National Lakes Assessment

A Collaborative Survey of the Nation’s Lakes
U.S. Environmental Protection Agency (USEPA). 

2009. National Lakes Assessment: A Collaborative 

Survey of the Nation’s Lakes. EPA 841-R-09-001. U.S. 

Environmental Protection Agency, Office of Water and 

Office of Research and Development, Washington, D.C.

This report was prepared by the U.S. Environmental Protection Agency (EPA), Office of Water 

and Office of Research and Development. It has been subjected to the Agency’s peer review and 

administrative review processes. This document contains information relating to water quality 

assessment. It does not substitute for the Clean Water Act or EPA regulations, nor is it a regulation 

itself. Thus, it cannot impose legally binding requirements on EPA, States, authorized Tribes or the 

regulated community, and it may not apply to a particular situation or circumstance.

Cover photo of Emerald Bay on Lake Tahoe courtesy of ©Ted C. McRae http://beetlesinthebush.wordpress.com
Acknowledgements

The EPA Office of Water (OW) and Office of Research and Development (ORD) would like to thank 

the many people who contributed to this project. Without the collaborative efforts and support by 

state and tribal environmental agencies, federal agencies, universities and other organizations, 

this groundbreaking assessment of lakes would not have been possible. In addition, the survey 

could not have been done without the dedicated help and support of enumerable field biologists, 

taxonomists, statisticians and data analysts, as well as program administrators, regional 

coordinators, project managers, quality control officers, and reviewers. To the many participants, 

EPA expresses its gratitude. 

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National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Collaborators

Alabama Department of Environmental 

 Management

Arizona Department of Environmental Quality

Blackfeet Tribe, Environmental Program

California Department of Fish and Game

California State Water Resources Control

 Board

Pueblo de Cochiti Department of Natural 

 Resources and Conservation

Colorado Department of Public Health 

 and the Environment

Connecticut Department of Environmental

 Protection

Delaware Department of Natural Resources

Eastern Shoshone Tribe and Northern Arapaho

 Tribe, Environmental Program

Florida Department of Environmental

 Protection

Georgia Department of Natural Resources

Idaho Department of Environmental Quality

Illinois Environmental Protection Agency

Indiana Department of Environmental 

 Management

Iowa Department of Natural Resources

Lac Courte Oreilles Band of Lake Superior

 Chippewa, Conservation Department

Lac du Flambeau Band of Lake Superior

 Chippewa, Tribal Natural Resources 

 Department

Leech Lake Band of Ojibwe, Division of 

 Resource Management 

Maine Department of Environmental

 Protection

Maryland Department of Natural Resources

Massachusetts Department of Environmental

 Protection

Michigan Department of Environmental 

 Quality

Minnesota Pollution Control Agency 

Mississippi Department of Environmental 

 Quality

Montana Department of Environmental 

 Quality

Nevada Division of Environmental Protection

New Hampshire Department of Environmental

 Services

New Jersey Department of Environmental 

 Protection

New York State Department of Environmental 

 Conservation

North Dakota Department of Health

Ohio Environmental Protection Agency

Oklahoma Water Resources Board

Oregon Department of Environmental Quality

Pennsylvania Department of Environmental 

 Protection

Pyramid Lake Paiute Tribe

Rhode Island Department of Environmental 

 Management
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National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Sisseton-Wahpeton Sioux Tribe,

 Environmental Program

South Dakota Department of 

Environment and Natural Resources

Spirit Lake Nation, Tribal Environmental

 Administration

Tennessee Department of Environment and

 Conservation

Texas Commission of Environmental Quality

Turtle Mountain Band of the Chippewa

 Indians Environmental Program

Utah Division of Environmental Quality

Vermont Department of Environmental

 Conservation

Virginia Department of Environmental Quality

Washington Department of Ecology

West Virginia Department of Environmental

 Protection

White Earth Band of Chippewa, Natural

 Resources Department

Wisconsin Department of Natural Resources

The following people played a pivotal role and lent their expertise to the data analysis of this 

project. These individuals painstakingly reviewed the dataset to ensure quality and consistency. 

These NLA analysts included Neil Kamman (lead, on detail from VT Department of Environmental 

Conservation), Richard Mitchell, and Ellen Tarquinio from EPA Office of Water; Phil Kaufmann, Tony 

Olsen, Dave Peck, Spence Peterson, Steve Paulsen, Amina Pollard, John Stoddard, John Van Sickle 

and Henry Walker from EPA Office of Research and Development; Donald Charles and Mihaele 

Enache from the Academy of Natural Sciences, Philadelphia PA; Charles Hawkins from Utah State 

University; Alan Herlihy from Oregon State University; Paul Garrison from WI Department of 

Natural Resources; Jennifer Graham and Keith Loftin from U.S. Geological Survey, Lawrence, KS; 

Jan Stevenson from Michigan State University, and Julie Wolin from Cleveland State University, OH.

Contributors

EPA would also like to thank those people who lent their scientific knowledge and/or writing 

talent to this report.

Steve Heiskary, Minnesota Pollution Control Agency, MN; Neil Kamman, Department of 

Environmental Conservation, VT; Terri Lomax, Department of Environmental Conservation, AK; 

Alice Mayio, EPA Office of Wetlands, Oceans and Watershed, Washington, DC: Amy Smagula, 

Department of Environmental Services, NH; Kellie Merrell, Department of Environmental 

Conservation, VT; Leanne Stahl, EPA Office of Science and Technology, Washington, DC.

The National Lakes Assessment survey project was led by Susan Holdsworth (OW) and Steve 

Paulsen (ORD) with significant programmatic help from Sarah Lehmann, Alice Mayio, Richard 

Mitchell, Dan Olsen, Carol Peterson, Ellen Tarquinio, Anne Weinberg, and EPA Regional Monitoring 

Coordinators. Contractor support was provided by Computer Sciences Corp., Dynamac Corp., 

EcoAnalysts, Inc., Great Lakes Environmental Center, Inc., Raytheon Information Services, 

TechLaw, Inc. and Tetra Tech, Inc.
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National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Additional Reports and Information

To augment the findings of this report, EPA is providing several additional reports. The first 

is the National Lakes Assessment: Technical Appendix. This appendix describes in detail the 

data analyses and scientific underpinnings of the results. It is intended to aid States and other 

institutions who would like a more in-depth explanation of the data analysis phase with the possible 

intention of replicating the survey at a smaller scale. Additional results are also forthcoming. Due 

to a number of reasons, EPA is not able to report at this time the results from several indicators 

(e.g., sediment mercury, enterococci, and benthic macroinvertebrates). Work is on-going for each 

of these indicators and results will be published when complete. The Technical Appendix, Field 

Methods and Laboratory Protocols are currently available on EPA’s web site at http://www.epa.gov/

lakessurvey/.

For those wishing to access data from the survey to perform their own analyses, EPA has made 

flat files of the data available via the internet at http://www.epa.gov/owow/lakes/lakessurvey/

web_data.html. Additionally, raw data and information on the sampled lakes will be uploaded to 

EPA’s STOrage and RETrieval (STORET) warehouse at http://www.epa.gov/STORET.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

iv

Table of Contents

Acknowledgements .................................................................................................................... i

Collaborators ........................................................................................................................... i

Contributors ........................................................................................................................... ii

Additional Reports and Information...........................................................................................iii

Tables and Figures ....................................................................................................................vi

Executive Summary................................................................................................................. viii

Chapter 1. Introduction ............................................................................................................. 2

A Highly Valued and Valuable Resource ...................................................................................... 2

Why a National Survey? ........................................................................................................... 2

The National Aquatic Resource Surveys ...................................................................................... 3

Chapter 2. Design of the Lakes Survey....................................................................................... 8

Areas Covered by the Survey.................................................................................................... 8

Selecting Lakes....................................................................................................................... 8

Lake Extent – Natural and Man-made Lakes.............................................................................. 11

Choosing Indicators ............................................................................................................... 12

Field Sampling ...................................................................................................................... 14

Setting Expectations .............................................................................................................. 15

Chapter 3. The Biological Condition of the Nation’s Lakes........................................................ 20

Lake Health – The Biological Condition of Lakes......................................................................... 20

Stressors to Lake Biota .......................................................................................................... 25

Ranking of Stressors.............................................................................................................. 31

Chapter 4. Suitability for Recreation........................................................................................ 36

Algal Toxins.......................................................................................................................... 36

Contaminants in Lake Fish Tissue............................................................................................ 39

Pathogen Indicators............................................................................................................... 40

Chapter 5. Trophic State of Lakes ............................................................................................ 44

Findings for Trophic State ....................................................................................................... 45
Chapter 6. Ecoregional Results ................................................................................................ 48

Nationwide Comparisons ........................................................................................................ 49 

Northern Appalachians ........................................................................................................... 52

Southern Appalachians........................................................................................................... 54

Coastal Plains ....................................................................................................................... 56

Upper Midwest...................................................................................................................... 58

Temperate Plains................................................................................................................... 60

Southern Plains..................................................................................................................... 62

Northern Plains ..................................................................................................................... 64

Western Mountains ................................................................................................................ 66

Xeric.................................................................................................................................... 68

Chapter 7. Changes and Trends ............................................................................................... 74

Subpopulation Analysis – National Eutrophication Survey............................................................ 74

Subpopulation Analysis – Trends in Acidic Lakes in the Northeast................................................. 76

Sediment Core Analysis.......................................................................................................... 76

Chapter 8. Conclusions and Implications for Lake Managers.................................................... 82

Overall Findings and Conclusions ............................................................................................. 82

Implications for Lake Managers ............................................................................................... 84

Chapter 9. Next Steps for the National Surveys ....................................................................... 92

Supplemental Reports............................................................................................................ 93

Tools and Other Analytical Support .......................................................................................... 93

Future National Assessments .................................................................................................. 93

Acronyms ................................................................................................................................ 95

Glossary of Terms.................................................................................................................... 96

Sources and References......................................................................................................... 100

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National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes
Tables and Figures

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

vi

Table 1. World Health Organization thresholds of risk associated with 

 potential exposure to cyanotoxins .......................................................................... 37

Table 2. Percent of U.S. lakes (natural and man-made) by trophic state, 

 based on four alternative trophic state indicators...................................................... 45

Figure ES-1. Biological condition of lakes nationally and based on lake origin ........................................ ix

Figure ES-2. Extent of stressor and relative risk of stressor to biological condition .................................. x

Figure ES-3. Proportion of national eutrophication survey (NES) lakes that exhibited improvement,

 degradation, or no change in trophic state based on the comparison of the

 1972 National Eutrophication Survey and the 2007 National Lakes Assessment ............. xi

Figure 1. The process of lake selection ....................................................................................... 10

Figure 2. Location of lakes sampled in the NLA ........................................................................... 11

Figure 3. Size distribution of lakes in the U.S. overall and for natural and man-made lakes ............... 12

Figure 4. NLA sampling approach for a typical lake ...................................................................... 14

Figure 5. Reference condition thresholds used for good, fair, and poor assessment .......................... 16

Figure 6. Assessment of quality using the Planktonic O/E Taxa Loss and Lake Diatom Condition

 Index ................................................................................................................. 24

Figure 7. Phosphorus, nitrogen, and turbidity in three lake classes ................................................ 26

Figure 8. Acid neutralizing capacity for lakes of the U.S ................................................................ 27

Figure 9. Dissolved oxygen for lakes of the U.S ........................................................................... 28

Figure 10. Schematic of a lakeshore ............................................................................................ 29

Figure 11. Lakeshore habitat for lakes of the U.S. as percent of lakes 

 in three condition classes ...................................................................................... 30

Figure 12. Shallow water habitat for lakes of the U.S. as percent of lakes 

 in three condition classes ...................................................................................... 30

Figure 13. Physical habitat complexity for lakes of the U.S. as percent of lakes 

 in three condition classes ...................................................................................... 31

Figure 14. Lakeshore disturbance for lakes of the U.S. as percent of lakes 

 in three condition classes ...................................................................................... 31 

Figure 15. Relative extent of poor stressors conditions. Relative risks of impact to 

 plankton O/E and Attributable risk (combining Relative extent and Relative risk) .......... 32

Figure 16. Percent of lakes, using three algal toxin indicators ......................................................... 37

Figure 17. Occurrence of microcystin in lakes ............................................................................... 38

Figure 18. Percentage predator fish with mercury and PCB levels above and below

 EPA recommended limits ....................................................................................... 39

Figure 19. Trophic state of lakes in the lower continental U.S .......................................................... 45

Figure 20. Ecoregions used as part of the National Lakes Assessment .............................................. 48

Figure 21. Biological condition (based on planktonic O/E taxa loss) across nine ecoregions ................. 49
Figure 22. Habitat condition of the nation’s lakes across nine ecoregions based on lakeshore

 habitat ................................................................................................................ 50

Figure 23. Trophic state across nine ecoregions (based on chlorophyll-a).......................................... 51

Figure 24. Comparison of exposure to cyanobacteria risk across nine ecoregions ............................... 51

Figure 25. NLA results for the Northern Appalachians .................................................................... 53

Figure 26. NLA results for the Southern Appalachians .................................................................... 55 

Figure 27. NLA findings for the Coastal Plains ............................................................................... 57

Figure 28. NLA findings for the Upper Midwest .............................................................................. 59

Figure 29. NLA findings for the Temperate Plains ........................................................................... 61 

Figure 30. NLA findings for the Southern Plains............................................................................. 63 

Figure 31. NLA findings for the Northern Plains ............................................................................. 65

Figure 32. NLA findings for the Western Mountains ........................................................................ 67

Figure 33. NLA findings for the Xeric ........................................................................................... 69

Figure 34. Proportion of NES lakes that exhibited improvement, degradation, or no change in

 phosphorus concentration based on the comparison of the

 1972 National Eutrophication Survey and the 2007 National Lakes Assessment ............. 75

Figure 35. Proportion of NES lakes that exhibited improvement, degradation, or no change in

 trophic state based on the comparison of the 1972 National Eutrophication

 Survey and the 2007 National Lakes Assessment ...................................................... 75 

Figure 36. Percentage and number of NES lakes estimated in each of four trophic classes 

 in 1972 and in 2007 based on chlorophyll-a concentrations ........................................ 76 

Figure 37. Change in percentage of chronically acidic lakes in the Adirondack Mountains 

 and New England ................................................................................................. 77

Figure 38. States with state-scale statistical surveys ..................................................................... 85

Figure 39. Comparison of lakes by trophic state for Vermont, the Northern Appalachians 

 ecoregion, and the Nation, based on chlorophyll-a .................................................... 87

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National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

viii

Executive Summary

“A lake is the landscape’s most 

beautiful and expressive feature. It 

is earth’s eye; looking into which the 

beholder measures the depth of his 

own nature.”

These words by the American 

poet Henry David Thoreau underscore 

America’s love of lakes. Lakes are 

places of reflection, relaxation, and 

repose, but like all our waters, they are 

being increasingly stressed. Growing 

anthropogenic pressures have prompted 

many governments, associations, and 

individuals to invest time in preserving or 

restoring the water quality of their lakes. 

To protect our nation’s lakes, Americans 

must strive to understand how their 

actions as individuals and as a society are 

affecting them. 

Under the Clean Water Act (CWA), 

the U.S. Environmental Protection Agency 

(EPA) must report periodically on the 

condition of the nation’s water resources 

by summarizing water quality information 

provided by the states. However, 

approaches to collecting and evaluating 

data vary from state to state, making it 

difficult to compare the information across 

states, on a nationwide basis, or over 

time. EPA and the states are continually 

working on ways to address this problem 

to improve water quality reporting.

Congress, environmental groups, 

and concerned citizens routinely ask 

EPA questions about the quality of the 

nation’s waters such as: What are the key 

problems in our waters? How widespread 

are the problems? Are there hotspots? 

Are we investing in water resource 

restoration and protection wisely? Are our 

waters getting cleaner? To better answer 

questions about the condition of waters 

across the country, EPA along with its 

state and tribal partners have embarked 

on a series of surveys to be conducted 

under the National Aquatic Resource 

Surveys (NARS) program. This relatively 

Executive Summary

Photo courtesy of Frank Borsuk
ix

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Executive Summary

new program provides statistically valid 

data and information vital to describing 

water resource quality conditions across 

the country, how these conditions vary 

with geographic setting, and the extent of 

human and natural influences.

 The National Lakes Assessment (NLA) 

is one in a series of annual NARS surveys. 

The NLA is the first statistical survey of 

the condition of our nation’s lakes, ponds, 

and reservoirs.1 Based on the sampling 

of over 1,000 lakes across the country, 

the survey results represent the state 

of nearly 50,000 natural and man-made 

lakes that are greater than 10 acres in 

area and over one meter deep. In the 

summer of 2007, lakes were sampled for 

their water quality, biological condition, 

habitat conditions, and recreational 

suitability. Field crews used the same 

methods at all lakes to ensure that results 

were nationally comparable. For many 

of the indicators, scientists analyzed the 

results against a reference condition. 

Reference conditions were derived from 

a set of lakes that were determined to be 

the least disturbed lakes for a region.

Key Findings

Biological Quality - 56% of the nation’s 

lakes are in good biological condition. 

Natural lakes had a higher percentage of 

lakes in good condition than man-made 

lakes (Figure ES-1).

Figure ES-1. Biological condition of lakes nationally and based on lake origin.

1

The full report including technical supporting documents is available on-line at http://www.epa.gov/lakessurvey/
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

x

Executive Summary

Lake Physical Habitat - Of the stressors 

included in the NLA, poor lakeshore 

habitat is the biggest problem in the 

nation’s lakes; over one-third exhibit poor 

shoreline habitat condition. Poor biological 

health is three times more likely in lakes 

with poor lakeshore habitat (Figure ES-2).

Nutrients - About 20% of lakes in the 

U.S. have high levels of phosphorus or 

nitrogen. High nutrient levels are the 

second biggest problem in lakes. Lakes 

with excess nutrients are two-and-a halftimes more likely to have poor biological 

health (Figure ES-2).

Algal Toxins - The NLA conducted the 

first-ever national study of algal toxins in 

lakes. Microcystin – a toxin that can harm 

humans, pets, and wildlife – was found to 

be present in about one-third of lakes and 

at levels of concern in 1% of lakes.

Fish Tissue Contaminants - A parallel 

study of toxins in lake fish tissue shows 

that mercury concentrations in game fish 

exceed health based limits in about half of 

lakes (49%); polychlorinated biphenyls 

(PCBs) at potential levels of concern are 

found in 17% of the lakes.

Figure ES-2. Extent of stressor and relative risk of stressor to biological condition.
xi

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Executive Summary

Trophic Condition - The NLA establishes 

the first nationally consistent baseline 

of trophic status. Over 36% of the 

nation’s lakes are mesotrophic, based on 

chlorophyll-a concentrations.

Changes in Trophic Condition - When 

compared to a subset of wastewaterimpacted lakes sampled 35 years ago, 

trophic status improved in one-quarter 

(26%) and remained stable in over half 

(51%) of those lakes (Figure ES-3). This 

could indicate that, when considering 

rising populations in these areas, 

investments in wastewater pollution 

control are working.

Implications

As these results show, EPA and its 

state and tribal partners have begun 

to answer important national questions 

about the condition of the country’s lakes. 

The results establish a national baseline 

status for future monitoring efforts which 

can be used to track scientifically credible 

trends in lake conditions. Successive 

surveys will help answer the question “Are 

our lakes getting better?” 

Figure ES-3. Proportion of National Eutrophication Survey 

(NES) lakes that exhibited improvement, degradation, or no 

change in trophic state based on the comparison of the 1972 

National Eutrophication Survey and the 2007 National Lakes 

Assessment. 
For water resource managers, 

policymakers, boaters, swimmers, and 

others, the NLA findings suggest:

• Poor lakeshore habitat condition 

imparts a significant stress on 

lakes and suggests the need for 

stronger management of shoreline 

development, especially as 

development pressures on lakes keep 

steadily growing. 

• Effective nutrient management 

continues to be needed in the nation’s 

lakes. Excess levels of nutrients 

contribute to algae bloom, weed 

growth, reduced water clarity, and 

other lake problems. The adverse 

impact of nutrients on aquatic 

life, drinking water, and recreation 

remains a concern.

• Local, state and national initiatives to 

protect the integrity of lakes should 

center on restoring the natural state 

of shoreline habitat – particularly 

vegetative cover and nutrient loading. 

Managers, residents, businesses, 

and community leaders should work 

together and enhance their efforts to 

preserve, protect, and restore their 

lakes and the natural environment 

surrounding them.

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

xii

Executive Summary
CHAPTER 1.

INTRODUCTION

Phelps Lake, Grand Teton National Park, WY. Photo courtesy of Great Lakes Environmental Center.

IN THIS CHAPTER

► A Highly Valued and Valuable Resource

► Why a National Survey?

► The National Aquatic Resource Surveys
Chapter 1 Introduction

2

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Chapter 1 

Introduction 

A Highly Valued and 

Valuable Resource

For anyone who went fishing as a child, 

water-skiing as a teen, or bird-watching as 

an adult, lakes are special places. Healthy 

lakes enhance the quality of life. In addition 

to supplying people with essential needs 

like drinking water, food, fiber, medicine, 

and energy, a lake’s ecosystem is important 

in providing habitat for wildlife, recreation, 

aesthetics, reducing the frequency and 

severity of floods, shaping landscapes, and 

affecting local and regional climates. Lakes 

provide habitat for wildlife and enjoyment for 

people while supporting intrinsic ecological 

integrity for all living things. 

It is difficult to put a price on a natural 

treasure. Certainly, from a vacationer’s 

perspective, lakes are invaluable, providing 

endless enjoyment and relaxation yearround. According to the U.S. Fish and 

Wildlife Service, 30 million Americans went 

fishing in 2006 and $42.2 billion was spent on 

recreational fishing. Locally, this translates 

into important economic and recreational 

benefits. For example, Lake Champlain, on 

the border of Vermont and New York, has 

over 65 beaches and 98 fishing-related 

businesses. According to the 2003 Lake 

Champlain Management Plan, in 1998 a total 

of $3.8 billion was generated from tourism. 

As more and more people use lakes for their 

livelihood and recreation, the competition for 

lake resources will continue. 

Protecting lake ecosystems is crucial 

not only to protecting this country’s public 

and economic health, but also to preserving 

and restoring the natural environment for 

all aquatic and terrestrial living things. 

Lake protection and preservation can only 

be achieved by making informed lake 

management policy decisions at and across all 

jurisdictional levels. 

Why a National Survey?

Water resource monitoring in the U.S. 

has been conducted by many different 

organizations over many decades using 

a variety of techniques. States and tribes 

conduct monitoring to support many Clean 

Water Act (CWA) programs. Section 305(b) 

of the CWA requires the U.S. Environmental 

Protection Agency (EPA) to report periodically 

on the condition of the nation’s water 

resources by summarizing information 

provided by the states. Yet approaches to 

collecting and assessing data vary from 

state to state, making it difficult to compare 

the information across states or on a 

nationwide basis. Each of these monitoring 

efforts provides useful information relative 

to the goals of the individual programs, 

but integrating the data into a nationwide 

assessment has been difficult. 
3

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Chapter 1 Introduction

In recent years, a number of independent 

reports have identified the need for improved 

water quality monitoring and analysis at a 

national scale. Among these, the General 

Accounting Office (2000) reported that 

EPA and states cannot make statistically 

valid assessments of water quality and 

lack the data to support key management 

decisions. The National Research Council 

(2001) recommended that EPA and states 

promote a uniform, consistent approach 

to water monitoring and data collection to 

better support core water management 

programs. The National Academy of Public 

Administration, in its 2002 report entitled, 

Understanding What States Need to Protect 

Water Quality, concluded that improved 

water quality monitoring is necessary to help 

state agencies make better decisions and 

use limited resources more effectively. These 

reports underscore the need 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 the problems. 

The National Aquatic 

Resource Surveys

To bridge this information gap, EPA, 

other federal agencies, states and tribes 

are collaborating to provide the public 

with improved environmental information. 

Statistical surveys are one way of addressing 

water resource assessment needs. By 

choosing a statistical design with standardized 

field and laboratory protocols, the EPA, states 

and tribes are able to collect and analyze 

data that are nationally consistent and 

representative of waterbodies throughout 

the U.S. These statistical surveys offer a 

cost-effective and scientifically valid way to 

fulfill statutory requirements, complement 

traditional monitoring programs, and support 

a broader range of management decisions.

The surveys are designed to answer such 

questions as:

• What is the extent of waters that 

support a healthy biological condition, 

recreation, and fish consumption?

