U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2013–1160

National Water-Quality Assessment Program

Design of Cycle 3 of the National Water-Quality Assessment 

Program, 2013–23:

Part 2: Science Plan for Improved Water-Quality Information and Management
Cover: Maps illustrating national-scale design elements for Cycle 3 of the National Water-Quality Assessment Program including: (upper left)-principal aquifers of the 

conterminous U.S., (center)-major rivers of the conterminous U.S., and (lower right) level-2 ecoregions of the conterminous U.S.
Design of Cycle 3 of the National WaterQuality Assessment Program, 2013–23: 

Part 2: Science Plan for Improved Water-Quality 

Information and Management

By Gary L. Rowe, Jr., Kenneth Belitz, Charlie R. Demas, Hedeff I. Essaid, 

Robert J. Gilliom, Pixie A. Hamilton, Anne B. Hoos, Casey J. Lee, 

Mark D. Munn, and David W. Wolock

National Water-Quality Assessment Program

Open-File Report 2013–1160

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2013

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as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner.

Suggested citation:

Rowe, G.L., Jr., Belitz, Kenneth, Demas, C.R., Essaid, H.I., Gilliom, R.J., Hamilton, P.A., Hoos, A.B., Lee, C.J., 

Munn, M.D., and Wolock, D.W., 2013, Design of Cycle 3 of the National Water-Quality Assessment Program, 

2013–23: Part 2: Science plan for improved water-quality information and management: U.S. Geological Survey 

Open-File Report 2013–1160, 110 p., http://pubs.usgs.gov/of/2013/1160/.
iii

Foreword

The United States has made major investments in assessing, managing, regulating, and conserving natural resources such as water, minerals, soils, and timber. Sustaining the quality of the 

Nation’s water resources and the health of our ecosystems depends on the availability of sound 

water-resources data and information to develop effective, science-based policies. Effective 

management of water resources also brings more certainty and efficiency to important economic sectors. Taken together, these actions lead to immediate and long-term economic, social, 

and environmental benefits that make a difference to the lives of millions of people (http://

water.usgs.gov/nawqa/applications/).

Two decades ago, the Congress established the U.S. Geological Survey’s (USGS) National 

Water-Quality Assessment (NAWQA) Program to meet this need. Since then it has served as a 

primary source of nationally consistent information on the quality of the Nation’s streams and 

groundwater; how water quality changes over time; and how natural features and human activities affect the quality of streams and groundwater. Objective and reliable data, water-quality 

models and related decision support tools, and systematic scientific studies characterize where, 

when, and why the Nation’s water quality is degraded—and what can be done to improve and 

protect it for human and ecosystem needs. This information is critical to our future because 

the Nation faces an increasingly complex and growing need for clean water to support population, economic growth, and healthy ecosystems. For example, two thirds of U.S. estuaries are 

impacted by nutrients and dead zones that no longer fully support healthy fish and other aquatic 

communities. Forty-two percent of the Nation’s streams are in poor or degraded condition compared to reference conditions. Eighty three percent of urban streams have at least one pesticide 

that exceeds criteria to protect aquatic life. Groundwater from about 20 percent of public and 

domestic wells—which serve almost 150 million people—contains at least one contaminant at 

a level of potential health concern.

This report presents a science plan for improved water-quality information and management 

for the third decade—Cycle 3—of the NAWQA Program.The science plan describes a 10-year 

strategy for national monitoring and assessment of the Nation’s freshwater quality and aquatic 

ecosystems during 2013–23 and builds on a foundation of over 20 years of NAWQA data collection, interpretative studies, and modeling activities. It represents the consensus of USGS 

scientists and managers, NAWQA Program stakeholders, and a National Research Council 

technical advisory committee (http://www.nap.edu/catalog.php?record_id=13464). 

Other recent NAWQA reports have focused on occurrence and distribution of nutrients, pesticides, and volatile organic compounds in streams and groundwater, the effects of contaminants 

and streamflow alteration on condition of aquatic communities in streams, and on the quality 

of untreated water from private domestic and public supply wells. Each report builds toward 

a more comprehensive understanding of the quality of regional and national water resources 

(http://water.usgs.gov/nawqa/nawqa_sumr.html). All NAWQA reports are available on-line at 

http://water.usgs.gov/nawqa/bib/.

The information in this report is intended primarily for those interested or involved in resource 

management and protection, conservation, regulation, and policymaking at regional and 

national levels. We hope this publication will provide you with insights and information to meet 

your needs, and will foster increased citizen awareness and involvement in the protection and 

restoration of our Nation’s waters.

William H. Werkheiser

Associate Director for Water

U.S. Geological Survey
iv

Contents

About this Report ..........................................................................................................................................xi

Introduction and Overview...........................................................................................................................1

Vision.......................................................................................................................................................1

Why Now?..............................................................................................................................................2

Priorities and Goals for NAWQA Cycle 3 ..........................................................................................8

Introduction to the Cycle 3 Approach .............................................................................................11

What Does the Nation Gain by This Plan?......................................................................................14

Cycle 3 Design Elements.............................................................................................................................19

Goals and Objectives of Cycle 3.......................................................................................................19

Study Components..............................................................................................................................20

Surface Water............................................................................................................................20

National Fixed-Site Network...........................................................................................21

Regional Synoptic Study..................................................................................................23

Integrated Watershed Study...........................................................................................25

Intensive Study..................................................................................................................28

Groundwater...............................................................................................................................28

Principal Aquifer Assessment ........................................................................................29

Regional Groundwater Studies ......................................................................................29

Local Groundwater Studies ............................................................................................30

National Implementation and Integration.....................................................................30

Goal 1—Assess the Current Quality of the Nation’s Freshwater Resources and How Water 

Quality is Changing Over Time......................................................................................................31

Products ...............................................................................................................................................31

Connections to other NAWQA Cycle 3 Goals.................................................................................31

Policy and Stakeholder Concerns Driving Key Management Questions .........................32

Objective 1a. Determine the Distributions and Trends for Contaminants in Current and 

Future Sources of Drinking Waters from Streams, Rivers, Lakes, and Reservoirs....34

Objective 1b. Determine Mercury Trends in Fish Tissue..............................................................36

Objective 1c. Determine the Distributions and Trends for Microbial Contaminants in 

Streams and Rivers Used for Recreation..........................................................................38

Objective 1d. Determine the Distributions and Trends of Contaminants of Concern in 

Aquifers Needed for Domestic and Public Supplies of Drinking Water ......................40

Objective 1e. Determine the Distributions and Trends for Contaminants, Nutrients, 

Sediment, and Streamflow Alteration that May Degrade Stream Ecosystems..........46

Objective 1f. Determine Contaminant, Nutrient, and Suspended-Sediment Loads to 

Coastal Estuaries and Other Receiving Waters ...............................................................49

Objective 1g. Determine Trends in Biological Condition at Selected Sites and Relate 

Observed Trends to Changes in Contaminants, Nutrients, Sediment, and 

Streamflow Alteration ..........................................................................................................51

Partnerships for Goal 1 ......................................................................................................................53

Goal 2—Evaluate How Human Activities and Natural Factors, Such as Land Use, Water Use, 

and Climate Change, are Affecting the Quality of Surface Water and Groundwater.........55

Products ...............................................................................................................................................55

Connections to other NAWQA Cycle 3 Goals.................................................................................55
v

Background..........................................................................................................................................55

Objective 2a. Determine How Hydrologic Systems—Including Water Budgets, Flow 

Paths, Travel-times and Streamflow Alterations—are Affected by Land Use, 

Water Use, Climate, and Natural Factors..........................................................................56

Objective 2b. Determine How Sources, Transport, and Fluxes of Contaminants, 

Nutrients, and Sediment are Affected by Land Use, Hydrologic System 

Characteristics, Climate, and Natural Factors..................................................................56

Objective 2c. Determine How Nutrient Transport Through Streams and Rivers is 

Affected by Stream Ecosystem Processes.......................................................................56

Objective 2d. Apply Understanding of How Land Use, Climate, and Natural Factors 

Affect Water Quality to Determine the Susceptibility of Surface-Water and 

Groundwater Resources to Degradation ..........................................................................57

Objective 2e. Evaluate How the Effectiveness of Current and Historical Management 

Practices and Policy is Related to Hydrologic Systems, Sources, Transport and 

Transformation Processes...................................................................................................57

Policy and Stakeholder Concerns Driving Key Management Questions ..................................57

NAWQA Progress During Cycles 1 and 2 .......................................................................................57

NAWQA’S Role in Cycle 3..................................................................................................................58

General Approach...............................................................................................................................59

Surface-Water Studies .............................................................................................................60

Contaminants.....................................................................................................................61

Nutrients.............................................................................................................................61

Sediment ............................................................................................................................62

Streamflow Alteration......................................................................................................63

Example of an Integrated Watershed Study .........................................................................63

Example of an Intensive Study for Sediment and Nutrient Transport...............................65

Groundwater Studies ................................................................................................................69

Critical Requirements for Technical Support and Data Support.................................................72

Partnerships for Goal 2 ......................................................................................................................73

Goal 3—Determine the Relative Effects, Mechanisms of Activity, and Management 

Implications of Multiple Stressors in Aquatic Ecosystems.....................................................74

Products ...............................................................................................................................................74

Connections to other NAWQA Cycle 3 Goals.................................................................................74

Background..........................................................................................................................................74

Objective 3a. Determine the Effects of Contaminants on Degradation of Stream 

Ecosystems, Determine which Contaminants Have the Greatest Effects in 

Different Environmental Settings and Seasons, and Evaluate Which Measures of 

Contaminant Exposure are the Most Useful for Assessing Potential Effects.............75

Objective 3b. Determine the Levels of Nutrient Enrichment that Initiate Ecological 

Impairment, What Ecological Properties are Affected, and Which Environmental 

Indicators Best Identify the Effects of Nutrient Enrichment on Aquatic 

Ecosystems.............................................................................................................................76

Objective 3c. Determine How Changes to Suspended and Depositional Sediment 

Impair Stream Ecosystems, Which Ecological Properties are Affected, and 

What Measures are Most Appropriate to Identify Impairment.....................................76

Objective 3d. Determine the Effects of Streamflow Alteration on Stream Ecosystems 

and the Physical and Chemical Mechanisms by Which Streamflow Alteration 

Causes Degradation .............................................................................................................76
vi

Objective 3e. Evaluate the Relative Effects of Multiple Stressors on Stream Ecosystems 

in Different Regions that are Under Varying Land Uses and Management 

Practices.................................................................................................................................76

Policy and Stakeholder Concerns Driving Key Management Questions ..................................77

NAWQA Progress in Cycles 1 and 2 ................................................................................................77

NAWQA’s Role in Cycle 3...................................................................................................................81

Approach..............................................................................................................................................81

Design Features .........................................................................................................................81

Study Designs and Outcomes for Each Individual Stressor...............................................84

Contaminants.....................................................................................................................84

Nutrients.............................................................................................................................84

Sediment ............................................................................................................................85

Streamflow Alteration......................................................................................................86

Example Designs for Integrated Intensive and Regional Studies Assessing 

Stressors in Urban and Agricultural Settings..........................................................87

Urban Example ..................................................................................................................87

Agricultural Example........................................................................................................88

Critical Requirements for Technical Support and Data Support.................................................90

Partnerships for Goal 3 ......................................................................................................................92

Goal 4—Predict the Effects of Human Activities, Climate Change, and Management 

Strategies on Future Water-Quality and Ecosystem Condition ..............................................93

Products ...............................................................................................................................................93

Connections to other NAWQA Cycle 3 Goals.................................................................................93

Background..........................................................................................................................................93

NAWQA Progress During Cycles 1 and 2 .......................................................................................94

NAWQA’s Role in Cycle 3...................................................................................................................95

Objective 4a. Evaluate the Suitability of Existing Water-Quality Models and Enhance 

as Necessary for Predicting the Effects of Changes in Climate and Land Use on 

Water-Quality and Ecosystem Conditions.........................................................................95

Objective 4b. Develop Decision-Support Tools for Managers, Policy Makers, and 

Scientists to Evaluate the Effects of Changes in Climate and Human Activities 

on Water Quality and Ecosystems at Watershed, State, Regional, and National 

Scales......................................................................................................................................97

Objective 4c. Predict the Physical and Chemical Water-Quality and Ecosystem 

Conditions Expected to Result from Future Changes in Climate and Land Use 

for Selected Watersheds ...................................................................................................101

Hypothetical Study in Chesapeake Bay........................................................................................101

Partnerships for Goal 4 ....................................................................................................................103

References Cited........................................................................................................................................105

Figures

1. Trends in the numbers of nitrate samples collected from streams and groundwater 

over time.........................................................................................................................................5

2. Conceptual model illustrating relations between environmental drivers, 

water-quality stressors, and human and aquatic ecosystem receptors ............................9
vii

3. Map showing locations of monitoring sites in the Cycle 2 fixed-site network for 

streams and rivers relative to the eight major river basins used for regional-scale 

synthesis and modeling of surface-water quality.................................................................13

4. Map of principal aquifer systems shaded according to percent of total pumping for 

public supply and locations domestic and public supply wells sampled in Cycles 1 

and 2..............................................................................................................................................14

5. Trend analysis for the insecticide diazinon in Accotink Creek, Virginia............................15

6. Modeled nitrate concentrations in shallow groundwater...................................................16

7. Results of laboratory tests showing reduced egg production in fathead minnows 

at atrazine concentrations as low as 0.5 microgram per liter with an exposure 

duration in the range of 21 days...............................................................................................17

8. Predicted maximum 21-day average atrazine concentration in streams for 

concentration levels shown to affect egg production of fathead minnows in 

laboratory studies.......................................................................................................................18

9. Map showing area of the southwestern United States for which the SPARROW 

model was used to predict nitrogen loads delivered to eastern Gulf of Mexico and 

South Atlantic estuaries based on a 50-percent reduction in agricultural nitrogen 

inputs ............................................................................................................................................19

10. Map showing locations of monitoring sites in the Cycle 2 fixed-site network for 

streams and rivers as a function of sampling frequency.....................................................22

11. Pie chart illustrating breakdown of National Fixed Site Network sites on large 

rivers .............................................................................................................................................24

12. Pie chart illustrating breakdown of National Fixed Site Network sites on wadeable 

streams.........................................................................................................................................24

13. Pie chart illustrating breakdown of National Fixed Site Network sites at 50 lake or 

reservoir drinking-water intakes..............................................................................................25

14. Hypothetical locations of 20 Integrated Watershed Study locations ................................26

15. Comparison of measured and regression-estimated fecal coliform bacteria 

concentrations in the Kansas River at Desoto, Kansas and the probability of 

exceeding recreational water-quality criteria.......................................................................39

16. Nitrate exceedance maps for California’s Central Valley principal aquifer......................43

17. Schematic diagram illustrating nested spatial scales for Cycle 3 surface-water 

studies ..........................................................................................................................................59

18. Example Integrated Watershed Study (IWS) design with embedded Intensive 

Study (IS)......................................................................................................................................60

19. Examples of geospatial information available for the White River Basin in Indiana 

that would be of use in an Integrated Watershed Study .....................................................66

20. Map of the White River Basin in Indiana showing proposed nested streamgages 

that could be added to the water-quality monitoring network ...........................................68

21. Nested spatial scales for Cycle 3 groundwater studies ......................................................70

22. Three-dimensional representation of a groundwater-flow system illustrating the 

depth intervals sampled by monitoring, domestic, and public-supply wells; flow 

paths and groundwater ages; and proximal and distal regions of the aquifer ................72

23. Schematic diagram showing the decrease in biological condition as stressors 

increase........................................................................................................................................75

24. Location of Effects of Urbanization on Stream Ecosystem topical studies and 

results of multiple regression modeling for identifying effects of multiple stressors 

on algae, invertebrate, and fish communities.79
viii

25. Location of the eight agriculturally dominated NAWQA study units included in 

the Effects of Nutrient Enrichment on Stream Ecosystems topical study and the 

national structural equation model..........................................................................................80

26. Relation between percent reduction in in-stream flow and the percentage of 

stream sites with impaired fish communities ........................................................................81

27. U.S. Environmental Protection Agency Level 2 Ecoregions ................................................83

28. Example of a regional-scale conceptual model based on existing studies and 

expert knowledge .......................................................................................................................84

29. Hypothetical conceptual model showing the primary stressors that determine 

ecosystem condition in an urban stream ecosystem...........................................................88

30. Study sites included in the Cycle 2 Effects of Urbanization on Stream Ecosystems 

(EUSE) study in the Raleigh-Durham metropolitan area in North Carolina.......................88

31. Regional Synoptic Study design for assessing key stressors and biological 

response.......................................................................................................................................90

32. Bayesian network model for hypothetical urban study .......................................................91

33. Conceptual model for testing the effects of land use, habitat, and nutrients on 

biological integrity in an agricultural setting .........................................................................92

34. Example of a structural equation model of a coastal plain agricultural setting 

showing relations between land use, habitat, water chemistry, and invertebrate 

community condition..................................................................................................................92

35. Simulated nitrate concentrations in streams and public-supply wells .............................94

36. Conceptual model illustrating relations between environmental drivers, stressors, 

and receptors ..............................................................................................................................96

37. Total suspended sediment load estimated by using the SPARROW model......................98

38. Estimated yield of sediment transported to streams and rivers from catchments, 

expressed on a per unit area basis, by using the SPARROW model .................................98

39. Sources of sediment in the Kansas River Basin estimated using the SPARROW 

Decision Support System..........................................................................................................99

40. Total sediment load in streams and rivers in south-central Texas overlaid on 

land-use classes.........................................................................................................................99

41. Sources of sediment in the Trinity River Basin upstream from Livingston Lake............100

42. Estimated annual mean atrazine concentration for conterminous U.S. streams 

based on 2007 atrazine use.....................................................................................................102

43. Probability that the estimated annual mean atrazine concentration exceeds the 

Maximum Contaminant Level of three micrograms per liter.............................................102

Tables

1. Changes from Cycle 2 to Cycle 3 in the National Fixed Site Network................................23

2. Sampling strategy for National Fixed Site Network..............................................................35

3. Water-quality constituents or contaminant groups to be monitored for 

characterizing surface-water quality for human health......................................................36

4. Approximate number of Cycle 3 groundwater networks and wells...................................44

5. Water-quality constituents or contaminant groups to be monitored for 

characterizing groundwater quality for human health.........................................................45

6. Water-quality models to be used in Cycle 3 for prediction and forecasting ....................96

7. Scenarios for forecasting changes in land use and climate.............................................101

8. Potential climate and land-use change effects study areas. Note that additional 

study areas are likely to be added.........................................................................................103
ix

Conversion Factors

SI to Inch/Pound

Multiply By To obtain

Length

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

Area

square kilometer (km2

) 247.1 acre

square kilometer (km2

) 0.3861 square mile (mi2)

Volume

liter (L) 33.82 ounce, fluid (fl. oz)

liter (L) 2.113 pint (pt)

liter (L) 1.057 quart (qt)

liter (L) 0.2642 gallon (gal)

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

Altitude, as used in this report, refers to distance above the vertical datum.

Concentrations of chemical constituents in water are given in milligrams per liter (mg/L) or 

micrograms per liter (μg/L).

Abbreviations and Acronyms

AGNPS Agricultural Nonpoint Source Pollution Model

CADDIS Causal Analysis/Diagnosis Decision Information System

CMAQ Community Multiscale Air Quality Modeling System

DDT dichlorodiphenyltrichlorethane

DSS Decision Support System

E. coli Escherichia coli

ELOHA Ecological Limits of Hydrologic Alteration

ETN Enhanced Trends Network

EUSE Effects of Urbanization on Stream Ecosystems

FIFRA Federal Insecticide, Fungicide, and Rodenticide Act

FPS Flow-Path Study

GSFLOW Coupled Groundwater and Surface Water Flow Model

GWRP Groundwater Resources Program

HBSL Health-Based Screening Level

HPV high-production volume chemicals

HSPF Hydrologic Simulation Program—Fortran

IS Intensive Study

IWS Integrated Watershed Study

LGS Local Groundwater Study
x

LOADEST Load Estimator

LUS Land-Use Study

MAS Major Aquifer Survey

MCL Maximum Contaminant Level

MOC3D Method of Characteristics Solute Transport Model

MODFLOW Modular Groundwater Flow Model

MODPATH MODFLOW Particle Tracking Model

MOWS Modeling of Watershed Systems 

MRB major river basin

MT3D Modular 3-D Groundwater Solute Transport Model

NARS National Aquatic Resource Surveys

NASQAN National Stream Quality Accounting Network

NAWQA National Water-Quality Assessment

NEET Effects of Nutrient Enrichment on Stream Ecosystems

NEON National Ecological Observatory Network

NFSN National Fixed-Site Network

NMN National Monitoring Network

NOAA National Oceanic and Atmospheric Administration

NRP National Research Program

NTAS NAWQA National Target Analyte Strategy

O/E ratio of the observed value to the estimated reference condition value

PAA Principal Aquifer Assessment

PAH polycyclic aromatic hydrocarbons

PCB polychlorinated biphenyl

P-GWAVA Process-based Groundwater Vulnerability Assessment

PRMS Precipitation Runoff Modeling System

QPCR quantitative polymerase chain reaction

RGS Regional Groundwater Study

RSS Regional Synoptic Studies

SDWA Safe Drinking Water Act

SFIREG State FIFRA Issues Research and Evaluation Group

SPARROW Spatially Referenced Regressions on Watersheds

STREON Stream Experimental and Observatory Network

SWAT Soil and Water Assessment Tool

TANC Transport of Anthropogenic and Natural Contaminants to Supply Wells

TMDL Total Maximum Daily Load

TOPMODEL Topography-based Model

USDA U.S. Department of Agriculture

USEPA U.S. Environmental Protection Agency

USGS U.S. Geological Survey

WARP Watershed Regressions for Pesticides

WaterSMART Water (Sustain and Manage America’s Resources for Tomorrow)
xi

About this Report

This report presents a science plan for improved water-quality information and management for the third decade—Cycle 3—of the National Water-Quality Assessment (NAWQA) 

Program, which since 1991, has provided long-term, nationally consistent information on the 

quality of the Nation’s streams and groundwater. These plans for monitoring and assessment 

of the Nation’s freshwater quality and aquatic ecosystems during 2013–23 are based on an 

extensive evaluation of assessment progress by NAWQA and its partners during Cycles 1 and 2 

(1991–2012) and an updated analysis of stakeholder priorities. 

