements of at least 2,500 people.  

From the 1,924 sites sampled for the NRSA, a subset of 164 urban river sites across the country were 

sampled for additional data analysis. Fish tissue samples at these locations were analyzed for chemicals 

of emerging concern, including perfluorinated compounds (PFCs) and synthetic musks, in addition to 

contaminants, such as mercury, PCBs, polybrominated diphenyl ethers (PBDEs), and organochlorine 

pesticides. Results for mercury and one PFC, perfluorooctane sulfonate (PFOS), are presented below; 

complete analysis and reporting on the remaining fish tissue analytical results for organic compounds 

will follow in a separate report. Additionally, comparisons between urban and non­urban waters will be 

examined in the future. 

February 2013  National Rivers and Streams Assessment, 2008–2009

53
Chapter 4. Human Health Considerations in the Nation’s Rivers and Streams

Urban rivers: findings for mercury 

Mercury is widely distributed in the environment through natural processes and through industrial 

activities, such as fossil fuel (e.g., coal) combustion and hazardous waste incineration. These activities 

release mercury into the atmosphere where it can be transported for long distances before being 

deposited in water or on land. Once mercury is deposited in water, certain microorganisms can 

change it into methylmercury, a highly toxic form that builds up in fish, shellfish, and animals that eat 

fish. Fish and shellfish are the main sources of human exposure to methylmercury. The levels of 

methylmercury in fish and shellfish depend on several factors, including what they eat, how long they 

live, and how high they are in the food chain. 

Mercury is widely found at detectable levels in fish tissue, and the amount of mercury measured in fish 

tissue usually increases with fish age and size. Fish tissue samples from 44 of the 163 urban sites 

assessed for mercury (or 26.9%) exceed the EPA fish­tissue­based human health water quality mercury 

criterion of 300 parts per billion (ppb) (see Figure 26). This represents 2,970 miles of the 11,002 

assessed urban river miles.  

Figure 26. Mercury in fish tissue from urban sites. 

National Rivers and Streams Assessment, 2008–2009 February 2013  54 
Chapter 4. Human Health Considerations in the Nation's Rivers and Streams

Urban rivers: findings for perfluorooctane sulfonate 

PFCs are artificial chemicals that persist in the environment and have been used for decades to make 

products that resist heat, oil, stains, grease, and water. They are used in many industrial applications 

and are found in stain­resistant fabrics, nonstick cookware, and some types of food packaging. One 

type of PFC, perfluorooctane sulfonate or PFOS, can accumulate to levels of concern in fish and 

wildlife.  

PFOS was the most commonly detected PFC in the fish tissue samples. Fish tissue samples from 19 of 

the 162 urban sites assessed for PFCs contained PFOS above the one­meal­per­week Minnesota 

advisory value of 40 ppb. This represents 11.6% of the 11,002 assessed urban river miles, or 1,276 river 

miles (Figure 27). EPA is currently re­assessing the risk of PFOS to human health and expects to have a 

peer­reviewed reference dose for PFOS in 2013. 

Figure 27. PFOS in fish tissue from urban sites. 

Elevated mercury levels in fish are the leading cause of fish consumption advisories in the U.S. Urban 

river results showed that mercury concentrations occurred above the 300 ppb human health screening 

value at about a quarter of the assessed urban river miles. These results demonstrate the pervasive 

nature of mercury deposition in watersheds of the U.S. and mercury’s subsequent accumulation in 

fish. PFCs are recognized as contaminants of emerging concern because they are toxic, ubiquitous, 

and persistent in the environment. Measured levels of PFOS in the fish tissue samples exceeded the 

one­meal­per­week screening value of 40 ppb at nearly 12% of the assessed urban river miles. To 

date, three states have issued fish consumption advisories based on elevated concentrations of PFOS 

in fish. 

February 2013  National Rivers and Streams Assessment, 2008–2009

55
            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 5. Changes in Stream Condition
�

Among the long-term goals of the National Aquatic Resource Surveys is detecting trends in 

both the condition of our aquatic resources and in the stressors that affect them. Policymakers 

need this information in order to evaluate whether policy decisions have been effective or 

whether a different approach is necessary to achieve important water quality goals. Trends can 

be tracked either at the individual water body scale or at the larger population scale. 

Typically, researchers and site managers are interested in changes at individual sites, while 

many policymakers are more driven by changes and trends in groups or populations. Both types 

of approaches are relevant to policy-making and complement each other in evaluating trends 

and causes This is analogous to human health considerations: for example, you and your doctor 

are interested in whether you are gaining or losing weight, but national health experts and the 

health policy debate will be driven more by whether there is an increase or decrease in the 

percentage of people in the U.S. who are gaining or losing weight. 

To detect trends in the condition of rivers and streams, more years of data will be 

necessary. However, comparison of the “wadeable streams” portion of the NRSA with the 2004 

WSA provides a preliminary assessment of change in conditions in wadeable streams only, 

between the two surveys. A change is not the same as a trend: it simply identifies the 

difference between two points in time. 

Some of the changes found in streams between 2004 and 2008–2009 are statistically 

significant, and some are not. More data and additional analyses are necessary to fully 

understand what these changes are telling us. 

Findings for changes in stream condition 

Comparing the WSA results to the NRSA’s wadeable stream results provides an initial look 

at changes for six of the survey indicators — the Macroinvertebrate MMI, total phosphorus, 

total nitrogen, in-stream fish habitat, riparian vegetative cover, and riparian disturbance. Some 

indicators were not included in the change analysis because they had not been evaluated in the 

WSA or because protocols were modified for the later study. The same evaluation thresholds 

were used for both studies. It is important to remember that results from the WSA cannot be 

56 National Rivers and Streams Assessment, 2008 2009 February 2013 
         

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 5. Changes in Stream Condition

compared to results in other chapters of this report because the NRSA evaluates both rivers 

and streams, not just streams. 

The figures below show the percent of stream length in good condition for a given indicator 

for the WSA in 2004 and the NRSA in 2008–2009. When the difference in the two estimates is 

statistically significant, it is noted with a red star. A detailed statistical analysis of the difference 

between surveys and the statistical confidence in that difference was performed and underlies 

the presentation of the results below. It should be noted that the WSA condition class 

percentages differ slightly from those in the WSA report to allow comparison between the 

target populations of wadeable streams across the country. Minor adjustments were made to 

the WSA percentages to be comparable to the NRSA design. 

In Figure 28, results for the macroinvertebrate community indicator and nutrient indicators 

(phosphorus and nitrogen) are shown for the nation and the three major climatic regions. 

Nationally, the percent of stream length in good macroinvertebrate condition dropped from 

27.4% in 2004 to 20.5% in 2008–2009. This difference is statistically significant for the nation 

and may be driven by a 13.3% decline in streams in good condition in the Plains and Lowlands. 

For the Eastern Highlands, the values also decline but the difference is not statistically 

significant. There is no difference in macroinvertebrate condition for streams in the West. 

A consistent, statistically significant drop is evident in the percentage of stream length in 

good condition for phosphorus. Nationally, 52.8% of stream length was in good condition for 

phosphorus in 2004, compared to 34.2% in 2008–2009. This pattern occurred in each of the 

three major climatic regions, with the largest change (a decline of 22.5%) in the Plains and 

Lowlands. 

February 2013 57

National Rivers and Streams Assessment, 2008 2009
         

            –

                       

                         

                             

                             

                   

Chapter 5. Changes in Stream Condition 

Figure 28. Change in macroinvertebrate condition and nutrients between 2004 and 2008–2009, based

on percent of length in good condition; red stars indicate statistically significant change (EPA/NRSA).

Note: WSA condition class percentages differ slightly from those in the WSA report to allow comparison

between the target populations of wadeable streams across the country. Minor adjustments were made to

the WSA percentages to be comparable to the NRSA design.

58 National Rivers and Streams Assessment, 2008 2009 February 2013 
         

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 5. Changes in Stream Condition

On the other hand, the percentage of stream length in good condition for nitrogen has risen 

nationally, from 46.6% in 2004 to 55.4% in 2008–2009. Increases occurred in the Eastern 

Highlands and the West, with each of those improvements being statistically significant. In the 

Plains and Lowlands, there was a slight decline in the percent of stream length in good 

condition but it is not statistically significant. 

Figure 29 presents change results for three of the habitat indicators: in-stream fish habitat, 

riparian vegetation cover, and riparian disturbance. The percent of stream length with good instream fish habitat rose nationally and in each of the three regions. Nationally and in the West, 

the percent of stream length in good condition for riparian vegetation cover also rose, with no 

statistically significant changes in the Eastern Highlands or Plains and Lowlands. The percent of 

stream length with low levels of riparian disturbance also showed statistically significant 

increases nationally, in the Eastern Highlands, and in the Plains and Lowlands. 

The fact that the differences noted above are statistically significant does not automatically 

mean they are the result of human activities. Already, analysts have examined the relationships 

between the change in nutrients and in natural phenomena such as precipitation, stream flow, 

and drought, but they have found no reasons to explain the differences. Additional work is 

underway to examine relationships to other signals of natural phenomena and to signals of 

human activity. EPA and the U.S. Geological Survey (USGS) are also examining how long-term 

trend data from USGS sites might help provide context for the changes seen between the WSA 

and the NRSA. Trends in water quality will emerge over time as more surveys are completed, 

and our understanding of the reasons for the trends will advance. 

February 2013 59

National Rivers and Streams Assessment, 2008 2009
         

            –

                       

                             

                     

                                 

                               

Chapter 5. Changes in Stream Condition 

Figure 29. Change in stream fish habitat, riparian vegetation cover, and riparian disturbance between

2004 and 2008–2009, based on percent of stream length in good condition; red stars indicate

statistically significant change (EPA/NRSA). Note: WSA condition class percentages differ slightly from

those in the WSA report to allow comparison between the target populations of wadeable streams across the

country. Minor adjustments were made to the WSA percentages to be comparable to the NRSA design.

60 National Rivers and Streams Assessment, 2008 2009 February 2013 
            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results
�

Introduction 

Ecoregions are geographic areas that display similar environmental characteristics, such as 

climate, vegetation, type of soil, and geology. EPA has defined ecoregions at various scales, 

from a continental scale (Level I) to fine scales that divide the land into smaller ecosystem units 

(Levels III or IV). This chapter will focus on NRSA results for the nine U.S. Level III ecoregions 

aggregated for use in the National Aquatic Resource Surveys. These nine ecoregions, shown in 

Figure 30, are: 

� Northern Appalachians 

� Southern Appalachians 

� Coastal Plains 

� Upper Midwest 

� Temperate Plains 

� Southern Plains 

� Northern Plains 

� Western Mountains 

� Xeric 

Ecoregions are designed to be used in environmental assessments, for setting water quality 

and biological criteria, and to set management goals for pollution control. This is because it is 

important to assess water bodies in their own ecological setting. For example, the rivers in the 

mountainous, cold-to-temperate Northern Appalachians will have many similar characteristics; 

they run through steep, rocky channels over glacial sediments, and are influenced by annual 

precipitation totals of 35 to 60 inches. These rivers will differ significantly from those in the dry 

plains, tablelands, and low mountains of the Xeric ecoregion, which drain erodible sedimentary 

rock and are subject to flash floods in a climate where precipitation ranges from 2 to 40 inches 

and average temperatures are much higher. 