• How widespread are major stressors 

that impact water resource quality?

• Are we investing in water resource 

restoration and protection wisely? 

• Are our waters getting cleaner?

State Water Quality Reports

Under section 305(b) of the Clean 

Water Act the states must submit 

biennial reports on the quality of their 

water resources. According to the 

most recently published National Water 

Quality Inventory Report (2004) the 

states assessed just over a third of the 

nation’s waters — 37% or 14.8 million 

acres of the nation’s 40.6 million acres 

of lakes, ponds and reservoirs. Of the 

lakes that were assessed, over half, 58% 

or 8.6 million acres, were identified as 

impaired or not supporting one or more 

of their designated uses such as fishing 

or swimming. The states cited nutrients, 

metals (such as mercury), sewage, 

sedimentation and nuisance species as 

the top causes of impairment. Leading 

known sources of impairment included 

agricultural activities and atmospheric 

deposition, although for many lakes, 

the sources of impairment remain 

unidentified.
Chapter 1 Introduction

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

4

The specific goals of NARS are to generate 

scientifically valid information on the condition 

of water resources at national and ecoregional 

scales, establish baseline information for 

future trends assessment, and assist states 

and tribes in enhancing their water monitoring 

and assessment programs. 

The focus of NARS is on waterbodies 

as groups or populations, rather than as 

individual waters. For example, a state or 

local manager may be interested in nutrient 

levels in a given lake over time. NARS, on 

the other hand, allows one to examine the 

percentage of the nation’s lakes that have 

experienced changes in nutrient levels over 

time. Findings such as these help drive 

national water quality management decisions. 

By generating population estimates of 

condition, the national statistical surveys 

and other statistical surveys have begun to 

provide answers to water resource questions 

with a known level of confidence. Working 

with its partners in states, tribes, territories, 

and other federal agencies, EPA has in recent 

years conducted statistical surveys of coastal 

waters, wadeable streams, and contaminants 

in lake fish tissue. The Agency’s plans are 

to survey each of the five waterbody types, 

(lakes, rivers, streams, wetlands, and 

estuaries), on a 5-year rotating basis. EPA 

and its partners anticipate that the national 

surveys will continue to foster collaboration 

across jurisdictional boundaries, build state 

and tribal infrastructure and capacity for 

enhanced monitoring efforts, and achieve 

a robust set of statistically-sound data for 

better, more informed water resource quality 

management policies and decisions. 

The National Lakes Assessment (NLA) 

is one component of the National Aquatic 

Resource Surveys. This report summarizes 

the first-ever assessment of lakes across the 

continental United States using consistent 

protocols and a modern, scientificallydefensible statistical survey approach. 

Using the National Aquatic 

Resource Surveys

Because of their scientific credibility, 

results from these surveys are being used 

in other scientific contexts. Most notably 

is the recent Heinz Center Report, The 

State of the Nation’s Ecosystems, 2008. 

The Heinz Center’s report is designed to 

provide a high level, comprehensive and 

scientifically sound account on the state 

of the nation’s ecosystems. The Heinz 

Center uses data derived from EPA’s 

Wadeable Streams Assessment report 

and National Coastal Condition Report to 

answer a number of outstanding questions 

about surface water health in our country. 

Information from on-going and upcoming 

national surveys will help fill gaps 

identified for other water resources and 

show trends in national water quality.

The help of state partners was essential. 

Photo courtesy of Frank Borsuk.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

5

HIGHLIGHT

Think Globally — Act Locally. 

Restoring Mousam Lake

 “Every little bit helps” is perhaps the fundamental tenet 

of the estimated 3,000 to 4,000 local watershed groups 

across the country. Many communities are proving that 

they can make a noticeable difference in their neighborhood 

water resource. In York County, Maine, the Soil and Water 

Conservation District (SWCD) and the Mousam Lake Regional 

Association (MLRA) together with residents, townships, state 

agencies and others embarked on the Mousam Lake Water 

Quality Improvement Project. With widespread collaboration 

and some funding, they were able to clean up an impaired 

lake.

Confronting Environmental Challenges

 Mousam Lake, a 863-acre lake located at the southern 

point of Maine, is a popular spot for boaters, anglers, and 

vacationers with its sandy shores and excellent cold and 

warm water trout fisheries. However, this 21- square mile 

watershed suffered from suburbanization and the conversion 

of forested land to driveways and parking lots. The lake’s 

shoreline is heavily developed with over 700 seasonal and 

year-round homes and a heavily used boat ramp. For the past 

several decades, Mousam Lake has endured increased soil erosion and pollution from stormwater runoff 

from home construction, lawns and roads, and from failing septic systems. Higher levels of phosphorus 

have led to increased algal growth, decreased water clarity and lower levels of dissolved oxygen. In the 

2003 Total Maximum Daily Load (TMDL) assessment, excess phosphorus was identified as the major 

impairment. This downward trend in water quality resulted in a steady decline in the lake’s once viable 

ecology and that of its surrounding aquatic habitats. Maine’s Department of Environmental Protection 

(MDEP) attributes the problem to soil erosion and polluted runoff from residential properties and camp 

roads and effluent from inadequate septic systems located in the sandy soils around the lake. The TMDL 

assessment estimated that to meet Maine water quality standards, the annual amount of phosphorus 

reaching the lake would need to be reduced by 27%. 

A Decade of Effort

Since 1997, the York County SWDC, MLRA, MDEP, and the towns of Acton and Shapleigh have 

been working together to address sources of pollution in Mousam Lake and foster long-term watershed 

stewardship. In 1999, the Mousam Lake Water Quality Improvement Project began. With help from EPA, 

the Maine Department of Transportation and the Maine Department of Agriculture negotiated cost share 

agreements with public and private landowners, and best management practices were initiated at 45 

priority sites. Technical assistance was provided to another 77 landowners. Projects included stabilizing 

shoreline erosion, improving gravel road surfaces and installing and/or upgrading roadside drainages. 

Twenty-one roads were repaired. In 2001, the Lake Youth Conservation Corps program was established 

to help with the implementation of best management practices, raise local awareness and commitment 
to lake protection, and involve local youth in environmental stewardship. Since 2007, the youth have 

completed over 115 projects and continue to repair an average of 18 sites each year with annual 

support from the towns of Acton and Shapleigh. The total cost for the project was $1.1 million with local 

townspeople and others contributing over $400,000 in matching funds or in-kind services.

A Cleaner, Healthier Lake

 In 1998 MDEP designated Mousam Lake as impaired and added it to the state’s section 303(d) list of 

waters not meeting water quality standards, a requirement of the federal Clean Water Act. From 1999 

through 2006, a galvanized community tackled the problem and in 2007, monitoring results indicated that 

pollution loads in the lake were reduced by more than 150 tons/per year of sediment and 130 pounds/

per year of phosphorus. Water clarity depth has increased by a full meter from what it was ten years ago. 

Today, erosion control projects continue, thus keeping an estimated 76 tons of sediment and 64 pounds of 

phosphorus out of the lake each year. In 2006, Mousam Lake was removed from the state’s 303(d) list of 

impaired waters. 

 Staff and a small cadre of local leaders are continuing their campaign to keep the lake in good health. 

Community outreach and education activities are ongoing to inform residents on how they can help. 

As part of the project, numerous newsletters have gone to every household in the watershed; MLRA 

holds annual meetings; the SWCD conducts workshops and delivers presentations; 30 construction sites 

have been acknowledged with “Gold Star” signs for environmental stewardship; and more than 200 

homeowners attended one of the thirteen “Septic Socials” to learn about septic system function, proper 

maintenance and water conservation.

Every Little Bit Helps

Vegetated buffer planting by Master Gardeners. 

Photo courtesy of Deborah Kendall. 

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

6
CHAPTER 2.

DESIGN OF THE LAKES SURVEY

Photo courtesy of Washington Department of Ecology

IN THIS CHAPTER

► Areas Covered by the Survey

► Selecting Lakes

► Lake Extent - Natural and Man-Made Lakes

► Choosing Indicators

► Field Sampling

► Setting Expectations
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

8

Chapter 2 Design of the Lakes Survey

Chapter 2

Design of the Lakes Survey

Lakes in the U.S. are as varied and 

unique as the landscape surrounding them. 

Receding glaciers formed thousands of lakes 

in the northwestern, upper midwestern, and 

northeastern parts of the country. Glacial 

action formed the Finger Lakes in New York, 

the Adirondack region, the kettle ponds in 

New England, as well as numerous lakes 

and “prairie potholes” located in Minnesota, 

Wisconsin, Iowa, and the Dakotas. In 

contrast, Oregon’s Crater Lake is a waterfilled volcanic depression, as is Yellowstone 

Lake in Wyoming. Lake Tahoe in California 

and Pyramid Lake in Nevada were formed 

by tectonic action. Along major rivers, like 

the Mississippi, oxbow lakes were formed 

from meandering river channels. Similarly, 

damming of the Columbia River and the 

Colorado River has created large man-made 

lakes and reservoirs. Smaller previously 

impounded streams comprise thousands of 

man-made lakes that provided energy for 

mills during industrialization. Natural lakes 

are scarce across the southern U.S. Many 

of the lakes in the arid southwestern and 

the humid southeastern U.S. are man-made 

lakes or reservoirs. The NLA survey included 

examples of all of these lake types.

Areas Covered By 

the Survey

The NLA encompasses the lakes, ponds 

and reservoirs of the continental U.S. 

including private, state, tribal and federal 

land. Although not included in this report, 

a lake-sampling project is underway in 

Alaska. Hawaii was not included in the 

national survey design. Information from the 

NLA is also presented for both natural and 

man-made lakes to present any difference 

in biological condition or responses to 

stressors.

NLA results are reported for the 

continental U.S. and for 9 ecological regions 

(ecoregions). Areas are included in an 

ecoregion based on similar landform and 

climate characteristics (see Chapter 6 and 

Figure 20). Assessments were conducted 

at the ecoregion level because the patterns 

of response to stress are often best 

understood in a regional context. Some 

states participating in the NLA assessed 

lake condition at an even finer state-scale 

resolution than the ecoregional scale by 

sampling additional random sites within their 

state boundaries. Although these data are 

included in the analysis described in this 

report, state-scale results are not presented.

Selecting Lakes

Since a census of every lake in the 

country is cost prohibitive and beyond the 

reach of any program, EPA used a statistical 

sampling approach incorporating state-ofthe-art survey design techniques. The first 

step, to ascertain the number of lakes in the 

country, was challenging because there is no 

comprehensive list or source for all lakes in 

the U.S. The best resource available is the 

USGS/EPA National Hydrography Dataset 

or NHD. The NHD is a multi-layered series 

of digital maps that reveal topography, 

Photo courtesy of Great Lakes Environmental Center
9

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Chapter 2 Design of the Lakes Survey

Alaska’s Lake Assessment

By Terri Lomax, AK Department of Environmental Conservation

The State of Alaska is about one-fifth the land mass of the continental U.S. Most of 

it is sparsely populated with extremely limited access. This limited access has helped 

preserve its rugged beauty and abundant natural resources. But Alaska is facing 

pressure from climate change and natural resource development. In the populated 

areas, the main causes of waterbody pollution are urban runoff and agricultural activity.

There are an estimated 3 million lakes in Alaska. Instead of being a full participant in the National Lakes 

Survey, the State of Alaska opted to conduct a regional assessment. It focused on the Cook Inlet Basin, an 

area located in the southcentral part of the state; at 39,325 square miles, it is slightly smaller than the state 

of Kentucky. The State selected this area because the only agricultural activity of significance occurs within 

the Cook Inlet Basin.

Alaska’s lake assessment began in 2007 with a pilot study of four lakes. This pilot study was focused 

on access and coordinating logistics of sampling, procedures, and analysis. In 2008, the full project was 

completed with sampling of 50 lakes in the Cook Inlet ecoregion. The field crew was from the Alaska 

Department of Environmental Conservation and the University of Alaska Anchorage Environment & Natural 

Institute. In addition to the National Lakes Assessment indicators, fish tissue for metals and mercury, 

sediment trace metals, and core dating were added to the study. 

To date, all water chemistry, habitat, and lake profile data has been analyzed. Biological indicators, 

sediment metals and mercury, and fish tissue samples are currently being analyzed. All data collected must 

undergo quality assurance review before a final release of the data. However, initial results indicate that lakes 

in the Cook Inlet ecoregion of Alaska are healthy.

area, flow, location, and other attributes of 

the nation’s surface waters. When queried, 

NHD has 389,005 features listed that could 

potentially be lakes, ranging in size from less 

than 2.4 acres (1 hectare) up to the largest 

lakes in the country. Figure 1 illustrates the 

sample framework for the survey.

Initial discussion by states and EPA 

regarding the scope of the survey focused on 

the size of lakes that were to be considered 

in the target population. It was agreed that, 

to be included, the site had to be a natural or 

man-made freshwater lake, pond or reservoir, 

greater than 10 acres (4 hectares), at least 

3.3 feet (1 meter) deep, and with a minimum 

of a quarter acre (0.1 hectare) open water. 

The Great Lakes and the Great Salt Lake 

were not included in the survey, nor were 

commercial treatment and/or disposal ponds, 

brackish lakes, or ephemeral lakes. After 

applying the criteria, 68,223 waterbodies 

were considered lakes by the NLA definition 

and thus comprised the target population 

(Figure 1, 3rd bar).

Other factors in lake selection included 

accessibility. In some cases, crews were 

either denied permission by the landowner or 

unable to reach the lake for safety reasons, 

such as sharp cliffs or unstable ridges. 

Using data from the crews’ experience 

and pre-sampling reconnaissance, it was 

estimated that 27% or 18,677 lakes fell into 

the inaccessible category. This left 49,546 

lakes which could be assessed - inference 
population (bottom bar). In the end, a total 

of 1,028 lakes were sampled in the survey. 

These 1,028 lakes represent the population. 

For quality assurance purposes, 10%, of the 

target lakes were randomly selected for a 

second sampling later in the summer.

Due to the selection process, the sampled 

NLA lakes represent 49,546 lakes or 73% 

of the target population. Thus, throughout 

this report, percentages reported for a given 

indicator are relative to the 49,546 lakes. For 

example, if the condition is described as poor 

for 10% of lakes nationally, this means that 

the number of lakes estimated to be poor for 

that indicator is 4,955 lakes. 

As an added feature, the design 

specifically included some sites from EPA’s 

1972 National Lake Eutrophication Study 

(NES). By including this subset of lakes EPA 

hoped to be able to evaluate changes that 

occurred between the 1970s and 2007.

In conjunction with the national survey, a 

number of states opted to sample additional 

lakes to achieve a state-wide probabilistic 

survey. EPA provided a list of additional lakes 

to the states so that any state wishing to 

conduct a state-scale statistical survey could 

do so. Sampling and processing methods from 

these additional lakes had to adhere to both 

the national field and laboratory protocols. 

Eight states (MI, WI, IN, MN, TX, OK, ID, 

and WA) took advantage of the opportunity 

and the results from the additional sites were 

analyzed along with the national data. Some 

states increased the number of sites, but only 

collected a subset of indicators. Still other 

states opted to expand the list of indicators 

to address issues specific to their state; for 

example, Minnesota used its state-scale 

survey to assess pesticides. 

Figure 2 shows the location of the lakes 

that were sampled for the NLA. The surveyed 

lakes cover an area of 3.8 million acres of 

surface water spread across the national 

landscape. 

The site selection for the survey ensures 

that EPA can make unbiased estimates 

concerning the health of the target population 

of lakes with statistical confidence. The 

greater the number of sites sampled, the 

more confidence in the results. The number 

of sites included in the survey allows EPA to 

determine the percentage of lakes nationwide 

and within predetermined ecoregions that 

exceed a threshold of concern with 95% 

confidence. In the graphs throughout this 

report, the margin of error is provided as thin 

lines on either side of the bars and represent 

the 95% confidence interval for the estimate.

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

10

Chapter 2 Design of the Lakes Survey

Figure 1. The process of lake selection. Starting with the NHD list 

of waterbodies, potential lakes are eliminated due to not meeting 

set criteria for inclusion in the survey (top bar), not being a lake 

(2nd bar), and inaccessibility (3rd bar) leaving the number of 

sampleable lakes or inference population (4th bar).
11

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

 For national estimates, the margin of error 

around the NLA findings is approximately 

±5% and for ecoregions the margin of error 

is approximately ±15%. For example, for the 

national biological condition findings, the NLA 

estimates that 22.4% of the nation’s lakes 

are in poor condition and that the margin of 

error is +/- 4%. This means that there is a 

95% certainty that the true value is between 

18.4% and 26.4%.

Lake Extent - 

Natural and Man-made Lakes

 NLA analysts, comprised of lake science 

experts both within and outside the Agency, 

examined available records for each sampled 

lake to determine its origin. They considered 

natural lakes as those that existed preEuropean settlement, even if presently 

augmented by means of an impoundment 

or other earthworks. Using this operational 

definition, 41% of the estimated 49,546 lakes 

are man-made reservoirs, while 59% are of 

natural origin. This means that nearly onehalf of today’s lakes were not here when the 

colonists arrived. 

 While natural lakes come in many different 

sizes, most man-made lakes are relatively 

small. A total of 52% of man-made lakes are 

10-25 acres (4-10 hectares) in size compared 

with only 34% of the natural lakes in that 

small lake size category. Large lakes, over 

12,500 acres (5,000 hectares), are rare in the 

U.S., comprising only 0.3% of natural lakes 

and 0.6% of man-made lakes (Figure 3).

Chapter 2 Design of the Lakes Survey

Figure 2. Location of lakes sampled in the NLA. Natural lakes are the blue dots; Man-made lakes are brown.
Chapter 2 Design of the Lakes Survey

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

12

Figure 3. Size distribution of lakes in the U.S. overall and for natural 

and man-made lakes.

Choosing Indicators

 Scientists and lake managers recognize 

that lake ecosystems are dynamic and 

indicators selected to characterize lakes 

must represent important aspects of water 

resource quality. For the NLA, a suite of 

chemical, physical and biological indicators 

were chosen to assess biological integrity, 

trophic state, recreational suitability, and key 

stressors impacting the biological quality of 

lakes. 

 Although there are many more indicators 

and/or stressors that affect lakes, NLA 

analysts believe these to be among the 

most representative at a national scale. The 

NLA survey marks the first time all these 

indicators have been applied consistently and 

simultaneously to lakes on a national scale. 

 For this assessment, NLA analysts looked 

at data of phytoplankton, zooplankton and 

sediment diatoms in an effort to characterize 

the biological condition of lakes. It was 

during the analysis that it was decided 

that the results of the phytoplankton and 

zooplankton assessment would serve as 

the primary biological indicator. To address 

recreational/human health related concerns, 

the NLA looked at actual levels of the algal 

toxin microcystin, along with cyanobacterial 

cell counts and chlorophyll-a concentrations 

as indicators of the potential for the 

presence of algal toxins. The presence and 

concentration of microcystin were used 

as the primary indicators for recreational 

condition. Chlorophyll-a was used as the 

primary indicator of trophic status. Although 

fish samples were not collected in the survey, 

NLA analysts also looked at the findings of a 

parallel study of contaminants in fish tissue. 

 Both physical and chemical stressor 

indicators were measured. For example, 

shorelines affect biological communities 

in many ways, such as providing food and 

Biological Recreational Chemical Physical

• Sediment diatoms • Pathogens*(enterococci) • Nutrients • Lakeshore habitat 

• Phytoplankton (algae) • Algal toxin (microcystins) (phosphorus & nitrogen) cover and structure 

• Zooplankton • Algal cell counts • Water column profile • Shallow water habitat 

• Benthic 

 macroinvertebrates*

• Algal density

 (Cyanobacteria) 

• Algal density

 (chlorophyll-a) 

 (dissolved oxygen, 

 temperature, pH, 

turbidity, acid neutralizing 

capacity, salinity)

 cover and structure

• Lakeshore human 

 disturbance

 (chlorophyll-a) • Sediment mercury*

• Invasive species*

* These indicators are still under evaluation and are not included in this report. Results will be published at a later date.
13

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

shelter for aquatic wildlife, and by moderating 

the magnitude, timing, and pathways 

of water, sediment, and nutrient inputs. 

Shorelines also buffer the lake from human 

activities. Water quality characteristics, such 

as nutrient levels and dissolved oxygen, 

create environments essential for aquatic 

organisms to survive and grow. At the 

bottom of the lake, sediment diatoms, a type 

of algae that live on the bottom and leave 

fossil remains, allow examination of current 

water quality conditions, such as phosphorus 

levels, along with historical conditions. These 

indicators of stress were selected because 

water quality stressors impact the biological 

health of lakes– from primary producers 

(phytoplankton or algae) to small openwater 

animals (zooplankton) to macroinvertebrates 

(insects, mollusks and crustaceans) and fish. 

Chapter 2 Design of the Lakes Survey

Lake Habitats

Lakes are highly interactive systems. The physical and chemical make-up of a lake supports a specialized 

community of biological organisms unique to the surrounding environment. Lakes and ponds are stillwater habitats that host a large array of floating organisms that cannot survive in flowing water. For many 

organisms, shoreline and shallow water habitats provide refuge from predation, living and egg-laying 

substrates, and food. In addition to aquatic inhabitants, a wide number of terrestrial animals rely on lakes for 

their food. For example, in a typical summer, a moose can eat over 171⁄2 lbs of aquatic plants per day. A 31⁄2 lb 

adult osprey can consume some 270 lbs of fish in one year

The indicators include both the vegetation and physical features along shorelines and adjacent upland areas. 

Shoreline structure affects nutrient cycling, biological production, and even sedimentation rates within the 

lake. The zone of transition between the lakeshore and the water’s edge is an area where considerable 

biological interactions occur and is critically important to benthic communities, fish, and other aquatic 

organisms. The relationship between the terrestrial and aquatic environments is characterized by the 

movement of nutrients/food from the shore to the water (e.g., fish making use of emergent plants for food or 

shelter), and the reverse movement from the water back to the shore (e.g., seasonal flooding of shorelines, 

shore birds feeding on aquatic insects and crustaceans). 

Human activities along lakeshores often adversely affect ecosystem functions by lessening the amount and 

type of optimal habitat available. Habitat cover or protection, in the form of woody snags, overhanging trees, 

and aquatic plants, becomes markedly reduced. A poor habitat cover adversely impacts aquatic plants, 

fish, and other living things in and around the lake. Alterations of these and other types of habitat features 

can affect biological integrity even in lakes where the water is not polluted. Therefore, the physical habitat 

condition of the land-water interface is critically important to overall lake condition.

Launching a field survey boat in Kansas. 

Photo courtesy of Ben Potter.
Chapter 2 Design of the Lakes Survey

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

14

Field Sampling

In preparation for the survey, each target 

lake was screened to verify that it met the 

established criteria for inclusion in the survey. 

Throughout the summer of 2007, 86 field 

crews, consisting of 2 to 4 people each, 

sampled lakes from Maine to California. To 

ensure consistency in data collection and 

quality assurance, the crews attended a 

three-day training session, used standardized 

field methods and data forms, and followed 

strict quality control protocols including field 

audits. 

At each lake site, crews collected samples 

at a single station located at the deepest 

point in the lake and at ten stations around 

the lake perimeter (Figure 4). At the midlake station, depth profiles for temperature, 

pH, and dissolved oxygen were taken with 

a calibrated water quality probe meter or 

multi-probe sonde. A Secchi disk was used 

to measure water clarity and depth at which 

light penetrates the lake (the euphotic 

zone). NLA analysts used these vertical 

profile measurements to determine the 

extent of stratification and the availability 

of the appropriate temperature regime 

and level of available oxygen necessary 

to support aquatic life. Single grab water 

samples were collected to measure nutrients, 

chlorophyll-a, phytoplankton, and the algal 

toxin microcystin. Zooplankton samples were 

collected using a fine mesh (80μm) and 

course mesh (243μm) conical plankton net. 

A sediment core was taken to provide data 

on sediment diatoms and mercury levels. The 

top and bottom layers of the sediment core 

were analyzed to detect possible changes in 

diatom assemblages over a period of time.

station.

Figure 4. NLA sampling approach for a typical lake. Sampling locations are denoted by letters A-J and Z. Riparian, 

littoral, sublittoral, and profundal lake zones are depicted, as is the schematic design of a shoreline physical habitat 
15

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

as a benchmark for setting thresholds for 

good, fair, and poor condition for each of the 

indicators. 