The purpose and scope of this report is to describe the science plan for Cycle 3 of the 

NAWQA Program. This plan describes four major goals for Cycle 3; the approaches for 

monitoring, modeling, and scientific studies; key partnerships required to achieve these goals; 

and products and outcomes that result from planned assessment activities. The science plan, as 

presented in this report, provides the framework for detailed design, but will still require much 

more detailed planning as decisions are made about the scope and implementation timeline for 

Cycle 3. A brief roadmap to the contents of this report follows. 

Introduction and Overview

The introduction explains the motivation and vision for Cycle 3 of NAWQA, why it is 

particularly needed now, how partnerships are vital to success, an overview of major goals and 

approaches, and finally, the information gained from Cycle 3 monitoring and modeling activities that can be used to improve, protect, and restore the Nation’s water quality. The guiding 

vision for the Cycle 3 design is that “Science-based strategies can protect and improve water 

quality for people and ecosystems even as population and threats to water quality continue to 

grow, demand for water increases, and climate changes.”

Cycle 3 Design Elements

This section outlines the specific objectives associated with each of the four Cycle 3 goals 

and describes each of the major design elements for implementing Cycle 3. These individual 

design elements for surface water and groundwater are then applied to specific design components for each objective in subsequent sections. The NAWQA Program strategy for waterquality assessment in Cycle 3 builds on proven approaches used in the previous two decades of 

the Program, including multi-scale, interdisciplinary assessments of critical hydrologic systems; 

systematic regional and national monitoring; detailed local-scale studies of governing processes 

and ecological effects; and modeling and statistical tools to integrate findings across multiple 

spatial and temporal scales. 

The surface-water design combines an enhanced national monitoring network that features 

perennial monitoring; greater contaminant coverage and application of continuous real-time 

water-quality monitoring; regional synoptic studies of specific topics; and integrated hydrologic 

and water-quality studies of representative large watersheds with local-scale intensive studies 

to answer specific questions. The groundwater design focuses on assessment of large principal aquifers, with a new goal of assessing groundwater quality in three dimensions, increased 

emphasis on groundwater quality from public supply wells, enhanced contaminant coverage, 

real-time continuous water-quality monitoring of shallow groundwater in selected aquifers, and 

groundwater flow and contaminant-transport modeling done at a range of scales. 
xii

Objectives and Approaches for Addressing Cycle 3 Goals

Remaining sections of the report describe the objectives and assessment approaches for 

each of the four Cycle 3 goals including: 

• objectives, 

• products, 

• policy and management relevance, 

• progress during Cycles 1 and 2, 

• study approaches, 

• planned studies, and 

• partnership opportunities

The objectives and approaches are presented somewhat differently for each of the goals, 

depending on the specific types of studies involved, their degree of integration, and the level of 

development for specific study designs.

Goal 1—Assess the Current Quality of the Nation’s Freshwater Resources 

and How Water Quality is Changing Over Time

The Cycle 3 design for monitoring surface water and groundwater addresses gaps in the 

current assessment of the Nation’s water-quality while also addressing issues identified by 

stakeholders as being important to maintaining or improving water quality in the future. A 

critical first step is to restore the NAWQA fixed-site network for monitoring water quality in 

the Nation’s streams and rivers; this network has suffered substantial declines in the number of 

sites and the frequency at which the sites are sampled between Cycles 1 and 2 (from approximately 500 sites monitored in Cycle 1 to 113 sites in 2011). Substantial increases in the number 

of surface-water sites (113 to 313 sites), annual sampling (at all sites), and the use of continuous water-quality monitoring (at most sites) are key features of the enhanced Cycle 3 design. 

In addition, several critical improvements that address key data gaps are included in the 

Cycle 3 design. These include (1) updated contaminant coverage; (2) enhanced characterization of contaminants in sources of public drinking-water supplies—with new emphasis on 

lakes, reservoirs, and on deeper parts of principal aquifers used for public supply; (3) expanded 

reference-site monitoring for tracking climate change and evaluating ecological background 

conditions; (4) a new effort to assess microbial contaminants in streams and rivers used for 

recreation; (5) enhanced monitoring of mercury trends in fish tissue; (6) a renewed emphasis on 

assessing trends in shallow groundwater quality; and (7) expanded assessment of contaminant, 

nutrient, and sediment loading to inland and coastal waters. 

The monitoring activities described for Goal 1 are essential for identifying and explaining 

trends in water-quality and ecosystem conditions (Goal 2), understanding the effects of climate 

change and human activities on water quality and aquatic biota (Goals 2 and 3), and also are 

essential for development and validation of water-quality models (Goals 2, 3, and 4).
xiii

Goal 2—Evaluate How Human Activities and Natural Factors, Such as 

Land Use, Water Use, and Climate Change, are Affecting the Quality of 

Surface Water and Groundwater

Studies to address Goal 2 are focused on developing explanations for, and understanding 

of, the observed patterns and trends in water quality. Such understanding is critical for evaluation of the effectiveness of implemented management practices and the susceptibility of water 

quality to degradation. Stressor studies examining sources and transport of contaminants, 

nutrients, and sediment, as well as streamflow alteration, will range in scale from individual 

stream reaches and groundwater flow paths to major river basins and principal aquifers. Modeling tools developed as part of this effort will be used to address Goals 1 and 3 by extrapolating findings to unmonitored areas, and new management strategies and the effects of potential 

future land use and climate change of water-quality and ecosystem conditions will be explored 

through Goal 4. 

Goal 3—Determine the Relative Effects, Mechanisms of Activity, and 

Management Implications of Multiple Stressors in Aquatic Ecosystems

Goal 3, which is receiving increased emphasis in Cycle 3, builds on Goals 1 and 2 by 

incorporating ecosystem processes and condition into water-quality assessment, understanding, 

and management. While Goals 1 and 2 provide the foundation for understanding the complex 

interactions of land use, climate, management practices, and major stressors (contaminants, 

nutrients, sediment, and streamflow alteration), Goal 3 focuses on understanding ecosystem 

response and on the development of regionally-based predictive models that relate stressors 

and management practices to effects on ecosystem condition. These models will be applied in 

Goal 4 to estimate the effects of future land use, climate change, and management strategies on 

aquatic ecosystems.

Goal 4—Predict the Effects of Human Activities, Climate Change, and 

Management Strategies on Future Water-Quality and Ecosystem Condition

A major new direction for NAWQA in Cycle 3 is the development of tools for waterresource managers and policy makers to forecast the effects that future changes in land use, 

water use, and climate may have on stressors and the suitability of water for human and aquatic 

ecosystem needs. These tools will be based on models that have been developed to meet other 

objectives of NAWQA assessments. Models assessing surface-water quality will be developed 

at regional (major river basin) to national scales, although time-varying models developed to 

assess the effects of changes in climate or land use will initially be developed at smaller scales. 

Groundwater models that couple flow and chemistry to assess groundwater availability will be 

developed at scales ranging from individual well fields to principal aquifers. Models to predict 

ecologic response will be done at the regional scale (level II or III ecoregion). NAWQA will 

evaluate which of the existing models are most suitable for estimating (within a quantified 

estimate of error) changes over time in water-quality and ecosystem conditions due to changes 

in climate, land and water use, and management practices.

Introduction and Overview

In 1991, the U.S. Congress established the National 

Water-Quality Assessment (NAWQA) Program within the 

U.S. Geological Survey (USGS) to develop long-term, nationally consistent information on the quality of the Nation’s 

streams and groundwater. During the last two decades, 

NAWQA has served as a primary source for nationwide 

information on the quality of streams and groundwater, how 

water quality changes over time, and how human activities and 

natural factors affect the quality of streams and groundwater. 

Objective and reliable data, water-quality models, and systematic scientific studies characterize where, when, and why 

the Nation’s water quality is degraded and what can be done 

to improve and protect it for human and ecosystem needs. 

This information is used by national, regional, state, and local 

stakeholders to develop effective, science-based policies 

for water-quality protection and management (see sidebar: 

“NAWQA Results Improve Water-Quality Management”).

This report presents the science plan for improved waterquality information and management for NAWQA’s third 

decade—Cycle 3—describing a 10-year strategy for national 

monitoring and assessment of the Nation’s freshwater quality 

and aquatic ecosystems during 2013–23. The science strategy 

for Cycle 3 is based on evaluation of progress by NAWQA and 

its partners during Cycles 1 and 2 (1991–2012) and an analysis 

of stakeholder priorities (Rowe and others, 2010). Specifically, 

input on key water issues and science needs has been solicited, 

reviewed, and supported by the National Research Council 

(2010, 2011, or 2012) and more than 50 internal and external 

stakeholders who provided input during the first three years of 

the planning effort (2008–11).

Vision

As the Program moves to its third decade, NAWQA’s 

guiding vision is that

“Science-based strategies can protect and improve 

water quality for people and ecosystems even as population and threats to water quality continue to grow, 

demand for water increases, and climate changes.”

NAWQA adheres to this vision by serving as one of the 

largest and most comprehensive programs that provides scientific information on the Nation’s freshwater resources. The 

Cycle 3 strategy was developed with the goal of meeting the 

Nation’s water-quality information needs, with a specific focus 

on meeting those particular needs that NAWQA is uniquely 

suited to fill (see sidebar: “NAWQA’s Unique Approach to 

National Assessment”). 

NAWQA’s approach combines nationally comprehensive 

and systematic monitoring with “targeted,” but nationally 

consistent, studies at multiple scales. The goal is to provide a 

better understanding of conditions, trends, and stressor-effects 

relations that are needed to improve the management of our 

Nation’s freshwater resources. Addressing questions such as 

“What is causing degradation of aquatic ecosystems?,” and 

“What can be done about it?” requires a “targeted” design 

such as NAWQA’s, which focuses on understanding the relations between water-quality conditions and human and natural 

factors that cause those conditions, including water sources, 

transport, seasonal differences, varying streamflow and groundwater contributions, and processes that control the movement 

of water. Information provided by NAWQA, as described 

further in this section of the report, complements information gathered by other national-scale water-quality programs, 

such as the U.S. Environmental Protection Agency (USEPA) 

National Aquatic Resources Surveys. The surveys assess 

water quality conditions in the Nation’s streams, rivers, lakes, 

wetlands, and coastal waters use a probability-based statistical 

design to address other important questions, such as “Is there 

a problem?” and “How prevalent is the problem?” NAWQA 

also complements state monitoring programs (which generally 

include multiple designs to address specific needs for the Clean 

Water Act or State regulatory programs) and many other government and academic programs that have varying and usually 

more specialized or research-oriented objectives.

The NAWQA 10-year strategy for 2013–23 is a comprehensive approach to fulfilling NAWQA’s unique and vital 

role in providing information needed to achieve the vision 

of science-based strategies that protect and improve water 

quality. The Cycle 3 plan continues strategies that have been 

central to the Program’s long-term success, but also adjusts 

Design of Cycle 3 of the National Water-Quality 

Assessment Program, 2013–23:

Part 2: Science Plan for Improved Water-Quality Information and Management

By Gary L. Rowe, Jr., Kenneth Belitz, Charlie R. Demas, Hedeff I. Essaid, Robert J. Gilliom, Pixie A. Hamilton, 

Anne B. Hoos, Casey J. Lee, Mark D. Munn, and David W. Wolock
2 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

approaches, monitoring intensity, and study design to address 

the needs of the next decade. Restoration of degraded monitoring networks and new directions in modeling and interpretative studies also are needed to meet the growing and evolving 

public and stakeholder needs for water-quality information and 

improved management, particularly in the face of increasing 

challenges related to population growth, increasing demands 

for water, and changing land use and climate.

Why Now?

Growing and constantly changing demands for clean water 

for humans and aquatic ecosystems are fueling an increasing 

urgency to protect our Nation’s water quality. Because water 

quality continues to decline, even as the demand for clean water 

is increasing, and Federal and state water-quality monitoring 

and assessment activities are decreasing, changes in historical 

approaches to water quality management are needed now. An 

updated assessment of water-quality monitoring needs is being 

conducted by the NAWQA Program and is important in shaping 

the Cycle 3 approach to rebuilding the Nation’s monitoring and 

assessment networks in conjunction with expanded Federal and 

State partnerships. 

Water-Quality Problems and Complexity are 

Increasing as Demand for Clean Water Grows 

Forty years ago, when “water quality” became a national 

issue and the Clean Water Act became law, national efforts 

were focused on the control of point-source contamination 

from “end-of-pipe” discharges, such as those associated with 

sewage treatment plants or factories. Substantial progress 

towards cleaner water resulted from engineering improvements in manufacturing processes and wastewater treatment 

(Dubrovsky and others, 2010). 

Unfortunately, continued advances in wastewatertreatment technology are no longer sufficient to address our 

Nation’s water-quality issues. The most important threats to 

the quality of our surface-water and groundwater resources 

are now spread over areas much larger than those affected by 

“end-of-pipe” point-source discharges, and include diffuse 

and widespread sources of contaminants that can affect entire 

watersheds. The sources of such “nonpoint” pollution, such as 

contaminants in runoff and groundwater recharge from urban 

or agricultural areas, are more difficult to pinpoint, evaluate, 

and control. In addition, specific effects on drinking-water 

quality or aquatic ecosystem condition usually are more difficult to define. Overall, we still haven’t answered the question 

“How do human activities in agricultural, urban, and natural 

settings affect water quality, cause changes in hydrologic 

systems, and degrade aquatic habitats?” at a level sufficient 

to meet the information needs of most water-resource managers. Also, the cumulative long-term effects of the introduction 

of hundreds of synthetic organic compounds on humans or 

aquatic biota, how to manage and reduce nutrient delivery to 

inland and coastal waters, and how to balance flow requirements in our streams and rivers to minimize habitat degradation 

and meet the needs of both humans and aquatic ecosystems are 

still largely unknown.

What we do know, however, is that we face a litany of 

water-quality issues that continues to grow. Key examples 

NAWQA Results Improve Water-Quality Management

Local, state, tribal, regional, and national stakeholders use NAWQA information to develop strategies for managing, 

protecting, and monitoring freshwater resources in different hydrologic and land-use settings across the Nation, such as to:

• Support development of regulations and guidelines that address the complex nature of contaminant occurrence, 

including contaminant mixtures, seasonal patterns, and variability among different environmental settings;

• Identify key sources and characteristics of nonpoint-source contamination in agricultural and urban areas;

• Prioritize geographic areas, aquifers, and watersheds in which water resources and aquatic ecosystems are most 

vulnerable to contamination; 

• Improve strategies and protocols for monitoring, sampling, and analysis of all hydrologic components, including 

the atmosphere, surface water, and groundwater;

• Contribute to State assessments of the beneficial uses of streams and impaired water (Total Maximum Daily Loads, 

or TMDLs), and development of strategies for source-water protection and management, pesticide and nutrient 

management plans, and fish-consumption advisories; and

• Sustain the health of aquatic ecosystems through improved stream protection and restoration management. 

Access http://water.usgs.gov/nawqa/xrel.pdf to see how local, State, regional, and national stakeholders use NAWQA 

information.
Introduction and Overview 3

NAWQA’s Unique Approach to National Assessment

The following describe unique aspects of NAWQA’s approach to national assessment:

• Interdisciplinary and dynamic studies that link chemical and physical conditions of streams (such as flow and habitat) with ecosystem health and the biological condition of algae, macroinvertebrate, and fish communities. Conditions are evaluated in a hydrologic context, which is important because contaminants and their potential effects on 

drinking-water supplies and aquatic ecosystems vary over time and depend largely on the amount of water flowing 

in streams and discharging from aquifers. By incorporating interconnections among water quality, hydrology, and 

biological systems, NAWQA assessments address the susceptibility of aquatic organisms to chemical and physical 

degradation and determine how ecosystem health and biological responses vary among the diverse environmental 

settings across the Nation.

• Targeted design, in which study areas and monitoring locations are chosen because they represent important 

environmental settings across the country. The NAWQA design targets sites that represent certain land uses (such 

as agricultural and urban areas) and monitors these sites over a range of hydrologic conditions to assess seasonal 

or climatic effects. Understanding sources of water and how that water is transported is critical to understanding 

and predicting water-quality conditions and effects on human and ecosystem health. The knowledge gained by this 

approach helps decision makers to identify streams and aquifers that are most vulnerable to contamination, target 

actions based on causes and sources of contamination, and monitor and measure the effectiveness of those actions 

over time. 

• National design that stresses consistent sampling and analytical methods, which allows water issues to be 

addressed at multiple scales, ranging from local to national. The design ensures that water-resource conditions—

including chemical, biological, and physical characteristics—in a specific locality or watershed can be compared 

to those in other geographic regions and can be aggregated for national assessment. NAWQA thereby builds local 

knowledge about the condition of water resources, emerging issues, and controlling processes in specific basins and 

aquifers. At the same time, NAWQA builds an understanding of how and why water conditions vary regionally and 

nationally. 

• Long-term monitoring so that trends in water quality can be analyzed to determine whether conditions are getting 

better or worse. Consistent and systematic information collected over many years helps to distinguish long-term 

trends from short-term fluctuations. Analysis of long-term trends is essential for assessing how environmental controls and best-management practices are working and for choosing cost-effective strategies for the future.

• Integration of modeling and monitoring so that water-quality understanding can be extrapolated to unmonitored 

areas, trends can be predicted, and future water-quality conditions can be better anticipated as a result of various 

resource, climatic, and land-management scenarios. Statistical and process-based models are used to address specific 

questions—now and into the future—with a focus on the linkages among sources, transport, and fate of contaminants.

include recognition that almost two-thirds of our major estuaries 

are affected by excess nutrients and related dead zones that no 

longer support fish and other life; 42 percent of our streams are 

impaired and not meeting beneficial uses, such as for drinking, 

recreation, and ecosystem health because of habitat degradation, nutrients, or sediment; 83 percent of our streams in urban 

areas were found to have at least one pesticide that exceeded 

criteria set to protect aquatic life; and more than 20 percent of 

our public and domestic wells—which serve about 150 million 

people—contain at least one contaminant at levels of potential 

health concern (see sidebar: “Ever-Increasing Water-Quality 

Issues Face the Nation”). 

These and other water-quality issues will not go away 

without improved, science-based strategies and, moreover, 

such issues will tend to worsen as our population grows. 

The U.S. Census Bureau projects that the Nation’s population will increase by approximately 130 million people 

by 2050, to a total of almost 440 million (Vincent and 

Velkhoff, 2010). With population growth comes expanded 

development of land for agricultural and urban use, 

increased use of fertilizers and pesticides for food production and urban landscaping, increased use of synthetic 

organic compounds, hydrologic modification of rural and 

urban landscapes, and increased demand for water to supply human and ecosystem needs. 

Increased climate variability and change (with associated changes in the amount and timing of precipitation 

and temperature) are expected in addition to increased 

stress on water quality related to human activities. The two 

pervasive factors that affect water-quality trends (changes 
4 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Ever Increasing Water-Quality Issues Facing Our Nation

• Forty-two percent of wadeable stream miles in the United States are in poor or degraded condition compared to reference conditions (U.S. Environmental Protection Agency, 2006). Widespread causes include nutrients and habitat 

disturbance, which are greatly affected by streamflow alteration and sediment. NAWQA findings indicate that one 

or more pesticides exceed concentrations of potential concern to aquatic life in 57 percent of streams in agricultural 

areas and in 83 percent of streams in urban areas (Gilliom and others, 2006). 

• Sixty-four of 99 major U.S. estuaries studied in 2004 have been adversely affected by excessive nutrient loading. 

The spread of coastal dead zones (areas of low dissolved oxygen) are projected to worsen through 2020 in 48 of 

these estuaries, as population growth, agricultural production, and other development results in an increase in nutrient inputs to coastal waters (Diaz and Rosenberg, 2008; Rockstrom and others, 2009). 