February 2013 61

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

             

Chapter 6. Ecoregional Results 

Figure 30. Ecoregional surveys for the NRSA (EPA/NRSA).

For purposes of the NRSA, least-disturbed reference sites in each ecoregion were used to 

set benchmarks for good, fair, and poor condition in that ecoregion, and reflect the variability 

within the ecoregion (see Chapter 2 and the NRSA Technical Report for more information on 

this approach). This allows sites in one ecoregion to be compared to the reference waters in 

that ecoregion. Because of this, it also allows results for one ecoregion to be compared to 

results for another. 

This chapter provides nationwide comparisons of key NRSA results for the nine ecological 

regions. It then describes each ecoregion in more detail, providing background information and 

describing NRSA results for the length of rivers and streams throughout the ecoregion. These 

results should not be extrapolated to an individual state or water body within the ecoregion 

because the study was not intended or designed to characterize conditions at these finer scales. 

This information also cannot be compared to the ecoregional results presented in the earlier 

WSA, which presented results only for streams. See Chapter 5 for the assessment of change for 

wadeable streams only between the WSA and the NRSA. A number of states implemented 

62 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

 

 

 

                       

                     

Chapter 6. Ecoregional Results

randomized designs at the state scale to characterize the condition of rivers and streams 

throughout their state, but these assessments are not described here. 

Nationwide comparisons 

The three most widespread stressors to rivers and streams — phosphorus, nitrogen, and 

riparian vegetative cover — are depicted by ecoregion in the following maps, along with 

summaries of macroinvertebrate condition and enterococci levels. These maps provide an 

overview of how conditions vary across the nation, and in some cases illustrate distinct 

ecoregional patterns. 

Biological condition — Macroinvertebrate Multimetric Index 

The proportion of rivers and streams in poor biological condition based on the 

Macroinvertebrate MMI ranges from 26% in the Western Mountains ecoregion to 71% in the 

Coastal Plains ecoregion (Figure 31). A clear pattern is evident: the easternmost ecoregions 

Figure 31. Biological condition in rivers and streams based on the Macroinvertebrate Multimetric Index across

the nine ecoregions (EPA/NRSA). Percents may not add up to 100% due to rounding.

February 2013 63

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

                         

             

Chapter 6. Ecoregional Results

(generally east of the Mississippi River) have a higher proportion of rivers and streams scoring 

in poor biological condition than those in the western U.S. In the east, the percent of river and 

stream miles in poor biological condition ranges from 55% to 71%. In the western ecoregions, 

the percent in poor condition ranges from 26% to 43%. 

Nutrients – total phosphorus and nitrogen 

The nutrients phosphorus and nitrogen are the most widespread stressors of those 

assessed in the NRSA. Figure 32 shows that in six of the nine ecoregions, phosphorus levels are 

consistently rated poor (i.e., high) in about a third or more of river and stream miles. In two 

more ecoregions — the Northern Plains and the Northern Appalachians — the proportion of 

miles rated poor is much higher (84% and 71%, respectively). Only in the Southern Plains 

ecoregion are half the river and stream miles rated good and only 23% rated poor for 

phosphorus levels. 

Figure 32. Total phosphorus levels in rivers and streams across the nine ecoregions (EPA/NRSA). Percents may

not add up to 100% due to rounding.

64 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

                         

           

Chapter 6. Ecoregional Results

The national picture shows less widespread impacts for nitrogen in many ecoregions (Figure 

33). The ecoregions with the highest proportion of miles in poor condition for nitrogen are the 

Northern Plains (60% rated poor), the Temperate Plains (58% rated poor), the Northern 

Appalachians (42% rated poor), and the Xeric (36% rated poor). Five ecoregions (Coastal Plains, 

Southern Plains, Southern Appalachians, Western Mountains, and Upper Midwest) have 

between 7% and 21% of river and stream miles rated poor for nitrogen. 

Figure 33. Total nitrogen levels in rivers and streams across the nine ecoregions (EPA/NRSA). Percents may not

add up to 100% due to rounding.

February 2013 65

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

                         

             

Chapter 6. Ecoregional Results 

Riparian vegetative cover 

One ecoregion — the Northern Plains — stands out as having the highest percentage of 

river and stream miles in poor condition for riparian vegetative cover, at 59% (Figure 34). The 

next highest is the Xeric ecoregion, at 37% of river and stream miles rated poor. In the 

remaining seven ecoregions, between 13% and 29% of river and stream miles are rated poor for 

riparian vegetative cover. 

Figure 34. Riparian vegetative cover in rivers and streams across the nine ecoregions (EPA/NRSA). Percents may

not add up to 100% due to rounding.

66 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

                       

                 

Chapter 6. Ecoregional Results

Enterococci 

In six of the nine ecoregions, less than a tenth of river and stream miles exceed thresholds 

protective of human health for enterococci bacteria (Figure 35). Of the three remaining 

ecoregions, the Southern Appalachians has 14% of river and stream miles exceeding thresholds, 

the Southern Plains has 13%, and the Central Plains has 11%. 

Figure 35. Enterococci human health threshold exceedance in rivers and streams across the nine ecoregions

(EPA/NRSA). Percents may not add up to 100% due to rounding.

February 2013 67

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results 

Northern Appalachians 

Setting 

The Northern Appalachians ecoregion covers all of the New England states, most of New 

York, the northern half of Pennsylvania, and northeastern Ohio. Included in the ecoregion are 

New York’s Adirondack and Catskill Mountains and Pennsylvania’s Allegheny National Forest. 

Major river systems include the St. Lawrence, Allegheny, Penobscot, Connecticut, and Hudson 

rivers. The total river and stream length represented in the NRSA for the Northern Appalachians 

ecoregion is 119,094 miles. 

Forests in this ecoregion were extensively cleared in the 18th and 19th centuries. Current fish 

stocks are lower than at the time of European contact, but the coastal rivers of the Northern 

Appalachians ecoregion still have a wide variety of fish including shad, alewife, salmon, and 

sturgeon that are born in fresh water, move to the sea for most of their lives, and then return 

to fresh water to spawn. Major manufacturing, chemical, steel, and power production occur in 

the large metropolitan areas around New York City, Connecticut, and Massachusetts. It is 

common for treated wastewater effluent to account for much of the stream flow downstream 

from major urban areas. 

This ecoregion is generally hilly, with some intermixed plains and mountain ranges. River 

channels in the glaciated uplands of the northern parts of the ecoregion are steep and rocky, 

and flow over glacial sediments. The climate is cold to temperate, with mean annual 

temperatures ranging from 39° to 48°F. Annual precipitation totals range from 35 to 60 inches. 

The Northern Appalachians ecoregion covers some 139,424 square miles of land (4.6% of the 

continental U.S.), with about 4,722 square miles of land under federal ownership. Based on 

satellite images from the 2006 National Land Cover Dataset, the distribution of land cover in 

this ecoregion is 61% forested, 15% planted/cultivated, and 9% developed; various other types 

of land cover (such as wetlands or scrubland) constitute the remaining 15% of the ecoregion. 

Summary of NRSA findings, Northern Appalachians 

A total of 206 NRSA sites were sampled to characterize the condition of rivers and streams 

in the Northern Appalachians ecoregion. Figure 36 shows an overview of the findings. 

68 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

 

                     

                                     

       

Chapter 6. Ecoregional Results 

Figure 36. NRSA survey results for the Northern Appalachians ecoregion (EPA/NRSA). Bars show the

percentage of river and stream length within a condition class for a given indicator. Percents may not add up

to 100% due to rounding.

Biological condition 

The Macroinvertebrate MMI shows that 57% of the river and stream length in the Northern 

Appalachians ecoregion is in poor condition, 22% is in fair condition, and 19% is in good 

condition. The Macroinvertebrate O/E Taxa Loss results show that 18% of river and stream 

length has lost more than 50% of taxa expected to occur, and 30% has lost between 20% and 

50% of taxa. 

The Periphyton MMI shows 53% percent of river and stream length in poor condition for 

periphyton, while for fish, 28% of river and stream length in this ecoregion is determined to be 

in poor condition. 

February 2013 69

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results 

Indicators of stress 

Of the indicators of stress measured for the NRSA, the most widespread in the Northern 

Appalachians ecoregion are phosphorus, nitrogen, riparian vegetative cover, streambed 

sediments, and riparian disturbance. Compared to least-disturbed conditions for this ecoregion: 

� Phosphorus is at high levels in 71% of river and stream length, medium levels in 23%, 

and low levels in 7%. 

� Nitrogen is at high levels in 42% of river and stream length, medium levels in 9%, and 

low levels in 49%. 

� Riparian vegetative cover is rated poor in 29% of river and stream length, fair in 21%, 

and good in 51%. 

� Streambed sediments are rated poor in 18% of river and stream length, fair in 21%, and 

good in 61%. 

� Riparian disturbance is at high levels in 11% of river and stream length, medium levels in 

50%, and low levels in 39%. 

Southern Appalachians 

Setting 

The Southern Appalachians ecoregion stretches over 10 states, from northeastern Alabama 

to central Pennsylvania, and includes the interior highlands of the Ozark Plateau and the 

Ouachita Mountains in Arkansas, Missouri, and Oklahoma. The topography of this ecoregion is 

mostly hills and low mountains, with some wide valleys and irregular plains. Its land area covers 

about 321,900 square miles (10.7% of the continental U.S.), with about 42,210 square miles in 

federal ownership. Many significant public lands, including the Great Smoky Mountains 

National Park, the George Washington and Monongahela National Forests, and Shenandoah 

National Park, are located within this ecoregion. 

The Southern Appalachians ecoregion has some of the greatest aquatic animal diversity of 

any area of North America, especially for species of amphibians, fishes, mollusks, aquatic 

insects, and crayfishes. Some areas, such as the Great Smoky Mountains National Park, 

continue to protect exceptional stands of old-growth forest riparian systems. Nevertheless, the 

70 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results

effects of habitat fragmentation, urbanization, agriculture, channelization, diversion, mining, 

and impoundments have altered many rivers and streams in this ecoregion. 

Rivers in this ecoregion flow mostly over bedrock and other resistant rock types, with steep 

channels and short meander lengths. A number of major rivers originate here, including the 

Susquehanna, James, and Potomac, along with feeders into the Ohio and Mississippi River 

systems such as the Greenbrier River in West Virginia. The total river and stream length 

represented in the NRSA for the Southern Appalachians ecoregion is 315,242 miles. It is 

considered temperate wet, with annual precipitation of about 40 to 80 inches and mean annual 

temperature ranging from 55° to 65°F. Based on satellite images in the 2006 National Land 

Cover Dataset, land cover in this ecoregion is 60% forested, 23% cultivated, and 9% developed; 

the remaining 8% is in various other types of land cover. 

Summary of NRSA findings, Southern Appalachians 

A total of 316 NRSA sites were sampled to characterize the condition of rivers and streams 

in the Southern Appalachians ecoregion. An overview of the findings is shown in Figure 37. 

Biological condition 

The Macroinvertebrate MMI shows that 65% of the river and stream length in the Southern 

Appalachians ecoregion is in poor condition; an additional 18% is in fair condition, and 17% is in 

good condition. The Macroinvertebrate O/E Taxa Loss results show that 17% of river and 

stream length has lost more than 50% of taxa expected to occur, and 37% has lost between 

20% and 50% of taxa. 