 EPA’s experience with past surveys 

showed that only a small portion of the 

sampled population of lakes will be of 

reference quality. EPA used both identified 

lakes that were thought to be of high quality 

as well as high quality lakes from the random 

site selection process to serve as candidate 

reference lakes that might ultimately serve 

as “least-disturbed” benchmark reference 

sites. The candidate lakes were sampled 

identically to, and in addition, to the target 

lakes. Subsequently, data results from all 

sampled lakes were evaluated against the 

reference screening criteria to determine 

the final set of lakes that would be used to 

characterize the reference condition. NLA 

analysts used a number of independent 

variables reflecting human influence as 

classification and screening criteria, e.g., 

limnological shoreline index, chloride content, 

total water column calcium, and others. Two 

parallel groups of reference lakes were set, 

one for biological condition, and another for 

Chapter 2 Design of the Lakes Survey

Retrieving a sediment core. 

Photo courtesy of Great Lakes Environmental Center.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

16

Chapter 2 Design of the Lakes Survey

nutrient stressors. The latter set of reference 

sites was developed so that nutrient levels 

could be used in screening reference lakes for 

biological condition.

 When considering reference condition, it 

is important to remember that many areas 

in the United States have been altered - with 

natural landscapes transformed by cities, 

suburban sprawl, agricultural development, 

and resource extraction. To reflect the 

variability across the American landscape, 

these least-disturbed lakes diverge from 

the natural state by varying degrees. For 

example, highly remote lakes like those in the 

upper elevation wilderness areas of Montana 

may not have changed in centuries and are 

virtually pristine, while the highest quality, 

least-disturbed lakes in other parts of the 

country, especially in urban or agricultural 

areas, may exhibit different levels of human 

disturbance. The least-disturbed reference 

sites in these widely influenced watersheds 

display more variability in quality than those 

in watersheds with little human disturbance. 

Thus in reference conditions across the 

country, i.e., the “bar” for expectations may 

be different. The resulting reference lakes 

represent the survey team’s best effort at 

selecting lakes that are the least disturbed 

nationally and in specific regions across the 

country.

Thresholds – Good, Fair, and Poor

 After the reference lakes were selected 

and reference condition was determined, 

thresholds against which the target lakes are 

compared were set. For NLA, each indicator 

for a lake was classified as either “good,” 

“fair,” or “poor” relative to the conditions 

found in reference lakes. That is, “good” 

denotes an indicator value similar to that 

found in reference lakes, “poor” denotes 

conditions definitely different from reference 

conditions, and “fair” indicates conditions 

on the borderline of reference conditions. 

Specifically, these thresholds are then applied 

to the results from the target lakes and are 

classified as follows: lake results above 25% 

of the reference range values are considered 

“good;” below the 5% of the reference range 

value are “poor;” and those between the 

5% and 25% are “fair” (Figure 5). These 

“good,” “fair,” “poor” designations however 

are not intended to be a replacement for the 

evaluation by states and tribes of the quality 

of lakes relative to specific water quality 

standards.

Figure 5. Reference condition thresholds used for good, fair, and poor assessment.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

17

HIGHLIGHT

Surveying the Nation’s Lakes for 

Invasive Aquatic Species

Amy P. Smagula

New Hampshire Department of Environmental Services

 On every continent, in nearly all aquatic habitat types, at all levels of the food web, invasive species 

have made an impact. Invasive aquatic species can be described as those species that live in water but are 

generally not native to a particular waterbody. In general they have traits or characteristics that suggest a 

competitive ecological advantage over native species. Invasive species grow rapidly and/or aggressively, 

so that they can eventually dominate a habitat to the detriment of native creatures that already live there. 

Invasive aquatic species include a whole range of organisms, including plants, animals, pathogens, and 

others. 

 The types of invasive aquatic species in our lakes are 

numerous and diverse, and can include aquatic plants that 

either root in substrate (like Eurasian watermilfoil or Hydrilla) 

or that float on the surface of the water (like the giant salvinia). 

They include larger animals such as fish (like the snakehead 

fish), and macroinvertebrates (like the zebra mussel). They also 

include those seen only with the aid of a microscope, such as 

filamentous algae or the spiny water flea.

 The pathways for invasive aquatic species introductions 

are varied, and include ballast water discharges from large 

vessels, retail industries like the aquarium and home water 

garden trades, and even internet suppliers of aquatic species. 

Once a species becomes established in a waterbody, either 

by accidental (e.g., contaminated boat) or intentional means 

(e.g., dumping of an aquarium or direct planting), it is transient 

recreational equipment (motor boats, kayaks, diving gear, etc.) 

that causes the lake-to-lake spread of these species. 

 Depending on the point of introduction and transport 

pathways, species can become widely distributed or remain 

as localized infestations. Unfortunately, many invasive aquatic 

species are highly adaptive, and can survive and thrive in a 

wide range of environmental conditions. Big or small, plant 

or animal, invasive aquatic species in our lakes can have 

detrimental effects on the very attributes of those waterbodies 

that scientists, citizens, and environmental stewards are trying 

to evaluate and preserve. 

How Can Data from the NLA Survey Help?

 One of the goals of the National Lakes Assessment (NLA) is to provide citizens and governments with 

current information on the health of our lakes so that they can take action to prevent further degradation. 

Data on invasive aquatic species can be used to help determine which of these species has been 

Invasive Aquatic Species:

• Grow very quickly and spread rapidly 

 to occupy large areas;

• Have various strategies for 

 reproduction;

• Survive in a range of conditions;

• Have no natural predators to 

 control them;

• Take over areas from native 

 plants/animals and can thus 

 be ecologically devastating;

• Pose serious economic problems

 in terms of control costs and costs 

 attributable to habitat loss and 

 recreational impairments to 

 waterbodies, including reductions 

 in property values on infested 

 waterbodies;

• Are very difficult if not impossible

 to control; and

• Threaten nearly half of the species

 listed under the Endangered 

 Species Act.
documented in a state or region, and if those are well established populations or if they are pioneering 

and can be eliminated or halted before other waterbodies in the area are affected. These data may also 

be used to assist with risk assessments for an area, based on what has been found in neighboring states, 

coupled with tourism and recreational data for that region. 

The Key is Prevention, Early Detection, & Rapid Response

 Preventing the introduction of invasive aquatic species is paramount to protecting a waterbody. Many 

states and regional working groups have established education campaigns to alert lake users and others 

about the threats posed by invasive aquatic species and to hopefully prevent a new infestation by proper 

care of transient recreational vessels and gear. Additionally, many states have developed prohibited 

species lists in an effort to prevent overland transport and sale of these invasive species.

 When prevention fails and an infestation does occur, early detection is critical. Individual lake 

associations, special interest groups, and homeowners are encouraged to look for new infestations on a 

regular basis during the growing season, particularly if they live on a waterbody that receives a high level 

of use by transient boaters. A small new infestation is much more easily contained or eradicated than a 

dense and large-scale infestation. A network of volunteer monitors around a waterbody can look for signs 

of invasive species and report to key officials who can effectively deal with a potentially new infestation.

 State officials should be knowledgeable and poised for a rapid response to contain and control an 

infestation. They should be aware of appropriate management actions for the species in question and how 

to best approach the problem. Fortunately, many states have developed specific plans for aquatic nuisance 

species management, so that an immediate response can be made. 

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

 Hydrilla

 (Hydrilla verticillata)

First Identified in US: 1960

Native Range: Africa

U.S. Distribution: Widespread throughout the east and 

southeast, CA as well as occurrence in other states in the U.S.

Description: Narrow leaves whorled around the 20 ft main 

stem. It is the most invasive submergent plant in the U.S., and 

can even out-compete invasive watermilfoil by canopying over 

the surface. It has been observed to grow up to a half-inch per 

day in optimum conditions. 

Impacts: This plant forms thick impenetrable growth in the 

water column of lakes. It can impact native aquatic plants and 

animals and cause problems for recreation and navigation on 

waterbodies that it infests.

 Zebra mussel 

 (Dreissena polymorpha)

First Identified in US: 1988

Native Range: Eurasia

U.S. Distribution: All of the Great Lakes and many 

associated tributaries, plus other states throughout the U.S.

Description: Sticky strands secreted from one side of shell. 

Can grow very thick on surfaces.

Impacts: Documented to grow very thick on surfaces, foul 

marine engines, clog intake pipes, wash up in windrows on 

beaches, and alter the aquatic food web by reducing the 

amount of algae in the water due to high filter-feeding rates. 

18

Photos credits: Hydrilla, Amy P. Smagula, NH DES. Zebra mussels, NH SeaGrant.
CHAPTER 3. THE BIOLOGICAL CONDITION 

OF THE NATION’S LAKES

IN THIS CHAPTER

► Lake Health – The Biological Condition of Lakes

► Stressors to Lake Biota

► Ranking of Stressors 
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

20

Chapter 3 The Biological Condition of the Nation’s Lakes

Chapter 3 

The Biological Condition 

of the Nation’s Lakes

The Clean Water Act explicitly aims “to 

restore and maintain the chemical, physical 

and biological integrity of the nation’s waters”. 

Although the NLA report does not include 

all aspects of biological integrity or review 

all possible chemical, physical or biological 

stressors known to affect water quality, it 

does present the findings of some important 

indicators for estimating the condition of the 

nation’s lakes and characterizing the key 

influences. 

This and the following two chapters 

describe the results of the NLA using three 

approaches to assess lake condition. The 

first approach evaluates whether lakes are 

able to support healthy aquatic plant and 

animal communities. Analysts evaluated key 

stressors to lake biota, such as chemical 

and physical habitat attributes, and ranked 

the stressors in order of importance. In 

the second approach, the recreational 

suitability of lakes was assessed and the risk 

of exposure to algal toxins was evaluated 

(Chapter 4). The third approach was to 

evaluate trophic state based on chlorophyll-a

levels (Chapter 5).

Lake Health – 

The Biological Condition of Lakes

The biology of a lake is characterized in 

terms of the presence, number, and diversity 

of fish, insects, algae, plants and other 

organisms that together provide accurate 

information about the health and productivity 

of the lake ecosystem. The number and kinds 

of plant and animal species present in a 

lake system are a direct measure of a lake’s 

overall well-being. 

The biological condition assessment is 

based on information from two biological 

communities or assemblages – phytoplankton 

and zooplankton — in its evaluation of lake 

condition. The primary basis for assessing 

biological health is an index of taxa loss 

which is applied to the phytoplankton and 

zooplankton data. The NLA uses a measure 

of planktonic taxa loss as the predominant 

measure of overall lake condition because it is 

based on both plant and animal data and thus 

will reflect a broader perspective of trends in 

lakes. A second method to assess biological 

health uses an index of biotic integrity that 

is applied to sediment diatoms, a distinct 

type of phytoplankton. Both models use the 

biological reference conditions developed from 

the set of reference lakes. 

Biological Indicators

Phytoplankton. Phytoplankton are microscopic plants (algae) that float in the water 

and are usually responsible for both the color 

Photo courtesy of Great Lakes Environmental Center
21

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Chapter 3 The Biological Condition of the Nation’s Lakes

and clarity of lakes. Because of their ability 

to photosynthesize (i.e., they use the sun’s 

energy to turn carbon dioxide and water into 

food and energy), they are a primary source 

of energy in most lake systems, providing the 

food source for higher order organisms such 

as zooplankton or small fishes. Phytoplankton 

are remarkably diverse. For example, certain phytoplankton can regulate the depth at 

which they reside, optimizing their ability to 

access both nutrients and light. Others are 

specific to certain habitats within lakes, and 

to certain nutrient and chemical conditions. 

Zooplankton. Zooplankton are small freefloating aquatic animals. The zooplankton 

community constitutes an important 

element of the aquatic food chain. These 

organisms serve as an intermediary species 

in the food chain, transferring energy from 

planktonic algae (primary producers) to 

larger invertebrate predators and fish. Both 

phytoplankton and zooplankton are highly 

sensitive to changes in the lake ecosystem. 

The effects of environmental disturbances 

can be detected through changes in species 

composition, abundance, and body size 

distribution of these organisms.

Diatoms. Diatoms are a group of algae. 

Typically abundant in marine and freshwater 

habitats, diatoms account for at least 20% of 

the primary production of energy on earth. 

Unique among the algae, diatoms have 

cell walls composed of silica (glass), which 

are intricate and beautiful as well as useful 

for identifying individual species. In lakes, 

diatoms grow suspended in water as well as 

attached to substrates. Biologists use the 

diatoms in the water column and those on the 

lake bottom as a reflection of conditions in 

the lake. When diatoms die, they settle to the 

bottom and their silica shells remain intact. 

Over time their silica shells are preserved in 

layer upon layer of lake sediments enabling 

researchers to look at conditions that existed 

in the past. Similar to other biological 

indicators, diatoms integrate the physical 

and chemical conditions of the lake and 

surrounding watershed in which they reside. 

The environmental conditions under which 

particular diatom species flourish vary greatly 

and have been well described, making them a 

useful indicator.

Index of Taxa Loss – 

The Observed/Expected (O/E) Ratio

NLA analysts used the planktonic O/E 

taxa loss model to assess the condition of 

the planktonic community, combining data 

from both phytoplankton and zooplankton. 

The O/E measure looks at whether or not 

organisms (taxa) one would expect to find, 

Centrate (left) and pinnate (right) diatoms.

Image courtesy of J. Smol as provided by D. Charles.

Collecting a zooplankton sample in Texas. 

Photo courtesy of Texas Commission of Environmental Quality.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

22

Chapter 3 The Biological Condition of the Nation’s Lakes

based on reference lakes, are in fact present. 

The model allows a precise matching of the 

taxa found in the sample — in this case 

phytoplankton and zooplankton taxa — with 

those that should occur under the specified 

natural environmental conditions defined 

by the reference sites. The list of expected 

taxa (or “E”) at individual sites are predicted 

from a model developed from data collected 

at reference sites. By comparing the list 

of taxa observed (or “O”) at a site with 

those expected to occur, one can quantify 

the proportion of taxa that have been lost 

presumably due to stressors present in 

the lake. The O/E model is widely used 

nationally and internationally to assess the 

condition of aquatic communities. The index 

is particularly attractive because it allows a 

direct comparison of conditions across the 

different types of aquatic systems (e.g., 

lakes, wetlands, streams, and estuaries) 

that will be assessed by the national aquatic 

resource surveys.

Typically O/E values are interpreted 

as the percentage of the expected taxa 

present. Each tenth of a point less than 1 

represents a 10% loss of taxa at the site; 

thus, an O/E score of 0.9 indicates that 90% 

of the expected taxa are present and 10% 

are missing. The higher the percentage, the 

healthier the lake. As with all indicators, 

O/E values must be interpreted in context 

of the quality of reference sites because the 

quality of reference sites available in a region 

sets the bar for what taxa may be expected. 

Regions with lower-quality reference sites 

may have fewer taxa or different taxa and 

thus will have a lower bar. Although an O/E 

value of 0.8 means the same thing regardless 

of a region, i.e., 20% of taxa have been 

lost relative to reference conditions in each 

region, the true amount of taxa loss will be 

under-estimated if reference sites are of 

lower quality, meaning more disturbed than 

reference sites in comparable regions.

For the phytoplankton and zooplankton 

data, NLA analysts developed regionallyspecific O/E models to predict the extent of 

taxa loss across lakes of the United States. 

They defined three categories of plankton 

taxa loss: good (<20% taxa loss), fair (20-

40% taxa loss), and poor (>40% taxa loss). 

Index of Biological Integrity - 

The Lake Diatom Condition Index

The Lake Diatom Condition Index 

(LDCI) — or the Diatom IBI — is similar in 

concept to an economic indicator (e.g., the 

Consumer Confidence Index) in that the 

total index score is the sum of scores for a 

variety of individual measures. To calculate 

economic indicators, economists look at a 

number of metrics, including new orders for 

consumer goods, building permits, money 

supply, and others that reflect economic 

growth. To determine the LDCI, ecologists 

Measuring physical habitat data with flooded terrestrial 

vegetation. Photo courtesy of Dave Mercer.
looked at taxonomic richness, habit and 

trophic composition, sensitivity to human 

disturbance, and other aspects of the 

assemblage that are reflective of a natural 

state. For the LDCI, NLA analysts calculated 

regionally-specific thresholds that were based 

on percentages of reference lake distributions 

of LDCI values.2

The development of the LDCI is a 

groundbreaking addition to the tools available 

to perform lake assessments. The metrics 

used to develop the LDCI for the NLA covered 

five characteristics of diatom assemblages 

that are routinely used to evaluate biological 

condition: 

Taxonomic richness: This characteristic 

represents the number of distinct taxa, or 

groups of organisms, identified within a 

sample. A greater number of different kinds 

of taxa, particularly those that belong to 

pollution-sensitive groups, indicate a variety 

of physical habitats and an environment 

exposed to generally lower levels of stress.

Taxonomic composition: Ecologists 

calculate composition metrics by identifying 

the different taxa groups, determining which 

taxa in the sample are ecologically important, 

and comparing the relative abundance of 

organisms in those taxa to the whole sample. 

Healthy (good quality) lake systems have 

diatoms from across a larger number of taxa 

groups, whereas stressed (poor quality) lakes 

are often dominated by a high abundance of 

organisms in a small number of taxa that are 

tolerant of pollution.

Taxonomic diversity: Diversity metrics 

look at all the taxa groups and the distribution 

of organisms among those groups. Healthy 

lakes should have a high level of diversity of 

diatoms present.

Morphology: Organisms are characterized 

by certain adaptations, including how they 

move and where they live. These habits 

are captured in morphological metrics. For 

example, some are designed to move freely 

up and down within the water column to 

maximize nutrient uptake or light exposure, 

while others may develop adaptations, such 

as coloration, to avoid predation. A diversity 

of such attributes is reflective of a lake 

that naturally includes a diversity of habitat 

niches.

Pollution tolerance: Each taxa can tolerate 

a specific range of chemical contamination, 

which is referred to as their pollution 

tolerance. Once this range is exceeded, the 

taxa are no longer present. Highly sensitive 

taxa, or those with a low pollution tolerance, 

are found only in lakes with good water 

quality. 

23

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Chapter 3 The Biological Condition of the Nation’s Lakes

2 The numerical threshold for the diatom index and many of the other NLA indicators can be found in the Technical Appendix.

Subsampling zooplankton samples.

Photo courtesy of EcoAnalysts.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

24

Chapter 3 The Biological Condition of the Nation’s Lakes

Findings of the Biological Assessments

Using the planktonic O/E, or taxa loss 

model, 56% of the nation’s lakes are in good 

condition, while 21% are in fair condition, 

and 22% are in poor condition (Figure 6). The 

LDCI shows similar results with 47% of lakes 

in good condition, 27% in fair condition, and 

23% in poor condition. For the continental 

U.S., this means about half of the country’s 

lakes are in good condition, while the other 

half are experiencing some level of stress that 

is negatively affecting the aquatic biological 

communities. 

Natural lakes in general exhibit slightly 

lower overall plankton taxa loss than manmade lakes. Sixty-seven percent of natural 

lakes are in good condition as compared 

to 40% of man-made lakes - a statistical 

difference. The LDCI, on the other hand, 

indicates that the proportion of lakes 

exhibiting good conditions does not vary 

significantly between natural and man-made 

lakes. However, 30% of natural lakes as 

compared to 13% of man-made lakes exhibit 

poor biological condition based on the diatom 

LDCI. 

Although in many cases the results of 

the planktonic O/E analysis are similar to 

the results of the diatom LDCI analysis, 

such agreement will not always occur. The 

taxa loss index examines a specific aspect 

of biological condition (biodiversity loss) 

and the index of biological integrity analysis 

3

For this and all figures in this report, values for good, fair and poor may not add to one hundred percent. Lakes sites that were not assessed and 

indicators for which no data was recorded are not included. Please refer to the Technical Appendix for further discussion.

Figure 6. Assessment of quality using the Planktonic O/E Taxa Loss and Lake Diatom Condition Index.3
25

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

combines multiple characteristics to evaluate 

biological condition. In this instance, the two 

communities may be responding differently 

to the stresses impacting lakes or to different 

stresses.

Stressors to Lake Biota

In the aquatic environment, a stressor 

can be anything (chemical, biological or 

physical) that has the potential to impact its 

inhabitants by altering their surroundings 

outside their normal ecological range. There 

are many external occurrences that can alter 

a creature’s ability to thrive, both natural and 

otherwise. Drought or rapid draw-down can 

be a stressor; contaminant (e.g., metals) 

can be a stressor; and human activity can 

be a stressor. An important dimension of the 

national lakes assessment is to evaluate key 

chemical and physical stressors of lake quality 

that, when altered, have the potential to 

impact lake biota.

1. Chemical Stressors 

For the assessment, five of the eight 

chemical indicators of lake stress were 

evaluated. These are total phosphorus 

concentration, total nitrogen concentration, 

turbidity, acid neutralizing capacity (ANC), 

and dissolved oxygen concentration (DO).

Phosphorus, Nitrogen, 

and Turbidity

Phosphorus and nitrogen are critical 

nutrients required for all life. In appropriate 

quantities, these nutrients support the 

primary algal production necessary to support 

lake food webs. In many lakes, phosphorus 

is considered the “limiting nutrient,” 

meaning that the available quantity of this 

nutrient controls the pace at which algae 

are produced in lakes. This also means that 

modest increases in available phosphorus can 

cause very rapid increases in algal growth. 

Some lakes are limited by nitrogen. In these 

lakes, modest increases in available nitrogen 

will yield the same effects. When excess 

nutrients from human activities enter lakes, 

cultural eutrophication is often the result. The 

culturally-accelerated eutrophication of lakes 

has a negative impact on everything from 

species diversity to lake aesthetics. 

Turbidity is a measure of light scattering, 

specifically, murkiness or lack of clarity. Lakes 

that are characterized by high concentrations 

of suspended soil particles and/or high 

levels of algal cells will have high measured 

turbidity. Turbidity in lakes is natural in 

some instances, resulting from natural soil 

deposition and resuspension within the lakes 

themselves. When human activities in lake 

watersheds and riparian zones increase soil 

erosion, increased turbidity often results 

in smothering of nearshore habitats by 

sediments and/or changing algae growth 

patterns. These changes affect biological and 

recreational conditions.

Chapter 3 The Biological Condition of the Nation’s Lakes

Boat fully loaded for a day on an Oklahoma lake. 

Photo courtesy of Paul Koenig.
Findings for Nutrients 

and Turbidity

Phosphorus, nitrogen, and turbidity are 

linked indicators that jointly influence both 

the clarity of water and the concentrations 

of algae in a lake. The levels of these 

three indicators vary regionally, as do the 

relationships between nutrients and turbidity, 

and between nutrients and algal growth. For 

phosphorus, nitrogen, and turbidity, lakes 

were assessed in relation to regionallyspecific thresholds based on the distributions 

in a distinct set of reference lakes.

Survey results show that slightly over half 

of the nation’s lakes are in good condition 

with respect to phosphorus and nitrogen 

(Figure 7). Fifty-eight percent and 54% of 

lakes are not stressed for the two nutrients, 

respectively. For all lake classes there was 

no significant difference between phosphorus 

and nitrogen indicators. For both nutrients, 

there are no significant differences between 

natural lakes and man-made lakes. 

For turbidity, 78% of lakes are in good 

condition, 16% are in fair condition, and 6% 

are in poor condition. When comparing the 

natural lakes to the man-made lakes for this 

indicator, 75% of natural lakes are in good 

condition as compared to 81% of man-made 

lakes. 

Lake Acidification

While not a widespread problem, lake 

acidification continues to be an important 

indicator of lake condition in a small number 

of areas around the country. Acid rain and 

acid mine drainage are major sources of 

acidifying compounds and can change the 

pH of lake water, impacting fish and other 

aquatic life. Acid neutralizing capacity 

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

26

Chapter 3 The Biological Condition of the Nation’s Lakes

Figure 7. Phosphorus, nitrogen, and turbidity in three lake classes.
(ANC) serves as an indicator for sensitivity 

to changes in pH. The ANC of a lake is 

determined by the soil and underlying geology 

of the surrounding watershed. Lakes with 

high levels of dissolved bicarbonate ions (e.g.,

limestone watersheds) are able to neutralize 

acid depositions and buffer the effects of acid 

rain. Conversely, watersheds that are rich in 

granites and sandstones and contain fewer 

acid-neutralizing ions have low ANC and 

therefore a predisposition to acidification. 

Maintaining stable and sufficient ANC is 

important for fish and aquatic life because 

ANC protects or buffers against drastic 

pH changes in the waterbody. Most living 

organisms, especially aquatic life, function at 

the optimal pH range of 6.5 to 8.5. Sufficient 

ANC in surface waters will buffer acid rain 

and prevent pH levels from straying outside 

this range. In naturally acidic lakes, the ANC 

may be quite low, but the presence of natural 

organic compounds in the form of dissolved 

organic carbon, or DOC, can mitigate the 

effects of pH fluctuations.