• Artificially modified landscapes—including straightened stream channels in agricultural areas and increases in the 

number and extent of impervious areas in urban areas—alter streamflow and degrade habitat. A NAWQA assessment found that 86 percent of 2,888 sites across the Nation with streamflow alteration had modified minimum and 

maximum flows (Carlisle and others, 2010b). Habitat changes and losses, often caused by streamflow alteration, are 

leading causes for the listing of more than 90 percent of threatened or endangered aquatic species under the Endangered Species Act (Wilcove and others, 1998).

• Population growth increases demand for drinking water at the same time it increases potential sources of contaminants. A USEPA national analysis of more than 15 million analytical records from public water systems during 

1998 to 2005 showed that exposure to concentrations of one or more regulated contaminants above a Maximum 

Contaminant Level was relatively common, including about 14 percent of the population for nitrate, 7 percent for 

tetrachloroethylene, and 12 percent for uranium (U.S. Environmental Protection Agency, 2009). 

• NAWQA findings for public-supply wells, which provide water to about 105 million people, showed that 22 percent of 

source-water samples contained at least one contaminant at levels of potential health concern (Toccalino and Hopple, 

2010). Similarly, 23 percent of samples from domestic (or privately owned) wells, which supply an additional 43 million people and are usually untreated, also had contaminant levels of potential concern (Desimone and others, 2009).

in land and water use with population growth, and climate 

variability) act simultaneously, but to varying degrees in 

different areas and at different times, sometimes the factors 

affect physical characteristics, such as streamflow, temperature, and sediment; sometimes they affect chemical 

characteristics; and sometimes both—but all factors ultimately affect the sustainability of available water supplies 

for current and future human and ecosystem needs.

The complexities of hydrologic systems and human 

activities on the landscape mean that we can no longer 

approach water issues through single-discipline science. 

Instead, meeting this challenge demands reliable and objective interdisciplinary data on the physical, chemical, and 

biological conditions of our water resources, as well as an 

understanding of the changes to human activities and natural 

factors that contribute to those conditions. Only by investing 

in improved monitoring and assessment will we be able to 

separate the effects of human activities from natural effects, 

identify the physical, chemical, and biological processes 

controlling the quality of our waters, and develop predictive 

tools that provide realistic and reliable projections of future 

conditions. These investments are essential for effective, 

science-based water-quality management strategies. 

Declining Monitoring Infrastructure and 

Investment in Water-Quality Science Threaten 

Our Ability to Assess and Solve Water-Quality 

Problems

Over the past 10–15 yr, Federal, State, and academic 

partners in the water community have faced substantial 

budget cuts that have reduced national monitoring networks and the collection of water-quality information. The 

NAWQA Program, for example, currently (2012) operates 

a “national” surface-water-trend network composed of 113 

stream and river sites, only about 40 of which are monitored 

during any given year. This represents a substantial decline 

from the 1990s, when almost 500 sites were monitored by 

NAWQA. The lack of maintained monitoring sites parallels 

similar declines in the amount of surface- and groundwaterquality data collected by other Federal and State agencies 

(fig. 1).

Some reductions in water-quality data collection and 

studies can be compensated for with models and other 

statistical tools, but models are only as good as the data 

that are available for their development and validation. For 

example, the USGS national model of nutrient sources and 
Introduction and Overview 5

transport—the Spatially Referenced Regression on Watersheds (SPARROW) model—was initially calibrated using 

data collected by both Federal and State agencies from 

435 sites (Smith and others, 1997). In 2012, only 35 of those 

sites were still being monitored for model calibration. The 

sparseness of ongoing data collection by USGS and other 

Federal and State agencies may limit model applications and 

will increase the uncertainty associated with future versions 

of the models and the accuracy of spatial extrapolations and 

predictions of future water-quality change. 

Of equal importance to the decline in water-quality data 

is that national investments in spatial and temporal information on the distribution and characteristics of factors that affect 

water quality (such as landscape features, human activities, 

and environmental settings) remain substantially inadequate 

and out-of-date. This includes, for example, spatial data on 

factors such as use of pesticides, fertilizers, and other chemicals; land- and water-use; land-management practices; hydrologic settings; and fluxes of chemicals from point sources. 

Overall, understanding the factors responsible for observed 

water-quality and stream ecosystem condition will advance 

only if current data on water-quality conditions and the related 

causative factors on the landscape are available. Our ability to 

design effective solutions will be remain greatly limited unless 

we invest in these essential geospatial and time-series environmental datasets as part of our investments in water-quality 

monitoring and science.

Scientific Foundation and Partnerships are Well 

Positioned to Make Rapid Progress

Fortunately, 20 yr of monitoring, modeling, and research 

have provided a solid foundation of data and scientific understanding to allow the water community to be able to address 

today’s increasingly complex water-quality issues (see, for 

example, sidebar: “Looking Back on NAWQA Since 1991”). 

Results of NAWQA studies have been used by stakeholders 

to inform water-resource policy and management decisions at 

scales ranging from local to national (http://water.usgs.gov/

nawqa/xrel.pdf). 

Moreover, the scientific foundation has also benefitted 

from periodic statistical surveys of the Nation’s waters by the 

USEPA in collaboration with its partners in the states, tribes, 

and other Federal agencies. The National Aquatic Resources 

Surveys, done in collaboration with the states, help to answer 

key questions, such as “What are the most significant waterquality problems?,” “Where are problems occurring?,” and 

“Is water quality improving?” USEPA and the state environmental agencies use the NARS data to develop and evaluate 

water-quality standards, identify impaired waters, and prioritize monitoring and management needs. Nationwide, coastal, 

lake, wetland, and wadeable stream assessments have been 

completed and a new survey of wadeable streams is scheduled 

for 2013 (http://water.epa.gov/type/watersheds/monitoring/

nationalsurveys.cfm). 

EXPLANATION

25,000

50,000

75,000

100,000

125,000

150,000

1925 1935 1945 1955 1965 1975 1985 1995 2005

Number of samples

Year

0

Streams

Groundwater

Figure 1.1

Figure 1. Numbers of nitrate samples from streams and groundwater illustrate the decline in monitoring 

by Federal and State agencies that has occurred over the past 20–25 years (yr), even for one of the most 

commonly monitored contaminants. Sample numbers are estimated from U.S. Environmental Protection 

Agency and U.S. Geological Survey (http://waterdata.usgs.gov/nwis/qw) databases and include nitrate 

and nitrite plus nitrate analyses. An exception to the overall trend is an increase in samples for streams 

and rivers in the early to mid 1990s; this short-term increase is attributed to NAWQA sampling during 

Cycle 1, but the peak was soon followed by an even sharper decline over the past 10–15 yr (Jerad Bales, 

U.S. Geological Survey, written commun., December 2010).
6 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Looking Back on NAWQA Since 1991—An Evolution of Approaches and Outcomes from Cycle 1 

and Cycle 2

The approaches and outcomes of NAWQA assessments during Cycles 1 and 2 provide a useful perspective for developing 

the Cycle 3 strategy. An overview is provided, with additional details available in noted online sources.

Cycle 1:

During 1991–2001, the NAWQA Program focused on interdisciplinary baseline assessments of the quality of streams, 

groundwater, and aquatic ecosystems in 51 of the Nation’s river basins and aquifers (referred to as “study units”). These 

assessments supported sampling of 505 stream sites and more than 6,000 wells. Each study-unit produced a USGS summary publication written for a broad audience interested in resource management, regulations, and policy at the local level 

(http://water.usgs.gov/nawqa/nawqa_sumr_complete.html). In each publication, the occurrence and distribution of pesticides, nutrients, volatile organic compounds, trace elements, dissolved solids, and radon are described, as well as the condition of aquatic habitat and algae, macroinvertebrate, and fish communities. The assessments relate contaminant sources, 

land and chemical use, hydrology, and other human and natural factors to water quality and the status of aquatic communities. Results are placed in the context of human-health and aquatic-life benchmarks, which indicate what these conditions 

imply for the protection and safety of drinking water, for the health of aquatic ecosystems, and for resource management. 

The consistent, multi-scale approach of Cycle 1 provided information that is needed to synthesize a broad understanding of 

how and why water quality varies regionally and nationally and enabled comparisons of how human activities and natural 

processes affect water-quality and biological conditions among the Nation’s diverse geographic and environmental settings. Major outcomes included comprehensive national assessments of pesticides, nutrients, volatile organic compounds, 

and aquatic ecology at the national scale and data synthesis and comparative analysis at the study-unit scale (http://water.

usgs.gov/nawqa/nawqa_sumr.html).

Cycle 2

During 2002–2012, NAWQA built on the baseline study-unit assessments of Cycle 1 by increasing emphasis on assessment of long-term trends. This was done by adding topical studies of priority water-quality issues that evaluated hydrologic 

processes and human activities that affect the quality of streams and groundwater. Selected new status assessments were 

also conducted, including an initial study of contaminants in currently used sources of drinking water. For trend assessment, long-term monitoring was established at 113 streams representing eight major river basins, and at groundwater 

sites representing 20 principal aquifers with more than 10 to 15 yr of consistent monitoring data available. Topical studies 

evaluated links among sources of contaminants, their transport through the hydrologic system, and the potential effects of 

contaminants and other water-quality disturbances on humans and aquatic ecosystems. The topical studies focused on: (1) 

the fate and transport of agricultural chemicals; (2) effects of urbanization on stream ecosystems; (3) effects of nutrient 

enrichment on stream ecosystems; (4) transport of contaminants to public-supply wells; and (5) bioaccumulation of mercury in stream ecosystems (http://water.usgs.gov/nawqa/studies/topical_studies.html). Each topical study included several 

nationally distributed study areas that ranged from a few square kilometers to a few hundred square kilometers that were 

nested within selected study units. 

The topical studies were integrated with continued regional and national synthesis assessments during Cycle 2. For 

example, the topical study of effects of nutrient enrichment on stream ecosystems is an integral part of the national synthesis summary report on nutrients in streams and groundwater. The topical study on mercury helps to explain occurrence 

and processes controlling mercury in fish, sediment, and water in streams across the Nation. Regional assessments consider 

water-quality conditions and trends in eight major river basins (http://water.usgs.gov/nawqa/studies/mrb) that discharge 

into some of the Nation’s key estuaries, including the Gulf of Mexico, Chesapeake Bay, Puget Sound, and the Great Lakes, 

as well as 19 of the Nation’s 62 principal aquifers (http://water.usgs.gov/nawqa/studies/praq/). 

The development and application of water-quality models has been integral to the success of the NAWQA Program in Cycle 2. 

The integration of modeling with monitoring helps to extend water-quality understanding to unmonitored areas under a range 

of possible circumstances. The models are essential tools for cost-effective management of water resources because managing 

contaminants requires far more information than we can afford to directly measure for all the places, times, and contaminants 

that are important. In addition, many management decisions—including how much to spend on implementing a management 

strategy, monitoring priorities, and registering pesticides—inherently depend on predicting the potential effects on water quality 

for locations that have never been monitored. The NAWQA models integrate information on water quality, chemical use, land 

use, and environmental drivers that help to explain how water-quality conditions vary regionally and nationally. A variety of 

models have been used in Cycle 2, including statistical models, detailed simulation models, and hybrid models.
Introduction and Overview 7

The surveys provide snapshots of water quality and 

ecosystem conditions that are not duplicated by NAWQA and 

provide information and data that are highly complementary 

to NAWQA. Integration of NAWQA and USEPA studies and 

data is an ongoing activity for both agencies, and has already 

resulted in an enhanced assessment of the factors affecting 

invertebrate communities and the condition of stream ecosystems across the country (Carlisle and others, 2008). 

Examples of important water-quality advances since 1991 

by NAWQA and its partners include: 

• Established interdisciplinary baseline assessments of 

streams, groundwater, and aquatic ecosystems in 51 of 

the Nation’s major river basins and aquifers; 

• Synthesis of water-quality conditions for the Nation’s 

streams and groundwater for nationally important 

water-quality concerns such as pesticides, nutrients, 

and volatile organic compounds VOCs; 

• Assessed trends in stream and groundwater quality 

based on almost two decades of monitoring in diverse 

environmental settings across the Nation; 

• Developed national- and regional-scale water-quality 

models; 

• Made important progress toward understanding (1) the 

interactions among sources of contaminants, and (2) 

physical, chemical, and biological processes that control the transport and transformation of contaminants 

through the hydrologic system; and

• Made important progress toward understanding the 

potential effects of nutrients, contaminants, and other 

stressors on aquatic ecosystems. 

Results of NAWQA studies have been used by stakeholders 

to inform water-resource policy and management decisions at 

scales ranging from local to national (http://water.usgs.gov/

nawqa/xrel.pdf). 

In addition to these and other advances in our scientific 

understanding, partnerships are now well developed for collaboration on water-quality assessment. Since its inception, 

NAWQA has striven to collaborate with Federal, state, and 

local governmental organizations, public interest groups, 

professional and trade associations, academia, and private 

industry to remain relevant to the needs and interests of these 

organizations. Such collaboration helps NAWQA address the 

most important water-resource issues facing our Nation, fill 

the most critical information niches, and get the most possible benefit from all available data and studies. The NAWQA 

Program remains committed to integrating information and 

data from other Federal and state agencies and other organizations into national assessments, where appropriate, so 

that findings more comprehensively span geographic and 

temporal scales and the different components of our water 

resources. Fortunately, such integration is increasingly possible as technology and expertise advance in the areas of data 

collection and exchange, assessment, modeling, compatible 

Web services, and reporting. 

Collaboration and partnerships not only increase 

geographic and temporal coverage through integration 

of multiple data sources, but also are critical to success 

because no single program can address all national water 

issues, and NAWQA’s approach cannot answer all of our 

water-quality questions. Some questions require a different approach and a specific set of data collected in certain 

places and times. For example, the scope of NAWQA is 

limited to freshwater streams, rivers, and aquifers. The 

NAWQA Program is not designed to assess water-quality 

conditions in estuaries, the near-shore marine environment, 

the oceans, or the Great Lakes. In these cases, partnerships 

are essential, and NAWQA information plays a key role 

in providing coordinated and consistent monitoring and 

modeling to other agencies that helps to track contaminant 

sources in watersheds and the amount and timing of sediment, nutrients, and contaminants delivered to receiving 

waters—information that is critical to supporting healthy 

coastal waters and ecosystems.

The following ongoing or potential external NAWQA 

partnerships are highlighted, but more detailed information on 

specific partnerships being explored is provided later in relation to specific goals, objectives, and approaches: 

• Partner with the National Water-Quality Monitoring 

Council and its Federal, state, tribal, and nongovernmental members to develop a national longterm collaborative network of reference sites;

• Partner with the National Ecological Observatory 

Network (NEON; http://neoninc.org/) to coordinate 

interdisciplinary monitoring for better understanding of 

nutrient processing in streams; 

• Partner with the National Oceanic and Atmospheric 

Administration (NOAA) and National Federation of 

Regional Associations to relate nutrient and sediment 

loadings from the land to ecosystem conditions in 

coastal estuaries; 

• Partner with the U.S. Department of Agriculture 

(USDA) to evaluate the effectiveness of conservation 

and management practices on water quality; and 

• Partner with USEPA, NOAA, and USDA to improve 

models and decision-support tools for predicting the 

effects of changing human activities and climate on 

water quality and aquatic ecosystems. 

In addition to partnerships with other agencies, partnerships with programs within USGS also are critical to success 

and for leveraging data collection, technical expertise, and 

complementary research topics. For example, this science plan 

is designed to deliver critical water-quality data and information that directly support other major USGS water programs, 

including evaluation of water availability and use as constrained by water quality and development of ecological flow 
8 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

requirements with the Water Census [WaterSMART—Water 

(Sustain and Manage America’s Resources for Tomorrow; 

http://www.doi.gov/watersmart/ ) Program. The science plan 

is also designed to deliver coordinated assessments of groundwater availabilitiy in specific aquifers by partnering with the 

Groundwater Resources Program (http://water.usgs.gov/ogw/

gwrp/). The strategy also contributes to the development of 

a national reference watershed-monitoring network, which 

will support the Global Change Program (http://www.usgs.

gov/global_change/), Toxic Substances Hydrology Program 

(http://toxics.usgs.gov/), and Contaminant Biology Program.

Topics for collaboration with other USGS programs are 

aligned along common goals outlined in the USGS science 

strategy for the decade 2007–2017 (U.S. Geological Survey, 

2007). The Cycle 3 design provides a national framework of 

monitoring and assessment for NAWQA and other programs 

to support recently reorganized mission areas of the USGS, 

particularly programs related to water, environmental health, 

ecosystems, and climate and land-use change. Selected contributions to specific mission areas include the following:

• Ecosystems Mission Area through continued monitoring and assessment of trends in the biological conditions of streams; improving our understanding of how 

environmental change affects ecosystem services; 

describing effects of chemical, physical, and hydrologic stressors on aquatic ecosystems; and developing 

models for predicting aquatic ecosystem response to 

land-use change and climate variability.

• Climate and Land Use Change Mission Area through 

continued long-term monitoring of flow, water quality, and biological condition in streams and rivers; 

increased monitoring of climate-sensitive reference 

streams; expanded collection of real-time data for temperature and other properties to differentiate short-term 

variability from long-term change; and development 

of models and decision-support tools that forecast how 

water quality and aquatic ecosystems will respond 

under different climate and land-use change scenarios. 

• Environmental Health Mission Area through 

expanded monitoring of source waters used for 

drinking-water supply including streams, rivers, lakes, 

reservoirs, and aquifers; assessments of sediment and 

fish-tissue quality for contaminants of concern for 

humans and aquatic biota; monitoring of microbial 

contaminants and algal toxins in surface water used 

for recreation; and enhanced tracking of contaminant 

movement at the watershed and aquifer scale. 

• Water Mission Area through assessments of the 

Nation’s water quality with respect to its suitability for 

human use and for maintaining healthy aquatic ecosystems, the extent and severity of streamflow alteration 

(changes in the hydrologic regime) and its effects on 

aquatic ecosystems; development of three-dimensional 

models of flow and chemistry in selected principal 

aquifers to assess groundwater availability; and development and testing of improved water-quality models 

for simulating concentrations and loads of nutrients, 

sediment, and other contaminants in streams and rivers 

from headwaters to receiving waters. 

• Core Science Systems by providing data and information on water quality and ecosystem condition available in a format that is understandable and accessible. Although this has been a long-term goal of the 

NAWQA Program, in Cycle 3 new emphasis will be 

placed on rapid delivery of data and findings and on 

the delivery of tools and models that facilitate management of critical water resources. 

Priorities and Goals for NAWQA Cycle 3

Periodic evaluations of assessment goals, approaches, 

and products have played a key role in enabling NAWQA 

to stay abreast of stakeholder priorities. In 2009, stakeholders identified 11 priority issues that they consider important 

for NAWQA to address (Rowe and others, 2010). Six of the 

issues reflected specific water-quality “stressors,” such as 

contaminants and sediment that directly affect water quality 

and its suitability for use by humans and aquatic ecosystems. 

The other five issues reflected large-scale “environmental 

drivers,” such as land use and climate change, which directly 

affect the water-quality stressors. Two “environmental drivers” 

of change—climate and shifts in land and water use related 

to population trends—and four water-quality stressors—

contaminants, nutrients, sediment, and streamflow alteration—

were identified as the most critical threats to the sustainability 

of water resources for the health of humans and aquatic 

ecosystems (fig. 2). 

Cycle 3 centers on four major goals that will guide 

development of the interdisciplinary studies that are needed to 

address the priority stressors and their effects on water quality. 

Goal 1 focuses on the physical, chemical, and biological characteristics of our waters and how they are changing over time. 

Goal 2 focuses on analyzing the effects of human and natural 

factors on water-quality stressors. Goal 3 assesses the effects 

of these stressors on stream ecosystem condition. Goal 4 is 

about forecasting the effects of the environmental change and 

stressors on water quality in the future. These interrelated 

goals maintain and expand on original NAWQA goals and 

collectively are critical to achieving the vision set forth for 

NAWQA in Cycle 3 (see sidebar: “Vital Connections Among 

Cycle 3 Goals”).

Goals 1 and 2 continue NAWQA goals that were initiated in 1991, which are to assess the status and trends in 

water-quality conditions and to evaluate the natural and 

human factors that affect those conditions. Although these 

broad goals have remained unchanged, greater emphasis 

has been placed since 2001 on evaluation of trends and 
Introduction and Overview 9

identifying the factors responsible for observed trends. Additional shifts related to Goals 1 and 2 are included in Cycle 3, 

based on stakeholder input and findings to date, notably 

including the addition of sediment and streamflow alteration, increased emphasis on the quality of deep groundwater 

used for public supply, and increased assessment of nutrient 

and sediment loads to estuaries. Goals 3 and 4, however, 

encompass the greatest changes in scope for Cycle 3 and 

extend NAWQA assessments much further into two critical 

areas: (1) determining the effects of multiple stressors on 

aquatic ecosystems and (2) forecasting future water-quality 

conditions. Examples of policy-relevant questions raised by 

water-resource managers and NAWQA stakeholders in relation to NAWQA Program goals established for Cycle 3 are 

listed below: 

Goal 1: Assess the current quality of the Nation’s freshwater resources and how water quality is changing over 

time: 

• Are water-quality goals, standards, and criteria being 

met for safe drinking and sustainable ecosystems at 

regional and national scales?

• Where are water-quality problems most severe?