The Periphyton MMI shows 68% percent of river and stream length in poor condition for 

periphyton, while for fish, 37% of river and stream length is in poor condition. 

Indicators of stress 

Of the indicators of stress measured for the NRSA, the most widespread in the Southern 

Appalachians ecoregion are phosphorus, riparian vegetative cover, riparian disturbance, 

nitrogen, and streambed sediments. Compared to least-disturbed conditions for this ecoregion: 

February 2013 71

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

                     

                                   

         

Chapter 6. Ecoregional Results 

Figure 37. NRSA survey results for the Southern Appalachian ecoregion (EPA/NRSA). Bars show the

percentage of river and stream length within a condition class for a given indicator. Percents may not add

up to 100% due to rounding.

� Phosphorus is at high levels in 40% of river and stream length, medium levels in 30%, 

and low levels in 30%. 

� Riparian vegetative cover is in poor condition in 26% of river and stream length, fair in 

25%, and good in 49%. 

� Riparian disturbance is at high levels in 26% of river and stream length, medium levels in 

43%, and low levels in 31%. 

� Nitrogen is at high levels in 17% of river and stream length, medium levels in 12%, and 

low levels in 71%. 

� Streambed sediments are rated poor in 13% of river and stream length, fair in 28%, and 

good in 58%. 

72 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results

Coastal Plains 

Setting 

The Coastal Plains ecoregion covers all of Florida, eastern Texas, and the Atlantic seaboard 

from Florida to New Jersey. It includes the Mississippi Delta and Gulf Coast, and ranges north 

along the Mississippi River to the Ohio River. The total land area of this ecoregion is about 

395,000 square miles, or 13.2% of the continental U.S. Of this, 25,890 square miles, or 6.6%, is 

in federal ownership. River systems within or intersecting the Coastal Plains ecoregion include 

the Mississippi, Suwannee, Savannah, Potomac, Delaware, Susquehanna, James, Sabine, Brazos, 

and Guadalupe. 

River habitats in the Coastal Plains ecoregion have high species richness and the greatest 

number of endemic species of aquatic organisms in North America. These include fish, aquatic 

insects, and mollusks, as well as unique species such as paddlefish, American alligators, and 

giant aquatic salamanders. However, it is estimated that about 18% of the aquatic species in 

this ecoregion are threatened or endangered. Historically, this ecoregion had extensive 

bottomlands that flooded for several months; these areas are now widely channelized and 

confined by levees. Acid mine drainage, urban runoff, air pollution, sedimentation, and the 

introduction of non-native species have affected riparian habitats and native aquatic fauna. 

In general, rivers in the Coastal Plains meander broadly across flat plains created by river 

deposition and form complex wetland topographies, with natural levees, back swamps, and 

oxbow lakes. Typically, they drain densely vegetated watersheds; well-developed soils and 

moderate rains and subsurface flows keep suspended sediment levels in the rivers relatively 

low. An exception is the Mississippi River, which carries large sediment loads from dry lands in 

the central and western portion of its drainage area. The total river and stream length 

represented in the NRSA for the Coastal Plains ecoregion is 176,510 miles. 

The topography of this ecoregion is mostly flat plains, barrier islands, many wetlands, and 

about 50 important estuary systems that lie along its coastal margins. The climate is temperate 

wet to subtropical, with average annual temperatures ranging from 50° to 80°F and annual 

precipitation ranging from 30 to 79 inches. Based on satellite images in the 2006 National Land 

February 2013 73

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

                     

                                   

         

Chapter 6. Ecoregional Results 

Cover Dataset, the distribution of land cover in this ecoregion is 28% forested, 26% cultivated, 

21% wetlands, 9% developed, and the remainder in various other types of land cover. 

Summary of NRSA findings, Coastal Plains 

A total of 308 NRSA sites were sampled to characterize the condition of rivers and streams 

in the Coastal Plains ecoregion. An overview of the findings is shown in Figure 38. 

Biological condition 

The Macroinvertebrate MMI shows that 71% of river and stream length in the Coastal Plains 

ecoregion is in poor condition compared to least-disturbed conditions, 17% is in fair condition, 

and 12% is in good condition. The Macroinvertebrate O/E Taxa Loss results show that 19% of 

river and stream length has lost more than 50% of the taxa expected to occur, and 44% of river 

Figure 38. NRSA survey results for the Coastal Plains ecoregion (EPA/NRSA). Bars show the

percentage of river and stream length within a condition class for a given indicator. Percents may not add

up to 100% due to rounding.

74 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results

and stream length has lost between 20% and 50% of taxa. 

The Fish MMI also shows a large percentage of river and stream length (52%) in poor 

condition for fish, while for periphyton, 28% of river and stream length is in poor condition. 

Indicators of stress 

Of the indicators of stress measured for the NRSA, the most widespread in the Coastal 

Plains ecoregion are phosphorus, in-stream fish habitat, riparian vegetative cover, riparian 

disturbance, and streambed sediments. Compared to least-disturbed conditions for this 

ecoregion: 

� Phosphorus is at high levels in 36% of river and stream length, medium levels in 31%, 

and low levels in 33%. 

� In-stream fish habitat is in poor condition in 24% of river and stream length, fair in 30%, 

and good in 45% of river and stream length. 

� Riparian vegetative cover is in poor condition in 18% of river and stream length, fair in 

13%, and good in 69%. 

� Riparian disturbance, or evidence of human influence in the riparian zone, is at high 

levels in 13% of river and stream length, fair in 40%, and good in 47%. 

� Streambed sediments are rated poor in 13% of river and stream length, fair in 34%, and 

good in 51%. 

Upper Midwest 

Setting 

The Upper Midwest ecoregion covers most of Minnesota’s northern half and southeastern 

area, two-thirds of Wisconsin, and almost all of Michigan, extending about 160,374 square 

miles or 5.3% of the continental U.S. National and state forests and federal lands account for 

about 25,000 square miles, or 15.5% of the area. The river systems in this ecoregion empty into 

portions of the Great Lakes regional watershed and the upper Mississippi River watershed. 

Major river systems include the upper Mississippi River in Minnesota and Wisconsin; the 

Wisconsin, Chippewa, and St. Croix rivers in Wisconsin; and the Menominee and Escanaba 

February 2013 75

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results 

rivers in Michigan. Other important water bodies include Lakes Superior, Michigan, Huron, and 

Erie. 

Virtually all of the virgin forest in this ecoregion was cleared in the 19th and early 20th 

centuries, and rivers and streams were greatly affected by logging. The Great Lakes aquatic 

systems are subject to increasing impact from invasive animal and plant species including the 

zebra mussel, round goby, river ruffe, spiny water flea, and Eurasian watermilfoil. Major 

manufacturing and chemical, steel, and power production occur in the large metropolitan areas 

of the Upper Midwest ecoregion. 

Streams in the Upper Midwest ecoregion typically drain relatively small catchments and 

empty directly into the Great Lakes or Upper Mississippi River. These streams generally have 

steep gradients, but their topography and soils tend to slow runoff and sustain flow throughout 

the year. The total river and stream length represented in the NRSA for the Upper Midwest 

ecoregion is 96,142 miles. 

The glaciated terrain of this ecoregion typically consists of plains with some hills. Lakes, 

rivers, and wetlands predominate in most areas. The climate is characterized by cold winters 

and relatively short summers, with mean annual temperatures ranging from 34° to 54°F and 

annual precipitation in the 20- to 47-inch range. Based on satellite images in the 2006 National 

Land Cover Dataset, the distribution of land cover in this ecoregion is 36% forested, 27% 

cultivated, 20% wetlands, and the remainder in various other types of land cover. 

Summary of NRSA findings, Upper Midwest 

A total of 161 NRSA sites were sampled to characterize the condition of rivers and streams 

in the Upper Midwest ecoregion. An overview of the findings is shown in Figure 39. 

Biological condition 

The Macroinvertebrate MMI shows that 59% of river and stream length in the Upper 

Midwest ecoregion is in poor condition compared to least-disturbed conditions, 23% is in fair 

condition, and 18% is in good condition. The Macroinvertebrate O/E Taxa Loss results show that 

76 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

                     

                                   

         

Chapter 6. Ecoregional Results 

Figure 39. NRSA survey results for the Upper Midwest ecoregion (EPA/NRSA). Bars show the

percentage of river and stream length within a condition class for a given indicator. Percents may not add

up to 100% due to rounding.

11% of river and stream length has lost more than 50% of the taxa expected to occur, and 12% 

of river and stream length has lost between 20% and 50% of taxa. 

The Fish MMI shows 41% of river and stream length in poor condition for fish; for 

periphyton, only 15% of river and stream length is in poor condition. 

Indicators of stress 

Of the indicators of stress measured for the NRSA, the most widespread in the Upper 

Midwest ecoregion are phosphorus, riparian vegetative cover, and nitrogen. Compared to leastdisturbed conditions for this ecoregion: 

February 2013 77

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results

� Phosphorus is at high levels in 33% of river and stream length, medium levels in 18%, 

and low levels in 50% of stream length. 

� Riparian vegetative cover is rated in poor condition in 23% of stream length, fair in 14%, 

and good in 63% of river and stream length. 

� Nitrogen is at high levels in 21% of river and stream length, medium levels in 39%, and 

low levels in 41%. 

� Streambed sediments and riparian disturbance are both rated poor in 11% of river and 

stream length. 

Temperate Plains 

Setting 

The Temperate Plains ecoregion includes Iowa; the eastern Dakotas; western Minnesota; 

portions of Missouri, Kansas, and Nebraska; and the flat lands of western Ohio, central Indiana, 

Illinois, and southeastern Wisconsin. This ecoregion covers about 342,200 square miles, or 

11.4%, of the continental U.S., with approximately 7,900 square miles under federal ownership. 

Many of the rivers in this ecoregion drain into the Upper Mississippi Ohio, and Great Lakes 

watersheds. 

Much of this ecoregion is now primarily arable cultivated land, including field crops such as 

corn, wheat, and alfalfa as well as hog and cattle production. Crops and grazing have reduced 

natural riparian vegetative cover, increased sediment yield, and introduced pesticides and 

herbicides. Rivers have many species of fish, including minnows, darters, killifishes, catfishes, 

suckers, sunfishes, and black bass. 

Rivers and streams in the tall grass prairie start from prairie potholes and springs and may 

be ephemeral (flowing for a short time after snowmelt or rainfall). Rivers carry large volumes of 

fine sediments and tend to be turbid, wide, and shallow. The total river and stream length 

represented in the NRSA for the Temperate Plains ecoregion is 227,017 miles. 

The terrain of this ecoregion consists of smooth plains and many small lakes and wetlands. 

The climate is temperate, with cold winters, hot and humid summers, and mean temperatures 

ranging from 36° to 55°F. Annual precipitation ranges from 16 to 43 inches. Based on satellite 

78 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

 

                     

                                   

         

Chapter 6. Ecoregional Results

images in the 2006 National Land Cover Dataset, the distribution of land cover in this ecoregion 

is 69% cultivated, 10% forested, 9% developed, and the remainder in other types of land cover. 

Summary of NRSA findings, Temperate Plains 

A total of 193 NRSA sites were sampled to characterize the condition of rivers and streams 

in the Temperate Plains ecoregion. An overview of the findings is shown in Figure 40. 