Findings for Lake Acidification

Results from the NLA indicate that almost 

all, or 99%, of the nation’s lakes can be 

classified as in good condition with respect 

to ANC (Figure 8). When looking at these 

results, however, it is also important to note 

that although the NLA indicates that lake 

acidification is not a widespread problem, 

acidification on a smaller scale, i.e., “hot 

spots,” do occur. While only a relatively small 

proportion of lakes may be impacted by 

acidification, the effects of acidification in the 

impacted lakes, and the contribution of acidity 

to other stressors, can be severe in specific 

geographic regions.

Dissolved Oxygen

Dissolved oxygen, or DO, is considered 

one of the more important measurements 

of water quality and is a direct indicator of a 

lake’s ability to support aquatic life. Aquatic 

organisms have different DO requirements 

for optimal growth and reproduction. 

Decreases in DO can occur during winter or 

summer when the available dissolved oxygen 

is consumed by aquatic plants, animals, 

and bacteria during respiration. While each 

organism has its own DO tolerance range, 

generally levels below 3 mg/L are of concern. 

Conditions below 1 mg/L are referred to as 

hypoxic and are often devoid of life.

27

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Chapter 3 The Biological Condition of the Nation’s Lakes

ANC Assessment Thresholds

Non-acidic >50 μeq ANC

Acidic-natural ≤ 50 μeq ANC 

and DOC ≤ 5 

mg/L

Anthropogenically

acidified

≤0 μeq ANC and 

DOC < 5 mg/L

Figure 8. Acid neutralizing capacity for lakes of the U.S.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

28

Chapter 3 The Biological Condition of the Nation’s Lakes

Findings for Dissolved Oxygen

For the NLA, DO assessment thresholds 

were established as high (≥ 5 mg/L), 

moderate (>3 to <5), and low (≤3 mg/L), 

and were based on measurements from 

the top two meters in the middle of the 

lake (Figure 9). Eighty-eight percent of the 

country’s lakes display high levels of DO and 

are in good condition based on the surface 

waters sampled (Figure 9). Natural lakes 

perform slightly better than the nation as a 

whole with 94% in good condition. Man-made 

lakes results show 80% with high levels of 

DO.

These findings indicate that, in general, 

low DO is not a chronic problem near the lake 

surface, which was not surprising given the 

sampling approach used in the survey. Future 

surveys may be able to more adequately 

address DO conditions in the bottom waters 

of lakes where low DO conditions are more 

likely to occur first.

2. Physical Stressors 

The condition of lakeshore habitats (Figure 

10) provides important information relevant 

to lake biological health. For the NLA, physical 

habitat condition was assessed based on 

observations for four indicators: 1) lakeshore 

habitat, 2) shallow water habitat, 3) physical 

habitat complexity (an index of habitat 

condition at the land-water interface), and 

4) human disturbance (extent and intensity 

of human activity). In assessing the physical 

habitat complexity indicator, NLA analysts 

looked at not only the total amount of cover 

present but also the diverse types of cover 

and the complex nature of potential ecological 

niches. For each lake habitat indicator, values 

were compared to the distribution of the 

indicator value in the reference sites.

Lakeshore Habitat

The lakeshore habitat indicator examines 

the amount and type of shoreline vegetation. 

It is based on observations of three layers 

of coverage (understory grasses and forbs, 

mid-story non-woody and woody shrubs, and 

overstory trees). In general, lakeshores are 

in better condition when shoreline vegetation 

cover is high in all three layers. It is important 

to note, however, that not all three layers 

naturally occur in all areas of the country. For 

example, in the Northern Plains areas, there 

is typically no natural overstory tree cover. 

Similarly, in some areas of the intermountain 

west, steep rocky shores are the norm for 

high-mountain and/or canyon lakes. These 

natural features have been factored into the 

calculation of the lakeshore habitat indicator.

Figure 9. Dissolved oxygen for lakes of the U.S.
29

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Shallow water habitat

The shallow water habitat indicator 

examines the quality of the shallow edge of 

the lake by utilizing data on the presence 

of living and non-living features such as 

overhanging vegetation, aquatic plants 

(macrophytes), large woody snags, brush, 

boulders, and rock ledges. Lakes with greater 

and more varied shallow water habitat are 

typically able to more effectively support 

aquatic life because they have more, and 

more complex, ecological niches. Like the 

lakeshore habitat indicator, the shallow water 

indicator is related to conditions in reference 

lakes and is modified regionally to account for 

differing expectations of natural condition.

Physical habitat complexity

The third indicator, physical habitat 

complexity, combines data on from the 

lakeshore and shallow water interface. This 

indicator estimates the amount and variety 

of all cover types at the water’s edge. Like 

the other indicators, this index is related 

to conditions in reference lakes and is 

modified regionally to account for differing 

expectations of natural condition. 

Chapter 3 The Biological Condition of the Nation’s Lakes

 Figure 10. Schematic of a lakeshore. 
Findings for Habitat Integrity

The findings for the three habitat stressor 

indicators are depicted in Figures 11, 12 

and 13. Nationally, 46% of lakes exhibit 

good lakeshore habitat condition, while 

18% of lakes are in fair condition and 36% 

are in poor condition. With respect to the 

shallow water areas of lakes, 59% of lakes 

exhibit good habitat condition, while 21% of 

lakes are in fair condition, and 20% are in 

the most disturbed, or poor condition. For 

physical habitat complexity of the land/water 

interface, 47% of lakes are in good condition, 

20% of lakes are in fair condition, and 32% 

are in poor condition. For all three habitat 

indicators, more natural lakes support healthy 

combined habitat condition than man-made 

lakes.

Lakeshore Human Disturbance

In the above discussion of the lakeshore 

environment, the condition of lakes was 

described in terms of habitat integrity in both 

the lakeshore and shallow water areas of the 

lake. The fourth indicator of physical habitat 

is lakeshore human disturbance and reflects 

direct human alteration of the lakeshore itself. 

These disturbances can range from minor 

changes (such as the removal of trees to 

develop a picnic area) to major alterations 

(such as the construction of a large lakeshore 

residential complex complete with concrete 

retaining walls and artificial beaches). The 

effects of lakeshore development on the 

quality of lakes include excess sedimentation, 

loss of native plant growth, alteration of 

native plant communities, loss of habitat 

structure, and modifications to substrate 

types. These impacts, in turn, can negatively 

affect fish, wildlife, and other aquatic 

communities. 

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

30

Chapter 3 The Biological Condition of the Nation’s Lakes

Figure 11. Lakeshore habitat for lakes of the U.S. as percent 

of lakes in three condition classes.

Figure 12. Shallow water habitat for lakes of the U.S. as 

percent of lakes in three condition classes.
31

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Chapter 3 The Biological Condition of the Nation’s Lakes

Findings for Lakeshore Disturbance

 Across the lower 48 states, 35% of lakes 

exhibit good conditions representative of 

relatively low human disturbance levels, while 

48% of lakes exhibit moderate disturbance, 

and 17% exhibit poor, or highly disturbed 

conditions (Figure 14). In contrast to the 

other three habitat indicators, the percentage 

of natural lakes that have minimal lakeshore 

disturbance is substantially higher than that 

of man-made lakes. Forty-six percent of 

natural lakes are in good condition compared 

to 18% of man-made lakes. These findings 

also show that there are twice as many manmade lakes with high lakeshore disturbance 

(poor condition) as natural lakes.

Ranking of Stressors

 An important key function of the national 

assessments is to provide a perspective on 

key stressors impacting biological condition in 

lakes and rank them in terms of the benefits 

expected to be derived from reducing or 

eliminating these stresses. For the NLA, 

analysts used three approaches to rank 

stressors. The first looks at how extensive or 

widespread any particular stressor is, e.g., 

how many lakes have excess phosphorus 

concentrations. The second examines the 

severity of the impact from an individual 

stressor when it is present, e.g., how 

severe is the biological impact when excess 

phosphorus levels occur. Ranking ultimately 

requires taking both of these perspectives 

into consideration. The third approach is 

attributable risk, which is a value derived 

by combining the first two risk values into a 

single number for ranking across lakes.

Figure 13. Physical habitat complexity for the lakes of the 

U.S. as percent of lakes in three condition classes.

Figure 14. Lakeshore disturbance for lakes of the U.S. as 

percent of lakes in three conditions classes.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

32

Chapter 3 The Biological Condition of the Nation’s Lakes

 Throughout this section, the stressors a small area (i.e., hot spots) or that occur 

over a wide area but are spread out have a 

low relative extent. It is important for water 

resource managers to take into account the 

extent of the stressor when setting priority 

actions at the national, regional, and state 

scale.

 Nationally, the most widespread stressors 

measured as part of the NLA are those that 

affect the shoreline and shallow water areas, 

which in turn can affect biological condition. 

Results from the NLA show that the most 

widespread of these is the alteration of 

lakeshore habitat. 

Figure 15. Relative extent of poor stressors conditions. Relative risks of impact to plankton O/E and Attributable risk (combining Relative 

extent and Relative risk).
Thirty-six percent of lakes nationally 

have poor lakeshore habitat (Figure 15, left 

graph). The second most prevalent stressor 

is physical habitat complexity, which is poor 

in 32% of lakes nationally. Total nitrogen 

and total phosphorus ranked fourth and fifth, 

respectively, in terms of how widespread 

excess levels are across the country.

The ranking of these stressors according 

to extent is similar across natural and 

man-made lakes with most stressors being 

more widespread in man-made lakes (e.g., 

lakeshores with poor habitats occurring at 

41% of man-made lakes compared with 33% 

of natural lakes). 

Relative Risk 

The evaluation of 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 10-

20 times more likely to get and die of lung 

cancer4. Similarly, one can examine the 

likelihood of having poor biological conditions 

when phosphorus concentrations are high 

compared with the likelihood of poor biological 

conditions when phosphorus concentrations 

are low. When these two likelihoods are 

quantified, their ratio is called the relative 

risk. For the NLA, only the relative risk of 

stressor to poor conditions is presented.

Results of the relative risk analyses are 

presented in the middle graph of Figure 15. 

The highest relative risk nationally was found 

for lakeshore habitat disturbance with a 

relative risk just over 3. This means that lakes 

with poor surrounding vegetation are about 3 

times more likely to also have poor biological 

conditions, as defined for this assessment. 

The remaining stressors, with the exception of 

dissolved oxygen and lakeshore disturbance, 

have relative risks near 2 (i.e., twice as 

likely to have poor biological conditions). The 

relative risks for stressors in natural lakes 

appear consistently greater than the relative 

risk values for man-made lakes.

Attributable Risk

As mentioned, attributable risk is 

derived by combining the relative extent 

and the relative risk into a single number 

for the purposes of ranking. Conceptually, 

attributable risk provides an estimate of 

the proportion of poor biological conditions 

that could be reduced if poor conditions of a 

particular stressor were eliminated. This risk 

value represents the magnitude or importance 

of a potential stressor and one that can be 

ranked and prioritized for policy makers and 

managers. 

Estimates for attributable risk based on 

the planktonic O/E indicator of biological 

condition are presented in right graph of 

Figure 15. Lakeshore habitat alteration has 

the highest attributable risk for plankton taxa 

loss while other stressors (with the exception 

of lakeshore disturbance, turbidity and 

33

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Chapter 3 The Biological Condition of the Nation’s Lakes

4 Centers for Disease Control. http://www.cdc.gov/cancer/lung/risk_factors.htm

Survey crew member records shoreline habitat data. 

Photo courtesy of Texas Commission of Environmental Quality.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

34

Chapter 3 The Biological Condition of the Nation’s Lakes

dissolved oxygen) have similar attributable 

risk values. Thus one might expect that 

to improve lake condition to the greatest 

extent, lakeshore vegetative habitat would 

have to be increased to the point that it is 

no longer a stressor. Natural lakes show a 

slightly different pattern in attributable risk 

with lakeshore habitat being a high priority 

followed closely by total nitrogen, total 

phosphorus and physical habitat complexity. 

For man-made lakes, three of the four habitat 

indicators rank the highest in attributable risk.

Human shoreline disturbance is an important stressor in lakes. 

Photo courtesy of Great Lakes Environmental Center.

Lakeshore Alteration Stress

By Kellie Merrell, VT Department of Conservation

Transformation of lakeshores from natural forested and wetland cover to lawns and sandy beaches, 

accompanied by residential homes development (and redevelopment) is a stressor to many lakes. In a survey 

of 345 lakes in the Northeast during the early 1990s, the U.S. Environmental Protection Agency and U.S. 

Fish and Wildlife Service determined that stress from shoreline alteration was a more widespread problem 

than eutrophication and acidification. In recent years, many state agencies have documented the effects of 

shoreline development on nearshore and shallow water habitat quality with notable results. 

As lakeshores are converted from forests to lawns, lakes are impacted by impervious surfaces, enhanced 

runoff, less shading, and in most cases, more abundant aquatic plant growth in shallow areas. Shallow water 

habitat is further simplified by the direct removal of woody structure, and interruption in the resupply of this 

critical habitat component. The Wisconsin Department of Natural Resources has estimated that unbuffered 

developed sites contribute five times more runoff, seven times more phosphorus and 18 times more sediment 

to a lake than the naturally forested sites. 

This alteration of the nearshore and shallow water habitat affects a variety of both terrestrial and aquatic 

wildlife and has been described in the literature. Green frog, dragonfly, and damselfly populations decline. 

The nesting success and diversity of fish species also declines, with sensitive native species being replaced 

by more tolerant species. Turtles lose basking sites and corridors to inland nest sites. Bird composition shifts 

from insect-eating to seed-eating species. Even white-tailed deer are affected, with reduction in winter browse 

along shorelines reducing winter carrying capacity. The removal of conifers along shores also reduces shoreline 

mink activity. Ultimately, the cumulative effects of lakeshore development have negative implications for many 

species of fish and wildlife.
CHAPTER 4.

SUITABILITY FOR RECREATION

IN THIS CHAPTER

► Algal Toxins

► Contaminants in Fish Tissue

► Pathogen Indicators

Photo courtesy of Washington Department of Ecology
Chapter 4 Suitability for Recreation

36

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Chapter 4

Suitability for Recreation 

Another perspective on lake condition 

views the quality of a lake in terms of its 

suitability or safety for recreational use. Lakes 

are used for a wide variety of recreational 

opportunities that include swimming, 

waterskiing, windsurfing, fishing, boating, 

and many other activities. However, a number 

of microbial organisms, algal toxins, and 

other contaminants present in lakes can 

make people sick. NLA analysts assessed 

three indicators with respect to recreational 

condition: 1) microcystin – a type of algal 

toxin, 2) cyanobacteria – a type of algae 

that often produces algal toxins, and 3) 

chlorophyll-a — a measure of all algae 

present. Results from a companion study of 

contaminants in fish tissue are also discussed. 

Samples were also collected for pathogens 

and sediment mercury; however, results 

for these two indicators are unavailable 

as of publication of this report and will be 

presented in a supplemental report available 

on http://www.epa.gov/lakessurvey/. 

Algal Toxins

One group of phytoplankton, 

cyanobacteria, (also called blue-green 

algae) are a natural part of all freshwater 

ecosystems. Eutrophication in lakes often 

results in conditions that favor their growth 

and cyanobacterial blooms frequently occur. 

Cyanobacterial blooms can be unsightly, often 

floating in a layer of decaying, odiferous, 

gelatinous scum. Many types of cyanobacteria 

have the potential to produce cyanotoxins, 

and several different cyanotoxins may be 

produced simultaneously. In assessing the risk 

of exposure to algal toxins for recreational 

safety, it is important to remember that algal 

density, i.e., chlorophyll-a concentrations 

and cyanobacteria cell counts, serve as 

proxies for the actual presence of algal 

toxins. This is because not all phytoplankton 

are cyanobacteria and not all cyanobacteria 

produce cyanotoxins. 

Although there are relatively few 

documented cases of severe human health 

effects, exposure to cyanobacteria or their 

toxins may produce allergic reactions such 
Chapter 4 Suitability for Recreation

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

37

as skin rashes, eye irritations, respiratory 

symptoms, and in some cases gastroenteritis, 

liver and kidney failure, or death. The most 

likely exposure route for humans is through 

accidental ingestion or inhalation during 

recreational activities, though cyanotoxins 

are also cause for concern in drinking water. 

Cyanotoxins can also kill livestock and 

pets that drink affected water. While many 

varieties of cyanotoxin exist, microcystin, 

produced by Microcystis taxa, is currently 

believed to be the most common in lakes. 

Microcystin is a potent liver toxin, a known 

tumor promoter, and a possible human 

carcinogen. 

Because of the potential for human 

illness, several states have issued guidelines 

for recreational use advisories associated with 

the presence of microcystin or associated 

indicators. These guidelines vary and rely on 

visual observations of algal scums, measured 

chlorophyll-a concentrations, cyanobacteria 

cell counts, and/or direct measurements of 

microcystin. While EPA does not presently 

have water quality criteria for microcystin, 

cyanotoxin, or any other algal toxins, the 

World Health Organization (WHO) has 

established recreational exposure guidelines 

for chlorophyll-a, cyanobacterial cell counts, 

and microcystin (Table 1).

Table 1. World Health Organization thresholds of risk associated with potential 

exposure to cyanotoxins.

Indicator 

(units)

Low Risk 

of Exposure

Moderate 

Risk 

of Exposure

High Risk

of Exposure

Chlorophyll-a

(μg/L) <10 10 - <50 >50

Cyanobacteria 

cell counts (#/L) < 20,000 20,000 - 

<100,000 ≥ 100,000

Microcystin 

(μg/L) <10 10 - ≤20 >20

Figure 16. Percent of lakes, using three algal toxin indicators. In the first two graphs the percentage numbers indicate the risk or exposure to 

algal toxins associated with the presence of chlorophyll-a and cyanobacteria, not the risk of exposure to cholorphyll-a and cyanobacteria per 

se.
Chapter 4 Suitability for Recreation

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

38

and because of this, the NLA results may 

underestimate certain types of recreational 

exposure when accumulations or scums are 

present. 

 Another important point to consider 

when looking at the data is whether the 

single sample of microcystin truly represents 

what is in the lake. Chlorophyll-a levels, 

cyanobacteria densities, and cyanotoxin 

concentrations may change quite rapidly, 

depending on bloom intensity and weather 

conditions. The concentrations of microcystin 

measured on one particular day may over 

or underestimate season-wide central 

tendencies. The NLA is not intended to assess 

the specific condition of any given lake, but 

rather provide information on the general 

conditions across the population of lakes. 

Finally, it is currently unknown how well 

microcystin occurrence correlates with the 

occurrence of other classes of cyanotoxins 

Figure 17. Occurrence of microcystin in lakes.
39

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

that were not measured, or how human 

health risks might be altered because of toxin 

mixtures. While the survey results are a good 

start in our understanding, much more is to 

be learned about algal toxins in lakes.

Contaminants in Lake Fish Tissue

 Fish acquire contaminants and 

concentrate them in their tissues by uptake 

from water (bioconcentration) and through 

ingestion (bioaccumulation). Fish can often 

bioaccumulate chemicals at levels of more 

than a million times the concentration 

detected in the water column. 

 In a study conducted by the Office of 

Water’s Office of Science and Technology, EPA 

surveyed contaminants in lake fish tissue. The 

National Study of Chemical Residues in Lake 

Fish Tissue characterized contaminant levels 

in fillet tissue for predators and in whole 

bodies for bottom-dwelling fish species. The 

study targeted pollutants that were classified 

as persistent, bioaccumulative, and toxic 

(PBT) chemicals, including mercury, arsenic, 

PCBs, dioxins and furans, DDT, and chlordane. 

This survey provided data to develop national 

estimates for 268 PBT chemicals in fish 

tissue from lakes and reservoirs in the 48 

continental states (excluding the Great Lakes 

and the Great Salt Lake).

 The study focused on fish species that 

are commonly consumed in the study area, 

have a wide geographic distribution, and 

potentially accumulate high concentrations of 

PBT chemicals. Fish samples were collected 

over a 4-year period (2000-2003) from 500 

randomly selected lakes and reservoirs, which 

ranged in size from 2.5 acres (1 hectare) to 

900,000 (365,000 hectares), were at least 3 

feet (1 meter) deep, and had permanent fish 

populations.

Chapter 4 Suitability for Recreation

Figure 18. Percentage predator fish with mercury and PCB levels 

above (red) and below (green) EPA recommended limits. 
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

40

Pathogen Indicators

Enterococci are believed to provide a 

better indication of the presence of pathogens 

than more traditional indicators for fecal 

coliform. Enterococci are bacteria that live 

in the intestinal tracts of warm-blooded 

creatures, including humans. 

They are most frequently found in soil, 

vegetation, and surface water because of 

contamination by animal excrement. Most 

species of enterococci are not considered 

harmful to humans. However, the presence 

of enterococci in the environment indicates 

the possibility that other disease-causing 

agents also carried by fecal material may be 

present. Epidemiological studies of marine 

and freshwater beaches have established 

a relationship between the density of 

enterococci in the water and the occurrence 

of gastroenteritis in swimmers. 

For the NLA, enterococci were measured 

using a method to assess ambient 

concentrations. This Quantitative Polymerase 

Chain Reaction (qPCR) method quantifies 

DNA that is specific to enterococci. Published 

epidemiological studies report a clear 

relationship between levels of qPCR-measured 

enterococci and sickness. EPA research is still 

underway to develop health-based thresholds 

for interpreting qPCR results. 

Analyzing phytoplankton samples.

Photo courtesy of EcoAnalysts.

Chapter 4 Suitability for Recreation
HIGHLIGHT

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

41

Atmospheric Contaminants: 

Mercury and Acid Rain

Neil C. Kamman

Vermont Department of Environmental Conservation

Of the many stressors that affect lakes, atmospheric contaminants are perhaps the most difficult to 

address. This is because sources of atmospheric contaminants are often hundreds or even thousands 

of miles from the lakes into which the contaminants are ultimately deposited. The intertwined issues of 

freshwater acidification and mercury contamination are not new. The popular press began reporting on 

acid rain in the 1970s. It took another 10-15 years for the press to also focus on mercury. Today, many 

people are aware of both issues, yet often do not fully comprehend nor appreciate the degree to which the 

two are linked. In the case of both these pollutants, the cycle is initiated by emissions into the air.

Mercury is a naturally occurring metal that is found in the environment in many forms, all of which 

are toxic to aquatic life in varying degrees. The release of mercury to the environment is enhanced by 

human activities such as the combustion of fossil fuels, such as coal and petroleum. In the U.S. the largest 

sources of mercury are coal-fired generation or utility boilers, followed by waste incinerators. Mercury is 

present in many household items, notably thermostats and fluorescent lamps, and is released when these 

items end up in landfills or incineration facilities. Depending on its chemical form, air-borne mercury may 

remain in the atmosphere for a period of minutes (as reactive gaseous mercury), days (as particulate 

mercury), or weeks or years (as gaseous elemental mercury). 

Methylmercury, one of the most toxic forms of mercury, can be prevalent in fish and has documented 

adverse health effects on humans. The U.S. Centers for Disease Control and Prevention estimates that 

up to 6% of women of childbearing age have blood mercury levels in excess of established safety levels. 

Fish and fish-eating wildlife such as the common loon and American bald eagle are also at risk from 

mercury toxicity. While the mercury cycle in lakes is quite complex, there are five basic stages: emission, 

deposition, methylation*, bioaccumulation, and finally sequestration to lake sediments.

Lake acidification is most commonly caused by acidic deposition (rain, snow and dust). The acidic 

deposition pathway begins with the release into the air of acid-forming chemicals, most notoriously sulfur 

dioxide and nitrogen oxides, and ends when sulfuric and nitric acids are deposited to the landscape. Sulfur 

dioxide, like mercury, results largely from the burning of fossil fuels. Some forms of coal are very rich in 

sulfur, and poorly controlled facilities released massive quantities, particularly during the period 1960-

1992. Both sulfur dioxide and nitrogen oxides are common components of vehicular emissions. Once 

emitted, these two compounds undergo complex atmospheric transformations, resulting in rain and snow 

that contain dilute concentrations of nitric and sulfuric acids. Thankfully, the Clean Air Act Amendments of 

1990 have resulted in profound reductions in acid-forming precursors. In very sensitive regions, however, 

lakes remain at risk for acidification even with reduced levels of acid rain. 