• Where and how are water-quality conditions changing 

over time?

• What are the freshwater inflows and loads of nutrients, 

sediment, and contaminants to estuarine ecosystems, 

the Great Lakes, and other receiving waters? 

Goal 2: Evaluate how human activities and natural factors, 

such as land use, water use, and climate, are affecting the quality of surface water and groundwater.

• Are the most important point and nonpoint sources of 

contaminants being addressed by current management 

strategies?

Contaminants Nutrients Sediment

Drivers

Stressors

Receptors

Streamflow

alteration

Human

health

Aquatic

ecosystems

Climate and

other natural

factors

Population

growth, land

and water use

Figure 1.2

Figure 2. The Cycle 3 design is based on an interdisciplinary approach to determine where, when, and how the 

physical, chemical, and biological quality of water resources is affected by four major stressors: contaminants, 

nutrients, sediment, and streamflow alteration, all of which are simultaneously affected by large-scale environmental 

drivers related to climate and other natural features or are related to population growth, land and water use, and 

associated human activities. Additional feedback loops, exist between human activities and climate, and between 

aquatic ecosystems and individual stressors; for example, the effects of biological activity on nutrient concentrations 

in streams, rivers, and coastal estuaries. These large, indeed global-scale environmental drivers are most important 

with respect to governing the ultimate sustainability of available water resources for human health and healthy aquatic 

ecosystems.
10 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

• Are protection, conservation, and remediation programs working effectively to control sources and 

transport of contaminants?

• What strategies are needed to protect sources of drinking water?

• What areas should be targeted for more intensive monitoring, protection, or remediation?

• What are the sources and transport processes controlling nutrient, contaminant, and sediment loads delivered to estuarine ecosystems, the Great Lakes, and 

other receiving waters? 

Goal 3: Determine the relative effects, mechanisms of activity, and management implications of multiple stressors on 

aquatic ecosystems. 

• What is the importance of various physical and chemical stressors on ecosystem condition, and which are 

most important to control?

• Which management strategies will most effectively 

improve and protect ecosystem condition? 

• What ecological measures are most appropriate as 

early warning indicators for assessing ecosystem 

degradation due to physical or chemical stressors and 

for monitoring recovery after changes in management 

practices? 

• What levels of stressors can be tolerated by aquatic 

ecosystems and how can this information best be used 

to develop regional thresholds for use in management 

issues such as nutrient criteria? 

Vital Connections Among Cycle 3 Goals

To achieve the vision expressed for Cycle 3, this science plan establishes four goals that represent an integrated approach 

to water-quality assessment. The goals are not intended to be pursued in exclusion to the other goals. Instead they represent 

high-priority areas identified by NAWQA stakeholders where Program resources should be directed over the next decade. 

Approaches used to achieve the four science goals will either depend on or affect products and outcomes from the other 

goals, as follows:

• Goal 1 continues NAWQA’s ongoing, long-term commitment to monitor surface-water and groundwater quality 

at multiple scales. Data collected will be used to assess geographic patterns and temporal trends in water quality 

across the Nation. These data are also essential for development and validation of water-quality models produced as 

part of Goals 2, 3, and 4. 

• Goal 2 continues NAWQA’s long-term goal to link the nature and distribution of water-quality conditions, as well 

as changes and trends in water quality and aquatic ecosystem condition, to the human and natural factors that affect 

water quality and aquatic ecosystem condition. Goal 2 studies focus on developing explanations for the observed 

patterns and trends in water quality identified by Goal 1 monitoring activities. This understanding is critical for 

evaluating the effectiveness of management practices and effects on ecosystem services. Modeling tools developed 

as part of Goal 2 studies will be used in Goal 1 assessments to extrapolate findings to unmonitored areas and in 

Goal 4 to explore the effect of different management strategies, changing land or water use, and climate-driven 

changes in hydrology on water quality and aquatic ecosystem condition. 

• Goal 3 studies evaluate relations between important water-quality and hydrologic stressors that cause degradation 

of stream ecosystems; findings will be incorporated into regional ecological models that examine the interdependent effects of multiple stressors. These models, which predict the effects of stressors on ecosystem condition for 

specific land-use and environmental settings, will be applied to meet the Goal 4 objective to evaluate the effects of 

management practices and future land use on stream ecosystem condition. Evaluating the effectiveness of strategies 

to control adverse effects on steam ecosystems will rely heavily on the understanding gained from Goal 2 studies 

and models. 

• Goal 4 predictions of the effects of future scenarios of land use, management strategies, and climate on waterquality and ecosystem conditions depend on the data and models developed from monitoring and studies conducted 

as parts of Goals 1, 2, and 3. Achieving Goal 4 also depends on scenarios of future management, land use, water 

use, and climate made by other USGS programs, agencies, and stakeholders.
Introduction and Overview 11

Goal 4: Predict the effects of human activities, climate 

change, and management strategies on future water-quality 

and ecosystem condition.

• How will projected changes in climate, population, 

land use, water use, management actions, and other 

human activities affect water quality for future beneficial uses?

• Which strategies will most effectively improve and 

protect biological communities and ecosystem conditions as land use and climate change over time?

• Which management strategies are most cost effective?

• What are the expected lag times between implementation of management practices and beneficial 

outcomes?

• Is water quality more sensitive to changes in climate or 

to human activities at the land surface?

Introduction to the Cycle 3 Approach

Partners, stakeholders, and the National Research Council 

(2011) offered two recommendations to guide the updated strategy for Cycle 3. First, NAWQA should stay on course with the 

overall approach used for national assessment in Cycles 1 and 

2 by maintaining priorities on national-scale policy relevance, 

continuity of long-term goals and design, national consistency, 

and building partnerships (see sidebar: “Guiding Principles 

for Cycle 3 Design”). Second, NAWQA needs to rebuild and 

enhance surface-water and groundwater quality monitoring 

networks, as well as expand its scope, in order to adequately 

meet new and continuing information needs for water management in the coming decade. The expansion in scope refers to 

addressing critical gaps in water-quality information, such as a 

need for expanded contaminant coverage, improved monitoring 

of water-quality trends, and development of the capability to 

forecast future water-quality conditions. 

Guiding Principles for Cycle 3 Design

• Maintain a priority on national-scale relevance: NAWQA achieves national-scale assessment by combining 

several interrelated approaches, including (1) cumulative interdisciplinary assessments of the most important 

hydrologic systems, (2) nationally consistent monitoring and data analysis that yield synthesis of findings at the 

national scale, (3) detailed topical studies of specific issues in relatively few locations, but with high transfer value 

to other parts of the Nation, and (4) development of statistical and water-quality models that enable extrapolation to 

unmonitored areas and resources. 

• Maintain continuity of long-term goals: The long-term goals of NAWQA are to (1) provide a nationally consistent 

description of current water-quality conditions for a large part of the Nation’s water resources, (2) define long-term 

trends (or lack of trends) in water quality, and (3) identify, characterize, and explain important factors that affect 

observed water-quality conditions and trends. These goals remain the foundation for Cycle 3 design, although specific goals for each 10-yr cycle are adjusted to reflect progress in earlier cycles, stakeholder priorities, and changing 

issues. 

• Maintain policy relevance: Priority in Cycle 3 is given to nationally relevant issues that align with the goals and 

strengths of NAWQA and that are considered a high priority by our stakeholders. Outcomes of Cycle 3 activities 

include data, scientific studies, and modeling and decision-support tools that can be used by water-resource managers and policy makers to evaluate the effectiveness of past, current, and proposed water-quality regulations and 

management practices. 

• Align with USGS science strategy: Cycle 3 of NAWQA will be aligned and closely coordinated with many mission-critical activities described in the USGS science strategy for the decade 2007–2017 (U.S. Geological Survey, 

2007). 

• Leverage resources through collaboration and partnerships: The ambitious vision for Cycle 3 cannot be fully 

achieved without integrating NAWQA assessment activities with other USGS programs, other governmental agencies (Federal, State, regional, and local), nongovernmental organizations, industry, and academia. Such partnerships 

expand the abilities of NAWQA and the Nation to assess the status and trends in water-quality and biological conditions spatially and temporally. Equally important is avoiding duplication of assessment and monitoring activities 

conducted by other USGS programs or external agencies.
12 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

The NAWQA approach to achieving Cycle 3 goals relies 

on the Program’s scientific foundation, existing networks, and 

proven approaches used during the past 20 yr. This includes 

systematic regional and national monitoring, multi-scale, 

interdisciplinary assessments in representative hydrologic 

systems and environmental settings, detailed local-scale 

studies of governing processes and ecological effects, and 

modeling and statistical analysis to integrate findings across 

multiple spatial and temporal scales. The details of significant 

design features and approaches for Cycle 3 are described in 

subsequent sections of the report but are introduced here with 

a focus on key aspects—some of which do not change for 

Cycle 3, while others do.

NAWQA will continue to assess the Nation’s water quality using the following approaches that remain essential to 

successful national-scale water-quality assessment:

• Adequate spatial representation of the hydrologic and 

environmental settings of the Nation, as well as specific 

areas of concentrated water-use and ecosystem need;

• Characterization of changes in the chemical, physical, and biological conditions at time scales (daily, 

seasonal, annual, decadal, and multi-decadal) most 

relevant to each type of problem in different environmental settings;

• Assessment of processes controlling the transport 

and fate of contaminants and other constituents by 

approaches that address their importance across multiple scales and that build transfer value of information 

to other settings; 

• Development of models and statistical approaches for 

extrapolation and forecasting of water-quality and 

biological conditions at varying spatial and temporal 

scales; 

• Synthesis of national and regional information for 

important water-quality issues; and

• Development of partnerships and data integration with 

other programs and agencies.

Even with the continued integration and collaboration 

with others, selective rebuilding of NAWQA surface-water 

and groundwater-monitoring networks that have been substantially reduced over the past decade due to fiscal constraints 

will be required. For example, the current (2012) NAWQA 

water-quality trend network for surface water monitors most 

sites only 1 yr out of every 4 yr. Such infrequent sampling is 

not sensitive enough to track changes in water chemistry over 

time and therefore cannot meet information needs for evaluating the effectiveness of management practices implemented to 

sustain clean water and healthy ecosystems. Some of the major 

changes in scope and emphasis that are part of the Cycle 3 science plan are the following:

• Expansion of the national surface-water monitoring 

network from 143 to 331 sites, including the addition 

of 30 reference sites, 70 drinking-water sites, 55 small 

watershed sites in specific land-use settings, and 33 large 

river coastal sites. Sampling of stream and river sites 

will change to every year instead of a 2- or 4-yr rotation, 

and real-time water-quality monitoring, including measurements of turbidity, will be added at most sites. 

• Initiation of integrated watershed studies in selected 

river basins to assess how water moves and transports 

contaminants, nutrients, and sediment over the land, 

from small headwater watersheds to downstream rivers, coastal ecosystems, and groundwater. Multi-scale 

monitoring and modeling approaches will be used to 

assess sources and transport. 

• Intensive studies nested within integrated watershed 

study areas will focus on the highest priority issues and 

concerns, such as effects of urbanization and agriculture on stream ecosystem condition.

• Increased monitoring and modeling of deep aquifers 

including sampling of approximately 2,000 publicsupply wells, the sampling of which was not emphasized in previous assessments. Overall, the number of 

groundwater samples collected in Cycle 3 will be twice 

the number collected during Cycle 2.

• Synoptic studies to assess regional biological conditions in streams across diverse environmental settings 

across gradients of key stressors (contaminants, nutrients, sediment, and streamflow alteration). Collected 

data will be used to test and extrapolate knowledge of 

processes demonstrated in intensive studies. 

• Development and application of predictive models and 

forecasts, accompanied by decision-support tools and 

estimates of model uncertainty, that can be used to 

assess the effectiveness of implemented or proposed 

regulatory policies and strategies, and potential effects 

of land-use and climate changes on water quality and 

ecosystem condition.

Although these assessment and study activities span a 

wide range of spatial scales, their implementation is highly 

interdependent. The locations selected for monitoring, modeling, and research will be based on their contribution towards 

supporting national-scale interpretations. Surface-water 

assessments will be systematically organized within the eight 

major river basins (MRB) that cover the conterminous United 

States, Alaska, and Hawaii (http://water.usgs.gov/nawqa/

studies/mrb). The MRBs are used by NAWQA for regionalscale analysis and modeling of surface-water quality. In addition to geographic organization by MRBs and environmental 

setting, the location of surface-water studies and regional 

or smaller-scale modeling efforts will be closely tied to the 

national network of stream-monitoring sites. This network 

serves to provide broad geographic coverage within the Basins 

and to provide anchors of consistent long-term data collection 

on which other studies are built (fig. 3). 
Introduction and Overview 13

Additional criteria for the selection of individual surface-water sites and ecologic monitoring and study locations 

include (1) availability of long-term water-quality, ecologic, 

or ancillary data (NAWQA or other sources) that supports or 

augments planned Cycle 3 assessment activities; (2) ability 

to partner with other USGS programs or external stakeholders that are conducting ongoing monitoring or research; 

and (3) an emphasis on geographic locations that exemplify nationally relevant water-quality issues and important 

ecosystem concerns. For example, NAWQA will continue 

to assess nutrient, sediment, and contaminant transport in 

key agricultural and urban settings in the Mississippi River 

Basin and watersheds flowing into other important estuaries, such as Chesapeake Bay and Puget Sound. Water-quality 

assessments also will focus on important watersheds where 

water quality is a factor in limiting water availability, such as 

in the arid Southwest, the upper Midwest, and the southeastern United States. 

Groundwater assessments in Cycle 3 will be designed to 

evaluate status and trends at the principal aquifer (PA; http://

water.usgs.gov/nawqa/studies/praq/) and national scales. 

Principal aquifers represent large areas (10,000 to greater than 

100,000 square kilometers (km2

)) with common lithostratigraphic and hydrogeologic characteristics (fig. 4). In Cycle 3, 

assessments are planned in 24 PAs; those PAs that account for 

the majority of current and future national groundwater use for 

drinking water will be selected. In each PA assessed, multiscale geographic and temporal monitoring will be combined 

ATLANTIC OCEAN

Puget Sound

Chesapeake

 Bay

GREAT LAKES

GULF OF MEXICO

PA

CIFIC

OCEAN

PACIFIC OCEAN

ARCTIC OCEAN

National Monitoring Network (NMN)—4 sites

National Stream Quality Accounting Network (NASQAN)—25 sites

National Water-Quality Assessment (NAWQA)—113 sites

Surface-water quality monitoring site

MRB 1

MRB 2

MRB 5

MRB 3

MRB 4

MRB 6

MRB 8

MRB 7

MRB 3

EXPLANATION

MRB1

MRB2

MRB3

MRB4

New England and Mid-Atlantic

South Atlantic-Gulf and Tennessee

Great Lakes, Ohio, Upper Mississippi, 

and Souris-Red-Rainy

Missouri

MRB5

MRB6

MRB7

MRB8

Lower Mississippi, Arkansas-White-Red, 

and Texas-Gulf

Rio Grande, Colorado, and Great Basin

Pacific Northwest

California

Major river basin (MRB)

0 250 500 MILES

0 250 500 KILOMETERS

#

"

Figure 1.3

Figure 3. The Cycle 3 fixed-site network for monitoring surface-water quality will include approximately twice the number of sites in 

the Cycle 2 network, shown in this figure, which is a combination of NAWQA, National Stream Quality Accounting Network (NASQAN), 

and National Monitoring Network (NMN) sites. The distribution of existing sites is shown in relation to the eight major river basins 

(MRBs) that NAWQA uses for regional-scale synthesis and modeling of surface-water quality. 
14 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

with groundwater flow modeling (done in collaboration with 

the USGS Groundwater Resources Program) to provide a 

three-dimensional assessment of groundwater quality and 

availability and of the factors that affect groundwater quality 

in different settings.

What Does the Nation Gain by This Plan?

Cycle 3 collaboration, monitoring, and assessment will 

produce the data and scientific information needed to develop 

effective solutions to protect and sustain clean water and healthy 

ecosystems. The strategy emphasizes the integration of interdisciplinary assessments of the natural and human factors that 

govern water quality across the Nation and uses this information 

to develop conceptual and mathematical models that can be used 

to forecast and assess effects of land-use activities and climate 

change. Moreover, the Cycle 3 strategy promotes the development 

and application of these models in the form of decision-support 

tools that can be used by managers to estimate conditions that 

cannot be directly measured and to predict how changes in human 

activities in a watershed, such as implementing best-management 

practices, are likely to affect water quality and aquatic ecosystems. 

50 percent or less

51 to 75 percent

76 to 90 percent

91 to 95 percent

96 to 100 percent

Glacial aquifer system

Principal aquifer not identified

EXPLANATION

Principal aquifer with percentage of total 

pumping for public supply Public-supply well sampled as part of Transport of Anthropogenic 

and Natural Contaminants to supply wells (TANC) studies or source 

water-quality assessment studies

Site type sampled in Cycles 1 and 2

Non-public-supply well sampled as part of major aquifer study network

Public-supply well sampled as part of a major aquifer study network

0 250 500 MILES

0 250 500 KILOMETERS

Figure 1.4

Figure 4. Groundwater monitoring and assessments are organized by principal aquifers, which are large areas (10,000 to 

greater than 100,000 square kilometers) with common lithostratigraphic and hydrogeologic characteristics. Those principal 

aquifers serving the majority of public drinking-water supplies (as indicated by the percentage by volume of pumping by publicsupply wells in each aquifer and the distribution of public-supply wells samples by NAWQA in Cycles 1 and 2) are shown on this 

map and are described at http://water.usgs.gov/nawqa/studies/praq/. 
Introduction and Overview 15

The Cycle 3 strategy also increases the priority on 

timely reporting of data, findings, and model results, because 

water-resource managers increasingly need rapid feedback on 

changing water-quality conditions. In addition to continuing 

national synthesis of multi-scale data and findings on nationally important topics such as nutrients and pesticides at regular 

(5- or 10-yr) intervals, the Program will regularly report key 

monitoring results and study findings by use of systematic 

annual reporting and accelerated online access to data, models, 

and decision-support tools. 

Cycle 3 will produce four general types of products 

that align with Cycle 3 goals. These products will advance 

water-quality science and improve the effectiveness of 

policies and strategies for water-quality management by 

increasing the availability and reliability of science and 

tools that support decisionmaking. Each product represents 

much-needed advances over our current (2012) knowledge 

and capabilities. Each general type of product described 

in this report will include scores of individual products 

that focus on specific water-quality issues within different 

geographic areas and with varying environmental settings. 

Although the details of these products are described later, 

a specific example of each category of Cycle 3 products is 

described to give the reader a visual sense of the outcomes. 

Reliable and Timely Status and Trend Assessments

NAWQA Cycle 3 will systematically fill information 

gaps in resource assessments and emphasize rapid feedback 

on changing water-quality conditions, so that managers can 

identify emerging problems, develop effective responses, and 

evaluate the performance of management strategies. 

Example: Tracking Trends and Change in Streams and 

Rivers

Policy- and management-relevant trend and change assessments must be sensitive enough to detect trends at the time 

scales in which important changes in contaminant sources or 

management strategies occur (fig. 5). Timely feedback enables 

policy-makers and managers to rapidly respond to changes in 

water-quality conditions and improves evaluation of (1) progress 

toward water-quality goals and (2) whether management strategies are working to improve water-quality conditions. The Cycle 

3 design for monitoring trends in surface-water quality calls for 

sampling at all sites every year, and for the collection of waterquality surrogate data in real time so that long-term trends typical 

of those caused by source changes or management strategies can 

be discerned and tracked relative to short-term changes caused 

by storms or other short-lived hydrologic events. 

EXPLANATION

1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

Measured concentration

Nondetection

Simulated concentration

Trend

Concentration of diazinon, in micrograms per liter

0.0001

0.001

0.01

0.1

1

Phase-out of

indoor residential

use of diazinon

Phase-out of

outdoor residential

use of diazinon

Figure 1.5

Figure 5. The trend analysis for the insecticide diazinon in Accotink Creek, an urban stream in Virginia, provides an 

example of the type of trend-analysis product that would result from implementation of the Cycle 3 design.
16 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Every-year monitoring of diazinon concentrations since 1997 

(with the exception of 2007) and continuous monitoring of flows 

throughout each year provided the data necessary to develop a 

time-series and trend model to simulate diazinon concentrations 

in Accotink Creek for 1996–2008. Every-year monitoring, as proposed in the Cycle 3 design, was the basis for the clear downward 

trend in diazinon concentrations during 2002–06, resulting in more 

than a 90-percent concentration decline. The decline corresponds 

to reduced residential uses resulting from a regulatory phase-out 

required by the USEPA. Understanding the effectiveness of the 

regulations in improving water quality is vital to USEPA and other 

stakeholders for tracking regulatory performance and determining 

implications for future strategies. 

Models and Decision-Making Tools

NAWQA models will quantitatively link sources and management practices to water-quality benefits and effects at multiple 

hydrologic scales, from headwater streams to rivers flowing into 

estuaries, and from shallow groundwater to deep regional aquifers.