Biological condition 

The Macroinvertebrate MMI shows that 55% of river and stream length in the Temperate 

Plains ecoregion is in poor condition compared to least-disturbed conditions, 30% is in fair 

condition, and 15% is in good condition. The Macroinvertebrate O/E Taxa Loss results show that 

Figure 40. NRSA survey results for the Temperate Plains ecoregion (EPA/NRSA). Bars show the

percentage of river and stream length within a condition class for a given indicator. Percents may not add

up to 100% due to rounding.

79 February 2013 National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results 

23% of river and stream length has lost more than 50% of the taxa expected to occur, and 21% 

of river and stream length has lost between 20% and 50% of taxa. 

The Fish MMI shows 35% of river and stream length in poor condition for fish; for 

periphyton, 29% of river and stream length is in poor condition. 

Indicators of stress 

Of the indicators of stress measured for the NRSA, the most widespread in the Temperate 

Plains ecoregion are nitrogen, phosphorus, riparian vegetative cover, riparian disturbance, and 

streambed sediments. Compared to least-disturbed conditions for this ecoregion: 

� Nitrogen is at high levels in 58% of river and stream length, medium levels in 13%, and 

low levels in 29%. 

� Phosphorus is at high levels in 31% of river and stream length, medium levels in 24%, 

and low levels in 46%. 

� Riparian vegetative cover is rated as poor in 24% of river and stream length, fair in 26%, 

and good in 50%. 

� Riparian disturbance is at high levels in 16% of river and stream length, medium levels in 

56%, and low levels in 29%. 

� Streambed sediments are rated poor in 14% of river and stream length, fair in 36%, and 

good in 50%. 

Southern Plains 

Setting 

The Southern Plains ecoregion covers about 405,000 square miles (13.5% of the continental 

U.S.) and includes central and northern Texas; most of western Kansas and Oklahoma; and 

portions of Nebraska, Colorado, and New Mexico. The Arkansas, Platte, White, Red, and Rio 

Grande rivers flow through this ecoregion, and most of the Ogallala aquifer (one of the world’s 

largest water table aquifers which supplies irrigation and drinking water to eight states) lies 

underneath it. Federal land ownership in this ecoregion totals about 11,980 square miles, or 

about 3% of the total. 

80 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results

The terrain is a mix of smooth and irregular plains interspersed with tablelands and low 

hills. The Great Prairie grasslands, which once covered much of the Southern Plains ecoregion, 

are the most altered and endangered large ecosystem in the U.S. About 90% of the original tall 

grass prairie was replaced by other vegetation; agriculture and livestock grazing and production 

are prevalent. Agriculture is, in fact, an important economic activity in this ecoregion, and 

includes sorghum, wheat, corn, sunflower, bean, and cotton production. Livestock production 

and processing is also prevalent. This ecoregion also contains a sizable portion of U.S. 

petroleum and natural gas production in Oklahoma, Kansas, and Texas. The total river and 

stream length represented in the NRSA for the Southern Plains ecoregion is 36,594 miles. 

Based on satellite images in the 2006 National Land Cover Dataset, the land in this 

ecoregion is 62% grassland/shrub, 27% cultivated, 5% forested, and the remainder in other 

types of land cover. The climate in this ecoregion is dry temperate, with mean annual 

temperatures ranging from 45° to 79°F. Annual precipitation is between 10 and 30 inches. 

Summary of NRSA findings, Southern Plains 

A total of 166 NRSA sites were sampled to characterize the condition of rivers and streams 

in the Southern Plains ecoregion. An overview of the findings is shown in Figure 41. 

Biological condition 

The Macroinvertebrate MMI shows that 42% of river and stream length in the Southern 

Plains ecoregion is in poor condition compared to least-disturbed conditions, 36% is in fair 

condition, and 21% is in good condition. The Macroinvertebrate O/E Taxa Loss results show that 

23% of river and stream length has lost more than 50% of the taxa expected to occur, and 28% 

of river and stream length has lost between 20% and 50% of taxa. 

The Fish MMI shows 31% of river and stream length in poor condition for fish. Forty-three 

percent of river and stream length is in poor condition for periphyton. 

Indicators of stress 

Of the indicators of stress measured for the NRSA, the most widespread in the Southern 

Plains ecoregion are riparian disturbance, streambed sediments, phosphorus, riparian 

February 2013 81

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

                     

                                 

           

Chapter 6. Ecoregional Results 

Figure 41. NRSA survey results for the Southern Plains ecoregion (EPA/NRSA). Bars show the

percentage of river and stream length within a condition class for a given indicator. Percents may not

add up to 100% due to rounding.

vegetative cover, and in-stream fish habitat. Compared to least-disturbed conditions for this 

ecoregion: 

� Riparian disturbance is rated at high levels in 30% of river and stream length, medium 

levels in 59%, and good levels in only 11% of river and stream length. 

� Streambed sediments are rated poor in 26% of river and stream length, fair in 34%, and 

good in 39%. 

� Phosphorus is at high levels in 23% of river and stream length, medium levels in 28%, 

and low levels in 50%. 

� Riparian vegetative cover is rated in poor condition in 18% of river and stream length, 

fair in 13%, and good in 70%. 

82 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results

� In-stream habitat is rated poor in 16% of river and stream length, fair in 25%, and good 

in 59%. 

� Salinity, though not a widespread stressor nationally or in most other ecoregions, is 

rated poor in 15% of river and stream length in the Southern Plains ecoregion. 

Northern Plains 

Setting 

The Northern Plains ecoregion covers approximately 205,084 square miles, or 6.8% of the 

continental U.S. It includes the western Dakotas, Montana east of the Rocky Mountains, 

northeast Wyoming, and a small section of northern Nebraska. This ecoregion is the heart of 

the Missouri River system and is almost exclusively within the Missouri River’s watershed. 

Federal lands account for 52,660 square miles, or nearly 26% of the total area. 

Human economic activity in this ecoregion is primarily agriculture, including cattle and 

sheep grazing and cropland. Coal mining occurs in the North Dakota, Montana, and Wyoming 

portions of the ecoregion, and petroleum and natural gas production are growing. 

This ecoregion’s terrain is irregular plains interspersed with tablelands and low hills. The 

Great Prairie grasslands were once an important feature of this ecoregion, but have largely 

been replaced by other vegetation or land uses, particularly cropland. The total river and 

stream length represented in the NRSA for the Northern Plains ecoregion is 27,227 miles. 

Based on satellite images in the 2006 National Land Cover Dataset, the land in this 

ecoregion is 68% grassland/shrub, 23% cultivated, 3% forested, and the remainder in other 

types of land cover. The climate in this ecoregion is dry and characterized by short, hot 

summers and long, cold winters. Temperatures average 36° to 46°F, and annual precipitation 

totals range from 10 to 25 inches. High winds are an important climatic factor in this ecoregion, 

which is also subject to periodic intense droughts and frosts. 

Summary of NRSA findings, Northern Plains 

A total of 175 NRSA sites were sampled to characterize the condition of rivers and streams 

in the Northern Plains ecoregion. An overview of the findings is shown in Figure 42. 

February 2013 83

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

                     

                                   

         

Chapter 6. Ecoregional Results 

Figure 42. NRSA survey results for the Northern Plains ecoregion (EPA/NRSA). Bars show the

percentage of river and stream length within a condition class for a given indicator. Percents may not add

up to 100% due to rounding.

Biological condition 

The Macroinvertebrate MMI shows that 33% of river and stream length in the Northern 

Plains ecoregion is in poor condition compared to least-disturbed conditions, 27% is in fair 

condition, and 40% is in good condition. The Macroinvertebrate O/E Taxa Loss results show that 

9% of river and stream length has lost more than 50% of the taxa expected to occur, and 18% of 

river and stream length has lost between 20% and 50% of taxa. 

The Fish MMI shows 29% of river and stream length in poor condition for fish; for 

periphyton, 30% of river and stream length is in poor condition. 

84 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results

Indicators of stress 

Of the indicators of stress measured for the NRSA, the most widespread in the Northern 

Plains ecoregion are phosphorus, riparian disturbance, nitrogen, riparian vegetative cover, and 

salinity. Compared to least-disturbed conditions for this ecoregion: 

� Phosphorus is at high levels in 84% of river and stream length, medium levels in 4%, and 

low levels in 13%. 

� Riparian disturbance is rated high in 60% of river and stream length, medium in 36%, 

and low in 3%. 

� Nitrogen is at high levels in 60% of river and stream length, medium levels in 17%, and 

low levels in 23%. 

� Riparian vegetative cover is rated poor in 59% of river and stream length, fair in 15%, 

and good in 26%. 

� Salinity is a widespread stressor in the Northern Plains and is found at high levels in 51% 

of river and stream length, at medium levels in 23%, and at low levels in 26% of river 

and stream length. 

Western Mountains 

Setting 

The Western Mountain ecoregion includes the Cascade, Sierra Nevada, and Pacific Coast 

ranges in the coastal states; the Gila Mountains in the southwestern states; and the Bitterroot 

and Rocky Mountains in the northern and central mountain states. The headwaters and upper 

reaches of the Columbia, Sacramento, Missouri, and Colorado River systems all occur in this 

ecoregion. This ecoregion covers about 397,832 square miles, with about 297,900 square miles, 

or 74.8%, classified as federal land. 

The terrain of the Western Mountains ecoregion is characterized by extensive mountains 

and plateaus separated by wide valleys and lowlands. Coastal mountains are transected by 

many fjords and glacial valleys, are bordered by coastal plains, and include important estuaries 

along the margins of the ocean. Soils are mainly nutrient-poor forest soils. Rivers drain dense 

forested catchments and contain large amounts of woody debris that provide habitat diversity 

February 2013 85

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results 

and stability. Rivers reaching the Pacific Ocean historically had large runs of salmon and trout, 

although many of these populations have been reduced by the effects of dams, flow regulation, 

overfishing, and introduced species. Smaller rivers generally start as steep mountain streams 

with staircase-like channels, steps, and plunge pools, with riffles and pools appearing as slope 

decreases. Upper river reaches experience debris flows and landslides when shallow soils 

become saturated by rainfall or snowmelt. The total river and stream length represented in the 

NRSA for the Western Mountains ecoregion is 150,975 miles. 

Based on satellite images in the 2006 National Land Cover Dataset, the land in this 

ecoregion is 55% forested, 36% shrub/scrub and grassland, and the remainder in other types of 

land cover. The climate is sub-arid to arid and mild in southern lower valleys, and humid and 

cold at higher elevations. The wettest climates of North America occur in the marine coastal 

rain forests of this ecoregion. Mean annual temperatures range from 32° to 55°F, and annual 

precipitation ranges from 16 to 240 inches. 

Summary of NRSA findings, Western Mountains 

A total of 210 NRSA sites were sampled to characterize the condition of rivers and streams 

in the Western Mountains ecoregion. An overview of the findings is shown in Figure 43. 

Biological condition 

The Macroinvertebrate MMI shows that 26% of river and stream length in the Western 

Mountains ecoregion is in poor condition compared to least-disturbed conditions, 31% is in fair 

condition, and 42% is in good condition. The Macroinvertebrate O/E Taxa Loss results show that 

6% of river and stream length has lost more than 50% of the taxa expected to occur, and 18% of 

river and stream length has lost between 20% and 50% of taxa. 