In one sense, the process of lake acidification is not as complex as that of mercury accumulation in 

that there is neither methylation nor bioaccumulation of the acids. Yet acidification has more pernicious 

effects that can exacerbate mercury problems. Acidification of watersheds renders the watersheds more 

efficient at creating and transporting methylmercury to lakes, along with other soil-bound toxic metals 

such as aluminium. Moreover, acidification of the lakes themselves renders the bioaccumulation of 

methylmercury more efficient. Therefore, acidic lakes: 1) receive more mercury from their watershed, 2) 

have more of the mercury in the toxic methylated form, and 3) have more efficient bioaccumulation of the 

methylmercury. 

*

The natural and biologically-mediated process by which mercury is transformed into toxic organic methylmercury.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

42

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Graphical depiction of methylmercury bioaccumulation in lake biota. This figure is reproduced from the Hubbard 

Brook Research Foundation’s ScienceLinks publication Mercury Matters: Linking Mercury Science with Public 

Policy in the Northeastern United States. Used with permission.
CHAPTER 5. TROPHIC STATE OF LAKES

IN THIS CHAPTER

► Findings for Trophic State

Photo courtesy of USEPA Region 10
Chapter 5 Trophic State of Lakes

44

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Chapter 5

Trophic State of Lakes

The third approach to assessing the 

condition of lakes is to look at lakes with 

respect to their primary production. Trophic 

state depicts biological productivity in lakes. 

Lakes with high nutrient levels, high plant 

production rates, and an abundance of plant 

life are termed eutrophic, whereas lakes 

that have low concentrations of nutrients, 

low rates of productivity and generally low 

biomass are termed oligotrophic. Lakes that 

fall in between are mesotrophic, and those 

on the extreme ends of the scale are termed 

hypereutrophic or ultra-oligotrophic. Lakes 

exist across all trophic categories; however 

hypereutrophic lakes are usually the result 

of excessive human activity and can be an 

indicator of stress conditions.

There is no ideal trophic state for lakes 

as a whole since lakes naturally fall in 

all of these categories. Additionally, the 

determination of “ideal” trophic state depends 

on how the lake is used or managed. For 

example, an oligotrophic lake is a better 

source of drinking water than a eutrophic lake 

because the water is easier or less expensive 

to treat. Swimmers and recreational users 

also prefer oligotrophic lakes because of their 

clarity and aesthetic quality. Eutrophic lakes 

can be biologically diverse with abundant fish, 

plants, and wildlife. For anglers, increased 

concentrations of nutrients, algae, or aquatic 

plant life generally result in higher fish 

production. 

Eutrophication is a slow, natural part 

of lake aging, but today human influences 

are significantly increasing the amount of 

nutrients entering lakes. Human activities 

such as poorly managed agriculture or 

suburbanization of lakeshores can result 

in excessive nutrient concentrations 

reaching lakes. This can lead to accelerated 

eutrophication and related undesirable effects 

including nuisance algae, excessive plant 

growth, murky water, odor, and fish kills.

Photo courtesy of Great Lakes Environmental Center
Chapter 5 Trophic State of Lakes

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

45

Findings for Trophic State

For NLA, the trophic state is characterized 

using nationally-consistent chlorophyll-a

concentrations (Figure 19). Based on these 

thresholds, 13% of lakes are oligotrophic, 

37% are mesotrophic, 30% are eutrophic, 

and 20% are hypereutrophic. The results 

also show that natural lakes tend towards 

mesotrophic conditions and man-made lakes 

towards eutrophic conditions. 

Many states and lake associations classify 

their lakes by trophic state using a variety 

of thresholds for nutrients (phosphorus 

or nitrogen), Secchi disk transparency, 

or chlorophyll-a, depending on the data 

available. For this assessment, NLA analysts, 

in consultation with a number of state and 

local lake experts, decided to base trophic 

state on chlorophyll-a concentrations. The 

group considered this indicator the most 

relevant and straightforward estimate of 

trophic state because it is based on direct 

measurements of live organisms, yet 

acknowledges that other indicators also could 

be used. Table 2 illustrates the percentages 

that would fall into the different trophic 

categories if different indicators were used. 

Total nitrogen and total phosphorus, (which 

ranked fourth and fifth in terms of how 

widespread excess levels are across the 

country) together or individually are primary 

drivers of eutrophication.

Table 2. Percent of U.S. lakes (natural and man-made) by trophic state, based on four alternative trophic state indicators.

Indicator Oligotrophic Mesotrophic Eutrophic Hypereutrophic

Chlorophyll-a 12.8 36.6 30.1 20

Secchi 

transparency 10.5 22.5 39.8 18.4

Total Nitrogen 22.1 37.5 22.0 18.4

Total Phosphorus 25.0 28.8 24.7 21.4

Figure 19. Trophic state of lakes in the lower continental U.S.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

46

HIGHLIGHT

Volunteer Power: 

Monitoring Lakes with Volunteers

Hundreds of organizations monitor lakes in the U.S. using 

trained volunteers. Some volunteer groups are run by state 

environmental agencies. Others are managed by local residential 

lake associations determined to protect the quality of their 

local lake, pond or reservoir. Universities, often as part of U.S. 

Department of Agriculture Cooperative Extension, manage a 

number of statewide lake volunteer monitoring programs. In some 

states, trained volunteers are the leading source of consistent, 

long-term lake data. Volunteer-collected lake data are widely used 

in state water quality assessment reports, identification of impaired 

waters, local decision making, and scientific study.

One national program designed to promote the use of 

volunteers in lake monitoring is the Secchi Dip-In (http://dipin.

kent.edu/index.htm). Run by limnologist Dr. Robert Carlson of Kent 

State University since 1994, the Dip-In encourages individuals 

who are members of a volunteer monitoring program to measure 

lake transparency on or around the 4th of July and report their 

results on a national website. These values are used to assess 

the transparency of volunteer-monitored waters in the U.S. and 

Canada. One goal of the Dip-In is to increase the number and 

interest of volunteers in environmental monitoring and to provide 

national level recognition of the work that they perform. 

Volunteer Monitoring and the National Lakes Assessment

 The relationship between lake volunteer monitoring and the National Lakes Assessment (NLA) is in 

its earliest stages. However, volunteers did participate in a few states where links between volunteer 

programs and state monitoring staff were strong. The Vermont Department of Environmental Conservation 

(DEC) conducted its own statistically valid assessment of 50 lakes including NLA-selected lakes, about half 

of which are also routinely sampled by volunteers in the DEC-managed Vermont Lay Monitoring Program. 

Volunteers were informed ahead of time when NLA sampling crews were going to arrive, and in some 

cases were able to provide boats for the crews as well as welcome local advice regarding lake navigation 

and access. In Rhode Island, some volunteers conducted side-by-side sampling with the NLA crews for 

later analysis and comparison using Rhode Island Watershed Watch methods. Volunteers observed the 

sampling, assisted crews with equipment, provided firsthand knowledge of local lakes, and contacted 

news media to provide publicity. In Michigan, at two lakes also monitored by Michigan’s Cooperative Lake 

Monitoring Program, volunteers sampled side-by-side with Michigan Department of Environmental Quality 

staff and NLA survey crews. Local newspaper reporters observed these monitoring events and provided 

press coverage of the volunteers working alongside the survey crews.

Volunteer monitors are important partners in the assessment and protection of the nation’s lakes, and 

state agencies and EPA should continue to explore pathways for improved communication and cooperation 

with volunteer programs in future surveys of the nation’s lakes.

A volunteer with the Michigan Cooperative 

Lakes Monitoring Program collects a water 

sample for chlorophyll analysis. 

Photo courtesy of Ralph Bednarz.
CHAPTER 6. ECOREGIONAL RESULTS

IN THIS CHAPTER

► Nationwide 

Comparisons 

► Northern 

Appalachians

► Southern 

Appalachians

► Coastal Plains

► Upper Midwest

► Temperate Plains

► Southern Plains

► Northern Plains

► Western Mountains

► Xeric

Photo courtesy of Tetra Tech
Chapter 6 Ecoregional Results

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

48

Chapter 6

Ecoregional Results

Taken individually, each lake is a reflection 

of its watershed. The characteristics of the 

watershed, i.e., its size relative to the lake, 

topography, geology, soil type, land cover, 

and human activities, together influence 

the amount and nature of material entering 

the lake. For example, a deep alpine lake 

located in a Rocky Mountain watershed will 

likely have clear, pristine water and little 

biological productivity. Conversely, a lake in a 

coastal plains watershed of the mid-Atlantic 

region, an area of nutrient-rich alluvial soils 

and a long history of human settlement, 

will more likely be characterized by high 

turbidity, high concentrations of nutrients and 

organic matter, prevalent algal blooms, and 

abundant aquatic weeds and other plants. 

Atmospheric deposition of airborne pollutants, 

as well as nutrients traveling in groundwater 

from hundreds of miles away, can affect the 

watershed and influence the lake condition. 

Lakes in high population areas are 

especially vulnerable. Combined sewer 

overflow and stormwater runoff can carry 

marked amounts of pollutants such as metals, 

excess sediment, bacteria, and most recently, 

pharmaceuticals. As a result, expectations 

and lake condition vary across the country.

Because of the diversity in landscape, it is 

important to assess waterbodies in their own 

geographical setting. The NLA was designed 

to report findings on an ecoregional scale. 

Ecoregions are areas that contain similar 

environmental characteristics and are defined 

by common natural characteristics such as 

climate, vegetation, soil type, and geology. 

By looking at lake conditions in these smaller 

ecoregions, decision-makers can begin to 

understand patterns based on landform and 

geography, and whether the problems are 

isolated in one or two adjacent regions or are 

widespread. 

Figure 20. Ecoregions used as part of the National Lakes Assessment.
Chapter 6 Ecoregional Results

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

49

Nationwide Comparisons

Biological Condition – Taxa Loss

 Regionally, the proportion of lakes with 

good biological condition ranges from 91% in 

the Upper Midwest to < 5% in the Northern 

Plains (Figure 21). In general, the glaciated 

and/or mountainous regions have the highest 

proportion of lakes exhibiting good biological 

condition, followed by Coastal Plains lakes. 

The Xeric west and Northern Plains exhibit the 

highest proportions of lakes in poor condition 

biologically. Forty nine percent of lakes are in 

poor biological condition in the Xeric region, 

while just under 85% of Northern Plains lakes 

are in poor biological condition. 

5 It is important to note that the geographic boundaries of the regionally-specific reference areas do not specifically match those of the nine 

ecoregions. More detailed information about how regional reference lakes were determined can be found in the Technical Report.

Figure 21. Biological condition (based on planktonic O/E taxa loss) across nine ecoregions.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

50

Habitat Stressors – 

Lakeshore Habitat

 In the NLA, habitat stress was assessed 

using four indicators: lakeshore habitat, 

shallow water habitat, physical habitat 

complexity and human disturbance. Of these, 

the most revealing indicator, based on the 

relative and attributable risk analyses, is 

lakeshore habitat. This analysis indicates that 

biological integrity of lakes is three times 

more likely to be poor when the lakeshore 

habitat area is classified as poor. Regionally, 

the proportion of lakes with poor lakeshore 

habitat ranges from a low of 25% in the 

Northern Appalachians to a high of 84% in the 

Northern Plains (Figure 22). Poor lakeshore 

habitat is most prevalent in the Plains and Xeric 

ecoregions.

Trophic Status

 Regionally, the proportion of lakes 

classified as oligotrophic, based on measures 

of chlorophyll-a, ranges from 54% in the 

Western Mountains to < 5% in the Temperate 

Plains (Figure 23). The highest proportion of 

mesotrophic waters are found in the Northern 

and Southern Appalachians, and the Upper 

Midwest. The proportion of eutrophic lakes is 

highest in the Coastal and Southern Plains. 

Hypereutrophic lakes are most prevalent in the 

Temperate Plains, where nearly 50% of lakes 

are classified hypereutrophic.

Recreational Suitability – Cyanobacteria 

(blue-green algae)

 Over 75% of lakes in the Western 

Mountains, Xeric west, Upper Midwest, and 

Northern and Southern Appalachians pose 

minimal risk of exposure to cyanobacteriaproduced toxins. The greatest proportions of 

lakes at high exposure risk (> 100,000 cells/L) 

occur in the Southern, Coastal, and Temperate 

Plains. The Northern Plains have over 50% of 

lakes in the moderate exposure risk category 

(Figure 24).

Figure 22. Habitat condition of the nation’s lakes across nine ecoregions based on lakeshore habitat.

Chapter 6 Ecoregional Results
51

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Figure 23. Trophic state across nine ecoregions (based on chlorophyll-a.)

Figure 24. Comparison of exposure to cyanobacteria risk across nine ecoregions.

Chapter 6 Ecoregional Results
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

52

Northern Appalachians 

The Landscape

 The Northern Appalachians ecoregion 

covers all of the New England states, most of 

New York, the northern half of Pennsylvania, 

and northeast Ohio. It encompasses New 

York’s Adirondack and Catskill Mountains and 

Pennsylvania’s mid-northern tier, including the 

Allegheny National Forest. Major waterbodies 

include Lakes Ontario and Erie, New York’s 

Finger Lakes, and Lake Champlain. There are 

5,226 lakes in the Northern Appalachians that 

are represented by the NLA, 54% of which 

are constructed reservoirs. The ecoregion 

comprises some 139,424 square miles (4.6% 

of the United States), with about 4,722 

square miles (3.4%) under federal ownership. 

Based on satellite images in the National Land 

Cover Dataset (1992), the distribution of 

land cover is 69% forested and 17% planted/

cultivated, with the remaining 14% of land in 

other types of cover.

 Many lakes in the region were created 

for the purpose of powering sawmills. During 

the 18th and early 19th centuries, lakes were 

affected by sedimentation caused by logging, 

farming, and damming of waterways. When 

agriculture moved west and much of eastern 

farmland converted back into woodlands, 

sediment yields declined in some areas. In 

many instances, lakes in what appears to 

be pristine forested settings are in fact still 

recovering from prior land use disturbances. 

In the mountainous regions of the Northern 

Appalachian ecoregion, many large reservoirs 

were constructed throughout the early 20th 

century for hydropower generation and/or 

flood control.

Findings

 A total of 93 of the selected NLA sites 

were sampled during the summer of 2007 to 

characterize the condition of lakes throughout 

the ecoregion. An overview of the NLA 

findings for Northern Appalachian lakes is 

shown in Figure 25. 

Biological Condition

 Fifty-five percent of lakes are in good 

biological condition based on planktonic 

O/E, and when using the diatom IBI, 67% of 

lakes in the ecoregion are in good biological 

condition relative to reference condition. 

Conversely, the percentages of lakes in poor 

condition are 15% and 10% based on the two 

analyses, respectively.

Trophic Status

 Based on chlorophyll-a, 26% of lakes 

are oligotrophic, 54% are mesotrophic, 17% 

are eutrophic, and only 3% are considered 

hypereutrophic.

Chapter 6 Ecoregional Results

Dick’s Pond in Massachusetts.

Photo courtesy of USEPA Region 1.
53

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Recreational Suitability

Using the indicators and World Health 

Organization guidelines described in Chapter 

3, most lakes in the Northern Appalachian 

ecoregion exhibit relatively low risk of 

exposure to cyanobacteria and associated 

cyanotoxins. Based on cyanobacterial counts, 

95% of lakes exhibit low exposure risk. 

Microcystin was present in 9% of lakes. 

Physical Habitat Stressors

Lakeshore habitat is considered good in 

66% of the lakes in this ecoregion. Given 

the long history of land use and settlement 

in this ecoregion, the shorelines of Northern 

Appalachian lakes exhibit relatively disturbed 

conditions due to human activities. Fiftyseven percent of lakes show moderate to high 

levels of lakeshore disturbance. 

Chemical Stressors

In contrast to physical habitat conditions, 

the majority of Northern Appalachian lakes 

exhibit high-quality waters based on the 

NLA chemical stressor indicators. Relative to 

regionally-specific reference expectations, 

total phosphorus and nitrogen, chlorophyll-a, 

and turbidity levels are considered good in 

80% or more of lakes in this ecoregion. Lakes 

are in good condition based on ANC and 

surface water DO levels when compared to 

nationally-consistent thresholds. 

Chapter 6 Ecoregional Results

Figure 25. NLA results for the Northern Appalachians. Bars show the percentage of lakes within a condition class for a given indicator. 

For Recreational Chlorophyll risk and Cyanobacteria risk, the percentage numbers indicate the risk of exposure to algal toxins associated 

with the presence of cholorphyll-a and cyanobacteria, not the risk of exposure to chlorophyll-a and cyanobacteria per se.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

54

Chapter 6 Ecoregional Results

Southern Appalachians 

The Landscape

The Southern Appalachians ecoregion 

stretches over 10 states, from northeastern 

Alabama to central Pennsylvania. Also 

included in this region are the interior 

highlands of the Ozark Plateau and the 

Ouachita Mountains in Arkansas, Missouri, 

and Oklahoma. The region covers about 

321,900 square miles (10.7% of the 

United States) with about 42,210 square 

miles (10.7%) under federal ownership. 

Many important public lands such as the 

Great Smoky Mountains National Park and 

surrounding national forests, the Delaware 

Water Gap National Recreation Area, 

the George Washington and Monongahela 

National Forests, and the Shenandoah 

National Park are located within the region. 

Topography is mostly hills and low mountains 

with some wide valleys and irregular plains. 

Piedmont areas are included within the 

Southern Appalachians ecoregion. 

Natural lakes are nearly non-existent 

in this ecoregion. The 4,690 lakes in the 

Southern Appalachians ecoregion represented 

by the NLA are all man-made. The 

configuration of the Southern Appalachian 

valleys has proven ideal for the construction 

of man-made lakes, and some of the nation’s 

largest hydro-power developments can be 

found in the Tennessee Valley. 

Findings

A total of 116 of the selected NLA 

sites were sampled during the summer of 

2007 to characterize the condition of lakes 

throughout the ecoregion. An overview of 

the NLA findings for lakes in the Southern 

Appalachians is shown in Figure 26. 

Biological Condition

 Forty-two percent of lakes are in good 

biological condition based on planktonic 

O/E and when using the diatom IBI, 63% of 

lakes in the ecoregion are in good biological 

condition relative to reference condition. 

Conversely, the percentages of lakes in poor 

condition are 31% and 13% based on the 

two analyses, respectively. The apparent 

difference between these two biological 

indices may suggest that the two indicators 

are responding to different stressors in lakes 

in this particular ecoregion. 

Trophic Status

Based on chlorophyll-a, 12% of lakes 

are oligotrophic, 46% are mesotrophic, 

17% are eutrophic, and 26% are considered 

hypereutrophic.

Recreational Suitability

While many lakes in the Southern 

Appalachians ecoregion exhibit relatively 

low risk of exposure to cyanobacteria and 

associated cyanotoxins, a quarter of lakes 

exhibit moderate risk levels based on 

chlorophyll-a and cyanobacteria values. 

Microcystin was present in 25% of lakes. 

Pennsylvania lake.

Photo courtesy of Frank Borsuk.
55

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Physical Habitat Stressors

 Lakeshore habitat is considered good in 

42% of the lakes in this ecoregion. Yet the 

shorelines of Southern Appalachians lakes 

indicate considerable lakeshore development 

pressure. Over 90% of lakes show moderate 

to high levels of lakeshore disturbance. 

Chemical Stressors

Based on the NLA chemical stressor 

indicators, a considerable proportion of 

Southern Appalachians lakes exhibit good 

quality waters. Total phosphorus and nitrogen 

are considered good in 66% and 68% of 

lakes, respectively. Relative to regionallyspecific reference expectations, chlorophyll-a

and turbidity levels are considered good 

in 72% or more of the man-made lakes in 

this ecoregion. Man-made lakes are in good 

condition based on ANC and surface water DO 

levels when compared to nationally consistent 

thresholds, although 9% of lakes were ranked 

poor due to low dissolved oxygen. 

Chapter 6 Ecoregional Results

Figure 26. NLA results for the Southern Appalachians. Bars show the percentage of lakes within a condition class for a given indicator. 

For Recreational Chlorophyll risk and Cyanobacteria risk, the percentage numbers indicate the risk of exposure to algal toxins associated 

with the presence of cholorphyll-a and cyanobacteria, not the risk of exposure to chlorophyll-a and cyanobacteria per se. 
Coastal Plains 

The Landscape

 The Coastal Plains ecoregion covers the 

Mississippi Delta and Gulf Coast, north along 

the Mississippi River to the Ohio River, all 

of Florida, eastern Texas, and the Atlantic 

seaboard from Florida to New Jersey. Total 

area is about 395,000 square miles (13% of 

the United States) with 25,890 square miles 

(6.6%) under federal ownership. Based on 

satellite images in the 1992 National Land 

Cover Dataset, the distribution of land cover 

is 39% forested, 30% planted/cultivated, 

and 16% wetlands, with the remaining 15% 

of land in other types of cover. Damming, 

impounding, and channelization in this 

ecoregion have altered the rate and timing of 

water flow and delivery to lakes. 

 A subset of major lakes of the region 

includes the Toledo Bend (TX) and 

Sam Rayburn Reservoirs (TX/LA), Lake 

Okeechobee (FL), Lake Marion (SC), and 

the massive lake-wetland complexes north 

of the Gulf Coast. The Coastal Plains is also 

home to a variety of lakes and ponds, such 

as Cape Cod kettleholes, New Jersey Pine 

Barren ponds, southeastern blackwater lakes, 

Carolina “Bays,” and the limestone-rich clear 

lakes of the Florida peninsula. A total of 7,009 

lakes and reservoirs in the Coastal Plains 

ecoregion are represented in the NLA, and 

69% of these are man-made.

Findings

 A total of 102 of the selected NLA sites 

were sampled during the summer of 2007 to 

characterize the condition of lakes throughout 

the ecoregion. An overview of the NLA 

findings for the Coastal Plains lakes is shown 

in Figure 27. 

Biological Condition

 Forty-seven percent of lakes are in good 

biological condition based on planktonic 

O/E, and when using the diatom IBI, 57% of 

lakes in the ecoregion are in good biological 

condition relative to reference condition. 

Conversely, the percentages of lakes in poor 

condition are 27% and 6% based on the two 

analyses, respectively

Trophic Status

 Based on chlorophyll-a, 6% of the lakes 

are mesotrophic, 60% are eutrophic, and 

34% are considered hypereutrophic. 

Recreational Suitability

 Lakes in the Coastal Plains ecoregion 

exhibit moderate risk of exposure to 

cyanobacteria and associated cyanotoxins. 

Based on cyanobacterial counts, 64% of lakes 

exhibited low exposure risk. Microcystin was 

present in 35% of lakes. 

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

56

Chapter 6 Ecoregional Results
57

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Physical Habitat Stressors

 Lakeshore habitat is considered good in 

22% of the lakes in this ecoregion. Moreover, 

the shorelines of the Coastal Plains lakes 

are highly disturbed, indicating considerable 

lakeshore development pressure in this 

region. About 84% of lakes show moderate to 

high levels of lakeshore human disturbance. 

Chemical Stressors

 Based on the NLA chemical stressor 

indicators, water quality is somewhat variable 

across the Coastal Plains. Total phosphorus 

and nitrogen are considered good in 48% and 

51% of lakes, respectively, and are poor in 

15% and 4% of lakes, respectively. Relative 

to regionally-specific reference expectations, 

chlorophyll-a concentrations are considered 

good in 65% of lakes, and turbidity levels 

are considered good in 85% of lakes in this 

ecoregion. Lakes are in good condition based 

on ANC and surface water DO levels when 

compared to nationally-consistent thresholds, 

although 13% of lakes were ranked fair due 

to low dissolved oxygen.

Chapter 6 Ecoregional Results

Figure 27. NLA findings for the Coastal Plains. Bars show the percentage of lakes within a condition class for a given indicator. For 

Recreational Chlorophyll risk and Cyanobacteria risk, the percentage numbers indicate the risk of exposure to algal toxins associated 

with the presence of cholorphyll-a and cyanobacteria, not the risk of exposure to chlorophyll-a and cyanobacteria per se. 
Upper Midwest 

The Landscape

 The Upper Midwest ecoregion covers 

most of the northern half and southeastern 

part of Minnesota, two-thirds of Wisconsin, 

and almost all of Michigan, extending about 

160,374 square miles (5.4% of the United 

States). A total of 15,562 lakes in the 

ecoregion are represented in the NLA, nearly 

all of which are of natural origin, reflecting 

the glaciation history of this region. Sandy 

soils dominate with relatively high water 

quality in lakes supporting warm and coldwater fish communities. Major lakes of the 

region include the Great Lakes (which, for 

design considerations, were not represented 

by the NLA), and also Lake of the Woods 

and Red Lake (MN). The glaciated terrain of 

this ecoregion is typically plains with some 

hill formations. The northern tier of this 

ecoregion has a very high number of smaller 

lakes, both drainage and seepage, which 

range widely in geochemical makeup. Much 

of the land is covered by national and state 

forest. Federal lands account for 15.5% of 

the area at about 25,000 square miles. Based 

on satellite images in the 1992 National Land 

Cover Dataset, the distribution of land cover 

is 40% forested, 34% planted/cultivated, 

and 17% wetlands, with the remaining 9% 

of land in other types of cover. Most of the 

landscape was influenced by early logging and 

agricultural activities.