Example: Prediction of Groundwater Quality

A key product of Cycle 3 will be models and decisionsupport tools that quantitatively link sources and management practices to water-quality conditions at the full range 

of management-relevant scales: from local to regional to 

national. In NAWQA Cycles 1 and 2, important progress was 

made on the application of process-based models to several 

case-study areas and on the application of statistical and 

hybrid models that link causal factors to individual contaminant occurrence, such as the effect of intensive agriculture 

on atrazine and nitrate concentrations. The model developed 

for predicting nitrate concentrations in shallow groundwater 

(Nolan and Hitt, 2006) provides an example of one type 

of model and its application to predicting conditions at the 

national scale (fig. 6).

Factors used to represent nitrogen sources in the model 

include farm fertilizer, manure from confined livestock, and 

population density. Factors in the model that represent the 

rate at which nitrate is transported to groundwater include 

water input, soil type, the presence of drainage ditches, and 

Predicted nitrate concentration, 

in milligrams per liter

EXPLANATION

Less than or equal to 1

Greater than 1 to 5

Greater than 5 to 10

Greater than 10

Missing data

0 250 500 MILES

0 250 500 KILOMETERS

Figure 1.6

Figure 6. A model of nitrate concentrations in shallow groundwater was used to predict nitrate concentrations across the 

conterminous United States. The model was used to show that the highest concentrations are predicted to be in the High Plains, 

northern Midwest, Central Valley of California, and other areas of intensive agriculture. These are areas with a combination 

of large nitrogen sources, natural factors that promote rapid transport of nitrogen in groundwater, and a lack of attenuation 

processes. (Modified from Nolan and Hitt, 2006.)
Introduction and Overview 17

percentage of clay. The nitrate model for shallow groundwater illustrates one type of model that can be further developed as data and understanding improve. Such models can 

be created for other contaminants and specific regions, and 

models of shallow groundwater quality provide an important 

starting point for evaluating deeper parts of aquifers used 

for domestic and public supply. Last, they can be used to 

develop groundwater models that couple groundwater quality 

with groundwater flow to evaluate the distribution and transport of contaminants in aquifers.

Understanding the Effects of Stressors on 

Stream Ecosystem Condition

NAWQA Cycle 3 includes analysis of relations between 

specific water-quality stressors—contaminants, nutrients, 

sediment, and streamflow alteration—and their individual and 

combined effects on aquatic ecosystems, so that management 

strategies can target the most critical causes of ecological 

degradation. 

Example: Evaluating Causes of Ecological Impacts

Improved protection and restoration of aquatic ecosystems requires an understanding of what factors have the 

potential to adversely affect aquatic organisms and where such 

factors may present the greatest risk. Data collected as part of 

NAWQA Cycles 1 and 2, and from assessments by USEPA 

and the states, have been used to develop statistical correlations between several different stressors and the biological 

condition of streams. Cycle 3 studies are designed to build on 

these correlation analyses by refining stressor effects relations 

and by combining the findings with ecological and waterquality models so that estimates can be made of the potential 

extent and conditions of potential concern. For example, a 

recent USGS study of fathead minnows (Tillitt and others, 

2010) showed that the herbicide atrazine affects egg production at relatively low concentrations (fig. 7). 

The atrazine Watershed Regressions for Pesticides 

model (WARP; Stone and Gilliom, 2008), which was developed from NAWQA Cycle 1 and 2 monitoring data (plus 

extensive data on atrazine use patterns, soils, precipitation, 

Exposure period, in days

0 5 10 15 20 25 30

0

200

400

600

800

1,000

1,200

Control

0.5 

5 

50 

Cumulative mean eggs per breeding tank

Atrazine exposure concentration, 

in micrograms per liter

Initial day of significant difference

 (p=0.05) from control

After 21 days, all

exposure levels

showed effects

EXPLANATION

Figure 1.7 Figure 7. Results of laboratory tests showing reduced egg production in fathead minnows at atrazine 

concentrations as low as 0.5 microgram per liter with an exposure duration in the range of 21 days. 

These findings raised the question as to where such atrazine levels are found in streams and may, 

therefore, be a concern warranting further investigation. (Modified from Tillitt and others, 2010; p=0.05; 

p, or more specifically, the p-value is the probability of rejecting the null hypothesis in a statistical test, 

defined here at a significance level of 0.05 or five percent).
18 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

and agricultural practices), allows rapid estimation of what 

areas of the country have streams that are likely to exceed the 

concentration levels identified as potential concerns by the 

laboratory results. The model was used to estimate the distribution of atrazine concentrations in streams where potential effects on actual fish populations may occur and can be 

used to guide follow-up investigations (fig. 8). This example 

illustrates one way in which new stressor-effects studies can 

be combined with statistical or simulation models developed 

from NAWQA’s sustained commitment to monitoring data to 

rapidly assess the characteristics and geographic extent of a 

potential management problem.

Forecasting and Scenario-Testing Tools

Forecasting and scenario-testing tools developed from 

Cycle 3 models will enable timely evaluation of current 

water-quality issues and future scenarios of changing land use, 

management practices, and climate.

Example: Forecasting Effects of a Reduction in Fertilizer 

Use on Nutrient Loadings

Cycle 3 assessments will apply hydrologic and statistical models to forecast how potential changes in climate, 

population, land-use, and other factors will affect groundwater and surface-water quality. These forecasts are needed 

by managers and policy-makers tasked with ensuring stable, 

clean water supplies for humans and ecosystem needs. The 

SPARROW model, for example, relates nutrient concentrations from a large network of monitoring stations to (1) 

upstream sources, such as fertilizer, manure, wastewater 

discharges, and the atmosphere; and (2) watershed characteristics affecting transport, including soil permeability, stream 

size, and streamflow (Smith and others, 1997). These sources 

and watershed characteristics are spatially referenced to a 

detailed network of stream reaches that represents pathways 

of water movement through the region included in the model. 

The SPARROW model can be used to provide information 

to address a variety of issues, including how changes in land 

EXPLANATION

Estimated maximum 21-day moving average concentration 

of atrazine, in micrograms per liter

Not modeled

Less than 0.5

0.5 to 5.0

Greater than 5 to 50

Greater than 50

Reduced egg production 

was found in these 

concentration ranges

0 250 500 MILES

0 250 500 KILOMETERS

Figure 1.8

Figure 8. Predicted maximum 21-day average atrazine concentration in streams for concentration levels shown to affect egg 

production of fathead minnows in laboratory studies. (Modified from Stone and Gilliom, 2009.)
Cycle 3 Design Elements 19

use or management actions, such as a 50 percent reduction in 

fertilizer usage, may affect water quality in the southeastern 

United States (fig. 9). 

This example shows that—in terms of total annual nitrogen load—a reduction of agricultural sources alone may not 

markedly improve eutrophication in some of these estuaries 

(fig. 9). Cycle 3 will expand the capabilities of SPARROW 

and other models to include additional contaminants and to 

simulate changes in nutrient (or other contaminant) fluxes over 

time. In addition, Cycle 3 includes plans to develop Webaccessible models and tools for managers to evaluate how 

water-quality and aquatic-ecosystem conditions may change in 

response to different management scenarios.

Cycle 3 Design Elements

The science plan strategy for water-quality assessment in 

Cycle 3 builds on proven approaches used in the previous two 

decades of the Program, including multi-scale, interdisciplinary assessments of critical hydrologic systems, systematic 

regional and national monitoring, detailed local-scale studies 

of governing processes and ecological effects, and modeling 

and statistical tools to integrate findings across multiple spatial 

and temporal scales. Although the basic approaches will 

remain the same, the increasing and changing demands for 

water-quality information, the improved technology for waterquality monitoring, and the need to rebuild from reductions in 

monitoring and assessment that occurred as Program resources 

declined over the past decade require that the Cycle 3 

approach incorporate a substantial evolution in emphasis and 

an expanded scope to meet the Nation’s current and future 

requirements for water-quality information. This section of 

the report lists specific objectives for each of the four major 

Cycle 3 goals and then provides a summary of recommended 

approaches and study components for the surface-water and 

groundwater design elements. 

Goals and Objectives of Cycle 3

The approach was developed by defining specific science 

objectives for each of the four Cycle 3 goals. The objectives are 

defined in relation to the four priority water-quality stressors—

contaminants, nutrients, sediment, and streamflow alteration—

and their potential effects on humans and aquatic ecosystems. 

These objectives, which are listed below for each of the four 

goals, will be addressed to varying degrees of comprehensiveness and detail (determined by scientific and stakeholder 

priorities) to meet each goal and provide information that is of 

greatest use in addressing water-quality management questions. 

Goal 1: Assess the current quality of the Nation’s freshwater 

resources and how water quality is changing over time. 

The following are objectives for Goal 1:

1a. Determine the distributions and trends for contaminants in current and future sources of drinking water 

from streams, rivers, lakes, and reservoirs;

1b. Determine mercury trends in fish tissue;

1c. Determine the distributions and trends for microbial 

contaminants in streams and rivers used for recreation;

1d. Determine the distributions and trends of contaminants of concern in aquifers needed for domestic and 

public supplies of drinking water;

1e. Determine the distributions and trends for contaminants, nutrients, sediment, and streamflow alteration 

that may degrade stream ecosystems;

1f. Determine contaminant, nutrient, and sediment loads 

to coastal estuaries and other receiving waters; and

1g. Determine trends in biological condition at selected 

sites and relate observed trends to changes in 

contaminants, nutrients, sediment, and streamflow 

alteration. 

GULF OF

MEXICO

ATLANTIC

OCEAN

!

!

!

!

!!! !

!!

!

!

!

!

!

!

25

20

15

10

5

0

Percent decrease

How will a 50 percent decrease in agricultural nitrogen

inputs change nutrient loads to eutrophic estuaries in the Southeast? 

EXPLANATION

Eutrophic estuary (Bricker and others, 1999)

Agricultural land use in watersheds of 

 eutrophic estuaries

Figure 9. Map showing area of the southeastern United 

States for which the SPARROW model was used to predict 

nitrogen loads delivered to eastern Gulf of Mexico and 

South Atlantic estuaries based on a 50-percent reduction 

in agricultural nitrogen inputs. The graph shows that the 

SPARROW model was used to predict that the response to 

a reduction of agricultural nitrogen inputs of this magnitude 

would be a decrease in estuarine loading from as little 

as 5 percent to a maximum of 24 percent, depending on 

the estuary. (Map constructed from dataset included in 

supplemental materials for Hoos and McMahon, 2009.)
20 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Goal 2: Evaluate how human activities and natural factors, 

such as land-use, water use, and climate change, are affecting 

the quality of surface water and groundwater.

The following are objectives for Goal 2:

2a. Determine how hydrologic systems—including 

water budgets, flow paths, traveltimes and streamflow alterations—are affected by land use, water use, 

climate, and natural factors;

2b. Determine how sources, transport, and fluxes of 

contaminants, nutrients, and sediment are affected by 

land use, hydrologic system characteristics, climate, 

and natural factors;

2c. Determine how nutrient transport through streams 

and rivers is affected by stream ecosystem processes;

2d. Apply understanding of how land use, climate, and 

natural factors affect water quality to determine the 

susceptibility of surface-water and groundwater 

resources to degradation; and

2e. Evaluate how the effectiveness of current and historical management practices and policy is related to 

hydrologic systems, sources, transport and transformation processes.

Goal 3: Determine the relative effects, mechanisms of activity, 

and management implications of multiple stressors on aquatic 

ecosystems. 

The following are objectives for Goal 3:

3a. Determine the effects of contaminants on degradation of stream ecosystems, determine which 

contaminants have the greatest effects in different 

environmental settings and seasons, and evaluate 

which measures of contaminant exposure are the 

most useful for assessing potential effects;

3b. Determine the levels of nutrient enrichment that initiate ecological impairment, what ecological properties are affected, and which environmental indicators 

best identify the effects of nutrient enrichment on 

aquatic ecosystems;

3c. Determine how changes to suspended and depositional sediment impair stream ecosystems, which 

ecological properties are affected, and what measures are most appropriate to identify impairment;

3d. Determine the effects of streamflow alteration on 

stream ecosystems and the physical and chemical 

mechanisms by which streamflow alteration causes 

degradation; and

3e. Evaluate the relative effects of multiple stressors on 

stream ecosystems in different regions that are under 

varying land uses and management practices.

Goal 4: Predict the effects of human activities, climate change, 

and management strategies on future water-quality and ecosystem condition.

The following are objectives for Goal 4:

4a. Evaluate the suitability of existing water-quality 

models and enhance as necessary for predicting the 

effects of changes in climate and land use on waterquality and ecosystem conditions;

4b. Develop decision-support tools for managers, policy 

makers, and scientists to evaluate the effects of 

changes in climate and human activities on water 

quality and ecosystems at watershed, state, regional, 

and national scales; and

4c. Predict the physical and chemical water-quality 

and ecosystem conditions expected to result from 

future changes in climate and land use for selected 

watersheds.

Study Components

Assessments of surface-water and groundwater quality 

for NAWQA Cycle 3 will each be based on several primary 

study components that have evolved from experience gained 

from Cycles 1 and 2. The study components for the surface 

water and groundwater design elements are described in this 

section separately. Each objective is highly dependent on 

information derived from other objectives and, thus, all objectives for surface and groundwater will depend on having study 

components that are flexible but closely coordinated. The 

study components provide a consistent structure for organizing 

multi-purpose, interrelated assessments across multiple scales 

of investigation for surface water and groundwater. A common 

study component for all types of assessments will be review 

and analysis of existing data and information, which will be 

referred to as “retrospective analysis.” Following the overview 

of the individual surface water and ground water study components provided here, subsequent sections will describe how 

these components are applied to the design of studies that will 

meet each goal and its related objectives.

Surface Water

The design for surface-water quality assessment addresses 

a complex array of objectives regarding the chemical and physical aspects of water quality and the effects of water-quality 

stressors on human health and aquatic ecosystems. Priority 

water-quality stressors for Cycle 3 are contaminants, nutrients, 

sediment, and streamflow alteration. Depending on the specific 

objective, spatial scales of interest extend from stream sites and 

reaches, to small watersheds, and to the entire Mississippi River 

Basin and the Nation; time scales of interest range from hours to 

decades; and environmental settings are diverse.
Cycle 3 Design Elements 21

In general terms, the array of Cycle 3 goals and objectives related to surface water has many similarities to those 

of Cycles 1 and 2, but the emphasis has evolved to reflect 

improved information and newly identified needs. The proposed Cycle 3 design, as described in this section, involves 

several broad enhancements and changes to the Cycle 2 

design that are needed to adequately address Cycle 3 goals 

and objectives. Individual components of the surface water 

design are briefly introduced in the following list and then 

explained in more detail in the following subsections, all as 

the foundation for explaining the specific approach to each 

goal and objective in subsequent parts of the report: 

• The National Fixed-Site Network (NFSN) is a 

national network of monitoring sites that serves as the 

foundation for long-term systematic tracking of the status and trends of stream and river water quality and for 

supporting and linking shorter-term studies at smaller 

scales. The Cycle 3 NFSN is expanded and upgraded 

from Cycle 2 to improve trend analysis and to provide 

support for model development and validation, analysis of drinking-water sources, analysis of reference 

conditions and climate change, analysis of nutrient and 

contaminant loads to coastal ecosystems, and other 

specific analysis requirements.

• Regional Synoptic Study (RSS) is a short-term, targeted water-quality or biological assessment of specific 

regions or environmental settings. The RSS assessments are a flexible design component that help fill 

spatial gaps between national fixed-site monitoring and 

the geographically limited Integrated Watershed Study 

and Intensive Study assessments (described in the following bullets). The RSS assessments are well suited 

for assessing water-quality or biological conditions 

where spatial variability is more important than temporal variability. These types of studies are particularly 

important for the development and testing of regional 

ecological models in support of Goal 3. The RSS 

assessments were used to a limited degree in Cycles 1 

and 2, but will take on a larger role in Cycle 3.

• Integrated Watershed Study (IWS) is a large-scale, 

holistic water quality assessment introduced in 

Cycle 3 to address the increasing need for integrated 

understanding of contaminant, nutrient, and sediment 

sources and transport in large watersheds and for 

developing reliable predictive models at these scales. 

The IWSs will fill gaps in water-quality assessments 

that were created by the phase-out of Study-Unit 

investigations during Cycle 2. 

• Intensive Study (IS) is a focused assessment that 

will be conducted at a few sites, reaches, or small 

watersheds, selected to investigate specific topics in 

comparative designs. The IS component is vital to 

meet Cycle 3 objectives for improving understanding of specific sources, processes, and stressor effects 

relationships in aquatic ecosystems. The IS were also 

an important part of the approach of NAWQA Topical Studies done in Cycle 2. In Cycle 3, the IS will be 

nested in IWS study areas to facilitate up-scaling of 

findings and to leverage monitoring, modeling, and 

ancillary data in the IWS study areas.

With these components as the building blocks for 

design, Cycle 3 can accommodate multiple scales of monitoring and assessment with sufficient structure to enable 

systematic integration of findings to address objectives at 

regional and national scales. The components also enable 

timely and targeted studies of specific topics with unique 

design requirements. Although policies often target regional 

and national scales, land- and water-management strategies 

usually are implemented locally. Thus, to ensure success in 

providing scientific information that improves management, 

NAWQA places a high priority on making the linkages of 

cause and effect across the scales.

In the following subsections, more detailed descriptions 

are provided for the four surface-water study components. The 

NFSN is described most completely, although not with detailed 

specifics on factors such as site selection and analytical strategy, whereas the IWS, IS, and RSS components are illustrated 

with examples and will be highly dependent on design details 

developed by focused study implementation teams.

National Fixed-Site Network

The Cycle 3 National Fixed-Site Network is a national 

network of monitoring sites with a long-term commitment to 

(1) perennial and systematic water-quality sampling, with timing, frequencies, and laboratory analyses designed for Cycle 3 

objectives, including assessment of long-term trends; and (2) 

continuous monitoring of streamflow (all sites) and selected 

water-quality properties (selected sites). The Cycle 3 design 

relies on, and is composed of, monitoring sites and activities 

supported to varying degrees http://www.usgs.gov/climate_

landuse/), and the interagency National Monitoring Network 

(NMN; http://acwi.gov/monitoring/network/index.html). 

The NFSN produces the consistent and common core of 

information that is essential for other Cycle 3 components. 

Fixed-site monitoring has been a vital component of the 

NAWQA design since the beginning of Cycle 1. During Cycle 

1, 505 sites were operated for varying periods of time during 

Study-Unit Investigations. By 2007, these sites were reduced 

to a national network of 113 sites, about three quarters of 

which (83) were sampled intensively only 1 yr out of every 

4 yr. When combined with 25 NASQAN sites and 4 NMN 

sites, the fixed-site monitoring network operated during the 

latter half of Cycle 2 consists of 142 sites (fig. 10). 

To meet Cycle 3 objectives, the NFSN needs to be 

substantially expanded and enhanced, including the following 

changes:

• Monitoring is planned to be conducted every year 

rather than using rotational schedules. Trend analysis 

of water-quality data from 1992–2008 has shown 
22 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

that important trends, such as those for many pesticides, are happening within a few years and are not 

adequately characterized with rotational sampling 

(see fig. 5).

• Continuous, real-time water-quality monitoring of 

selected water-quality properties is planned for most 

sites. Continuous monitoring of selected properties, 

such as specific conductance and turbidity—now 

more economically and technically feasible than in 

the past—will enable detailed and accurate estimates 

of concentrations and loads for dissolved solids and 

suspended sediment and will contribute to improving 

estimates of other water-quality properties through 

correlation analysis. Continuous data also yield 

improved understanding of the effects of short-term 

hydrologic events (such as storms, floods, dam 

releases) on water quality and provide time-dense data 

for developing dynamic simulation models. 

• Additional sites will be added to support improved 

assessment of sources of drinking water, loadings of 

nutrients, contaminants, and sediment to coastal ecosystems, and background conditions. These sites fill 

information gaps, and this information from new sites 

is essential to meet Cycle 3 goals.

ATLANTIC OCEAN

Puget Sound

Chesapeake

 Bay

GREAT LAKES

GULF OF MEXICO

PA

CIFIC

OCEAN

PACIFIC OCEAN

ARCTIC OCEAN

National Monitoring Network (NMN)—4 sites

National Stream Quality Accounting Network (NASQAN)—25 sites

National Water-Quality Assessment (NAWQA)—113 sites

Surface-water quality monitoring site

EXPLANATION

0 250 500 MILES

0 250 500 KILOMETERS

Sampling schedule

Every year Every other year Every fourth year

Figure 2.1

Figure 10. The Cycle 2 fixed-site network for monitoring surface-water quality is a combination NAWQA, NASQAN (National Stream 

Quality Accounting Network), and NMN (National Monitoring Network) sites. Of the 142 sites included in the combined network, only 

44 are monitored every year; 15 sites are sampled one in every two years, and the remaining 83 sites are monitored only 1 out of every 

4 years.
Cycle 3 Design Elements 23

Specific Roles

The following are specific roles of the NFSN in the 

NAWQA Cycle 3 design:

• Primary data source for basic assessments of the 

distributions and trends in contaminants, nutrients, and 

sediment, including associated models;

• Perennial “anchor” sites for IWS and IS assessments 

that have short-term study periods;

• Primary data source for assessing contaminant, nutrient, and sediment loading to coastal ecosystems;

• Primary data source for assessing the quality of 

surface-water sources of drinking water; and

• Primary source of reference watershed data for evaluating effects of changing climate and human activities on 

water quality and aquatic ecosystems. 