The Fish MMI shows 21% of river and stream length in poor condition for fish, while for 

periphyton, 36% of river and stream length is in poor condition. 

86 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

 

 

                     

                                   

         

Chapter 6. Ecoregional Results 

Figure 43. NRSA survey results for the Western Mountains ecoregion (EPA/NRSA). Bars show the

percentage of river and stream length within a condition class for a given indicator. Percents may not add

up to 100% due to rounding.

Indicators of stress 

Of the indicators of stress measured for the NRSA, the most widespread in the Western 

Mountains ecoregion are phosphorus, nitrogen, riparian disturbance, riparian vegetative cover 

and streambed sediments. Compared to least-disturbed conditions for this ecoregion: 

� Phosphorus is at high levels in 37% of river and stream length, medium levels in 25%, 

and low levels in 39%. 

� Nitrogen is at high levels in 18% of river and stream length, medium levels in 15%, and 

low levels in 67%. 

� Riparian disturbance is rated high in 18% of river and stream length, medium in 50%, 

and low in 32%. 

February 2013 87

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results

� Riparian vegetative cover is rated poor in 13% of river and stream length, fair in 18%, 

and good in 69%. 

� Similarly, streambed sediments are rated poor in 13% of river and stream length, fair in 

26%, and good in 62%. 

Xeric 

Setting 

The Xeric ecoregion covers the largest area of all NRSA aggregate ecoregions and includes 

the most total land under federal ownership. It covers portions of 11 western states and all of 

Nevada, for a total of about 636,583 square miles, or 21% of the continental U.S. Around 

453,000 square miles, or 71% of the land, is classified as federal lands, including the Grand 

Canyon National Park, Big Bend National Park, and the Hanford Nuclear Reservation. 

The terrain of the Xeric ecoregion is composed of a mix of physiographic features, including 

plains with hills and low mountains, high-relief tablelands, piedmont, high mountains, and 

intermountain basins and valleys. The ecoregion includes the flat to rolling topography of the 

Columbia/Snake River Plateau; the Great Basin; Death Valley; and the canyons, cliffs, buttes, 

and mesas of the Colorado Plateau. Its relatively limited surface water supply contributes to the 

Upper and Lower Colorado, Great Basin, California, Rio Grande, and Pacific Northwest regional 

watersheds. Large rivers flow all year, are supplied by snowmelt, and peak in early summer. 

Small rivers are mostly ephemeral. Rivers are often subject to rapid change due to flash floods 

and debris flows. In southern areas of the ecoregion, internal drainages often end in saline 

lakes or desert basins without reaching the ocean (e.g., Utah’s Great Salt Lake). 

Rivers in this ecoregion create a riparian habitat oasis for plants and animals. Many fish are 

endemic and have evolved to cope with warm, turbid waters. Many are threatened or 

endangered due to flow regulations from dams, water withdrawals, and introduced non-native 

species. The total river and stream length represented in the NRSA for the Xeric ecoregion is 

44,974 miles. 

Based on satellite images in the 2006 National Land Cover Dataset, the land in this 

ecoregion is 77% shrub/scrub and grassland, 8% cultivated, 7% forested, and the remainder in 

88 National Rivers and Streams Assessment, 2008 2009 February 2013 
     

            –

 

 

 

 

 

 

 

 

 

                     

                                       

Chapter 6. Ecoregional Results

various types of land cover. The climate in this ecoregion varies widely from warm and dry to 

temperate, with mean annual temperatures ranging from 32° to 75°F and annual precipitation 

in the 2- to 40-inch range. 

Summary of NRSA findings 

A total of 189 NRSA sites were sampled to characterize the condition of rivers and streams 

in the Xeric ecoregion. An overview of the findings is shown in Figure 44. 

Biological condition 

The Macroinvertebrate MMI shows that 43% of river and stream length in the Xeric 

ecoregion is in poor condition compared to least-disturbed conditions, 15% is in fair condition, 

Figure 44. NRSA survey results for the Xeric ecoregions (EPA/NRSA). Bars show the percentage of river

and stream length within a condition class for a given indicator. Percents may not add up to 100% due to

rounding.

89 February 2013 National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 6. Ecoregional Results

and 41% is in good condition. The Macroinvertebrate O/E Taxa Loss results show that 13% of 

river and stream length has lost more than 50% of the taxa expected to occur, and 31% of river 

and stream length has lost between 20% and 50% of taxa. 

The Fish MMI shows 40% of river and stream length in poor condition for fish; for 

periphyton, 50% of river and stream length is in poor condition. 

Indicators of stress 

Of the indicators of stress measured for the NRSA, the most widespread in the Xeric 

ecoregion are riparian disturbance, riparian vegetative cover, phosphorus, nitrogen, and 

streambed sediments. Compared to least-disturbed conditions for this ecoregion: 

� Riparian disturbance is rated high in 46% of river and stream length, medium in 36%, 

and low in 18%. 

� Riparian vegetative cover is in poor condition in 37% of river and stream length, fair 

condition in 19%, and good condition in 44%. 

� Phosphorus is at high levels in 38% of river and stream length, medium levels in 26%, 

and low levels in 36%. 

� Nitrogen is at high levels in 36% of river and stream length, medium levels in 24%, and 

low levels in 40%. 

� Streambed sediments are rated poor in 34% of river and stream length, fair in 31%, and 

good in 34%. 

90 National Rivers and Streams Assessment, 2008 2009 February 2013 
            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 7. Summary and Next Steps
�

This first National Rivers and Streams Assessment was an unprecedented sampling and 

analytical effort by EPA and its state and tribal partners. Over two summers, 85 field crews 

sampled nearly 2,000 sites along the nation’s wide-ranging rivers and streams. Twenty-two 

separate field training sessions were held to prepare for this survey. The efforts of the field 

crews yielded over 25,000 samples shipped to laboratories across the country. For example, 

over the course of the survey, 3,300 benthic macroinvertebrate samples (each sample with 

hundreds of individual preserved macroinvertebrates) were shipped to eight laboratories for 

sorting, identification, and analysis. Seventeen different indicators were sampled or evaluated 

at the NRSA sites. Ten million bits of data were collected in field and analyzed in laboratories. 

These data from the NRSA are available at www.epa.gov/aquaticsurveys. 

Overall, the NRSA finds that biological communities in our rivers and streams are being 

heavily affected and degraded across the country. More than half of the nation’s river and 

stream length is in poor condition, based on an index that combines different measures of the 

condition of aquatic benthic macroinvertebrates. The eastern and mid-western ecoregions tend 

to have the most waters in poor biological condition, with the percentage of rivers and streams 

rated poor ranging from 55% to 71%. In the west (including the Northern and Southern Plains 

ecoregions), the percentage of rivers and streams in poor biological condition ranges from 26% 

to 42%. 

Of the four chemical stressors assessed, phosphorus and nitrogen are the most widespread. 

Biological communities are 50% more likely to be in poor condition when phosphorus levels are 

high and 40% more likely to be in poor condition when nitrogen levels are high. Phosphorus is 

the most widespread stressor in six of the nine ecoregions, and nitrogen is the most widespread 

in one ecoregion. Analysis of the NRSA data suggest that if phosphorus levels were reduced in 

areas where levels are currently high, we might see 17% of the nation’s river and stream length 

improve to good conditions for macroinvertebrates. 

Of the four physical habitat stressors assessed in the NRSA, poor riparian vegetative cover 

and high levels of riparian disturbance are reported in 24% and 20% of the nation’s river and 

stream length respectively, and are the most widespread. Riparian disturbance is the most 

February 2013 91

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 7. Summary and Next Steps

widespread stressor in two of the nine ecoregions. However, excess streambed sediments have 

a somewhat greater impact on biological condition. Poor biological condition is 60% more likely 

in rivers and streams with excessive levels of streambed sediments. Nearly 9% of river and 

stream length in poor biological condition might improve to good conditions for 

macroinvertebrates if excess levels of streambed sediments were reduced or eliminated. 

The NRSA also includes two indicators that provide insight into potential risks to human 

health. It finds that in 9% of the nation’s river and stream length, levels of enterococci bacteria 

exceed threshold levels for protecting human health. Additionally, the NRSA is able to report 

that over 13,000 miles of rivers have mercury levels in fish tissue that exceed human health 

screening values. 

As we continue to implement these surveys over time, an important element of the NRSA is 

the ability to track changes in the condition of our rivers and streams. This report provides a 

first glimpse of that capability by examining the differences between stream conditions as 

reported in 2004 and wadeable systems assessed as part of the NRSA. Several NRSA indicators 

show statistically significant change compared to the 2004 WSA. An increase in stream length in 

good condition is evident for nitrogen, in-stream fish habitat, riparian disturbance, and riparian 

vegetation; however, there is also a decrease in stream length in good condition for 

phosphorus and overall biological condition as measured by the macroinvertebrate index. 

These findings of change apply only to streams and are only identifying differences between 

two points in time; they should not be interpreted as trends in water quality conditions. 

Reasons for the changes have not been determined although work continues in evaluating 

possible human or natural explanations. Future assessments of the nation’s rivers and streams 

will be able to provide more robust trend assessments as additional years of data become 

available and as our understanding of the relationship between human activity, natural 

phenomena, and environmental change mature. 

The survey’s finding that more than half of river and stream length is in poor biological 

condition and that excess nutrients and poor habitat are widespread contributors to poor 

condition supports continued management attention to these problems at the national, 

regional, state, and watershed scales. Management actions should be focused not only on 

92 National Rivers and Streams Assessment, 2008 2009 February 2013 
         

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 7. Summary and Next Steps

improving those areas where biological conditions are poor, nutrient levels are high, and 

habitat conditions are already degraded, but on protecting those areas that are still in good 

condition. 

Moving the science forward 

Many of the contributions of the NRSA go beyond the findings discussed in this report. 

Scientists developed new methods of sampling and assessing important water indicators such 

as streambed sediments; data were collected on leading-edge indicators that will be analyzed 

and reported separately; and state and tribal partners gained — and shared — new expertise in 

state-of-the-art field monitoring methods and probability-based surveys. 

EPA scientists and collaborators are continuing to move the science forward to assess the 

core indicators that are part of the NRSA. Many of these efforts are focused on new ways to 

assess the benthic macroinvertebrate community using a method similar to the one used for 

the fish assemblage and periphyton assemblage indicators. This advanced approach uses a 

modeling technique — called random forest modeling — to improve the establishment of 

reference condition and our ability to assess the condition of biological communities. NRSA 

scientists will publish supplemental benthic analysis using the random forest model and set the 

stage for incorporating this procedure into the next NRSA report. 

NRSA scientists are also working toward developing assessment and reporting methods that 

will more fully integrate the three biological indicators into one to evaluate the overall 

condition of rivers and streams. Transferring NRSA methods and technology to state and tribal 

programs is another key aspect of moving the science forward. 

As additional data continue to come back from laboratories, they will be analyzed and 

published as NRSA supplemental reports. For example, many analytes that were included in the 

fish tissue analysis are still waiting for final laboratory analysis. These include pesticide data, 

PCBs, and chemicals of emerging concern such as pharmaceuticals. In urban rivers, crews also 

collected water samples to look at the presence and amount of chemicals of emerging concern. 