Findings

 A total of 148 of the selected NLA sites 

were sampled during the summer of 2007 to 

characterize the condition of lakes throughout 

the ecoregion. An overview of the NLA 

findings for the Upper Midwest lakes is shown 

in Figure 28. 

Biological Condition

 Ninety-one percent of lakes are in good 

biological condition based on planktonic 

O/E, and when using the diatom IBI, 47% of 

lakes in the ecoregion are in good biological 

condition relative to reference condition. 

Conversely, the percentages of lakes in poor 

condition are 4% and 22% based on the two 

analyses, respectively. The difference between 

these two biological indices may suggest that 

the two indicators are responding to different 

stressors in lakes in this particular ecoregion.

Trophic Status

 Based on chlorophyll-a, 9% of lakes are 

oligotrophic, 54% are mesotrophic, 26% 

are eutrophic, and 10% are considered 

hypereutrophic. 

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

58

Chapter 6 Ecoregional Results

Minnesota prairie pothole lake.

Photo courtesy of Steve Heiskary.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

59

Recreational Suitability

 Lakes in the Upper Midwest exhibit 

relatively low risk of exposure to 

cyanobacteria and associated cyanotoxins. 

Based on cyanobacterial counts, 81% of lakes 

exhibited low exposure risk. Microcystin was 

present in 23% of lakes. 

Physical Habitat Stressors

 Lakeshore habitat is considered good 

in 54% of the lakes in this ecoregion. The 

shorelines of the Upper Midwest lakes, 

indicate considerable lakeshore development 

pressure. Forty-six percent of lakes show 

moderate to high levels of lakeshore human 

disturbance. 

Chemical Stressors

 Based on the NLA chemical stressor 

indicators, water quality is relatively good 

across the Upper Midwest. Total phosphorus 

and nitrogen are considered good in 66% and 

59% of lakes, respectively, and are poor in 

9% and 8%, of lakes respectively. Relative 

to regionally-specific reference expectations, 

chlorophyll-a concentrations are considered 

good in 68% of lakes, and turbidity levels 

are considered good in 77% of lakes in this 

ecoregion. Lakes are in good condition based 

on ANC and surface water DO levels when 

compared to nationally-consistent thresholds. 

Chapter 6 Ecoregional Results

Figure 28. NLA findings for the Upper Midwest. Bars show the percentage of lakes within a condition class for a given indicator. For 

Recreational Chlorophyll risk and Cyanobacteria risk, the percentage numbers indicate the risk of exposure to algal toxins associated 

with the presence of cholorphyll-a and cyanobacteria, not the risk of exposure to chlorophyll-a and cyanobacteria per se. 
Temperate Plains 

The Landscape

 The Temperate Plains ecoregion includes 

the open farmlands of Iowa; eastern North 

and South Dakota; western Minnesota; 

portions of Missouri, Kansas, and Nebraska; 

and the flat farmlands of western Ohio, 

central Indiana, Illinois, and southeastern 

Wisconsin. This ecoregion covers some 

342,200 square miles (11.4% of the United 

States), with approximately 7,900 square 

miles (2.3%) in federal ownership. The terrain 

consists of smooth plains, numerous small 

lakes, prairie pothole lakes, and wetlands. A 

total of 6,327 lakes in the Temperate Plains 

ecoregion are represented in the NLA, of 

which 75% are of natural origin. Lakes of 

this region are generally small, with over 

60% of lakes smaller than 100 hectares in 

size. Agriculture is the predominant land 

use. Based on satellite images in the 1992 

National Land Cover Dataset, the distribution 

of land cover is 9% forested and 76% 

planted/cultivated, with the remaining 15% of 

land in other types of cover.

Findings

 A total of 137 of the selected NLA sites 

were sampled during the summer of 2007 to 

characterize the condition of lakes throughout 

this ecoregion. An overview of the NLA 

findings for the Temperate Plains lakes is 

shown in Figure 29. 

Biological Condition

 One quarter, or 24%, of lakes are in 

good biological condition based on planktonic 

O/E, and when using the diatom IBI, 17% of 

lakes in the ecoregion are in good biological 

condition relative to reference condition. 

Conversely, the percentages of lakes in poor 

condition are 35% and 52% based on the two 

analyses, respectively.

Trophic Status 

 Based on chlorophyll-a, 2% of lakes are 

oligotrophic, 32% are mesotrophic, 21% 

are eutrophic, and 45% are considered 

hypereutrophic. 

Recreational Suitability

 Lakes in the Temperate Plains exhibit 

moderate risk of exposure to cyanobacteria 

and associated cyanotoxins. Based on 

cyanobacterial counts, 48% of lakes exhibited 

low exposure risk. Microcystin was present in 

67% of lakes. 

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

60

Chapter 6 Ecoregional Results

Sampling with a D-net for benthic macroinvertebrates. 

Photo courtesy of Great Lakes Environmental Center.
61

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Physical Habitat Stressors

Lakeshore habitat is considered good 

in 56% of the lakes in this ecoregion. The 

shorelines of the Temperate Plains lakes 

exhibit human activity disturbances, urban 

development, and agricultural pressures 

in this region. Sixty percent of lakes show 

moderate to high levels of lakeshore human 

disturbance. 

Chemical Stressors

Based on the NLA chemical stressor 

indicators, water quality in the Temperate 

Plains is somewhat variable. Total phosphorus 

and nitrogen are considered good in 38% and 

27% of lakes, respectively, and are poor in 

30% and 40% of lakes, respectively. Relative 

to regionally-specific reference expectations, 

chlorophyll-a concentrations are considered 

good in 56% of lakes, and turbidity levels 

are considered good in 84% of lakes in 

this ecoregion. Lakes are generally in good 

condition based on ANC and surface water DO 

levels when compared to nationally-consistent 

thresholds. However, dissolved oxygen is fair 

in 12% of lakes. 

Chapter 6 Ecoregional Results

Figure 29. NLA findings for the Temperate Plains. Bars show the percentage of lakes within a condition class for a given indicator. For 

Recreational Chlorophyll risk and Cyanobacteria risk, the percentage numbers indicate the risk of exposure to algal toxins associated 

with the presence of cholorphyll-a and cyanobacteria, not the risk of exposure to chlorophyll-a and cyanobacteria per se. 
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

62

Southern Plains

The Landscape

The Southern Plains ecoregion covers 

approximately 405,000 square miles (13.5% 

of the United States) and includes central 

and northern Texas; most of western 

Kansas and Oklahoma; and portions of 

Nebraska, Colorado, and New Mexico. The 

terrain is a mix of smooth and irregular 

plains interspersed with tablelands and low 

hills. Most of the great Ogallala aquifer lies 

underneath this region. 

Based on satellite images in the 1992 

National Land Cover Dataset, the distribution 

of land cover is 45% grassland, 32% planted/

cultivated, and 14% shrubland, with the 

remaining 9% of land in other types of 

cover. The Great Prairie grasslands, which 

once covered much of the Southern Plains 

region, are considered the most altered and 

endangered large ecosystem in the United 

States. About 90% of the original tall grass 

prairie has been replaced by other vegetation 

or land use. Federal land ownership in the 

region totals about 11,980 square miles or 

approximately 3% of the total, the lowest 

share of all NLA aggregate ecoregions. A 

total of 3,148 lakes in the Southern Plains 

ecoregion are represented in the NLA, 97% of 

which are constructed reservoirs. 

Findings

A total of 128 of the selected NLA sites 

were sampled during the summer of 2007 to 

characterize the condition of lakes throughout 

this ecoregion. An overview of the NLA 

findings for the Southern Plains lakes is 

shown in Figure 30. 

Biological Condition

Thirty-four percent of lakes are in good 

biological condition based on planktonic 

O/E, and when using the diatom IBI, 41% of 

lakes in the ecoregion are in good biological 

condition relative to reference condition. 

Conversely, the percentages of lakes in poor 

condition are 29% and 23% based on the two 

analyses, respectively.

Trophic Status

Based on chlorophyll-a, 9% of lakes are 

oligotrophic, 14% are mesotrophic, 51% 

are eutrophic, and 26% are considered 

hypereutrophic.

Recreational Suitability

Lakes in the Southern Plains exhibit 

moderate risk of exposure to cyanobacteria 

and associated cyanotoxins. Based on 

cyanobacterial counts, 57% of lakes exhibit 

low exposure risk. Microcystin was present in 

21% of lakes. 

Chapter 6 Ecoregional Results

Comanche Creek Reservoir. 

Photo courtesy of Texas Commission of Environmental Quality.
63

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Physical Habitat Stressors

Lakeshore habitat is fair to poor in 63% 

of the lakes in this ecoregion. The shorelines 

of Southern Plains lakes exhibit considerable 

disturbed conditions due to human activities. 

Ninety percent of lakes show moderate to 

high levels of lakeshore human disturbance.

Chemical Stressors

Water quality, based on the NLA chemical 

stressor indicators, is relatively good in 

the Southern Plains. Total phosphorus and 

nitrogen are considered good in 73% and 

55% of lakes, respectively, and are poor in 

7% and 20% of lakes, respectively. Relative 

to regionally-specific reference expectations, 

chlorophyll-a concentrations and turbidity 

levels are considered good in over 80% of 

lakes in this ecoregion. Lakes are generally 

in good condition based on ANC and surface 

water DO levels when compared to nationallyconsistent thresholds. However, dissolved 

oxygen is fair in 12% of lakes. 

Chapter 6 Ecoregional Results

Figure 30. NLA findings for the Southern Plains. Bars show the percentage of lakes within a condition class for a given indicator. For 

Recreational Chlorophyll risk and Cyanobacteria risk, the percentage numbers indicate the risk of exposure to algal toxins associated 

with the presence of cholorphyll-a and cyanobacteria, not the risk of exposure to chlorophyll-a and cyanobacteria per se. 
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

64

Northern Plains 

The Landscape

The Northern Plains ecoregion covers 

approximately 205,084 square miles (6.8% 

of the United States), including western 

North and South Dakota, Montana east of the 

Rocky Mountains, northeast Wyoming, and a 

small section of northern Nebraska. Federal 

lands account for 52,660 square miles or 

a relatively large 25.7% share of the total 

area. Terrain of the area is irregular plains 

interspersed with tablelands and low hills. 

This ecoregion is the heart of the Missouri 

River system and is almost exclusively within 

the Missouri River’s regional watershed. 

Several major reservoirs are along the 

Missouri River mainstem, including Lake Oahe 

and Lake Sacajawea. The total surface area 

of lakes in this region is growing owing to 

increased runoff coupled with flat topography. 

Devil’s Lake (ND) is one example, which in 

1993 had a surface area of 44,000 acres and 

presently covers in excess of 130,000 acres. 

Based on satellite images in the 1992 

National Land Cover Dataset, the distribution 

of land cover is 56% grassland and 30% 

planted/cultivated, with the remaining 14% 

of land in other types of cover. A total of 

2,660 lakes in the Northern Plains ecoregion 

are represented in the NLA, 77% of which are 

of natural origin. 

Findings

A total of 65 of the selected NLA sites 

were sampled during the summer of 2007 to 

characterize the condition of lakes throughout 

this ecoregion. An overview of the NLA 

findings for the Northern Plains ecoregion is 

shown in Figure 31. 

Biological Condition

The Northern Plains has the highest 

proportion of lakes in poor biological condition 

of any of the ecoregions. Ninety percent of 

lakes are in poor biological condition based 

on planktonic O/E, and 88% are in poor 

condition based on the diatom IBI.

Trophic Status

Based on chlorophyll-a, 8% of lakes are 

oligotrophic, 22% are mesotrophic, 48% 

are eutrophic, and 22% are considered 

hypereutrophic. 

Recreational Suitability

Lakes in the Northern Plains exhibit the 

greatest risk of exposure to cyanobacteria 

and associated cyanotoxins of all ecoregions. 

Based on cyanobacterial counts, 59% of 

lakes exhibit moderate to high exposure risk. 

Microcystin was present in 75% of lakes.

Physical Habitat Stressors

Lakeshore habitat cover is considered 

good in only 7% of the lakes in this 

ecoregion. Regionally-specific habitat 

reference condition for the Northern Plains 

Chapter 6 Ecoregional Results

A Northern Plains lake. 

Photo courtesy of Tetra Tech.
65

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

is comprised of grasses and shrubs and is 

different from many of the other ecoregions 

where expectations include a tree layer in 

addition to a middle and lower story. Even 

taking into account the regional-specific 

expectations, the NLA data show that the 

Northern Plains lake shorelines exhibit very 

high levels of disturbance due to human 

activities. Ninety-nine percent of lakes show 

moderate or high levels of lakeshore human 

disturbance. 

Chemical Stressors

Based on the NLA chemical stressor 

indicators, water quality is variable in 

the Northern Plains. In general, lakes in 

this ecoregion tend to have high levels of 

nutrients. Relative to regionally-specific 

reference expectations, total phosphorus 

concentrations are considered poor in 71% of 

lakes, while total nitrogen concentrations are 

considered poor in 91% of lakes. By contrast, 

based on chlorophyll-a, 78% of lakes are 

considered in good condition, and turbidity 

levels are good in 70% of lakes. 

In the Northern Plains ecoregion, the 

traditional limnological concept that biomass 

production is controlled simply by nutrient 

concentrations may not apply. Lakes are 

generally in good condition based on ANC and 

surface water DO levels when compared to 

nationally-consistent thresholds.

Chapter 6 Ecoregional Results

Figure 31. NLA findings for the Northern Plains. Bars show the percentage of lakes within a condition class for a given indicator. For 

Recreational Chlorophyll risk and Cyanobacteria risk, the percentage numbers indicate the risk of exposure to algal toxins associated 

with the presence of cholorphyll-a and cyanobacteria, not the risk of exposure to chlorophyll-a and cyanobacteria per se. 
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

66

Western Mountains

The Landscape

The Western Mountains ecoregion 

includes the Cascade, Sierra Nevada, 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. This 

region covers approximately 397,832 square 

miles, with about 297,900 square miles or 

74.8% classified as federal land — the highest 

proportion of federal property among the 

nine aggregate ecoregions. The terrain of this 

area is characterized by extensive mountains 

and plateaus separated by wide valleys and 

lowlands. Lakes in this region, in particular 

those within smaller, high-elevation drainages, 

are very low in nutrients, are very dilute in 

other water chemistry constituents (e.g., 

calcium). Therefore biological productivity 

in these systems is limited in their natural 

condition. Accordingly, these smaller, high 

elevation lakes are very sensitive to effects of 

human disturbances.

Lakes and ponds of the region range 

from large mainstem impoundments to highmountain caldera and kettle lakes. Most 

famous among these mountain caldera lakes 

are Crater Lake (OR) and Lake Yellowstone 

(WY). The single deepest measurement of 

Secchi disk transparency recorded during 

the NLA – 122 feet (37 meters) – occurred 

in this ecoregion in Waldo Lake (OR). Based 

on satellite images in the 1992 National Land 

Cover Dataset, the distribution of land cover 

is 59% forest, 32% shrubland and grassland 

with the remaining 9% of land in other types 

of cover. A total of 4,122 lakes in the Western 

Mountains ecoregion are represented in the 

NLA, 67% of which are of natural origin. 

Findings

A total of 155 of the selected NLA sites 

were sampled during the summer of 2007 to 

characterize the condition of lakes throughout 

this ecoregion. An overview of the NLA 

findings for the Western Mountains lakes is 

shown in Figure 32. 

Biological Condition

Fifty-eight percent of lakes are in good 

biological condition based on planktonic 

O/E, and when using the diatom IBI, 50% of 

lakes in the ecoregion are in good biological 

condition relative to reference condition. 

Conversely, the percentages of lakes in poor 

condition are 11% and 3% based on the two 

analyses, respectively.

Trophic Status

Based on chlorophyll-a, 54% of lakes 

are oligotrophic, 26% are mesotrophic, 

16% are eutrophic, and 4% are considered 

hypereutrophic. The Western Mountains 

ecoregion has the highest proportion of 

oligotrophic lakes (very clear with low 

productivity) of any of the ecoregions across 

the country.

Chapter 6 Ecoregional Results

Survey crews travel on horseback to reach remote lakes. 

Photo courtesy of Tetra Tech.
67

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Recreational Suitability

Lakes in the Western Mountains exhibit 

the lowest risk of exposure to cyanobacteria 

and associated cyanotoxins of all ecoregions. 

Based on cyanobacterial counts, 96% of lakes 

exhibit low exposure risk. Microcystin was 

present in only 5% of lakes. 

Physical Habitat Stressors

Lakeshore habitat is considered good in 

48% of the lakes in this ecoregion. Similar 

to the Northern Plains, regionally-specific 

reference conditions were modified in this 

ecoregion to account for sparse natural 

vegetation cover types expected in this 

mountainous region. With respect to human 

activity along the lakeshore, this ecoregion 

has the lowest percentage of lakes with 

human disturbance of all regions. Forty-three 

percent of lakes show moderate to high levels 

of lakeshore human disturbance.

Chemical Stressors

Based on the NLA chemical stressor 

indicators, water quality in the Western 

Mountains is consistently in the medium 

range. Relative to regionally-specific reference 

expectations, total phosphorus concentrations 

are considered good in 56% of lakes, fair 

in 11%, and poor in 33%. Total nitrogen 

concentrations are considered good in 52% 

of lakes, fair in 10%, and poor in 38%. Based 

on chlorophyll-a, 48% of lakes are considered 

in good condition, 17% in fair condition, and 

35% in poor condition. Turbidity levels are 

good in 56% of lakes and fair in 31% of lakes. 

Lakes are in good condition based on ANC and 

surface water DO levels when compared to 

nationally-consistent thresholds. 

Chapter 6 Ecoregional Results

Figure 32. NLA findings for the Western Mountains. Bars show the percentage of lakes within a condition class for a given indicator. For 

Recreational Chlorophyll risk and Cyanobacteria risk, the percentage numbers indicate the risk of exposure to algal toxins associated with the 

presence of cholorphyll-a and cyanobacteria, not the risk of exposure to chlorophyll-a and cyanobacteria per se. 
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

68

Xeric

The Landscape

The Xeric ecoregion covers the largest 

area of all NLA aggregate ecoregions. This 

ecoregion covers portions of eleven western 

states and all of Nevada for a total of about 

636,583 square miles (21.2% of the United 

States). Some 453,000 square miles or 

71.2% of the land is classified as federal 

lands, including large tracts such as the 

Grand Canyon National Park (AZ), Big Bend 

National Park (TX), and the Hanford Nuclear 

Reservation (WA). The Xeric ecoregion is 

comprised of a mix of physiographic features. 

The region 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. All of the non-mountainous 

area of California falls in the Xeric ecoregion. 

In southern areas, dry conditions and 

water withdrawals produce internal drainages 

that end in saline lakes or desert basins 

without reaching the ocean. Large lakes in 

the southwestern canyon regions are the 

products of large dam construction projects. 

Water levels in these lakes fluctuate widely 

due to large-scale water removal for cities 

and agriculture. Recently, shifts in climate and 

rainfall patterns have resulted in considerably 

reduced water levels on several of the major 

Colorado River impoundments including Lake 

Mead, Lake Powell, and Lake Havasu. Based 

on satellite images in the 1992 National Land 

Cover Dataset, the distribution of land cover is 

61% shrubland and 15% grassland, with the 

remaining 24% of land in other types of cover. 

A total of 802 lakes in the Xeric ecoregion are 

represented in the NLA, 91% of which are 

constructed reservoirs.

Findings

A total of 84 of the selected NLA sites 

were sampled during the summer of 2007 to 

characterize the condition of lakes throughout 

the ecoregion. An overview of the NLA results 

for the Xeric ecoregion is shown in Figure 33. 

Biological Condition

Thirty-seven percent of lakes are in good 

biological condition based on planktonic 

O/E, and when using the diatom IBI, 70% of 

lakes in the ecoregion are in good biological 

condition relative to reference condition. 

Conversely, the percentages of lakes in poor 

condition are 49% and 6% based on the two 

analyses, respectively. The difference between 

these two biological indices may suggest that 

the two indicators are responding to different 

stressors in lakes in this particular ecoregion. 

Trophic Status

Based on chlorophyll-a, 22% of lakes 

are oligotrophic, 27% are mesotrophic, 

22% are eutrophic, and 28% are considered 

hypereutrophic.

Chapter 6 Ecoregional Results

Lewis Lake, NM. 

Photo courtesy of Tetra Tech. 
Figure 33. NLA findings for the Xeric. Bars show the percentage of lakes within a condition class for a given indicator. For Recreational 

Chlorophyll risk and Cyanobacteria risk, the percentage numbers indicate the risk of exposure to algal toxins associated with the 

presence of cholorphyll-a and cyanobacteria, not the risk of exposure to chlorophyll-a and cyanobacteria per se. 

Recreational Suitability

Lakes in the Xeric ecoregion exhibit 

low to moderate risk of exposure to 

cyanobacteria and associated cyanotoxins. 

Based on cyanobacterial counts, 82% of 

lakes exhibit low exposure risk. Microcystin 

was present in 23% of lakes. 

Physical Habitat Stressors

Lakeshore habitat is considered good 

in 34% of the lakes in this ecoregion. In 

the Xeric ecoregion, regionally-specific 

reference conditions were modified to 

account for sparse natural vegetation cover 

types expected in this dry region. Lakes 

in the Xeric ecoregion exhibit considerably 

disturbed conditions due to human activities. 

Over 89% of lakes show moderate to high 

levels of lakeshore human disturbance.

Chemical Stressors

Like the Western Mountains ecoregion 

to the north, the water quality in the Xeric 

ecoregion is in the medium range. Relative 

to regionally-specific reference expectations, 

total phosphorus concentrations are 

considered good in 45% of lakes, fair in 

28%, and poor in 28%. Total nitrogen 

concentrations are considered good in 

40% of lakes, fair in 57%, and poor in 

3%. Based on chlorophyll-a, 50% of lakes 

are considered in good condition, 21% in 

fair condition, and 29% in poor condition. 

Turbidity levels are good in 41% of lakes, 

and fair in 39%. Lakes are good condition 

based on ANC and surface water DO levels 

when compared to nationally-consistent 

thresholds. 

6869

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Chapter 6 Ecoregional Results
Partnerships for a Statewide Assessment 

of Lake Condition

Steve Heiskary

Minnesota Pollution Control Agency

 In 2007, the Minnesota Pollution Control Agency (MPCA) 

along with the Minnesota Department of Natural Resources 

(MDNR) led the State’s participation in USEPA’s National Lakes 

Assessment survey. Various other collaborators were engaged in 

this study as well, including the U.S. Forest Service (USFS), the 

Minnesota Department of Agriculture (MDA), and U.S. Geological 

Survey (USGS). MPCA and MDNR combined on initial planning 

of the survey and conducted the vast majority of the sampling. 

USFS staff were instrumental in sampling remote lakes in the 

northeastern Boundary Waters Canoe Area Wilderness.

 Minnesota was assigned 41 lakes as a part of the original draw 

of lakes for the national survey – the most of any of the lower 

48 states. The State then chose to add nine additional lakes 

(randomly selected) to the survey to yield the 50 lakes needed 

for statistically-based statewide estimates of lake condition. In 

addition to the 50 lakes, three reference lakes were later selected 

and sampled by USEPA as a part of the overall NLA effort. 

As part of its statewide assessment, Minnesota opted to add several measurements of unique interest 

to its overall state program. Examples of these add-ons are: pesticides; water mercury; sediment analysis 

of metals, trace organics and other indicators; macrophyte species richness; fish-based lake Index of 

Biotic Integrity (IBIs); and microcystin (at the index site and at a random near-shore site). A few of the 

findings are highlighted here. All of the reports completed to date can be found at: http://www.mpca.

state.mn.us/water/nlap.html.