Design Characteristics

The design of the NFSN for Cycle 3 is described in comparison to the Cycle 2 design in table 1; figures 11, 12, and 13 

show the general distribution of large river, wadeable stream, 

and drinking-water intakes sites by land use. Site selection and 

site-specific sampling and analysis plans for NFSN monitoring 

sites will be completed after Cycle 3 plans develop further and 

more is known about the budget, analytical methods, external partnerships, and coordination with other NAWQA study 

components and USGS programs. 

Relation to Other Components

The following describe the relation of the NFSN to other 

surface-water and groundwater components:

• IWS component: On average, each IWS basin will 

contain from one to four NFSN sites that provide a 

core of consistent, long-term data at key locations.

• IS component: Most IS will be anchored by one or two 

NFSN sites that provides a longer-term temporal reference for the shorter-term intensive study.

• Regional Synoptic Study (RSS) component: Most 

RSSs will include 10 to 20 NFSN sites that will serve 

as long-term temporal references for the short-term 

synoptic approach of the RSS.

• Local Groundwater Study (LGS), Regional Groundwater Study (RGS), and Principal Aquifer Assessment 

(PAA) components: Most LGS, RGS, and PAA will 

include one or more NFSN sites that will be used to 

perform base-flow separation analyses to determine 

water-quality and quantity contributions from groundwater to monitored watersheds. 

Regional Synoptic Study

The RSS component consists of short-term, targeted 

water-quality assessments of specific regions and conditions. 

Generally, the number of sampling sites for a RSS in a 

particular region is much greater than the number of NFSN 

Table 1. Changes from Cycle 2 to Cycle 3 in the National Fixed Site Network.

[NAWQA, National Water-Quality Assessment; NASQAN, National Stream Quality Accounting Network; NMN, National Monitoring Network]

Characteristic Cycle 2 Cycle 3

Total sites

142 total sites consisting of: 

113 NAWQA sites, 

25 NASQAN sites, and 

4 NMN sites)

313 total sites

Sampling schedule Most sites every 2 or 4 years All sites sampled all years

Sampling frequency 12–26 samples per year 6–26 samples per year

Real-time monitors None 50 percent of sites

Ecological monitoring sites 58 88 (includes 30 new reference sites)

Reference sites 19 58 (includes 30 new reference sites listed above)

Drinking-water intake sites on streams and rivers Temporary at selected intakes 20 perennial

Drinking-water intake sites on lakes and reservoirs None 50 perennial

Coastal sites 7 56 sites

Contaminant analyses Limited Expanded

Suspended sediment Limited Suspended sediment and continuous turbidity 

monitoring
24 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Cycle 2: 43 large rivers

Cycle 3: 138 large rivers

(including 20 sites at drinking water intakes)

Coastal: Every year (4)

Coastal: rotate4 (3)

Inland: Every year (11)

Inland: rotate4 (25)

Coastal rivers

(56)

Large inland rivers

(62) 

Drinking water intake

(20) 

rotate4

EXPLANATION

Dominant watershed land use and 

number of sites (in parentheses)

Sampled once every 4 years

Large inland rivers

(62) 

Figure 2.2

Figure 11. The number of National Fixed Site Network sites on 

large rivers (nonwadeable) increases from 43 sites in Cycle 2 

to 138 sites in Cycle 3. Important changes in Cycle 3 include 53 

additional coastal sites, 20 sites at drinking-water intakes, and 

annual monitoring at each site every year.

rotate2

rotate4 Sampled once every 4 years

EXPLANATION

Dominant watershed land use and 

number of sites (in parentheses)

Sampled once every 2 years

Urban (31)

Cycle 2: 70 Wadeable Streams

Cycle 3: 125 Wadeable Streams

Agricultural: rotate2 (3)

Agricultural: rotate4 (24)

Urban: rotate2 (12)

Urban: rotate4 (12)

Undeveloped: rotate4 (19)

Agricultural (36)

Urban (31)

Undeveloped (58)

Figure 2.3

Figure 12. The number of National Fixed Site Network sites on 

wadeable streams increases from 70 sites in Cycle 2 to 125 sites 

in Cycle 3. Important changes in Cycle 3 include an increase in 

undeveloped reference sites from 19 to 58 sites and increased 

monitoring at each site throughout the year, every year. 

sites in the same geographic area (typically in the range of 

10 to 20 times more) depending on the scale characteristics 

and variability of natural and human features on the landscape. The RSS is a very flexible design component. Some 

RSS assessments may be unique, one-time studies aimed at 

specific topic in a region, such as the distribution of a specific 

contaminant in spring runoff within a particular setting such 

as row-crop agriculture. Others will be part of long-term 

rotational series of RSS assessments, such as geographic 

assessments of the biological condition of streams as related 

to a consistent set of important stressors, that are conducted 

using a similar design. Within such assessments, regions are 

rotated over time to build a national dataset on a particular set 

of scientific and management questions.

The RSS assessments fill a gap between NFSN and geographically limited IS and IWS components by increasing the 

spatial extent of assessment for issues that are expected to be 

primarily dominated by spatial variability more than temporal 

variability. The RSS assessments are particularly important 

for evaluating biological conditions and contaminants in bed 

sediments or fish tissue.

Specific Roles

The following are specific roles of the RSS assessments 

in the NAWQA Cycle 3 design:

• Expand geographic assessment for water-quality 

characteristics identified from other studies to be of 
Cycle 3 Design Elements 25

potential regional interest, particularly biological conditions; and 

• Provide geographically extensive reconnaissance 

assessments of particular water-quality characteristics, such as bed sediment contaminants, which are 

expected to vary more spatially then temporally.

Design Characteristics

Most RSS assessments are studies of a contiguous large 

region spanning multiple states, such as a major river basin 

or ecoregion, depending on the objective. Some RSS assessments, however, may target a specific environmental setting 

that is not contiguous, such as urban areas. Most RSS assessments will be one-time, short-term studies, usually with one 

sampling visit or with multiple samplings during a single 

season, but some trend-assessment objectives may require 

repeated RSS assessments over appropriate time intervals. 

Each RSS generally targets a relatively narrow range of 

water-quality conditions.

Relation to Other Components and Associated Analyses

The following items describe the relation between RSS 

assessments and other surface-water components:

• Point-in-time testing and verification of predictions for 

selected constituents and biological conditions from 

national and regional models developed from NFSN 

and RSS assessments; and

• Up-scaling of findings for selected constituents from 

IWS and IS assessments to a regional scale.

Integrated Watershed Study

The IWS component consists of long-term, interdisciplinary water-quality assessments of large watersheds. The IWS 

assessments are nationally distributed examples of regional 

environmental settings, each of which is characterized by a 

defined range of human activities and natural hydrologic settings. The IWS assessments consist of a stable set of 10–20 

watersheds that are generally in the range of 5,000–50,000 km2, 

depending on the scale characteristics and variability of the 

human and natural environmental setting in a particular region. 

Example candidate IWS locations are shown in figure 14 to 

illustrate potential distribution and scale. The regions and IWS 

watersheds will be prioritized and selected with the goal of 

representing the national range of important human effects on 

water quality. Most, if not all, IWS assessments will be large 

watersheds selected from the NAWQA Cycle 2 trend network 

and will consist of either entire NAWQA Cycle 1 study units or 

one of their major sub-basins. Characterization and prioritization of IWS assessments will follow the same type of process 

and will use similar information as was used to prioritize study 

units and topical study areas for Cycle 2. There will likely be 

one or two IWS in each NAWQA Cycle 2 major river basin 

(MRB), but selection and implementation of IWS will be 

phased to coordinate with IS priorities, partnerships with other 

agencies, and available resources.

An important role of the IWS is to bridge the gap in 

scale between NFSN monitoring and the IS component 

so that large-scale and multi-scale source and transport 

objectives, predominantly for contaminants, nutrients, and 

sediment, can be addressed. In the context of the NAWQA 

Study-Unit -investigations that evolved through Cycle 1 

(52 study units) and Cycle 2 (started with 42 study units but 

most activities were phased out), IWS can be considered to 

be more selective, more intensive, surface-water focused 

“study units.” Although primarily focused on surface water, 

the IWS watersheds also will be the primary locations where 

monitoring and modeling studies will examine relations 

between surface water and groundwater in different hydrologic settings.

Specific Roles

The following are specific roles of the IWS component in 

the NAWQA Cycle 3 design:

• Serves as focus areas for developing intensive and 

high-quality information on water-quality and hydrologic-system characteristics and the human and natural 

factors that affect water surface and groundwater 

quality, including data derived from continuous waterquality sensor technology;

• Provides a real-world laboratory for developing and 

testing hydrologic and water-quality models that link 

human activities and natural factors to sources and 

transport of contaminants, nutrients, and sediment from 

headwaters to large rivers. Ultimately, data obtained 

EXPLANATION

Dominant watershed land use and 

number of sites (in parentheses)

Agricultural (20)

Cycle 3: 50 Reservoir and Lake Drinking-Water Sources

Mixed (20)

Agricultural (20)

Urban (10)

Figure 2.4

Figure 13. The Cycle 3 allocation of 50 National Fixed Site 

Network sites at lake or reservoir drinking-water intakes is 

a new assessment component that was not part of Cycle 2.
26 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

from the IWS locations will be used for development 

and testing of predictive models used to forecast waterquality conditions under various scenarios of climate 

or land-use change;

• Defines the geographic areas for locating IS so that 

IS study areas are nested in a well-characterized large 

watershed for analysis of larger-scale significance and 

linkage to downstream waters;

• Contributes to evaluating the importance of land- and 

water-management practices to large-scale improvements in water quality by linking local-scale studies and land-use activities to effects on downstream 

systems in larger watersheds;

• Is well-suited for developing collaborative partnerships with local, state, and Federal agencies (such as 

USDA and USEPA) and with academic researchers 

because of their focus on linking across scales, from 

site-specific studies to large watershed water-quality 

conditions. The IWS component thus spans a variety 

of research and management interests in key settings and is supported by NAWQA’s monitoring and 

assessment infrastructure.

Design Characteristics

In general, each IWS will focus on a watershed that previously was included in NAWQA studies. These watersheds 

generally have a solid baseline of hydrologic, water-quality, 

and ancillary information from Cycles 1 and 2, combined 

with other data sources. A potential exception may occur 

if high-value partnerships can be formed between multiple 

agencies in watersheds that have large amounts of waterquality and ancillary data or that have existing water-quality 

models that can be leveraged to advance NAWQA and other 

agency goals. As an initial step for Cycle 3 planning and 

implementation, approximately 20-50 candidate IWS basins 

will be characterized using existing information, following a 

consistent approach. As Cycle 3 plans evolve, this will facilitate selecting IWS basins for detailed assessment.

White

River

Basin

0 250 500 MILES

0 250 500 KILOMETERS

Figure 2.5

EXPLANATION

Hypothetical Integrated Watershed Study areas

Additional Cycle 1 and Cycle 2 Study Units

Major River Basin boundaries

Figure 14. Hypothetical map of 20 possible Integrated Watershed Study watersheds distributed among the 8 NAWQA major river 

basins (fig. 3) in the conterminous United States. The actual number of Integrated Watershed Study assessments and timing of 

implementation will be determined based on coordination with Intensive Study priorities, partnerships with other agencies, available 

resources, and other factors to be evaluated as Cycle 3 begins. Also indicated is the location of the White River Basin, which is 

used as an example to illustrate design features of an Integrated Watershed Study in the section on Goal 2. As illustrated here, the 

20 hypothetical Integrated Watershed Study areas were selected from the 51 watersheds studied by NAWQA in Cycles 1 and 2; 

however additional watersheds with extensive water-quality data and models will be considered during the implementation phase.
Cycle 3 Design Elements 27

Initial Characterization of Candidate Integrated Watershed 

Study Areas

The initial characterization of candidate IWS areas will 

serve as a well-defined starting point for a design that can be 

used to identify critical issues in each watershed as they relate 

to the Cycle 3 objectives, inventory the available information 

and critical gaps, and begin to explore potential partnerships. 

Initial characterization will include, but not be limited to, the 

review, update, and synthesis of readily available existing 

information, such as:

• Geographic characterization of human and natural 

characteristics;

• Land-use characteristics and distribution;

• Point-source discharges;

• Drinking-water intakes;

• Active streamgages and current monitoring programs;

• Current water-quality issues and stakeholders; and

• Information from other studies and related activities in 

progress in the IWS study area, such as other USGS 

studies, USDA Agricultural Research Service research 

sites (http://www.ars.usda.gov/), and Long Term Ecological Research (LTER) sites (http://www.lternet.edu/sites/).

Selection and Implementation of Integrated Watershed Study 

Assessments

All IWS assessments will not be implemented at the same 

time because of constraints on funding and personnel, as well 

as the timing of study priorities. A range of implementation 

options will be considered, but the favored approach to begin 

Cycle 3 is to implement approximately 6 to 10 IWS assessments within a 10-yr study period. The 10-yr study period 

for a comparatively small number of studies is preferred over 

the alternative of having more IWS assessments on a shorter 

rotational schedule. The 10-yr study period is essential for 

developing sustainable study partnerships and efficiently phasing in data collection and modeling. Although several specific 

issues warrant consideration regarding the number of IWS 

assessments that can be implemented at one time (which will 

not be resolved until later during the implementataion phase), 

examples of some of the primary factors that will determine 

priorities for implementation follow:

• Relevance to highest priority IS assessments;

• Relevance to current regional issues, such as nutrient 

loading to the Mississippi River Basin, Chesapeake Bay, 

and other large estuaries affected by eutrophication;

• Readiness of data and infrastructure for studies;

• Suitability of staff;

• Geographic distribution; and

• Likelihood of partnering with other USGS programs, 

Federal or state agencies, and academic researchers on 

shared scientific interests. 

Core Assessment Activities 

Each implemented IWS assessment will have a standard 

core of assessment and modeling activities that generally are 

similar among all selected IWS assessments, but will also be 

customized to address local conditions, and supplemented 

as needed for support of RSS and IS assessments. Although 

details of assessment activities will be determined separately 

by a later planning effort, basic core activities would include:

• Detailed updates and enhancements of ancillary information on all human activities in the watershed that 

affect water quality;

• Inventory of the locations and quantities of water withdrawals for drinking water and other purposes;

• Compilation and verification of historical and ongoing 

water-quality data collection and studies;

• Enhanced fixed-site monitoring. Typically this would 

involve supplementing one to four NFSN sites typically in an IWS with 10–12 additional sites that would 

be monitored using a similar sampling and analytical 

strategy as the NFSN sites. The additional sites will be 

located to measure water quality and fluxes at outlets 

of major sub-basins in the watershed, to support model 

development and analysis, and for selected land-use or 

best management practice settings;

• Streamflow and mass-balance analysis for fluxes of 

water, dissolved solids, sediment, and other constituents, through and from the watershed as data allow; and

• Development of water-quality models to simulate water 

and constituent movement through the watershed and 

to account for the distribution and characteristics of 

point and nonpoint sources.

Relation to Other Components

The following items describe the relation between the 

IWS assessments and other surface-water and groundwater 

components:

• Testing and verification of predictions from national 

and regional models developed from NFSN and 

regional synoptic studies;

• Up-scaling of findings from IS assessments to a larger 

watershed context; and

• Nesting within LGS and RGS studies to examine 

groundwater/surface-water interactions, including flow 

and transport modeling. 
28 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Intensive Study

Intensive Study assessments are interdisciplinary studies ranging in scale from individual stream reaches to small 

(50–200 km2) watersheds. The primary purpose of these assessments is to address specific process- or effects-based objectives 

that cannot be studied at larger scales but that are critical for 

understanding processes and effects at the larger scale. Examples of these studies include assessment of the following:

• Effects of stream-ecosystem processes on the transport 

of nutrients by streams and rivers, and how ecosystem 

processes are affected by watershed alterations and 

management practices;

• Effects of sediment and sedimentation on the function 

and structure of aquatic ecosystems;

• Effects of contaminants in water, sediment, or the 

aquatic food chain on degradation of stream ecosystems; and

• Effects of reach-scale geochemical and hydrologic 

processes on contaminant transport from groundwater 

to streams and streams to groundwater and how these 

processes are affected by hydromodification of a 

watershed in agricultural and urban areas. 

Design Characteristics

• The IS assessments could include single sites for 

addressing the interactions of flow, contaminants, 

nutrients, or sediment, or multiple sites for studies that 

address nutrient processing in small watersheds or the 

importance of groundwater/surface-water interactions. 

The IS will be nested inside the larger IWS, with one 

or two IS sites per IWS, depending on the specific 

questions being addressed. Similar to the IWS, the IS 

will be anchored by sites in the NFSN. 

• The IS assessments provide an important scale for collaborative work with other USGS long-term programs 

like the National Research Program (http://water.

usgs.gov/nrp/) and the Toxic Substances Hydrology 

Program (http://toxics.usgs.gov/) and are well suited 

for coordinating with NEON and other non-USGS 

programs. 

• Each IS site will be selected primarily from sites or 

small watersheds that have been studied during Cycle 

1 or 2 to take advantage of the amount of baseline 

data already available. Because monitoring for each IS 

assessment will be used to address different questions, 

no single design will necessarily work for all questions. 

Due to the variable levels of effort at these sites, IS 

assessments will rotate among the different IWS study 

areas, with some IS assessments lasting 2–4 yr and 

others lasting longer.

Relation to Other Components

The following items describe the relation between the IS 

assessments and other surface-water components:

• Include at least one NFSN site for each IS and locate 

within an IWS study area;

• Provide understanding of specific processes or causeeffect relations for interpreting findings from all other 

components; and

• Provide information on rates of key hydrologic, 

geochemical, and biological processes for use 

in water-quality and hydrologic models used to 

extrapolate and forecast water-quality conditions. 

Groundwater

In Cycle 3, NAWQA will provide a comprehensive 

national assessment of groundwater quality in the context of 

its suitability as a source of drinking water and with respect 

to its effect on ecosystem conditions. In Cycles 1 and 2, 

NAWQA implemented a targeted design that provided an 

opportunity to assess groundwater quality across a broad range 

of conditions representative of the Nation, with a particular 

focus on evaluating the relation between land use and shallow 

groundwater quality. In Cycle 3, NAWQA will implement an 

integrated design that uses data and models at multiple scales, 

with an emphasis on developing a three-dimensional view 

of groundwater quality in selected principal aquifers. The 

Cycle 3 groundwater design will complement and build on 

data and models developed by NAWQA during Cycles 1 and 

2, by other USGS Programs, such as the National Cooperative 

Geologic Mapping Program (http://ncgmp.usgs.gov/), Groundwater Resources Program (http://water.usgs.gov/ogw/gwrp/), 

and Cooperative Water Program (http://water.usgs.gov/coop/), 

and other Federal and non-Federal entities. 

In Cycle 1, NAWQA groundwater studies were implemented within study units (2000–10,000 km2

), with National 

Synthesis teams focusing on specific contaminant groups 

(pesticides, volatile organic compounds, nutrients, and trace 

elements). In Cycle 2, NAWQA evaluated previously collected 

data in the context of principal aquifers (10,000–100,000 

km2), implemented topical studies designed to develop a better understanding of groundwater quality at local to regional 

scales (100–1,000 km2), maintained a groundwater-sampling 

network for the purposes of assessing trends, assessed trends 

at multiple scales, and also built and sampled new networks 

to fill in data gaps from Cycle 1. During Cycle 1, NAWQA 

sampled about 2,700 observation wells, 3,000 domestic 

wells, approximately 500 public-supply wells, and 500 wells 

with other uses (mainly irrigation). Observation wells were 

installed in randomly selected locations at shallow depths, 

generally less than 50 feet (15 m) below land surface, in 

areas of specific land uses such as row-crop agriculture or 

urban areas as part of Land-Use Study (LUS) networks. 

Results were used to assess the effects of specific land uses on 
Cycle 3 Design Elements 29

shallow groundwater quality. Existing domestic and publicsupply wells randomly selected within the target aquifer were 

sampled as part of Major Aquifer Survey (MAS) studies; data 

from these wells were intended to provide a snapshot of waterquality conditions in the used resource. In Cycle 1, NAWQA 

used statistical analysis and statistical models to evaluate 

groundwater quality at the study-unit and national scales. In 

Cycle 2, NAWQA used statistical summaries and statistical 

models to assess groundwater quality at the principal aquifer 

and national scales, and developed groundwater models to 

understand the distribution, transport, and trends of contaminants at local to regional scales.

The primary organizational unit for Cycle 3 groundwater studies will be the principal aquifer, rather than the 

study unit. Principal aquifers represent large areas (approximately 200,000 to greater than 3,000,000 km2

) with common 

lithostratigraphic and hydrogeologic characteristics, whereas 

study units correspond to surface-water basins (watersheds) or 

smaller aquifer units. Within the context of Principal Aquifer 

Assessments (PAA), NAWQA will collect data and develop 

models at multiple scales. In Cycle 3, NAWQA will develop 

models that can be used to extrapolate groundwater quality 

into unmonitored areas and to forecast changes in groundwater 

quality that might occur due to changes in broad-scale factors. 