EPA included several leading-edge indicators as part of the NRSA. These indicators were 

selected to address emerging issues and developments in aquatic sciences and were included 

February 2013 93

National Rivers and Streams Assessment, 2008 2009
     

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 7. Summary and Next Steps 

to support innovative research within the EPA. For example, the EPA Office of Research and 

Development led an effort to study microbial sediment enzyme activity (or sediment enzymes), 

an indicator that focuses on nutrient concentration within the streambed sediment. The work 

to collect and analyze sediment enzymes is helping EPA and our partners better understand 

nutrient limiting factors within the stream or river channel that affect the biological community. 

The result may prove to be a sensitive indicator that can help us implement the most effective 

management action to address nutrient pollution. A number of peer-reviewed journal articles 

focus on the technical aspects of the analysis and assessment of this innovative indicator. 

Next steps 

As this report was being written, planning was already underway for the 2013–2014 

National Rivers and Streams Assessment. EPA and its state and tribal partners have taken stock 

of the lessons learned from the 2008–2009 survey as well as from other National Aquatic 

Resource Surveys; they have met to discuss possible changes in indicators, methods, reference 

sites, logistics, and analytical approaches; sites for the 2013–2014 sampling seasons have been 

selected; and manuals for field and laboratory methods and quality assurance are being 

updated and prepared. Supplemental reports based on these 2008–2009 findings will be issued 

as assessments are completed. These supplemental reports will be made available on the 

National Aquatic Resource Surveys main website at www.epa.gov/aquaticsurveys. 

EPA, states, tribes, and other federal partners expect to continue to produce national water 

quality assessments on a regular cycle under the National Aquatic Resource Surveys program. A 

new national coastal assessment report will be released in 2013 based on field sampling that 

took place in 2010. A first-ever national wetlands condition assessment, based on field sampling 

in 2011, is also scheduled for 2013. A second national lakes assessment is planned for 2014 

based on sampling during the summer of 2012. 

As these national assessments continue, many states are developing and conducting their 

own state-scale probability surveys of their rivers and streams, lakes, and coastal waters. EPA 

will continue to explore ways to best support states as they sample, analyze, and report on 

their waters using these surveys. For example, EPA is working to build and refine tools states 

94 National Rivers and Streams Assessment, 2008 2009 February 2013 
         

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Chapter 7. Summary and Next Steps

can use to assess survey data at different scales and is exploring options for providing direct 

technical support. As a first step, EPA will make available the statistical codes that were used to 

develop the MMIs and thresholds for assessment. EPA is also piloting in-person training on the 

statistical tools and methods that were used in the National Lakes Assessment. Modifications 

and refinements will be made to this pilot effort to train states and tribes for the NRSA and 

other NARS programs. 

This survey would not have been possible without the assistance and collaboration of 

hundreds of scientists working for state, federal, and tribal agencies and universities across the 

country. These scientists helped plan and design the survey, select sites and indicators, develop 

and improve monitoring methods, train crew members, conduct sampling, track samples, 

screen and analyze results, and review and write up the findings. Working together on future 

surveys, and on state-scale surveys of similar design, EPA and its partners will continue 

developing a high quality baseline of information on rivers and streams that can be used to 

evaluate our progress in protecting and restoring them. 

February 2013 95

National Rivers and Streams Assessment, 2008 2009
Chapter 7. Summary and Next Steps

California uses the NARS approach to enhance monitoring capacity 

Introduction 

One of the strengths of the NARS program has 

been its ability to transfer significant technical 

advances in monitoring approaches and 

techniques to states and tribes. Partnerships with 

states and tribes were designed to help build 

local capacity to take advantage of the new tools 

that NARS was developing. 

Over the last 12 years, California has embraced 

this technical and partnership approach. First 

participating in the EPA Environmental 

Monitoring and Assessment Program (EMAP) 

Western pilot to monitor streams and rivers, 

California used what it learned to produce a 

thriving program that is transforming the way 

water quality monitoring is conducted and data 

Figure 45. Map of about 1,200 probability sites in  are evaluated throughout the state. Since 2000,  California sampled since 2000 using compatible  California has leveraged about 250 EMAP/NRSA  EMAP­style survey designs. 

sites into a probability dataset of over 1,200 sites

(Figure 45). The list of data applications and opportunities for partnerships keeps growing every year.

Regional assessments and land use assessments 

The high density of sites in California supports the development of regional assessments and 

analyses (e.g., of stressor extent and risk) that are more relevant to the scale at which policy and 

management decisions are made (Figure 46). California also added the ability to produce summaries 

for major land cover classes such as forested, agricultural, or urban land (Figure 47). This was the first 

attempt to use a probability survey to produce land­use­specific assessments. Knowing the 

probability­derived distribution of stressors and indicators in urban, agricultural, and forested 

landscapes gives managers context for interpreting the results of monitoring done in these types of 

landscapes. 

National Rivers and Streams Assessment, 2008–2009 February 2013  96 
Chapter 7. Summary and Next Steps

Figure 46. Biological condition of perennial streams in the six major 

ecological regions of California. (Green = good biological condition, 

yellow = altered biological condition, and red = very altered biological 

condition.)

Figure 47. Percentage of California stream length that exceeds severe (red) 

and moderate (yellow) threshold values for various chemical and physical 

habitat stressor variables in streams associated with each of three major 

land cover types. 

February 2013  National Rivers and Streams Assessment, 2008–2009

97
Chapter 7. Summary and Next Steps

Beyond condition assessments 

Exploring stressor–condition relationships    

CA measures a large suite of water chemistry and in­stream and riparian habitat parameters in 

addition to ecological condition indicators such as benthic invertebrates and algae. Site­specific 

information is supplemented with over a hundred layers of GIS data that look across the site, 

watershed and region. This provides a dataset that can be used to explore stressor–condition 

relationships for a wide variety of objectives (Figure 48). The ability to produce objective descriptions 

of stressor extent and relationships between stressors and biological condition holds even greater 

potential to influence CA’s resource management programs. Better understanding of these 

relationships is leading to significant improvements in the state’s ability to prioritize limited 

resources and to have more meaningful discussions about issues of concern with the public and with 

other agencies (Figure 49). 

Figure 49. The combination of probability and 

reference distributions provides objective context 

for interpreting targeted monitoring data. 

Figure 48. Relative risk of biological 

impairment associated with a series of 

habitat and chemistry variables in southern 

California streams. 

National Rivers and Streams Assessment, 2008–2009 February 2013  98 
Chapter 7. Summary and Next Steps

Support for biocriteria development 

California’s extensive probability datasets have given the state a solid foundation to move toward 

using ecological indicators for regulatory purposes, such as biocriteria development and refining 

reference condition. Probability data have also played an important role in the development of 

the technical elements of California’s biocriteria policy, which is currently in progress.  

Fostering inter-agency collaboration 

California’s statewide probability survey, the Perennial Streams Assessment, serves as a highly 

effective tool for encouraging collaboration with regional monitoring programs and federal 

agencies. For example, two successful monitoring partnerships in urban areas (southern coastal 

California and the San Francisco Bay Area) worked with the Assessment to create monitoring 

programs that were compatible with the Assessment’s design and that allowed them to 

coordinate efforts and effectively use data across regional groups. Partnerships with federal 

agencies have the potential for similar benefits in rural areas. 

Partnerships like those in California enable programs to do more with limited monitoring 

resources and provide feedback that improves the monitoring program. They help connect 

partners’ management needs to the right data. California is using this approach to accelerate its 

progress toward the widespread use of ecological indicators in aquatic resource protection, 

including the development of multiple indicator assemblages (such as algae and wetland 

vegetative condition) and tools for a variety of aquatic resource types, including non­perennial 

streams, wetlands, and large rivers. 

February 2013  National Rivers and Streams Assessment, 2008–2009

99
            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Glossary of Terms
�

Benthic macroinvertebrates: Aquatic insects (often in larval stages) such as dragonfly larvae 

and beetles, crustaceans such as crayfish, worms, and mollusks. These small creatures live 

throughout the stream bed attached to rocks, vegetation, and logs and sticks or burrowed 

into stream bottoms. 

Biological assemblages: Key groups of animals and plants — such as benthic 

macroinvertebrates, fish, or algae — that are studied to learn more about the condition of 

water resources. 

Biological integrity: The state of being able to support and maintain a balanced community 

of organisms with a species composition, diversity, and functional organization comparable 

to that of the natural habitat of the region. 

Ecoregions: Ecological regions that are similar in climate, vegetation, soil type, and geology; 

water resources within a particular ecoregion have similar natural characteristics and 

similar responses to stressors. 

In-stream fish habitat: Areas fish need for concealment and feeding, such as large wood 

within the stream banks, boulders, undercut banks, and tree roots. 

Intermittent (ephemeral) streams: Streams that flow only during part of the year, such as in 

the spring and early summer after snowmelt, or only in direct response to precipitation. 

Macroinvertebrate Multimetric Index: The sum of a number of individual measures of 

biological condition, such as the number of taxa in a sample, the number of taxa with 

different habits and feeding strategies, etc. 

National Hydrography Dataset (NHD) Plus: Comprehensive set of digital spatial data — 

based on U.S. Geological Survey 1:100,000 scale topographic maps — that contains 

information on surface water features such as streams, rivers, lakes, and ponds. 

Nutrients: Substances such as nitrogen and phosphorus that can over-stimulate the growth 

of algae and other plants in water. Nutrients in streams and lakes can come from 

agricultural and urban runoff, leaking septic systems, sewage discharges, and similar 

sources. 

O/E (Observed/Expected) Ratio of Taxa Loss: A ratio comparing the number of taxa 

expected (E) to exist at a site to the number that are actually observed (O). The taxa 

expected at individual sites are based on models developed from data collected at 

reference sites. 

Perennial streams: Steams that flow throughout the year. 

100 National Rivers and Streams Assessment, 2008 2009 February 2013 
   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Glossary of Terms 

Physical habitat: For streams and rivers, the area in and around the stream or river, 

including its bed, banks, in-stream and overhanging vegetation, and riparian zone. 

Probability-based design: A type of random sampling technique in which every element of 

the population has a known probability of being selected for sampling. 

Reach: Stream segment. 

Reference condition: The least-disturbed condition available in an ecological region, 

determined based on specific criteria, used as a benchmark for comparison with sampled 

sites in the region. 

Riparian: Pertaining to a stream or river and its adjacent area. 

Riparian disturbance: A measure of the evidence of human activities in and alongside 

streams and rivers, such as dams, roadways, construction, pastureland, and trash. 

Riparian vegetative cover: The vegetation corridor alongside streams and rivers. Intact 

riparian vegetative cover reduces pollution runoff, prevents streambank erosion, and 

provides shade, lower temperatures, food, and habitat for fish and other aquatic 

organisms. 

Streambed sediments: Fine sediments and silt on the streambed. In excess quantities, they 

can fill in the habitat spaces between stream cobbles and boulders, and suffocate 

macroinvertebrates and fish eggs. 

Stream order: Stream size, based on the confluence of one stream with another. First-order 

streams are the origin or headwaters. The confluence or joining of two first-order streams 

forms a second-order stream, the confluence of two second-order streams forms a thirdorder stream, and so on. 

Stressors: Effects or substances that are stressful to — and therefore degrade — aquatic 

ecosystems. Stressors can be chemical (e.g., nutrients), physical (e.g., excess sediments on 

the streambed), or biological (e.g., competing invasive species). 