Pesticides

With the exception of the corn herbicide atrazine, pesticide degradates were more frequently detected 

than were the parent compounds. Possibly more of these parent compounds may have initially been 

present in a greater number of lakes, but had degraded prior to sampling. Alternately, parent compounds 

may have degraded early in the process, with degradates being subsequently transported to the lakes via 

overland runoff. Since the peak pesticide application period is late spring to early summer, mid-summer 

(July – August) lake sampling may have allowed ample time for degradation products to reach affected 

lakes. MDA was a key collaborator in this effort and conducted the pesticide analysis.

HIGHLIGHT

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

70
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

71

Mercury levels

Measurement of total mercury (THg) and methyl mercury (MeHg) concentrations indicate that 

high levels of THg and MeHg are distributed throughout the state. The northeastern region has higher 

THg and MeHg concentrations compared to the southwestern region, although the MeHg fraction may 

actually be somewhat higher in the southwestern region. Otherwise, high THg and MeHg concentrations 

are distributed throughout the range of NLA lakes. These data can be used as a baseline against which 

to evaluate the efficacy of mercury emissions controls in MN. The USGS was an important partner in this 

effort 

Aquatic Macrophytes

Plant species richness was assessed at ten 

random near-shore sites on each lake. Generally, 

species richness increases from south to north 

peaking in the north central portion of the State 

before decreasing in the northeastern arrowhead 

region. The general trend of increasing species 

richness from north to south can be explained 

by water clarity, water chemistry, and human 

disturbance, and reaffirms previous observations. 

The decrease in species richness in the northeastern 

portion of the state can be attributed to tannin 

stained waters and rocky substrate associated 

with Canadian Shield lakes located throughout this 

region. 

Continuing Partnerships

Minnesota also is collaborating on a regional 

assessment of lakes in the Prairie Pothole Region 

with the states of North Dakota, South Dakota, 

Montana and Iowa and EPA Regions V and VIII. This 

collaboration will expand applications of statisticallyderived data and serve to enhance state, regional 

and national lake assessment efforts.

Atrazine

Deisopropylatrazine

Desethyatrazine MetolachlorMetolachlor 

ESA

Metolachlor 

OXA

Detection present non-detect present present present present

Detection freq. 87% 2% 64% 4% 27% 7%

Detection of Pesticides and Pesticide Degradates in Minnesota Lakes
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

72
CHAPTER 7. CHANGES AND TRENDS

Photo courtesy of Great Lakes Environmental Center

IN THIS CHAPTER

► Subpopulation Analysis of Change – National 

Eutrophication Study

► Subpopulation Analysis – Trends in Acidic Lakes 

in the Northeast

► Sediment Core Analysis
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

74

Chapter 7

Changes and Trends

Among the long term goals of the National 

Aquatic Resource Surveys is the detection 

of changes and trends in both the condition 

of our Nation’s aquatic resources and in the 

stressors impacting them. Trends in particular 

can be critical for policy makers i.e., whether 

policy decisions have been effective or 

whether a different approach is needed to 

achieve important water quality goals.

This first survey of lakes and reservoirs 

provides clear information on current status 

and serves as the baseline for future changes 

and trends analyses. At this early stage the 

National Lakes Assessment is, however, 

able to incorporate three ancillary analyses 

to provide a cursory look at what changes 

have occurred. Over time, EPA intends to use 

further analysis and future surveys to start 

the trends analyses.

The first indication of change comes from 

the analysis of a subset of lakes surveyed 

in the 1970’s and again in 2007. Between 

1972 and 1976 the Agency and the states 

implemented the National Eutrophication 

Survey (NES) – a survey that included more 

than 800 lakes. The NLA was designed to 

allow for the comparison of some of the same 

lakes. 

The second example of change is based 

on data in a regional study of acidic lakes in a 

subpopulation of lakes, i.e., the northeastern 

U.S. Finally, a third examination of change 

involves the evaluation of cores from the 

lake sediments. By examining different cross 

sections within the sediment core and the 

microscopic diatoms present, analysts can 

infer past conditions in each lake.

Subpopulation Analysis

- National Eutrophication Survey

Between 1972 and 1976, EPA conducted 

the National Eutrophication Survey. This 

study was designed to assess the trophic 

condition (defined as nutrient enrichment) 

of lakes influenced by domestic wastewater 

treatment plants (WWTP). The purpose of the 

survey was to measure nutrient inputs from 

all sources in the watershed relative to those 

of the WWTP source to determine if WWTP 

upgrades might be successful in modifying the 

lake or reservoir trophic state. While national 

in scope, it was unlike the NLA in that it was 

not probability-based. Instead it targeted 

a specific set of 800 wastewater impacted 

lakes.

For the NLA, a subset of 200 lakes from 

the 1972-1976 NES survey was randomly 

selected using the same probability design 

principles from the broader survey. This 

allowed the condition of all 800 lakes from 

the original NES survey to be inferred from 

Chapter 7 Changes and Trends
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

75

the subsample of 200 lakes sampled in 

2007. The phosphorus levels, chlorophyll-a

concentrations, and trophic condition of 

the NES population in 2007 could then be 

compared to what was observed in the 1970s 

to determine how these metrics have changed 

over the last thirty-plus years.

When making comparisons between then 

and now, some design differences between 

the two studies must be considered. NLA 

sampling consisted of a single, mid-summer 

integrated water sample at the deepest spot 

in the lake and from just below the surface to 

a depth of up to 2m (a sampling tube). The 

NES sampling consisted of sampling several 

sites on the lake as well as the inlets and 

outlets. NES sampling also included a site 

at the perceived deepest spot in the lake. 

Sampling was done with a depth-specific 

sampler (bottle) at just below the surface and 

at 1-2m depth intervals. Analysts compared 

the integrated sample NLA chlorophyll 

concentrations and NES samples taken at the 

site nearest the NLA site and from depth(s) 

that most nearly mimicked the depth of the 

NLA integrated depth sample. The accuracy 

and precision of chemical analytical results 

were considered comparable to each other 

based on the methods and the quality 

assurance of both surveys.

The NLA analysts looked at changes 

in the NES lakes over the past thirty-plus 

years using two approaches: by comparing 

concentration levels of key indicators and 

by examining trophic status. In both cases, 

researchers were able to estimate the number 

and percentage of NES lakes that showed 

a change since the original sampling in the 

1970s. It is worth noting that this type of 

analysis provides an estimate of net change, 

but little information on change in individual 

lakes.

Phosphorus levels have decreased in more 

than 50% of the NES lakes (403) and for 24% 

(189) no change was detected. An increase 

in phosphorus levels was seen in 26% of the 

lakes (207) (Figure 34). 

Trophic status based on chlorophyll-a also 

changed (Figure 35). Trophic status improved 

in 26% (184) of the lakes, and remained 

Chapter 7 Changes and Trends

Figure 34. Proportion of NES lakes that 

exhibited improvement, degradation, or no 

change in phosphorus concentration based 

on the comparison of the 1972 National 

Eutrophication Survey and the 2007 National 

Lakes Assessment

Figure 35. Proportion of NES lakes that 

exhibited improvement, degradation, 

or no change in trophic state based on 

the comparison of the 1972 National 

Eutrophication Survey and the 2007 National 

Lakes Assessment.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

76

unchanged in over half (51% or 408 lakes) 

of the NES lakes. Trophic state degraded in 

23% (208) of the NES lakes. Specifically, 

using chlorophyll-a as the indicator of trophic 

state, 49% of the lakes (394 lakes) in NES 

were classified as hypereutrophic in 1972. In 

2007, that number had fallen to 35% (279) of 

the lakes. In 1972, just over 5% of the lakes 

were classified as oligotrophic and by 2007, 

over 14% of the lakes (117) were classified 

as oligotrophic (Figure 36).

Subpopulation Analysis - Trends 

in Acidic Lakes in the Northeast

A similar approach to assessing changes 

and trends was taken for lakes that are either 

acidic or sensitive to acidification as part of 

EPA’s EMAP Temporally Integrated Monitoring 

of Ecosystems/Long Term Monitoring (TIME/

LTM) program. During the 1980s, the National 

Surface Water Survey was conducted on 

lakes in acid sensitive regions across the 

country. Again, EPA was able to make some 

comparisons. The NLA results show that 

acidification of lakes affects a very small 

number of lakes nationally. However, in 

certain regions of the country, the problem 

is of concern, particularly when lakes smaller 

than 10 acres (4 hectares) are included. 

Between the early 1990s and 2005, 

the acid neutralizing capacity in lakes in 

the Adirondack Mountains increased to a 

degree where many water bodies that were 

considered “chronically acidic” in the early 

1990s were no longer classified as such in 

2005 (Figure 37). Specifically, between 1991-

1994 and 2005, the percent of chronically 

acidic waterbodies decreased in the 

Adirondack Mountains from 13.0% to 6.2%. 

Additionally, acid-sensitive lakes in New 

England were beginning to show a decrease in 

acidity. The percent of chronically acidic lakes 

in this region decreased from 5.6% in 1991-

1994 to 4.3% in 2005. This trend suggests 

that lakes in these two regions are beginning 

to recover from acidification, though acidic 

surface waters are still found in these regions.

The trend of increasing ANC in lakes 

in the Adirondack Mountains and New 

England between the early 1990s and 

2005 corresponds with a decrease in 

acid deposition in each of these regions 

and reduced air emissions of the main 

components to acid deposition, which are 

sulfur dioxide and nitrogen oxides.

Sediment Core Analysis

In the third examination of change, the 

NLA incorporated paleolimnological analyses, 

a technique that uses lake sediment cores 

to obtain insights about past conditions. NLA 

analysts looked at thin slices of sediment 

cores and identified diatom silica casings. 

The community of diatoms present in 

each slice gives clues to the chemical and 

physical conditions in the lake when that 

Chapter 7 Changes and Trends

Figure 36. Percentage and number of NES lakes estimated in each of four 

trophic classes in 1972 and in 2007 based on chlorophyll-a concentrations.
77

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

layer was deposited. Models have been 

developed to relate the diatom community 

to lake chemistry characteristics, such 

as total phosphorus, and to lake physical 

characteristics, such as clarity. Using these 

relationships, the diatoms in deeper layers of 

the sediment were identified and the chemical 

conditions present at that point in time 

were inferred. This technique was used very 

effectively during studies of acidification in 

lakes during the 1980s. Individual states and 

other organizations have also used sediment 

cores in this manner on more localized/

regional scales to improve our understanding 

of what lakes were like in the past. 

EPA piloted this technique for application 

at a national scale to examine temporal 

change in a subset of lakes included in 

the NLA. In the field, the top layer of the 

sediment core was collected along with a 

layer deep in the core. Unfortunately, EPA 

was unable to date the sections of the core 

to confirm their age. Instead, NLA analysts 

used independent techniques, their own 

expertise, and the knowledge of regional 

experts to determine whether the cores 

were sufficiently deep for NLA purposes. The 

Agency acknowledges that this approach is a 

less reliable means of estimating the age of 

the cores. 

For man-made lakes the bottom layer 

of the sediment cores was not collected 

because it was presumed sediment cores in 

these more recent lakes would not represent 

a pre-industrial condition. Three hundred 

ninety-two lakes, representing 34% of the 

target population, were in this category and 

also were not evaluated. In addition, 334 

lakes, representing about 22% of the target 

population, were not evaluated because 

the core length was insufficient. In the end, 

change estimates were possible for 426 lakes, 

representing 55% of the target population.

Even though the percentage of target 

population is less than optimum, some 

information can be gleaned from the data. 

Results from the cores showed that an 

estimated 17% of lakes in the lower 48 states 

exhibited no significant change in inferred 

total phosphorus between the bottom of the 

core and the top of the core. A decrease 

in total phosphorus was estimated to have 

Chapter 7 Changes and Trends

Figure 37. Change in percentage of chronically acidic lakes in the 

Adirondack Mountains and New England.

Slicing off the top layer of the sediment core for diatom 

analysis. Photo courtesy of Frank Borsuk.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

78

occurred in 12% of the lakes while almost 7% 

of lakes were estimated to have experienced 

an increase in total phosphorus. The 

pattern in changes for total nitrogen differs 

somewhat. Nationally, the percentage of lakes 

showing no change between the top and 

bottom of the core is less than 5%. Sixteen 

percent of the lakes showed an increase in 

total nitrogen while 18% showed a decrease 

in total nitrogen. 

 The difference between the top and 

bottom of the sediment cores suggests that 

many lakes may have lower total phosphorus 

and total nitrogen levels now than they once 

did. Without dating the cores, however, 

more information and analysis are needed in 

explaining these results.

While results from this approach are 

presented below, further analyses will be 

necessary to determine if sediment core 

dating should be included in future lake 

surveys. Issues for consideration include 

evaluating:

• Whether the approach used is sufficiently 

robust to identify cores reaching preindustrial times across the country;

• Whether the assessment of change 

in a relatively small subset of lakes merits 

the effort expended in the context of a 

national survey; and

• Whether alternative coring and/or dating 

approaches should be considered for 

future iterations of the NLA.

Chapter 7 Changes and Trends

Photos courtesy of USEPA Region I Measuring lake depth. 
 

HIGHLIGHT

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

79

Climate Impacts on Lakes

Warmer Temperatures and Lake Condition

The preponderance of information indicates that the planet is warming and significant changes in 

climate are expected around the globe. The International Panel on Climate Change (IPCC) unequivocally 

attributes the climate change to human activities that have increased greenhouse gases in the 

atmosphere. The United States alone saw an increase 

of 1° (F) over the last century. Most of the warming 

has occurred in the last three decades and the largest 

observed warming across the country has taken place 

in the winter months. In southern areas, surface water 

temperatures are surpassing those of air temperatures, 

while in the north, there is ample evidence of earlier 

ice-out dates. For lakes, these changes will impact 

reservoirs and drinking water sources, hydroelectric 

power facilities, irrigation regimes, shipping and 

navigation, and recreational opportunities. From an 

ecosystem standpoint, warmer lakes will result in 

changes in water depth, thermal regime, nutrient 

loading, retention time, mixing and oxygen availability, 

and suspended sediments – all of which will alter 

habitat suitability and lake productivity.

Changes in the Upper Midwest — The Great Lakes

While scientists generally agree that the nation will get slightly wetter over the next century, 

precipitation trends at a regional level are uncertain. In many areas, however, increased rainfall could 

be offset by increased evaporation, both in terms of soil moisture and surface water. The Great Lakes, 

which hold 18% of the world’s fresh surface water, are being watched carefully. Many agree that warming 

trends throughout the region will lead to a climate more comparable to the Deep South thus making the 

lakes themselves smaller and muddier. Since 1988, temperature in Lake Erie has risen 1° (F) and while 

predictions vary, some researchers forecast that by 2070, lake level will fall about 34 inches and surface 

area will shrink 15%. This scenario would leave 2,200 square miles of new land exposed. Lower water 

levels and less ice cover will lead to more sediment delivery, and therefore more algae and potentially 

more waterborne diseases. Excessive algal blooms can affect aquatic life and harm animals and humans. 

Climate changes will also affect fish populations and zooplankton communities due to the disruptions in 

lake dynamics such as the timing and severity of ice-cover, winter-kill and spring/fall turn-over.

Photo courtesy of Great Lakes Environmental Center
Changes in the Southwest – Lake Tahoe and Lake Mead

Persistent drought conditions, increased extreme rainfall events, more wildfires, and heightened 

flooding, runoff and soil erosion are all expected to afflict the already arid southwest. Since 1988, the 

average surface water temperature of Lake Tahoe has increased by 1° (F). Other signs of persistent 

warming are decreased snowfall, later snowfall, and earlier 

snowmelt. In Tahoe City, California, the percentage of precipitation 

falling as snow has dropped from 52% in 1910 to 35% in 2007 

and since 1961, peak snowmelt throughout the lake region has 

shifted earlier by two and a half weeks. In Tahoe: State of the Lake 

Report 2008, researchers reported that algal growth, considered 

an indicator of warming’s acceleration, has increased rapidly with 

concentrations now five times what they were in 1959. Levels of 

nitrogen and phosphorus deposited from the Angora forest fire (also 

considered a climate indicator) also were 2-7 times greater than 

normal. 

Fluctuations in precipitation and snowpack have critical impacts 

on life in the desert. In Nevada, the water level in Lake Mead is 

steadily dropping and with it the hydroelectric production capacity 

by Hoover Dam. Studies cited by the National Conference of State Legislatures and Center for Integrative 

Environmental Research (2008) indicate that there is a 10% chance that Lake Mead could dry up by 2021 

and a 50% chance it will be dry by 2050. Lake Mead provides drinking water for over 2 million people 

and generates electricity for over 1.3 million. Water-based recreation brings in more than $1 billion to the 

area’s economy. Major changes in annual precipitation and snowpack are proving difficult for reservoir 

managers who must balance winter flooding with maximum capture and storage for summer water needs 

— all within the context of overall declining water levels. 

What the Experts Say

How a changing climate will impact the country’s lakes is far from understood and not easy to grasp. 

The Climate Change Science Program, in its 2008 report, underscores that most observed changes in 

water quality across the continental U.S. are likely attributable to causes other than climate change and 

are instead primarily due to changes in pollutant loadings. Nevertheless, there is general agreement with 

the IPCC (2007) conclusion that higher water temperatures, increased precipitation intensity and longer 

periods of low levels are likely to exacerbate many forms of water pollution, with impacts on ecosystem 

integrity, and water system reliability and operating costs. Both groups agree that a mix of mitigation and 

adaptation will be necessary to address the impacts.

Photo courtesy of Great Lakes Environmental 

Center

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

80
CHAPTER 8. CONCLUSIONS AND IMPLICATIONS 

FOR LAKE MANAGERS

Photo courtesy of Great Lakes Environmental Center

IN THIS CHAPTER

► Overall Findings and Conclusions

► Implications for Lake Managers
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

82

Chapter 8 

Conclusions and 

Implications for 

Lake Managers

Overall Findings and Conclusions

The NLA offers a unique opportunity to 

frame discussions and planning strategies 

based on environmental outcomes and across 

jurisdictional lines. It serves as a first step 

in the evaluation of the collective successes 

of management efforts to protect, preserve, 

or restore water quality. Attributable risk 

analyses can serve as a useful tool to help 

prioritize individual stressors. As EPA and its 

partners repeat the survey, the NLA will be 

able to track changes in water quality over 

time for lakes as a whole rather than just 

for a few individuals. This will help advance 

the understanding of important regional and 

national patterns in water quality, and speak 

to the cumulative effectiveness of the national 

water program.

Taken together, the results of the 

NLA provide a broad range of information 

necessary to understand the condition of our 

nation’s lakes and some of the key stressors 

likely to be affecting them. The results are 

especially important because they establish a 

national baseline for future monitoring efforts 

which can be used to track statistically-valid 

trends in lake condition. These stressors in 

lake systems are now placed in context of 

their relative importance for restoring and 

maintaining lake integrity. 

Condition of the Nation’s Lakes

The results of the survey provide 

information relating to the fundamental 

question of “what is the condition of the 

nation’s lakes?” The NLA reports on condition 

in three important ways. Biological indicators 

are especially useful in evaluating national 

condition because they integrate stress of 

combined problems over time. The NLA 

shows that 56% of the nation’s lakes are in 

good condition, 21% are in fair condition, 

and 24% are in poor condition based on 

Chapter 8 Conclusions and Implications for Lake Managers

Photo courtesy of Jim Anderson and Dennis McCauley
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

83

a measure of planktonic O/E taxa loss. 

Recreational suitability is based on the algal 

toxin, microcystin. Microcystin was found 

to be present in approximately one-third 

of lakes and at levels of concern in 1% of 

lakes. Finally, trophic status results based on 

chlorophyll-a concentrations show that 20% 

of lakes are hypereutrophic, while 80% are in 

lower nutrient enrichment categories.

Ecoregional assessments reveal broadscale patterns in lake condition across state 

lines and across the country. Again using 

biological condition as the primary indicator 

of lake health, the Northern Appalachians, the 

Upper Midwest and the Western Mountains 

ecoregions have the greatest proportion of 

lakes in good condition – over half of the 

lakes in each of these regions are classified as 

good. 

While it is too early in the survey program 

to determine if overall lake condition is 

improving, NLA analysts were able to examine 

changes in one subset of lakes, first sampled 

more than thirty years ago. It is encouraging 

to see that trophic status improved in 26% 

of the NES lakes and remained unchanged 

in 51% of the lakes. This means that trophic 

status in over three-quarters of these lakes 

remained the same or even improved despite 

growth of the U.S. population.

Major Physical and Chemical 

Stressors to Biological Quality

The NLA results show that of the physical 

indicators measured in the study, degraded 

lakeshore habitat is the most significant 

stressor to poor biological integrity. Using 

this as the primary habitat indicator, just 

under half of the country’s lakes (45%) are 

in good condition. The NLA results also show 

that lakes in poor condition for habitat are 

3 times more likely to be in poor biological 

condition. Another physical habitat indicator 

examined was the presence of human 

activities. From the standpoint of human 

disturbances along lakeshores, just one-third 

(35%) of the country’s lakes are in good 

condition. Conversely, in addition to exhibiting 

good biological conditions, about half of 

the lakes in the relatively healthy Northern 

Appalachians, the Upper Midwest and the 

Western Mountains ecoregions, are in good 

habitat condition relative to other ecoregions 

across the country. 

Nutrients in the form of phosphorus and 

nitrogen are the second most important 

stressor to lake biological health. Fifty-eight 

percent of lakes are in good condition relative 

to total phosphorus levels and 54% are in 

good condition relative to total nitrogen. 

Lakes in poor condition for either of these 

stressors are twice as likely to be in poor 

biological condition. Yet, unlike habitat 

condition, nutrient levels vary widely across 

the country. The Northern Appalachians 

ecoregion has the greatest percentage of 

lakes in good condition relative to total 

phosphorus (TP) and total nitrogen (TN) 

(79% for TP and 88% for TN) while the 

Temperate Plains (38% for TP and 27% for 

TN) and the Northern Plains (22% for TP and 

9% for TN) ecoregions have the lowest.

Chapter 8 Conclusions and Implications for Lake Managers

About 40% of the nation’s lakes are constructed reservoirs.

Photo courtesy of Eric Vance.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

84

Implications for Lake Managers

While survey results fill key informational 

gaps in regional and national monitoring 

programs by generating estimates of the 

condition of water resources, evaluating the 

prevalence of key stressors, and documenting 

trends in the population of waters over time, 

they do not address all management concerns 

at all scales. For example, the lakes survey 

does not address causal factors or sources 

of stress. For water resource managers and 

city planners, efforts to reduce stresses and 

improve water quality entails confronting 

the source(s) of the stress (such as energy 

generation, agricultural production, or 

suburban development) and working toward 

implementing viable but often difficult 

solutions. 

Address Major Lake Stressors

State lake management programs 

increasingly report that development 

pressures on lakes are steadily growing. 

The NLA findings show that local, state, and 

national initiatives should center on shoreline 

habitats, particularly vegetative cover, and 

nutrient loads to protect the integrity of lakes. 

The findings of the four physical habitat 

indicators show that poor habitat condition 

imparts a significant stress on lakes and could 

suggest the need for stronger management 

of lakeshore development at all jurisdictional 

levels. Of the four, degradation of lakeshore 

habitat cover is the most important stressor 

of lakes. The attributable risk analysis 

suggests that eliminating this stressor could 

restore the biological condition in 40% of 

lakes that are classified as poor, or 8.8% 

of lakes nationwide. Development and 

disturbance stressors along lakeshores (such 

as tree removal, residential construction, 

and grazing and cropping practices) impact 

the integrity of lakeshore and shallow water 

habitats, affecting terrestrial and aquatic 

biota alike. 

These NLA results support the continuing 

need for national, state, and local efforts to 

ameliorate the impacts of human activities 

in and around lakes to protect the lake 

ecosystem. For example, USDA’s Conservation 

Reserve Enhancement Program supports 

the planting of buffers to serve as natural 

boundaries between water bodies and 

farm land. EPA’s Low Impact Development 

(LID) program helps address lakeshore 

development pressures (see text box on page 

86).

Nutrients have been a longstanding 

stressor of waterbodies in this country. 

Nationally, over 40% of the lakes exhibit 

moderate or high levels of nitrogen or 

phosphorus concentrations. In addition, 

regional hotspots are evident - in the 

Temperate and Northern Plains, nearly 

all lakes have high levels of nutrients. 

The NLA findings emphasize the need for 

continuing implementation of Federal-State 

partnership programs to control point and 

non-point sources of nutrient pollution. 