The Cycle 3 study components for assessment of groundwater 

quality are briefly introduced in the following list and then 

explained in more detail in the following subsections:

• Principal Aquifer Assessment: The PAA component 

will be the primary organizational unit for groundwater 

studies in Cycle 3, and PAA studies will be designed 

for assessment of status and trends at principal aquifer 

to national scales. 

• Regional Groundwater Study: The RGS assessments 

will be nested within principal aquifers, and selected 

RGS assessments will be co-located with surface-water 

IWS areas. The RGS assessments will be designed 

for assessment of status and trends at regional scales 

with an emphasis on improving understanding of how 

human activities and natural factors affect groundwater 

quality. 

• Local Groundwater Studies: The LGS assessments 

will be co-located with surface-water IS areas or nested 

within RGS areas, and are designed to improve understanding of the human activities and natural factors 

that affect groundwater quality at a more specific level 

of cause and effect than RGS assessments. 

With these components as the building blocks for design, 

Cycle 3 can accommodate multiple scales of monitoring, 

assessment, and modeling with sufficient structure to enable 

systematic integration of findings, yet with sufficient flexibility to enable timely and targeted studies of specific topics with 

unique design requirements. The following subsections provide detailed descriptions of each study component, followed 

by a description of initial plans for national implementation.

Principal Aquifer Assessment

The PAA studies will be designed for assessment of 

groundwater status and trends at the principal aquifer to 

national scales. Figure 4 shows the distribution of principal 

aquifers in relation to use as public supplies of drinking water 

and to public-well sampling during Cycles 1 and 2. In Cycle 3, 

NAWQA will evaluate existing regional groundwater networks and develop new regional networks in the context of 

principal aquifers. This plan also outlines two new types of 

monitoring networks for Cycle 3, the Principal Aquifer Survey 

(PAS) network and the Enhanced Trends Network (ETN). 

Data from PAS wells will be used to assess groundwater quality in aquifers at depths used for public supply. ETN wells 

will be selected from existing networks, instrumented with 

continuous recorders (water level, specific conductance, and 

temperature), and sampled bimonthly for selected constituents 

to gain a better understanding of short-term variability and 

long-term trends in groundwater quality. The ETN wells will 

target shallow groundwater in aquifers and hydrogeologic settings where changes in climate or land use are expected to be 

quickly reflected in groundwater. 

In Cycle 3, NAWQA will use statistical and quantitative groundwater models to assess the status and trends in 

groundwater quality at the principal aquifer scale. Output 

from statistical modeling could take the form of constituent 

concentrations or probabilities associated with a constituent 

concentration exceeding a specified threshold, for example, 

a Maximum Contaminant Level (MCL) or a Health-Based 

Screening Level (HBSL) or some fraction thereof. Modeling studies will include three-dimensional groundwaterflow simulation (Harbaugh, 2005) and particle tracking 

(Pollock, 2012). Where available, NAWQA will use or build 

on models previously developed by the USGS Groundwater Resources Program (http://water.usgs.gov/ogw/gwrp/). 

Output from quantitative flow models, such as hydrologic 

position and residence time, may be used as explanatory factors in statistical models.

Regional Groundwater Studies

The Cycle 3 Regional Groundwater Study (RGS) 

assessments will be designed to contribute to assessment 

of status and trends at regional to national scales and to 

improve understanding of the human activities and natural 

factors affecting groundwater quality. The RGS assessments 

(with study areas of approximately 1,000 to greater than 

100,000 km2) were a major component of NAWQA during 

Cycles 1 and 2 and included LUS and MAS networks, largescale networks sampled by the Transport of Anthropogenic 

and Natural Contaminants to Supply Wells topical study 

(TANC; http://oh.water.usgs.gov/tanc/NAWQATANC.htm), 

and networks of public supply wells sampled by the Source 

Water-Quality Assessments (http://water.usgs.gov/nawqa/

swqa/). In Cycle 3, NAWQA will use existing data when 

available (retrospective data), continue to sample selected 

existing networks to evaluate trends in groundwater quality, 
30 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

implement additional networks where needed, and develop 

quantitative models. Additional networks will fill gaps in the 

existing NAWQA networks, with a particular emphasis on 

evaluating groundwater quality in three dimensions, and in 

areas where groundwater is an important source of drinking 

supply. With the shift to assessment at the principal aquifer 

scale, new networks may be located outside of Cycle 1 or 2 

study-unit boundaries. 

Quantitative models can include groundwater simulation with particle tracking and groundwater simulation 

with solute transport. Quantitative models will account 

for the three-dimensional and temporal aspects of regional 

groundwater-flow systems. Where available, NAWQA will 

use or build on previously developed models, including 

those developed for large- and small-scale TANC studies or 

models produced by the USGS Cooperative Water Program 

(http://water.usgs.gov/coop/). Refinement of the models 

may include simulation of the flow system as a dual-domain 

system; this consists of a mobile domain where transport 

is dominated by advection and immobile pore space where 

advective transport does not occur, in order to better represent residence time and transport of contaminants. The RGS 

study areas will be nested within PAA study areas and may 

be co-located with surface-water IWS study areas. Knowledge gained from RGS assessments will provide a basis for 

extrapolating groundwater quality into unmonitored areas.

Local Groundwater Studies

Cycle 3 Local Groundwater Study (LGS) assessments 

will be designed to develop a better understanding of the 

human activities and natural factors that affect groundwater 

quality. These studies can include two-dimensional FlowPath Studies (FPSs) that examine how groundwater quality 

changes as groundwater flows from recharge to discharge 

areas at scales ranging from a few hundred meters to several kilometers. The LGS assessments also can be threedimensional at scales ranging from tens to hundreds of 

square kilometers, and can address questions related to the 

human, hydrologic, and geochemical processes affecting 

groundwater quality (as done at small-scale TANC studies). 

The LGS assessments will use existing (retrospective) data 

when available, newly acquired data, and quantitative modeling. Quantitative models could range from relatively simple 

mass-balance models to complex simulation models of 

groundwater flow coupled with reactive chemical transport. 

The LGS study areas will be nested within surface-water 

Intensive Studies or RGS study areas.

National Implementation and Integration

In Cycle 3, NAWQA will provide a national perspective on the quality of groundwater, particularly focused on 

groundwater used now or needed in the future for domestic 

and public supplies of drinking water. NAWQA will develop 

national or principal aquifer-scale exceedance maps for 

selected constituents that have concentrations of concern; 

concentrations of concern will be defined relative to USEPA 

MCLs or USGS HBSLs (Toccalino, 2007), and for emerging constituents of concern, on other criteria. Exceedance 

maps will be based on statistical models and incorporate data 

collected by NAWQA and others. The exceedance maps will 

include explanatory factors identified through RGS and PAA 

data collection and statistical models. 

In Cycle 3, about 24 principal aquifers will be identified 

for assessment; these aquifers supply more than 90 percent 

of the groundwater used for domestic and public supply. 

About one third of the principal aquifers will be evaluated 

at a high level of intensity, one third at a moderate intensity, 

and one third at low intensity. High-intensity studies will 

involve sampling of about 200 PAS wells; implementation 

of two to four new MAS, LUS, or FPS networks; development of one to three regional-scale groundwater flow and 

particle-tracking models; development of a principal aquiferscale groundwater-flow and particle-tracking model; and 

development of principal aquifer-scale statistical models for 

selected constituents. Regional-scale models of flow and 

solute transport may be implemented in two to four highintensity PAA study areas, and local-scale models of coupled 

flow and reactive chemistry may be implemented in one or 

two high-intensity PAA study areas.

Moderate-intensity studies will involve sampling of 

about 100 PAS wells; may or may not include implementation of new MAS, LUS, or FPS networks; development of 

one or two regional-scale groundwater-flow and particletracking models; development of a principal aquifer-scale 

flow model (with or without particle tracking); and development of principal aquifer-scale statistical models for selected 

constituents. Low-intensity studies will involve sampling of 

about 50 PAS wells. The low-intensity studies also would 

involve development of principal aquifer-scale statistical 

models for selected constituents.

Enhanced Trend Network (ETN) wells could be located 

within any of the PAA study areas, but it is expected that 

ETN wells would mostly be located in high- or moderateintensity PAA study areas. Criteria for selection of a PAA 

as a high-, moderate-, or low-intensity study may include 

population served by public and domestic supply wells (or 

volume of pumping), climate, hydrogeologic setting, availability of previous data and models, and the geographic 

distribution of other PAAs. Details on the number of networks and wells proposed for the Cycle 3 design can be 

found in section “Objective 1d. Determine the Distributions 

and Trends of Contaminants of Concern in Aquifers Needed 

for Domestic and Public Supplies of Drinking Water” in the 

section on Goal 1.
Goal 1 31

Goal 1—Assess the Current Quality of 

the Nation’s Freshwater Resources and 

How Water Quality is Changing Over 

Time

Objectives, approaches, and partnership opportunities that 

will be used to address the four Cycle 3 goals are described 

in this and subsequent sections. For each of the four Cycle 3 

science goals and their associated objectives the following 

information is described: 

1. Progress made during Cycles 1 and 2, 

2. Data or information gaps not addressed during 

Cycles 1 or 2,

3. NAWQA role in Cycle 3

4. Planned outcomes, 

5. Approach

6. Critical data or technical support requirements, 

7. Partnerships and collaborative opportunities

In this section Goal 1 objectives and approaches are 

described individually; however, in subsequent sections 

on Goals 2, 3, and 4, study objectives are grouped together 

because of similar information requirements, and a description 

of the overall approach that will be used to achieve the science 

goal objectives is given.

Goal 1 Outcome: An updated and enhanced assessment 

of spatial patterns and temporal trends of the quality of the 

Nation’s freshwater resources. 

Products

The following are planned products for Goal 1:

1. Annual Web-based reports on contaminant, nutrient, 

and sediment concentrations and loads based on an 

expanded monitoring network of over 260 streams 

and large rivers with expanded analytical coverage per 

prioritization of constituents by the NAWQA National 

Target Analyte Strategy (NTAS) work group (see 

sidebar “NAWQA NationalTarget Analyte Strategy”).

2. Annual Web-based reports on source- and finishedwater quality at 20 large river and 50 lake or reservoir drinking-water intakes with expanded analytical 

coverage per NTAS prioritization.

3. Annual Web-based reports on contaminant concentrations and trends in groundwater used for domestic 

and public supply with expanded analytical coverage 

per NTAS prioritization. 

4. Continuous monitoring of selected water-quality 

properties and constituents (for example, temperature, 

specific conductance, dissolved oxygen, turbidity, and 

nitrate) or related surrogate water-quality constituents 

(salinity, nutrients, sediment, or bacteria) at a subset 

of NFSN and shallow groundwater-monitoring sites.

5. Annual Web-based reports on trends in mercury 

in fish tissue at the national scale based on annual 

sampling at 100 to 200 locations.

6. Annual Web-based reports on trends in waterquality and biological conditions at approximately 

50 streams in watersheds undergoing rapid landuse change (urbanizing) and at approximately 40 

reference-condition watersheds. 

7. Exceedance maps for groundwater contaminants of 

human-health concern (for example, nitrate, trace 

elements, radionuclides, microbial constituents, and 

organic compounds) at depth zones used for domestic and public supply at the principal aquifer scale 

and for different time periods. 

8. Updated (annual or 5-yr) versions of steady-state 

statistical and hybrid water-quality models such as 

WARP and SPARROW that provide estimates of 

contaminant, nutrient, and sediment concentrations 

and loads at monitored and unmonitored sites at 

national and regional scales.

9. Web-based delivery of steady-state model results 

that allow users to access model predictions for particular aquifers, streams, or watersheds.

10. National-scale synthesis reports that summarize data 

and findings on water-quality conditions and trends 

for surface water and groundwater at regular intervals (every 5 or 10 yr). 

Connections to other NAWQA Cycle 3 Goals

Data, analyses, models, and decision-support systems 

associated with the seven Goal 1 objectives described in 

the following subsections represent the continuation of the 

original NAWQA Program goals of assessing the status and 

trends of the Nation’s water quality and the factors that affect 

water quality and aquatic ecosystems. The data collected 

using the Cycle 3 design will be needed to 

• Develop the understanding necessary to build nationalscale statistical models that allow extrapolation of 

water-quality conditions to unmonitored parts of the 

country (Goal 2);

• Understand trends in water quality at a timescale relevant to changing regulatory policies and 

management practices (Goal 2);
32 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

• Assess the effects of changing land-use and climatic 

conditions on key water-quality and aquatic ecosystem 

stressors (Goal 2);

• Assess the effects of key stressors (contaminants, 

excess nutrients, sediment, and altered streamflow) on 

aquatic ecosystems (Goal 3); and

• Support the development of transient (time-varying) 

models that forecast and predict water-quality and 

stream ecosystem response to changing land-use and 

climatic conditions (Goal 4).

Policy and Stakeholder Concerns Driving Key 

Management Questions

Water-quality legislation enacted in this country at the 

Federal level has been prompted by two primary concerns: 

protection of human health and restoring and maintaining the 

chemical, physical, and biological integrity of the Nation’s 

surface water and groundwater. Hence, stakeholders and 

policy makers are focused on mitigating ongoing persistent 

water-quality problems as well as new or emerging issues 

that relate to human health and aquatic-ecosystem conditions. 

Because most of the concerns and related policies and regulations that prompted the need for water-quality assessment 

apply to assessing the current condition of the Nation’s water 

resources and how those resources are changing over time, the 

following subsections give a brief overview of those policies 

and concerns per the two major receptors of interest: human 

health and aquatic ecosystems. 

Policies and Concerns Related to Human Health

The occurrence of contaminants in source and treated 

drinking water is the primary water-quality concern related 

to human health. Also of concern are (1) threats related to 

consumption of aquatic organisms (primarily fish in freshwater) and (2) microbial contamination of waters used for 

NAWQA National Target Analyte Strategy (NTAS)

A high priority for many stakeholders is for NAWQA to assess new or previously unrecognized contaminants that are 

currently unregulated but that may pose a threat to humans or aquatic ecosystems. Emerging contaminants include, but 

are not limited to pharmaceuticals, antimicrobials, personal-care products, algal toxins, newly introduced pesticides 

and high-use industrial chemicals, various breakdown products, and selected microbial contaminants. Recognizing the 

need to weigh the addition of new contaminants against the need to continue monitoring of Cycle 1 and 2 NAWQA 

contaminants as well as a need to upgrade NAWQA’s existing analytical portfolio, the Cycle 3 Planning Team established a NTAS work group in spring 2009. The work group was instructed to prioritize constituents with respect to:

• Which current NAWQA contaminants are important for continued monitoring;

• Which contaminants could be dropped from lab schedules used by the NAWQA Program; and

• Which emerging contaminants should be added to monitoring plans, in view of current understanding of the 

national significance of different contaminants to Cycle 3 activities.

The NTAS work group was initially tasked with prioritizing current NAWQA analytes and candidate contaminants in 

water and sediment (an evaluation of priority contaminants in fish tissue was dropped due to lack of data) with a focus 

on organic chemicals and trace elements. Microbial contaminants were evaluated separately. Several thousand candidate 

contaminants known to partition in either water or sediment were evaluated. Prioritization of candidate contaminants was 

based on:

• Relevance to human or aquatic ecosystem health based on toxicity data, human- or aquatic-health benchmarks, or 

other documented or suspected health effects noted in the scientific literature;

• Actual or predicted occurrence in the environment at concentrations approaching or exceeding health benchmarks based on existing data, chemical-use information, physiochemical properties, or literature reports; and

• Other agency priorities such as a compound’s presence on the USEPA Contaminant Candidate List 3 or the 

Unregulated Contaminant Monitoring Rule list.

After prioritization was complete, NTAS, in collaboration with the Cycle 3 Planning Team, research chemists at the 

National Water Quality Laboratory, and scientists from the USGS Toxics Substances Hydrology Program, produced a plan 

to upgrade existing methods and develop new ones for the highest priority contaminants.

Information regarding the contaminants evaluated, their relative importance within specific contaminant groups, and the 

methods used to develop the NTAS work group’s recommendations is described in Olsen and others (2013).
Goal 1 33

recreation and drinking. Safe drinking water is essential to 

public health, and the quality of the Nation’s drinking-water 

supply is an issue of growing national importance. Surface 

water is the largest source of drinking water for the United 

States; it accounts for about two thirds of the water used for 

public supply in 2005, and over 10,000 community water 

systems relied on surface-water sources for drinking water 

(Kenny and others, 2009). Reservoirs supply more than twice 

as much drinking water as rivers and streams (Hutson and 

others, 2004). Remaining drinking water for public supply is 

provided by water systems that rely on groundwater sources. 

In 2005, about 258 million Americans received their water 

from public suppliers; the remaining 43 million Americans 

were self-supplied with the vast majority (about 98 percent) 

obtaining their water from private wells (Kenny and others, 

2009). The critical importance of surface and groundwater sources of drinking water makes it a high priority for 

NAWQA to provide a National perspective on the quality 

of both present-day sources of supply and resources that are 

likely to be used in the future. 

The Safe Drinking Water Act (SDWA) provides a 

national framework for the protection of water quality 

provided by public suppliers, and the SDWA thus applies to 

virtually all surface-water sources (very few are private). The 

SDWA also regulates groundwater sources used for public 

supply and suppliers who rely on groundwater under the direct 

influence of surface water. The SDWA authorizes and directs 

the USEPA to establish health-based standards for drinking 

water and requires public suppliers to test for regulated and 

selected non-regulated contaminants in the water they provide 

to their customers. The Source Water Protection Program, 

established in a 1996 amendment to the SDWA, requires delineation of well-head protection areas for public-supply wells, 

identification of potential sources of contamination in those 

areas, determination of susceptibility of public-supply wells to 

contamination, and communication of findings to the public. 

However, the quality of water from privately-owned domestic 

wells is not regulated by the SWDA, nor in most cases is it 

regulated by the states. 

States are responsible for determining the need for and 

issuing of fish-consumption advisories, but USEPA acts as a 

central repository for national information on the advisories, 

and USEPA has published guidance to states, territories, tribes, 

and local governments to use in establishing fish-consumption 

advisories (for example, see http://water.epa.gov/scitech/

swguidance/fishshellfish/fishadvisories/index.cfm). Most advisories involve five contaminants known to bioaccumulate in 

the environment: mercury, polychlorinated biphenyls (PCBs), 

chlordane, dioxins, and dichlorodiphenyltrichlorethane (DDT). 

These contaminants persist for long periods in sediments 

where bottom-dwelling animals accumulate and pass them up 

the food chain to fish. Mercury, PCBs, chlordane, dioxins, and 

DDT were at least partly responsible for 97 percent of all fish 

consumption advisories in effect in 2008, with 80 percent of 

all advisories based at least partly on mercury (http://www.epa.

gov/waterscience/fish/advisories/fs2008.html).

Monitoring, treatment, and disinfection aimed at eliminating the threat of water-borne disease caused by microbiological contamination of public water supplies is regulated by 

the SDWA. The Clean Water Act also addresses microbial contamination and enables protection of surface water for drinking water, recreation, and aquatic food source uses. Although 

the recreational water quality of beaches, lakes, and reservoirs 

is monitored by the USEPA, the states, and local health departments, the recreational water quality of streams and rivers 

used for recreation is only infrequently monitored. 

Policies and Concerns Related to Aquatic Ecosystems

The Clean Water Act is the cornerstone for protection of 

surface-water quality in the United States and for restoring and 

maintaining the chemical, physical, and biological integrity of 

the Nation’s waters so these waters can support high-quality 

aquatic ecosystems and the services those ecosystems provide. 

The statute uses a variety of regulatory and non-regulatory tools 

to reduce direct pollutant discharges into waterways, finance 

municipal wastewater-treatment facilities, and manage polluted 

runoff. The Clean Water Act requires a series of biennial national 

reports, known as 305(b) reports, which summarize water-quality assessments by states, territories, tribes, and jurisdictions of 

the United States. This is the primary source used by the USEPA 

for informing Congress and the public about water-quality conditions as they have been monitored and analyzed by states and 

other jurisdictions. These reports have major weaknesses from 

a national perspective, however, because of the inconsistency in 

approaches among states and overall sparse data. 

Understanding the factors that govern the status and 

trends in the quality of aquatic ecosystems is a national 

concern because of the present extent of impaired waters and 

the potential that the amount of impaired waters and associated ecosystems may increase in the future. As of 2004, 42 

percent of wadeable stream miles in the United States were 

found to be in poor condition, compared to least-disturbed 

reference conditions, and 25 percent were in fair condition 

(U.S. Environmental Protection Agency, 2009). The most 

widespread stressors identified in this USEPA national study 

were nutrients, riparian habitat disturbance, and streambed 

sediment. However, contaminants and other known stressors 

were not extensively assessed, resulting in an incomplete 

understanding of causes. In addition, concerns are increasing 

regarding the potential effects of less well understood threats 

to aquatic ecosystems, including endocrine disrupting chemicals, low-concentration mixtures of multiple contaminants, 

and changing climate.