Taxa: Plural of “taxon”; groupings of living organisms, such as phylum, order, family, genus, 

or species. Scientists organize organisms into taxa in order to better identify and 

understand them. 

Transect: A path or line along which one counts and studies various aspects of a stream, 

river, or other study area. 

Wadeable streams: Streams that are small and shallow enough to adequately sample by 

wading, without a boat. 

February 2013 101

National Rivers and Streams Assessment, 2008 2009
            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Sources and References
�

General references 

Lang, B. n.d. Columbia River. www.ccrh.org/river/history.htm (accessed August 15, 2012). 

Delaware River Basin Commission. 2012. Basin information. www.state.nj.us/drbc/basin 

(accessed August 15, 2012). 

General Accounting Office. 2000. Water Quality — Key EPA and State Decisions Limited by 

Inconsistent and Incomplete Data. GAO/RCED-00-54. 

H. John Heinz 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. New York: Cambridge University Press. 

Moving Waters: The Colorado River and the West. 2001. Information droplets. 

www.movingwaters.org/faq.html (accessed August 15, 2012). 

National Academy of Public Administration. 2002. Understanding What States Need to Protect 

Water Quality. Academy Project Number 2001-001. 

National Research Council. 2001. Assessing the TMDL Approach to Water Quality Management. 

Committee to Assess the Scientific Basis of the Total Maximum Daily Load Approach to 

Water Pollution Reduction. Washington, DC: National Academies Press. 

Stoddard, J.L., J.S. Kahl, F.A. Deviney, D. DeWalle, C.T. Driscoll, A. Herlihy, J.H. Kellogg, P. 

Murdoch, J.R. Webb, and K. Webster. 2003. Response of Surface Water Chemistry to the 

Clean Air Act Amendments of 1990. EPA/620/R-03/001. Washington, DC: U.S. 

Environmental Protection Agency. 

U.S. Department of the Interior, National Park Service. 2012. Mississippi River facts. 

www.nps.gov/miss/riverfacts.htm (accessed August 2, 2012). 

U.S. EPA. 2001. National Coastal Condition Report. EPA/620/R-01/005. Washington, DC: U.S. 

Environmental Protection Agency, Office of Research and Development and Office of Water. 

U.S. EPA. 2004. National Coastal Condition Report II. EPA/620/R-03/002. Washington, DC: U.S. 

Environmental Protection Agency, Office of Research and Development and Office of Water. 

U.S. EPA. 2006. National Estuary Program Coastal Condition Report. Draft. EPA/842/B-06/001. 

Washington, DC: U.S. Environmental Protection Agency, Office of Water. 

U.S. EPA. 2006. Wadeable Streams Assessment: A Collaborative Survey of the Nation’s Streams. 

EPA/841/B-06/002. Washington, DC: U.S. Environmental Protection Agency, Office of Water 

and Office of Research and Development. 

February 2013 102

National Rivers and Streams Assessment, 2008 2009
   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Sources and References 

U.S. EPA. 2009. National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes. 

EPA/841/R-09/001. Washington, DC: U.S. Environmental Protection Agency, Office of Water 

and Office of Research and Development. 

U.S. EPA. 2012. The Missouri River mainstem. 

www.epa.gov/region07/citizens/care/missouri.htm (accessed August 2, 2012). 

Water Education Foundation. 2012. Colorado River facts. 

www.watereducation.org/doc.asp?id=1025 (accessed August 15, 2012). 

Stream and river sampling and laboratory methods 

Flotemersch, J.E., J.B. Stribling, and M.J. Paul. 2006. Concepts and Approaches for the 

Bioassessment of Non-wadeable Streams and Rivers. EPA/600/R-06/127. Cincinnati, OH: 

U.S. Environmental Protection Agency. 

Lazorchak, J.M., B.H. Hill, D.K. Averill, D.V. Peck, and D.J. Klemm, eds. 2000. Environmental 

Monitoring and Assessment Program—Surface Waters: Field Operations and Methods for 

Measuring the Ecological Condition of Non-Wadeable Rivers and Streams. EPA/620/R00/007. Cincinnati (OH): U.S. Environmental Protection Agency. 

Peck, D.V., D.K. Averill, A.T. Herlihy, R.M. Hughes, P.R. Kaufmann, D.J. Klemm, J.M. Lazorchak, 

F.H. McCormick, S.A. Peterson, M.R. Cappaert, T. Magee, and P.A. Monaco. 2005. 

Environmental Monitoring and Assessment Program — Surface Waters Western Pilot Study: 

Field Operations Manual for Non-Wadeable Rivers and Streams. EPA/620/R-06/003, 

2006.Washington, DC: U.S. Environmental Protection Agency. 

U.S. EPA. 2004. Wadeable Streams Assessment: Benthic Laboratory Methods. EPA/841/B04/007. Washington, DC: U.S. Environmental Protection Agency, Office of Water and Office 

of Environmental Information. 

U.S. EPA. 2004. Wadeable Streams Assessment: Field Operations Manual. EPA/841/B-04/004. 

Washington, DC: U.S. Environmental Protection Agency, Office of Water. 

U.S. EPA. 2004. Wadeable Streams Assessment: Quality Assurance Project Plan. EPA/841/B04/005. Washington, DC: U.S. Environmental Protection Agency, Office of Water and Office 

of Environmental Information. 

U.S. EPA. 2004. Wadeable Streams Assessment: Site Evaluation Guidelines. EPA/841/B-04/006. 

Washington, DC: U.S. Environmental Protection Agency, Office of Water and Office of 

Environmental Information. 

U.S. EPA. 2004. Wadeable Streams Assessment: Water Chemistry Laboratory Manual. 

EPA/841/B-04/008. Washington, DC: U.S. Environmental Protection Agency, Office of Water 

and Office of Environmental Information. 

U.S. EPA. 2007. National Rivers and Streams Assessment: Field Operation Manual. EPA/841/B07/009. Washington, DC: U.S. Environmental Protection Agency. 

February 2013 103

National Rivers and Streams Assessment, 2008 2009
   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Sources and References 

U.S. EPA. 2007. National Rivers and Streams Assessment: Laboratory Operations Methods 

Manual. EPA/841/B-07/010. Washington, DC: U.S. Environmental Protection Agency. 

U.S. EPA. 2007. National Rivers and Streams Assessment: Quality Assurance Project Plan. 

EPA/841/B-07/007. Washington,, DC: U.S. Environmental Protection Agency. 

U.S. EPA. 2007. National Rivers and Streams Assessment: Site Evaluation Guidelines. EPA/841/B07/008. Washington, DC: U.S. Environmental Protection Agency. 

Probability designs 

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, D.L., Jr. 1997. Variable density grid-based sampling designs for continuous spatial 

populations. Environmetrics 8: 167-195. 

Stevens, D.L., Jr., and N.S. Urqhart. 2000. Response designs and support regions in sampling 

continuous domains. Environmetrics 11: 11-41. 

Stevens, D.L., Jr., and A.R. Olsen. 1999. Spatially restricted surveys over time for aquatic 

resources. Journal of Agricultural, Biological, and Environmental Statistics 4: 415-428. 

Stevens, D.L., Jr., and A.R. Olsen. 2003. Variance estimation for spatially balanced samples of 

environmental resources. Environmetrics 14: 593-610. 

Stevens, D.L., Jr., and A.R. Olsen. 2004. Spatially-balanced sampling of natural resources in the 

presence of frame imperfections. Journal of American Statistical Association 99: 262-278. 

Ecological regions 

Griffith, G.T., T. Loveland, T. Olsen, and J. Omernik (contributors). 1997. Ecological Regions of 

North America — Toward a Common Perspective. Montreal, QC: Secretariat of the 

Commission for Environmental Cooperation. 

Hamilton, P.A., T.L. Miller, and D.N. Myers. 2004. Water quality in the nation’s streams and 

aquifers — overview of selected findings, 1991-2001. U.S. Geological Circular 1265. Reston, 

VA: U.S. Department of the Interior, U.S. Geological Survey. 

Jacobson, R.B., S.R. Femmer, and R.A. McKenney. 2001. Land-use change and the physical 

habitat of streams: a review with emphasis on studies within the U.S. Geological Survey 

Federal-State Cooperative Program. U.S. Geological Circular 1175. U.S. Department of the 

Interior, U.S. Geological Survey, Reston, Va. 

Laroe, E.T., G.S. Farris, C.E. Puckett, P.D. Doran, and M.J. Mac, eds. 1995. Our Living Resources: 

A Report to the Nation on the Distribution, Abundance, and Health of U.S. Plants, Animals, 

and Ecosystems. Washington, DC: U.S. Department of the Interior, National Biological 

Service. 

104

National Rivers and Streams Assessment, 2008 2009 February 2013 
   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Sources and References 

Mac, M.J., P.A. Opler, C.E. Puckett Haecker, and P.D. Doran. 1998. Status and Trends of the 

Nation’s Biological Resources. 2 volumes. Reston, VA: U.S. Department of the Interior, U.S. 

Geological Survey. 

Omernik, J.M. 1987. Ecoregions of the conterminous United States. Annals of the Association of 

American Geographers 77: 118-125. 

U.S. EPA. 2000. National Water Quality Inventory: 1998 Report to Congress. EPA/841/R-00/001. 

Washington, DC: U.S. Environmental Protection Agency, Office of Water. 

Fish multimetric indices 

Blocksom, K.A. 2003. A performance comparison of metric scoring methods for a multimetric 

index for Mid-Atlantic Highlands streams. Environmental Management 31: 0670-0682. 

Bramblett, R.G., T.R. Johnson, A.V. Zale, and D.G. Heggem. 2005. Development and evaluation 

of a fish assemblage index of biotic integrity for northwestern Great Plains streams. 

Transactions of the American Fisheries Society 134: 624-640. 

Cutler, D.R., T.C. Edwards, K.H. Beard, A. Cutler, K.T. Hess, J. Gibson, and J.J. Lawler. 2007. 

Random forests for classification in ecology. Ecology 88: 2783-2792. 

Emery, E.B., T.P. Simon, F.H. McCormick, P.L. Angermeier, J.E. DeShon, C.O. Yoder, R.E. Sanders, 

W.D. Pearson, G.D. Hickman, R.J. Reash, and J.A. Thomas. 2003. Development of a 

multimetric index for assessing the biological condition of the Ohio River. Transactions of 

the American Fisheries Society 132: 791-808. 

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

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. 

Meador, M.R., and D.M. Carlisle. 2009. Predictive models for fish assemblages in eastern U.S. 

streams: Implications for assessing biodiversity. Transactions of the American Fisheries 

Society 138: 725-740. 

Indices of biotic integrity 

Barbour, M.T., J.B. Stribling, and J.R. Karr. 1995. Chapter 6: Multimetric approach for 

establishing biocriteria and measuring biological condition. In W.S. Davis and T.P. Simon, 

eds. Biological Assessment and Criteria: Tools for Water Resource Planning and Decision 

Making. pp. 63-77. Boca Raton, FL: Lewis. 

Frey, D.G. 1977. The integrity of water — an historical approach. In S.K. Ballentine and L.J. 

Guarala, eds. The Integrity of Water. pp. 127-140. Washington, DC: U.S. Environmental 

Protection Agency. 