The NLA data can be used to support and 

enhance collaboration between jurisdictional 

authorities and the use of programs such as 

the Environmental Quality Incentives Program 

and Conservation Reserve and Enhancement 

Programs managed by USDA’s Natural 

Resources Conservation Service, and the 

Section 319 Program and National Pollutant 

Discharge Elimination System run by EPA.

Chapter 8 Conclusions and Implications for Lake Managers
85

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Track Status and Trends Information

Lake managers should consider the 

national trend information as well as the 

ecoregional data in evaluating site specific 

information in a broader context. Conducted 

on a five-year basis, subsequent lake surveys 

will help water resource managers to assess 

temporal differences in the data and perform 

trends analyses. Future surveys will also help 

EPA and its partners evaluate national and 

ecoregional stressors to these ecosystems, 

track changes, and explore the relative 

importance of each in restoring or maintaining 

waterbody health. Wide-area or regional 

changes in stressors over time can potentially 

be linked to human factors such as land 

use changes (e.g., development) or natural 

causes (e.g., increased storm surges).

Implement Statewide 

Statistical Surveys

Statistical survey designs provide water 

resource managers and the public with 

consistent, statistically-valid assessments 

of the broader population of waters in the 

area of interest (nationally, state-wide, 

etc.) based on data from a relatively small 

representative sample. Information provided 

by these surveys can help managers monitor 

the effectiveness of their lake restoration and 

pollution control activities as well as target 

resources and additional monitoring where 

they are most needed. To date, 40 states 

are implementing statistical surveys (Figure 

38). These states are leveraging their limited 

monitoring resources to gain state-wide 

insights into their water resource quality. EPA 

encourages states to implement state-wide 

statistical surveys as a component of their 

CWA monitoring program.

Chapter 8 Conclusions and Implications for Lake Managers

Figure 38. States with state-scale statistical surveys.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

86

Chapter 8 Conclusions and Implications for Lake Managers

Low Impact Development Protects Lake Quality

Low impact development (LID) is a set of approaches and practices that are designed to reduce runoff 

of water and pollutants from the site at which they are generated. LID techniques manage water and water 

pollutants at the source through infiltration, evapotranspiration, and reuse of rainwater, preventing many 

pollutants from ever reaching nearby surface waters. LID practices include rain gardens, porous pavements, 

green roofs, infiltration planters, trees and tree boxes, and rainwater harvesting for non-potable uses such as 

toilet flushing and landscape irrigation. The primary goal of LID is to design each development site to protect, 

or restore, the natural hydrology of the site so that the overall integrity of the watershed is protected. 

Development typically causes an imbalance in the natural hydrology of a watershed by replacing pervious 

surfaces (e.g., fields, forests, wetlands etc.) with impervious surfaces (e.g., rooftops, parking lots, roads, 

etc.). This change in ground cover not only increases runoff because of decreased infiltration, it also reduces 

the potential for the removal of nonpoint source pollutants.

By engineering terrain, vegetation, and soil features, LID practices promote infiltration of runoff close to 

its source and help prevent sediment, nutrients, and toxic loads from being transported to nearby surface 

waters. Once runoff is infiltrated into soils, plants and microbes can naturally filter and break down many 

pollutants and restrict movement of others.

Implementing LID practices in watersheds will contribute to groundwater recharge, improve water 

quality, reduce flooding, preserve habitat, and protect lake quality. In addition, LID practices increase land 

value, aesthetics and recreational opportunities, and public/private collaborative partnerships while reducing 

stormwater management costs. For more information visit: http://www.epa.gov/owow/nps/lid.

States with statistical survey programs 

are already using the results to develop 

watershed-scale or site-specific protection or 

restoration projects. Virginia, for instance, 

has established an intensive water quality 

monitoring program incorporating statistical 

sampling methods. South Carolina’s 

monitoring program includes a statisticallybased component to complement its targeted 

monitoring activities. Each year a new 

statewide set of statistical random sites 

is selected for each waterbody type, i.e., 

streams, lakes/reservoirs, and estuaries. 

The State of Florida also implements an 

annual probabilistic monitoring program. 

Their program will be an enhancement of its 

2000 Status Monitoring Network — a five-year 

rotating-basin, statistical design sampling of 

six water resources, including small lakes 

(1-10 hectares) and large lakes (>10 

hectares). Florida is currently in the fifth year 

of the Network and will report its findings in 

2010. 

State-wide surveys can be leveraged with 

the national survey and the information can 

be used in conjunction with other existing 

state monitoring programs to get a better 

understanding of the state’s waters. In the 

same way that a lake association might relate 

the conditions it measures in a particular 

lake to other lakes, state/tribal managers can 

relate the conditions of lakes statewide to 

relevant ecoregional or national conditions. 

For example, Vermont compared its lakes’ 

trophic status to the lakes in the Northern 

Appalachians ecoregion and nationwide 
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National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

(Figure 39). This assessment shows that lakes 

in Vermont are more oligotrophic than lakes 

at the NLA ecoregional or national scale. Lake 

managers in states with a statistical survey 

network can use information such as this to 

target resources and management efforts. 

Incorporate New and 

Innovative Approaches

EPA is encouraging states, tribes, and 

others to utilize NLA data and methods for 

their own customized purposes. The NLA 

provides lake managers with new tools and 

techniques to adopt into existing programs. 

Managers are encouraged to consider the host 

of new assessment indicators and methods 

that are applicable within assessment 

programs of any scale. For example, the 

quantitative assessment of physical habitat 

at the land-water interface is an area of 

intensifying focus within the lakes community. 

The NLA physical habitat assessment 

method provides a ready approach that has 

already been implemented by field crews 

across the lower 48 states and Alaska. The 

resulting data are readily reduced to four 

components of habitat integrity that relate 

directly to ecological integrity in lakes. For 

lake assessment programs lacking a physical 

habitat assessment component, the NLA 

method provides a low-cost and informationrich enhancement. 

Chapter 8 Conclusions and Implications for Lake Managers

Figure 39. Comparison of lakes by trophic state for Vermont, the Northern Appalachians 

ecoregion, and the Nation, based on chlorophyll-a.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

88

The incorporation of recreational 

indicators within lake assessment 

programs can also yield useful information 

to lake managers. Public awareness 

of cyanobacteria and related toxins is 

increasing, fueled in part by an increasing 

number of beach closures and related media 

reports. In the NLA, while only a small 

proportion of lakes exhibited moderate or 

high-risk concentrations of microcystin, the 

proportions of lakes with concentrations 

of chlorophyll-a or cyanobacteria cells 

associated with the development of 

elevated microcystin was considerably 

greater. Routine monitoring of chlorophyll-a, 

cyanobacterial cell counts, and/or 

microcystin can be implemented using a 

tiered approach tailored to the likelihood 

of microcystin occurrence. Many states are 

now adopting such programs, resulting 

in greater protection of human health in 

instances where cyanobacteria blooms may 

limit or prohibit swimming.

Work Beyond 

Jurisdictional Boundaries

Survey data on a national scale allows 

for aggregation of data and comparability of 

the results across several ecoregional levels. 

Within each of these ecoregions, states 

often share common problems and stressors 

to shared watersheds. The NLA offers a 

unique opportunity for adjacent states to 

work together, establish coalitions, and put 

into place collaborative actions that cross 

state boundaries. As a starting point, EPA 

and its state partners are working together 

to develop approaches to monitoring that 

will allow comparisons on a state-wide basis 

and across state boundaries as well. EPA 

and the states are committed to finding 

mutually-beneficial and scientifically-sound 

ways to integrate and exchange data 

from multiple sources, as well as options 

to improve both sample collection and 

analytical methods.

Chapter 8 Conclusions and Implications for Lake Managers

Aquatic weed harvesting is one way to manage plant growth.

Photo courtesy of Frank Borsuk.

Pennsylvania spillway. 

Photo courtesy of Frank Borsuk.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes 89

HIGHLIGHT

State, Tribal, and Regional Lake Surveys: 

Examples From Across the Country 

State-wide Lake Assessments

Oklahoma: Oklahoma was one of several states that chose to add to the number of nationally-selected 

lake sites within its boundaries to achieve a state-wide assessment. Oklahoma is looking into using 

National Lakes Assessment (NLA) survey data for further development of nutrient and biological criteria, 

incorporating new parameters into its established monitoring program, and nesting a probability-based 

survey into its fixed station rotation.

Michigan: Twenty-nine Michigan lakes were randomly 

selected as part of the NLA. To allow for a state-scale 

assessment, the state added 21 additional randomly-chosen 

lakes. Michigan’s surveyed lakes ranged from an unnamed 

10-acre lake in Clare County to 13,000-acre Gogebic Lake 

in Gogebic County. The state will continue to analyze its 

lake data set to further evaluate the condition of Michigan’s 

inland lakes based on the national survey assessment tools. 

 

Oregon: Oregon sampled 30 lakes across the state as 

part of the NLA. In Oregon, the results from the 2007 

NLA will help answer two key questions about the quality 

of lakes, ponds and reservoirs: What percent of Oregon’s 

lakes are in good, fair or poor condition for key indicators 

of nutrient status, ecological health and recreation? What 

is the relative importance of key lake “stress factors” such 

as nutrients and pathogens? The random design took field 

crews to a wide variety of sites. Elevation at the target lakes 

ranged from 30 feet to 7,850 feet. Lake depths ranged from 

1 meter to 128 meters (Waldo Lake); maximum sampling 

depth, however, was 50 meters. The most difficult lake 

to reach was Ice Lake in the Eagle Cap Wilderness, which 

required the use of an outfitter and horses for the eight-mile 

and 3,300-foot elevation gain journey.

Enhancing Lake Monitoring for the 

Lac du Flambeau Tribe, Wisconsin

The Lac du Flambeau Tribe is using the NLA study to enhance its own water program. The ability to 

develop protective site-specific water quality criteria and assess lake health is limited when available data 

cover only a small geographic area such as the Lac du Flambeau Reservation. Participation in the NLA 

enabled the Tribe to compare Reservation lake data to national and regional lake health. The Tribe used 

the NLA protocols for physical habitat, water chemistry, and vertical water profiles on an additional 11 

lakes within the Reservation. These data are being entered into EPA’s Water Quality Exchange (WQX) using 

Ice Lake in the Eagle Cap Wilderness.

Photo courtesy of Oregon Department of 

Environmental Quality.
an Excel template to ensure data uniformity for comparison. The Tribe will develop lake report cards for 

the general public, managers, and decision makers assessing the health of Reservation lakes as compared 

to national and regional lake health. The Tribe will also be able to evaluate development of criteria using 

these data. 

Assessing Prairie Potholes: A Collaborative Effort. 

The Prairie Pothole Region crosses the north central U.S. and Canada and includes nearly 8,000 prairie 

pothole lakes. Prairie pothole lakes are intrinsically shallow and defined as natural lakes where 80% or 

more of the lake is less than 15 feet deep. Prairie Pothole 

lakes are part of a major waterfowl fly-way and are a 

valuable regional and national resource. In order to more 

fully understand this unique ecosystem, North Dakota, 

Iowa, Minnesota, South Dakota, Montana, USGS, and 

EPA undertook an assessment of these lakes. Analysts 

have found that nutrient and chlorophyll-a levels in Prairie 

Pothole lakes are quite high compared to the nation’s 

lakes. A combination of high nutrient levels, elevated 

algae growth, low transparency, presence of roughfish, 

and broad, wind-swept basins serve to limit rooted plant 

growth. Maintaining rooted plant growth is important for 

Prairie Pothole health. More detailed information on the 

results of the Prairie Pothole survey will be provided in a 

NLA supplemental report.

90

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Photo courtesy of Wes Weissenburger
CHAPTER 9.

NEXT STEPS FOR 

THE NATIONAL SURVEYS

IN THIS CHAPTER

► Supplemental Reports 

► Tools and Other Analytical Support

► Future National Assessments

Bayley Lake in Stevens County was one of the lakes the Department of Ecology sampled during the survey. 

Photo courtesy of Washington State Department of Ecology.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

92

Chapter 9

Next Steps for the 

National Surveys

EPA is committed to continually enhance 

the National Aquatic Resource surveys in 

order to improve the quality and quantity 

of information it needs to understand the 

condition of the aquatic environment and 

how it is changing over time. As technologies 

advance, future surveys and collaborations 

can also lead to new indicators, new 

monitoring approaches, and new water 

resource management programs and policies. 

With the publication of this report, the 

lakes survey moves into a design/planning 

phase in preparation for the next survey in 

2012. This phase will incorporate lessons 

learned from the first lakes survey, other 

national surveys, and state, tribal and local 

experiences. Additionally, EPA anticipates 

that states and other partners will continue 

to utilize data from the first lakes survey and 

issue supplemental reports based on their 

findings.

During 2010, EPA and its state and tribal 

partners will take stock of the survey and 

begin planning for 2012. Issues for discussion 

may include changes to the design, field 

methods, equipment, laboratory methods, 

and/or analyses procedures. Other items 

include improving reference site selection, 

refining regionally representative reference 

sites, and adding more reference sites to the 

survey. Consideration will be given not only 

Chapter 9 Next Steps for the National Surveys

Lakes

2006 2007 2008 2009 2010 2011 2012

Design Field Lab and 

Data 

Analysis

Report Design and 

Planning

Field

Photo courtesy of Lauren Wilkinson, Great Lakes Environmental Center.
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

93

to how alternate approaches will improve 

future data, but how the Agency can ensure 

comparability to the initial baseline. 

Supplemental Reports

The NLA included data collection for 

several indicators for which analysis could 

not be completed in time for this report. 

These included benthic macroinvertebrates, 

sediment mercury, and enterococcus. 

Analysts are currently developing 

macroinvertebrate indicators to add to our 

understanding of biological integrity of lakes. 

Sediment mercury samples are still in the 

data analysis phase, as is the enterococcus

dataset. EPA plans to produce supplements 

to this report with the macroinvertebrate, 

sediment mercury, and enterococcus findings. 

Supplemental information will be posted on 

http://www.epa.gov/lakessurvey.

In the next few years, EPA plans to 

continue additional analyses of the survey 

data to develop tools and strategies that will 

provide a better understanding of lakes and 

water resources in general. One important 

undertaking will be to conduct an in-depth 

analysis of the relationship between lake 

condition, stressors, and management actions 

such as point and nonpoint controls and other 

restoration activities. EPA plans to publish its 

progress and findings in interim lake survey 

reports.

Tools and Other 

Analytical Support

The next two years will also provide an 

opportunity for states to tailor their own 

statewide program to complement the 

national programs. Extensive discussion 

during the upcoming research and design 

phase will focus on ways to leverage and 

integrate national and state-scale surveys. 

This approach will improve the efficiency 

and value investment in monitoring. One 

EPA near-term project will be to work with 

the states to develop tools that can be 

used to re-create the survey for state-wide 

assessments and for customized purposes. 

EPA is committed to providing technical 

support to assist states, tribes and other 

partners in using these tools. Such an 

“assessment tool kit” might include IBI or O/E 

model development, habitat data analysis 

techniques, decision-support tools, and webbased trainings session.

Future National Assessments

EPA and its state, tribal and federal 

partners expect to continue to produce 

national assessments on a yearly cycle. Rivers 

and stream sampling was completed in 2008 

and 2009 and a report will be released in 

2011. A national coastal assessment report 

will be published in 2012 based on field 

sampling in 2010. Wetlands will be surveyed 

in 2011, followed by a report in 2013. In 

2012, field sampling for lakes will occur again 

and the assessment report that follows in 

2014 will include an evaluation of changes in 

biological condition and key stressors. Each of 

the water type surveys will then continue with 

changes and trends becoming a greater focus 

for each resource type. 

The continued utility of these national 

surveys and their assessment reports 

depends on continued consistency in design, 

as well as in field, lab and assessment 

methods from assessment to assessment. 

However, the surveys should also provide the 

flexibility that allows the science of monitoring 

to improve over time. Maintaining consistency 

while allowing flexibility and growth will 

continue to be one of the challenges of the 

coming years.

Chapter 9 Next Steps for the National Surveys
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

94

This national lakes survey would not 

have been possible without the involvement 

of hundreds of scientists working for state, 

tribal, and federal agencies and universities 

across the nation. Future National Aquatic 

Resource Surveys will continue to rely on 

this close collaboration, open exchange of 

information, and the dedication, energy, and 

hard work of its participants. EPA will continue 

to work to help its partners translate the 

expertise they gained through these national 

surveys to studies of their own waters. It also 

will work to ensure that this valuable and 

substantial baseline of information be widely 

used to evaluate the success of efforts to 

protect and restore the quality of the Nation’s 

waters.

Chapter 9 Next Steps for the National Surveys
95

National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Acronyms

ANC Acid Neutralizing Capacity

CPL Coastal Plains

CWA Clean Water Act

DO Dissolved Oxygen

DOC Dissolved Organic Carbon

EMAP Environmental Monitoring and Assessment Program

EPA Environmental Protection Agency

GIS Geographic Information System

IBI Index of Biological Integrity

ITIS Integrated Taxonomic Information System

LDCI Lake Diatom Condition Index

NAP Northern Appalachians

NARS National Aquatic Resource Surveys

NES National Eutrophication Study

NHD National Hydrography Dataset

NLA National Lakes Assessment

NLCD National Land Cover Dataset

NPL Northern Plains

O/E Observed/Expected

ORD Office of Research and Development, EPA

OW Office of Water, EPA

PPR Prairie Pothole Region

QA/QC Quality Assurance/Quality Control

QAPP Quality Assurance Project Plan

qPCR Quantitative Polymerase Chain Reaction

REMAP Regional Environmental Monitoring and Assessment Program

SAP Southern Appalachians

SPL Southern Plains

TIME/LTM Temporally Integrated Monitoring of Ecosystem/Long Term Monitoring

TMDL Total Maximum Daily Load

TPL Temperate Plains

TN Total Nitrogen

TP Total Phosphorus

UMW Upper Midwest

USDA U.S. Department of Agriculture

USGS U.S. Geological Survey

WMT Western Mountains

WQX EPA’s Water Quality Exchange

WWTP Wastewater Treatment Plant

XER Xeric

Chapter 9 Acronyms
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

96

Glossary of Terms

Glossary of Terms 

Acid Neutralizing Capacity (ANC): A lake’s ability to adapt to, i.e. neutralize, increases in 

acidity due to acidic deposition from anthropogenic sources (automobile exhausts, fossil fuels) and 

natural geologic sources.

Attributable risk: Magnitude or significance of a stressor. Is determined by combining the 

relative extent of a stressor (prevalence) and the relative risk of the stressor (severity).

Benthic macroinvertebrates: Benthic meaning “bottom-dwelling”. Aquatic larval or adult 

insects, crayfish, worms and mollusks. These small creatures live on the lake bottom attached to 

rocks, vegetation, logs and sticks, or burrow into the sediment.

Biological assemblage: Key group or community of plant or animal being studied to learn 

more about the biological condition of water resources.

Biological integrity: State of being capable of supporting and maintaining a balanced 

community of organisms having a species composition, diversity, and functional organization.

Chlorophyll-a: A type of plant pigment present in all types of algae sometimes in direct 

proportion to the biomass of algae. A chemical indicator used to assess trophic condition. 

Complexity: Used to describe the diversity and intricacy of an ecosystem. A complex habitat is 

one that has a wide range of different niches for optimum growth and reproduction for both plants 

and animals. 

Condition: State or status of a particular indicator. For example, the biological condition of a 

lake is the status of a biological assemblage, such as diatoms. Often measured against a reference 

value or threshold.

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.

Epilimnion: The uppermost, warmest, well-mixed layer of a lake during summertime.

Euphotic zone: The uppermost layer of the lake defined as the depth at which light penetrates.

Eutrophic: See Trophic state.
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National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Eutrophication: The process of increased productivity of a lake or reservoir as it ages. Often this 

process is greatly accelerated by human influences and is termed cultural eutrophication.

Hypereutrophic: See Trophic state.

Hypolimnion: The lower, cooler layer of lake during the summer.

Lakes Diatom Condition Index (LDCI): The sum of individual measures of a diatom 

assemblage, such as number and composition of taxa present, diversity, morphology, and other 

characteristics of the organisms.

Limnological: Of or pertaining to the study of fresh waters.

Littoral zone: The water’s edge. The lake bottom extending from the shoreline lakeward to the 

greatest depth occupied by rooted plants. 

Macrophyte: Literally meaning “large plant.” An aquatic plant that can grow emergent, 

submergent or floating.

Mesotrophic: See Trophic state.

National Hydrography Dataset: Comprehensive set of digital spatial data that contains 

information on surface water features across the U.S.

Nutrients: In the context of the NLA, substances such as nitrogen and phosphorus that are 

essential to life but in excess can overstimulate the growth of algae and other plants in aquatic 

environments. Excess nutrient can come from agricultural and urban runoff, leaking septic systems, 

sewage discharges and similar sources.

O/E (Observed/Expected) Ratio of Taxa Loss: A comparison of the number of taxa that 

are observed (O) at a site relative to the number of taxa expected (E) to exist for a site of similar 

nature. The taxa expected at individual sites are based on models developed from data collected at 

reference sites.

Oligotrophic: See Trophic state.

Pelagic zone: The open area of a lake, from the edge of the littoral zone to the center of the 

lake.

Primary productivity: The production of organic compounds from atmospheric or aquatic 

carbon dioxide, principally through the process of photosynthesis. All life on earth is directly or 

indirectly reliant on primary production. In aquatic ecosystems, the organisms responsible for 

primary production are the phytoplankton, and form the base of the food chain.

Glossary of Terms
National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

98

Probability-based design: A type of random sampling technique in which every site in the 

population has a known probability of being selected for sampling. Results from the sampled sites 

can be used to represent the population as a whole.

Profundal zone: The deepest part of the lake. The lake bottom located below the depth of light 

penetration.

Reference condition: The least-disturbed condition available in an ecological region, 

determined based on specific criteria, and used as the benchmark for comparison with the 

surveyed sample sites in the region.

Regionally-specific reference: A subset of the reference condition based on reference lake 

sites of similar type and geography. For ecoregional assessments, the lakes are only compared to 

the particular reference lakes that are similar for that area.

Relative extent: The relative prevalence of a specified condition (such as poor) for a stressor 

or biological indicator. A stressor with a high relative extent means that it is relatively widespread 

when compared to other stressors.

Relative risk: The severity of the stressor. Like attributable risk and relative extent of the risk, 

this term is used to characterize and quantify the relative importance of the stressor. Stressors with 

low relative extent and high relative risk are called “hot spots”.

Riparian zone: The banks or shoreline of a lake or waterbody.

Riparian or Shoreline disturbance: A measure of the evidence of human activities alongside 

lakes, such as roadways, dams, docks, marinas, crops, etc.

Riparian vegetative cover: Vegetation alongside lakeshore. Intact riparian vegetative cover 

reduces pollution runoff, prevents streambank erosion, and provide shade, food, and habitat for 

fish and other aquatic organisms.

Secchi transparency: A measure of the clarity of water obtained by lowering a black and 

white, or all white, disk (Secchi disk) into the water until it is no longer visible. Measured in feet or 

meters.

Stressors: Factors that adversely affect, and therefore degrade, aquatic ecosystems. Stressors 

may be chemical (e.g., excess nutrient, pesticides, metals), physical (e.g., pH, turbidity, habitat), 

or biological (e.g., invasive species, algal bloom).

Glossary of Terms
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National Lakes Assessment: A Collaborative Survey of the Nation’s Lakes

Stressor-response: Change in biological condition due to the presence of one or more 

stressors.

Sublittoral zone: The lake bottom area between the littoral (rooted plants) to the depth at 

which there is no more light penetration.

Taxa: Taxonomic grouping of living organisms, such as family, genus or species, used for 

identification and classification purposes. Biologists describe and organize organisms into taxa in 

order to better identify and understand them.

Threshold: The quantitative limit or boundary. For example, an assessment threshold is the 

particular percentage of the reference condition or cut-off point at which a condition is considered 

good, fair or poor.

Trophic state: Meaning “nourishment.” Used to describe the level of productivity of a lake. 

Oligotrophic: A nutrient poor lake. Describes a lake of low biological productivity and high 

transparency or clarity.

Mesotrophic: A lake that is moderately productive.

Eutrophic: A well-nourished lake, very productive and supports a balanced and diverse array

of organisms. Usually low transparency due to high algae and chlorophyll-a content.

Hypereutrophic: Characterized by an excess of nutrients. These lakes usually support algal 

blooms, vegetative overgrowth, and low biodiversity.

Watershed: A drainage area or basin in which all land and water areas drain or flow toward a 

central repository such as a lake, river or the ocean. 

Glossary of Terms
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100

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