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

February 2013 105

National Rivers and Streams Assessment, 2008 2009
   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Sources and References 

Karr, J.R., and D.R. Dudley. 1981. Ecological perspective on water quality goals. Environmental 

Management 5: 55-68. 

Mebane, C.A., T.R. Maret, and R.M. Hughes. 2003. An index of biological integrity (IBI) for 

Pacific Northwest rivers. Transactions of the American Fisheries Society 132: 239-261. 

Observed/expected models 

Hawkins, C.P. 2006. Quantifying biological integrity by taxonomic completeness: Its utility in 

regional and global assessments. Ecological Applications 16: 1277-1294. 

Hawkins, C.P., R.H. Norris, J.N. Hogue, and J.W. Feminella. 2000. Development and evaluation 

of predictive models for measuring the biological integrity of streams. Ecological 

Applications 10: 1456-1477. 

Hawkins, C.J., Y. Cao, and B. Rober. 2010. Method of predicting reference condition biota 

affects the performance and interpretation of ecological indices. Freshwater Biology 55: 

1066-1085. 

Van Sickle, J., C.P. Hawkins, D.P. Larsen, and A.T. Herlihy. 2005. A null model for the expected 

macroinvertebrate assemblage in streams. Journal of the North American Benthological 

Society 24: 178-191. 

Wright, J.F. 2000. An introduction to RIVPACS. In J.F. Wright, D.W. Sutcliffe, and M.T. Furse, eds. 

Assessing the Biological Quality of Fresh Waters. pp. 1-24. Ambleside, UK: Freshwater 

Biological Association. 

Periphyton 

Bahls, L.L. 1993. Periphyton Bioassessment Methods for Montana Streams. Helena, MT: 

Montana Department of Health and Environmental Sciences. 

Baker, E.A., K.E. Wehrly, P.W. Seelbach, L. Wang, M.J. Wiley, and T. Simon. 2005. A multimetric 

assessment of stream conditoin in the Northern Lakes and Forests ecoregion using spatially 

explicit statistical modeling and regional normalization. Transactions of the American 

Fisheries Society 134: 697-710. 

Clarke, R.T., M.T. Furse, J.F. Wright, and D. Moss. 1996. Derivation of a biological quality index 

for river sites: Comparison of the observed with the expected fauna. Journal of Applied 

Statistics 23: 311-332. 

Stevenson, R.J. 2006. Refining diatom indicators for valued ecological attributes and 

development of water quality criteria. In: N. Ognjanova-Rumenova and K. Manoylov, eds. 

Advances in Phycological Studies. pp. 365-383. Moscow, Russia: Pensoft Publishers. 

Stevenson, R.J., R.C. Bailey, M.C. Harass, C.P. Hawkins, J. Alba-Tercedor, C. Couch, S. Dyer, F.A. 

Fulk, J.M. Harrington, C.T. Hunsaker, and R.K. Johnson. 2004. Designing data collection for 

ecological assessments. In M.T. Barbour, S.B. Norton, H.R. Preston, and K.W. Thornton, eds. 

106

National Rivers and Streams Assessment, 2008 2009 February 2013 
   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Sources and References 

Ecological Assessment of Aquatic Resources: Linking Science to Decision-Making. pp. 55-84. 

Pensacola, FL: SETAC Press. 

Stevenson, R.J., R.C. Bailey, M.C. Harass, C.P. Hawkins, J. Alba-Tercedor, C. Couch, S. Dyer, F.A. 

Fulk, J.M. Harrington, C.T. Hunsaker, and R.K. Johnson. 2004. Interpreting results of 

ecological assessments. In M.T. Barbour, S.B. Norton, H.R. Preston, and K.W. Thornton, eds. 

Ecological Assessment of Aquatic Resources: Linking Science to Decision-Making. pp. 85-111. 

Pensacola, FL: SETAC Press. 

Stevenson, R.J., B.E. Hill, A.T. Herlihy, L.L. Yuan, and S.B. Norton. 2008. Algal-P relationships, 

thresholds, and frequency distributions guide nutrient criterion development. Journal of the 

North American Benthological Society 27: 783-799. 

Stevenson, R. J., Y. Pan, K. Manoylov, C. Parker, D. P. Larsen, and A.T. Herlihy. 2008. 

Development of diatom indicators of ecological conditions for streams of the western 

United States. Journal of the North American Benthological Society 27: 1000-1016. 

Physical habitat 

Bryce, S.A., G.A. Lomnicky, P.R. Kaufmann, L.S. McAllister, and T.L. Ernst. 2008. Development of 

biologically-based sediment criteria in mountain streams of the western United States. 

North American Journal of Fisheries Management 28: 1714-1724. 

Bryce, S.A., Lomnicky, G.A., and P.R. Kaufmann. 2010. Protecting sediment-sensitive aquatic 

species in mountain streams through the application of biologically-based streambed 

sediment criteria. Journal of the North American Benthological Society 29(2): 657-672. 

Buffington, J.M., and D.R. Montgomery. 1999. Effects of hydraulic roughness on surface 

textures of gravel-bed rivers. Water Resources Research 35: 3507-3521. 

Buffington, J.M., and D.R. Montgomery. 1999. Effects of sediment supply on surface textures of 

gravel-bed rivers. Water Resources Research 35: 3523-3530. 

Cummins, K.W. 1974. Structure and function of stream ecosystems. BioScience 24: 631-641. 

Gorman, O.T., and J.R. Karr. 1978. Habitat structure and stream fish communities. Ecology 59: 

507-515. 

Gregory, S.V., F.J. Swanson, W.A. McKee, and K.W. Cummins. 1991. An ecosystem perspective 

of riparian zones. BioScience 41: 540-551. 

Kaufmann, P.R., P. Levine, E.G. Robison, C. Seeliger, and D. Peck. 1999. Quantifying Physical 

Habitat in Wadeable Streams. EPA/600/3-88/021a. Washington, DC: U.S. Environmental 

Protection Agency. 

Kaufmann, P.R., J.M. Faustini, D.P. Larsen, and M.A. Shirazi. 2008. A roughness-corrected index 

of relative bed stability for regional stream surveys. Geomorphology 199: 150-170. 

February 2013 107

National Rivers and Streams Assessment, 2008 2009
   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Sources and References 

Kaufmann, P.R., D.P. Larsen, and J.M. Faustini. 2009. Bed stability and sedimentation associated 

with human disturbances in Pacific Northwest streams. Journal of the American Water 

Resources Association 45(2): 434-459. 

Kaufmann, P.R., and J.M. Faustini, 2011. Simple measures of channel habitat complexity predict 

transient hydraulic storage in streams. Hydrobiologia 685(1): 69-95. 

Reference condition 

Bailey, R.C., R.H. Norris, and T.B. Reynoldson. 2004. Bioassessment of Freshwater Ecosystems: 

Using the Reference Condition Approach. New York, NY: Kluwer Academic Publishers. 

Hughes, R.M. 1995. Chapter 4: Defining acceptable biological status by comparing with 

reference conditions. In W. Davis and T. Simon, eds. Biological Assessment and Criteria: 

Tools for Water Resource Planning and Decision Making for Rivers and Streams. pp. 31-47. 

Boca Raton, FL: Lewis. 

Stoddard, J.L., D.P. Larsen, C.P. Hawkins, R.K. Johnson, and R.H. Norris. 2006. Setting 

expectations for the ecological condition of streams: The concept of reference condition. 

Ecological Applications 16: 1267-1276. 

Other EMAP assessments 

Stoddard, J.L., A.T. Herlihy, B.H. Hill, R.M. Hughes, P.R. Kaufmann, D.J. Klemm, J.M. Lazorchak, 

F.H. McCormick, D.V. Peck, S.G. Paulsen, A.R. Olsen, D.P. Larsen, J. Van Sickle, and T.R. 

Whittier. 2006. Mid-Atlantic Integrated Assessment (MAIA) — State of the Flowing Waters 

Report. EPA/600/R-06/001. Washington, DC: U.S. Environmental Protection Agency. 

U.S. EPA. 2000. Mid-Atlantic Highlands Streams Assessment. EPA/903/R-00/015. Philadelphia, 

PA: U.S. Environmental Protection Agency, Region 3. 

Biological condition gradient/quality of reference sites 

Davies, S.P., and S.K. Jackson. 2006. The Biological Condition Gradient: A conceptual model for 

interpreting detrimental change in aquatic ecosystems. Ecological Applications 16: 1251-

1266. 

Lattin, P.D. In preparation. A process for characterizing watershed level disturbance using 

orthophotos. 

Relative risk 

Van Sickle, J., J.L. Stoddard, S.G. Paulsen, and A.R. Olsen. 2006. Using relative risk to compare 

the effects of aquatic stressors at a regional scale. Environmental Management 38(6): 1020-

1030. 

108

National Rivers and Streams Assessment, 2008 2009 February 2013 
   

            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Sources and References

Nutrients 

Bourassa, N., and A. Cattaneo. 1998. Control of periphyton biomass in Laurentian streams 

(Quebec). Journal of the North American Bentholological Society 17: 420-429. 

Dodds, W.K., and E.B. Welch. 2000. Establishing nutrient criteria in streams. Journal of the 

North American Benthological Society 19(1): 186-196. 

Kelly, M.G. 1998. Use of community-based indices to monitor eutrophication in rivers. 

Environmental Conservation 25: 22-29. 

Kelly, M.G., and B.A. Whitton. 1995. The trophic diatom index: A new index for monitoring 

eutrophication in rivers. Journal of Applied Phycology 7: 433-444. 

Miltner, R.J., and E.T. Rankin. 1998. Primary nutrients and the biotic integrity of rivers and 

streams. Freshwater Biology 40: 145-158. 

Nordin, R.N. 1985. Water Quality Criteria for Nutrients and Algae: Technical Appendix. Victoria, 

BC: Ministry of Environment. 

www.env.gov.bc.ca/wat/wq/BCguidelines/nutrients/nutrientstech.pdf. 

Pan, Y., R.J. Stevenson, B.H. Hill, A.T. Herlihy, and G.B. Collins. 1996. Using diatoms as indicators 

of ecological conditions in lotic systems: A regional assessment. Journal of the North 

American Benthological Society 15: 481-495. 

Welch, E.B. 1992. Ecological Effects of Wastewater. 2nd edition. London, UK: Chapman and Hall. 

February 2013 109

National Rivers and Streams Assessment, 2008 2009
            –

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

List of Abbreviations and Acronyms
�

ANC acid-neutralizing capacity 

CPL Coastal Plains 

EMAP Environmental Monitoring and Assessment Program 

EPA U.S. Environmental Protection Agency 

GIS geographic information system 

MMI multimetric index 

NAP Northern Appalachians 

NARS National Aquatic Resource Surveys 

NHD USGS National Hydrography Dataset 

NOAA National Oceanic and Atmospheric Administration 

NPL Northern Plains 

NRSA National Rivers and Streams Assessment 

O/E observed/expected 

PCB polychlorinated biphenyl 

qPCR quantitative polymerase chain reaction 

RBS relative bed stability 

SAP Southern Appalachians 

SPL Southern Plains 

TPL Temperate Plains 

UMW Upper Midwest 

USGS U.S. Geological Survey 

WMT Western Mountains 

WSA Wadeable Streams Assessment 

XER Xeric region 

110

National Rivers and Streams Assessment, 2008 2009 February 2013