Within this backdrop of clear-cut documentation of widespread impairment, but uncertainty regarding dominant causes, 

contaminants are an important class of ecosystem stressors 

that need to be characterized and understood in relation to 

their importance in affecting aquatic ecosystems. Without an 

understanding of the relative importance of contaminants and 

their relation to other stressors, management strategies aimed 

at improving aquatic ecosystems cannot be reliably and efficiently devised or implemented.
34 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Management questions related to the Goal 1 status- and 

trend-assessment activities described throughout this section 

include the following examples:

• Are water quality goals, standards, and criteria being 

met for safe drinking and sustainable ecosystems at 

regional and national scales?

• Where are water-quality problems most severe?

• Where and how are conditions changing over time?

• What are the freshwater inflows and loads of nutrients, 

contaminants, and sediment to estuarine ecosystems, 

the Great Lakes, and other receiving waters? 

Objective 1a. Determine the Distributions and 

Trends for Contaminants in Current and Future 

Sources of Drinking Waters from Streams, 

Rivers, Lakes, and Reservoirs

NAWQA Progress During Cycles 1 and 2 

NAWQA monitoring of contaminants in sources of drinking water in Cycles 1 and 2 was primarily focused on assessing 

ambient water quality in streams and rivers across the Nation 

with a primary focus on pesticides and nitrate. Pesticide and 

nitrate studies supported basic assessments of conditions by 

region and land use, as well as the development of predictive 

models that allow extrapolation of results to current and potential source waters in unmonitored watersheds. In addition to 

the national assessment of ambient stream conditions, selected 

stream and river sources of drinking water were monitored for 

about 280 organic contaminants, including selective analysis 

of both source and finished water, to assess occurrence patterns 

in source water and to determine if these patterns also occurred 

in finished water prior to distribution. With the exception of a 

USEPA-sponsored study of pesticide occurrence in reservoirs 

conducted in the latter stages of Cycle 1 (Blomquist and others, 

2001), NAWQA has not addressed contaminant occurrence in 

lakes and reservoirs used for drinking-water supply. 

Information Needs Not Addressed During Cycles 

1 and 2

Remaining information needs that are identified in the 

following bullets include those resulting from a combination 

of design decisions, budget deficiencies, and technological 

constraints during Cycles 1 and 2. The needs have a wide 

range of importance and are not listed in priority order.

• Reservoirs and lakes were not assessed;

• Few source-water intakes were directly monitored—the 

design was oriented toward characterization of ambient 

stream waters, with inference or extrapolation to particular intakes;

• Contaminants were not extensively assessed in surface 

water (not at all or only in a few, selected locations) 

including (1) many pesticides and their degradates and 

adjuvants; (2) numerous additional unregulated organic 

contaminants, including high-production volume chemicals and pharmaceuticals; (3) disinfection by-products; 

(4) algal toxins; (5) microbial contaminants (including 

pathogens); and (6) many types of contaminant mixtures;

• Finished water was assessed for only a small subset of 

sampled public systems; and

• Gradual erosion of geographic and temporal coverage of the surface-water status- and trends-monitoring 

network has reduced the reliability and completeness 

of ambient stream-quality data.

NAWQA’s Role in Cycle 3

The Cycle 3 design for assessing the status and trends of 

contaminants in surface-water sources of drinking water focuses 

on (1) assessing the quality of current and potential future 

source waters, including potentially important new or previously unrecognized environmental contaminants, (2) identifying 

contaminants of potential human-health significance, (3) limited 

monitoring of lakes and reservoirs used to supply drinking water, 

(4) evaluating trends with a particular focus on contaminants of 

greatest concern, and (5) relating observed status and trends to 

natural and human factors that cause observed conditions.

Planned Outcomes

The following are planned outcomes for Objective 1a:

• Enhanced and updated occurrence and distribution 

assessments for current and potential future source 

waters that (1) build on previous assessments by 

updating and expanding target contaminants (based on 

prioritization by the NTAS work group as described 

by Olsen and others, 2013); (2) expand the scope of 

assessment to include 50 lakes and reservoirs that 

currently or potentially supply drinking water; (3) 

improve geographic coverage of contaminant monitoring for streams and rivers to increase the reliability 

of assessments for the most important present and 

future drinking-water sources (importance determined 

by balancing vulnerability to contamination against 

population served); (4) improve statistical models that 

extrapolate contaminant occurrence in streams, rivers, 

lakes, and reservoirs used for public supply based on 

watershed characteristics, chemical use, and other 

relevant ancillary data; and (5) provide regular (annual 

and 5-yr summaries) of water-quality data via the web 

and online reports;

• Targeted assessments of relations between source- and 

finished-water quality;
Goal 1 35

• Assessment of water-quality trends for selected contaminants in source waters and at intake sites for the 

duration of Cycle 3. These assessments will feature 

improved tracking of the most critical contaminants in 

important surface-water supplies; and

• Periodic national reports on the status and trends of 

source-water quality.

Approach

Overview

Objective 1a will mostly be accomplished through 

expanded data collection conducted at NFSN sites, and, to a 

lesser extent, through data provided by RSS assessments and 

other agencies. The most significant changes for the NFSN 

in Cycle 3 include a return to perennial (each site monitored 

each year, every year) instead of rotational (sites monitored 

1 yr out of every 2 or 4 yr) monitoring strategy and a recommendation to incorporate continuous water-quality sensor 

technology at 50 percent of the NFSN sites. Table 2 lists other 

components of the recommended monitoring strategy for the 

NFSN, including sampling frequency and constituents to be 

monitored using continuous water-quality sensors. 

In addition to an upgraded network of ambient streamand river-monitoring sites in which each monitoring site is 

sampled each year of Cycle 3, new monitoring components 

recommended to assess the suitability of surface-water sources 

for drinking-water supply include a sub-network of 20 stream 

and river sites that are at or near public-supply intakes. These 

sites would be selected to represent intakes that are most 

vulnerable to contaminants, based on watershed characteristics 

such as agricultural or urban land use. Blended water systems 

(that is, those systems with multiple surface-water sources or 

those that include a mix of surface water and(or) groundwater 

sources) would be avoided so that the sites are suitable for 

source-water/finished-water comparisons. The 20 sites would 

be distributed geographically across different environmental 

settings with locations weighted towards serving the greatest 

population and having the greatest exposure to contaminants. 

Locations will be selected to balance the distribution of sampling sites across a gradient of system size and vulnerability 

to contamination while also filling critical needs in the NFSN 

with respect to geography, environmental setting, and stream 

size. Site locations will also be nested within IWS areas to the 

extent possible. 

To more fully assess a key source of the Nation’s drinking water, NAWQA will create a new network of 50 lakes 

and reservoirs used for public supply. The focus will be on 

monitoring intake water quality (1 site per supply location) 

with a subset of 10–25 percent of sites selected for sourcewater/finished-water comparisons. The subset of sites selected 

for source-water/finished-water comparisons will focus on the 

most contaminated source waters in a variety of environmental 

and land-use settings based on an initial round of sampling. 

Subject to the above constraints, sites serving the largest 

number of people will be selected. Lake and reservoir studies 

will be strictly focused on water-quality monitoring and will 

not involve detailed studies of lake or reservoir hydrodynamics. Site-selection criteria will be similar to those used for the 

20 stream sites. 

Regional Synoptic Study assessments, in which a selected 

set of contaminants are targeted for sampling during specific 

periods of interest (for example, chemical application periods 

and specific climatic or hydrologic conditions) in water-bodies 

used for drinking-water supply may also be conducted to fill 

gaps in spatial or temporal occurrence. Note that variable 

sampling frequencies at different site types reflect different 

requirements for characterizing contaminant concentrations 

over the annual hydrologic cycle. For example, weekly sampling of small (wadeable) streams over a period of several 

months is warranted to fully characterize the concentrations of 

pesticides during spring application periods. 

Table 2. Sampling strategy for National Fixed Site Network.

Site type

Number

of

sites

Site sampled

every year?

Sampling frequency 

(samples per year)

Continuous water-quality monitoring constituentsa

Streamflow Temperature Specific

conductance Turbidity Dissolved oxygen

Ambient large river 118 Yes 6–18 Yes Yes Yes Yes Yes

Ambient wadeable 

stream

125 Yes 26 Yes Yes Yes Yes Yes

Stream or river drinking 

water intake 20 Yes 18 Yes Yes Yes Yes Yes

Lake or reservoir 

drinking-water intake 50 Yes 12 Possibly Possibly Yes No No

a Continuous water-quality monitoring sensors for the constituents listed will be installed in 50 percent of National Fixed Site Network sites.
36 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Contaminant Coverage

Proposed contaminant coverage for Objective 1a by site 

type is given in table 3 and is based on data needs for this and 

other Cycle 3 objectives. The proposed addition of new or 

emerging contaminants to Cycle 3 monitoring for this objective 

is based on prioritiziation by the NAWQA National Target Analyte Strategy (NTAS) work group (see sidebar) and is subject to 

having approved analytical methods and adequate funding. A 

key step will be continued development of HBSLs (Toccalino, 

2007) for new contaminants that are added to NAWQA analytical schedules. Development of new HBSLs, which is critical 

for assessing which contaminants are of greatest concern, will 

continue to be done in collaboration with USEPA.

Use of continuous-monitoring technology that yields realtime water-quality information for basic properties such as temperature, specific conductance, dissolved oxygen, turbidity, and 

other related constituents is an integral feature of the NFSN 

monitoring design (table 2). It is recommended that such sensors be installed at 50 percent of NFSN sites. Data from such 

monitoring will provide information regarding short-term (minutes to days) responses of water quality to hydrologic, climatic, 

or human effects and will provide an improved understanding 

of stressor-effects relations and will also provide time-dense 

data for the development of transient water-quality models. 

Expand Compilation and Analysis of Non-USGS Data

NAWQA will continue to selectively compile and analyze non-USGS data collected by the states and other organizations to improve spatial coverage of both regulated and 

unregulated contaminants relevant to human water use. An 

important step will be to improve tracking of new data from 

ongoing monitoring efforts. Such tracking will benefit from 

improved methods of data sharing that are being developed 

by USGS, USEPA, and the states. Such data will be critical for working with the USGS WaterSMART Program to 

produce assessments of water availability relative to water 

quantity and quality in selected parts of the country. 

Critical Requirements for Technical Support and Data 

Support

An initial design requirement for Objective 1a will be a 

reliable analysis of the locations of water-supply intakes and 

the boundaries of their watersheds. Reliable data on surfacewater-quality conditions in candidate streams, rivers, lakes, 

and reservoirs considered for drinking-water studies will be 

needed from states, water utilities, and the USEPA. For the 

lake and reservoir studies, data and analysis of the physical 

characteristics of supply reservoirs, such as volume, flushing 

rate, and seasonal mixing and turnover characteristics, will be 

needed for site selection. Finally, continued development of 

appropriate statistical and process-based water-quality models 

to support source and transport analysis (as described in the 

section on Goal 2) will be needed to extrapolate occurrence 

and distribution data to unmonitored areas. 

Objective 1b. Determine Mercury Trends in Fish 

Tissue

NAWQA Progress During Cycles 1 and 2 

Substantial progress was made during Cycle 1 on 

assessing concentrations of organic contaminants in whole 

fish (approximately 1,000 sites were sampled nationally), 

which resulted in national assessments that yielded 

Table 3. Water-quality constituents or contaminant groups to be monitored for characterizing surface-water quality for human health.

Site type

Water-quality constituents to be monitored

Major

Ions

Nutrients

(nitrogen, 

phosphorus, 

carbon)a

Suspended

sedimenta Pesticides

Volatile 

organic 

compoundsb

Human

and

veterinary

drugsc

Semivolatile 

organic 

chemicalsd

Algal

toxins Pathogense

Ambient large river Yes Yes Yes Yes No Yes Yes No Yes

Ambient wadeable stream Yes Yes Yes Yes No Yes Yes No Yes

Large river drinking-water intake No Yes No Yes Yes Yes Yes Yes No

Lake or reservoir drinking-water 

intake No Yes No Yes Yes Yes Yes Yes No

 a Nutrient and sediment monitoring at ambient stream and river sites reflects monitoring requirements for Goal 1 Objectives 1f and 1g.

b

Covers volatile organics, selected high-production volume chemicals, and disinfection by-products of potential human-health concern per findings of the 

NAWQA Target Analyte Strategy (NTAS) work group.

c

Covers pharmaceuticals, antimicrobials, and hormones of potential human-health concern per findings of the NTAS work group. 

d

Covers wide variety of trace organic chemicals including compounds found in personal-care products, detergents, flame retardants, and other organic contaminants of potential human-health concern per findings of the NTAS work group. Although some compounds may be of natural origin, most are associated 

with household, industrial, and agricultural waste or wastewater. 

e

Pathogen monitoring is proposed for a subset of the National Fixed Site Network sites under Objective 1c.
Goal 1 37

statistical-extrapolation models for key individual contaminants. However, trace elements, including mercury, were 

assessed in fish livers and other organisms such as Asiatic 

clams; the presence of these elements in these types of samples 

is difficult to relate to human consumption. From 1998 through 

2005, NAWQA and the Toxic Substances Hydrology Program 

collaborated on a national reconnaissance study of mercury in 

streams, streambed sediment, and fish fillets at approximately 

300 locations (Scudder and others, 2009). Explicit monitoring 

of mercury trends in fish was not a design feature of Cycle 2; 

however, progress was made in assessing the sources and 

factors that control mercury accumulation in water, streambed 

sediment, and fish in selected watersheds across the country 

(Brigham and others, 2009; Marvin-DiPasquale and others, 

2009; Chasar and others, 2009). A recent retrospective analysis 

of fish mercury data collected by state and Federal agencies 

found that out of several thousand locations where fish mercury 

samples had been collected, only about 60 sites had enough 

consistent, long-term data for evaluation of mercury trends in 

fish (Chalmers and others, 2011). 

Information Needs Not Addressed During Cycles 

1 and 2

Information needs that are noted in the following bullets 

include those needs resulting from a combination of design 

decisions, budget deficiencies, and technological constraints. 

The needs have a wide range of importance and are not listed 

in priority order.

• A nationally consistent monitoring program to assess 

trends in fish-tissue mercury and by implication, trends 

in atmospheric mercury caused by reductions related to 

policy changes, is lacking;

• New or emerging contaminants were not extensively 

assessed in fish tissue; 

• Cycle 1 assessments of mercury were based on whole 

fish or livers, emphasizing the use of fish as sampling 

media or wildlife food sources, rather than as human 

food sources; and

• Cycle 1 tissue sites were not resampled for trend 

analysis.

NAWQA’s Role in Cycle 3

The role of NAWQA with respect to addressing potential 

concerns with human consumption of contaminated fish is to 

build on existing regulatory monitoring of edible fish tissues such as the USEPA National Fish Contaminants Survey 

(http://water.epa.gov/scitech/swguidance/fishstudies/overview.

cfm) and to address information needs that are most critical to 

long-term protection of human health from contaminants that 

bioaccumulate in fish. Given that the USEPA and the states 

monitor contaminants responsible for consumption advisories, 

and that an extensive assessment of a variety of contaminants 

in fish of lakes, rivers, and coastal waters is being done by 

USEPA as part of the National Aquatic Resource Surveys 

Program (http://water.epa.gov/type/watersheds/monitoring/

aquaticsurvey_index.cfm), NAWQA will focus on trends in 

mercury concentrations in fish in Cycle 3. Nationally consistent long-term monitoring of trends in mercury is an important 

information gap that is not being addressed by others, yet 

such monitoring will be critical for evaluating the effectiveness of regulatory control strategies for mercury. As Cycle 3 

progresses, and if other priorities emerge, other contaminants 

may be added to assessments. Monitoring of various contaminants in fish tissue may be included in some studies for Goal 3 

objectives for evaluating ecological effects of contaminants on 

fish health.

Planned Outcomes

The following are planned outcomes for Objective 1b:

• Annual updates of trends in mercury in fish tissue 

within a selected set of watersheds that represent a 

range of mercury deposition and methyl-mercury 

production rates will be reported on the Web; and

• A substantial investment in the proposed national 

mercury monitoring network will be provided 

(MERCNET; see http://nadp.sws.uiuc.edu/mercnet/). 

Approach

Overview

The basic approach is to annually monitor mercury 

concentrations in fish in a network of stream and river sites 

over the duration of Cycle 3. Site selection will be based on 

the extent and quality of historical data and on coverage of 

a variety of watershed characteristics that have been shown 

to be important in methyl-mercury production and bioaccumulation in fish consumed by humans such as mercury 

deposition rates, percentage of wetlands, organic carbon in 

streambed sediment, dissolved sulfate, and pH. Candidate 

sites would include NFSN sites, USGS Biomonitoring of 

Environmental Status and Trends Program (http://www.

cerc.usgs.gov/data/best/search/) and National Contaminant 

Biomonitoring Program (http://www.cerc.usgs.gov/pubs/

center/pdfDocs/90341.PDF) sites, and NAWQA lake-coring 

sites. The total number of sites to be monitored would 

range from 100 to 200 sites, with a minimum 25-percent 

overlap with NFSN sites, especially those selected for 

ecosystem-trends monitoring. Mercury trend sites would 

be sampled annually, and one or more targeted fish species 

would be sampled that represent the top predator sport fish 

and that fall within a defined age range. At sites lacking 

predator sport fish, other species may be used as an indicator species. 
38 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Expand Compilation and Analysis of Non-USGS Data

NAWQA will continue to selectively compile and analyze 

non-USGS data collected by the states and other organizations 

on mercury in fish tissue. The primary reason to do so is to 

improve spatial and temporal coverage of mercury concentrations in fish tissue.

Critical Requirements for Technical Support and Data 

Support

A key ancillary data need is to improve current geographic and factual information on state-level monitoring 

programs. Finally, continued improvement on data sharing and 

infrastructure is needed to allow for more efficient and collaborative aggregation of state, Federal, and tribal fish mercury 

monitoring data. 

Objective 1c. Determine the Distributions and 

Trends for Microbial Contaminants in Streams 

and Rivers Used for Recreation

NAWQA Progress During Cycles 1 and 2

Although indicator bacteria were collected at NAWQA 

stream and river sites in Cycle 1, the data were never synthesized at the national level, and only a few Cycle 1 study 

units issued reports to describe the indicator organism datasets that were collected. A strategy for monitoring microbial 

contaminants in Cycle 2 developed by Francy, Myers, and 

Helsel (2000) was not implemented because of lack of funding, although a pilot study to evaluate the occurrence of several 

indicator organisms in streams and groundwater was conducted 

in the latter part of Cycle 1 (Francy, Helsel, and Nally, 2000). 

Information Needs Not Addressed During Cycles 

1 and 2

Newer, molecular, and polymerase-chain-reaction techniques that provide more accurate and pathogen-specific data 

could not be implemented because the methods were either 

still in development or not approved (Cycle 1) or because 

NAWQA did not have the funding (Cycle 2). 

NAWQA’s Role in Cycle 3

Microbial contamination of water is very relevant to 

a national water-quality assessment program. Unlike most 

chemical contaminants, microorganisms can cause nearly 

instant illness to people that are exposed to an infective 

dose. Water-borne diseases from microorganisms are readily 

understood by most people, and outbreaks of water-borne 

diseases, although not as widespread or deadly as in undeveloped countries, are relatively common in the United States as 

reported by the Centers for Disease Control and Prevention 

(http://www.cdc.gov/healthywater/surveillance/index.html). 

Beaches, lakes, and reservoirs used for recreation are monitored by USEPA, the states, and local health departments. 

However, although many people participate in recreational 

activities such as swimming, boating, or water skiing on 

rivers, few states routinely monitor streams and rivers for 

microbiological quality to determine suitability for watercontact recreation.

NAWQA can address three important deficiencies with 

respect to the microbiological assessment of streams and 

rivers: (1) assess the microbiological quality of streams and 

rivers used for body contact recreation, where a high degree 

of bodily contact with the water is likely, for example, swimming, water skiing, or tubing, (2) evaluate relations between 

rapid analytical methods that provide results within 4 hours 

to culture-based methods that take at least 18 hours to obtain 

results, and (3) determine if physical or hydrologic surrogates, such as turbidity or streamflow, are reliable predictors 

of microbial contaminants in inland streams or rivers.

Planned Outcomes

The following are planned outcomes of Objective 1c:

• In streams and rivers, the occurrence and distribution 

of indicator bacteria that are used as current and future 

measures of recreational water quality and the factors and sources that affect their distribution will be 

assessed using state-of-the-art monitoring technology 

and analytical methods;

• A determination will be made of whether rapid analytical methods for selected indicator bacteria are reliable substitutes for traditional culture methods. If it is 

shown that the new methods yield consistent results 

across different hydrologic and climatic settings, it is 

possible that state and local health departments tasked 

with monitoring recreational water quality will adopt 

these methods into state monitoring programs; and

• Statistical models would be developed and refined; 

these models rely on continuously measured surrogates 

to generate real-time predictions of bacterial concentrations and unsafe conditions in streams and rivers used 

for recreational activities. After development, calibration, and quality assurance, data and regression-based 

estimates of microbial contaminant concentrations will 

be placed on the USGS Water-Quality Watch Web site 

(http://waterwatch.usgs.gov/wqwatch/) on a near realtime basis (fig. 15)

Approach

Overview

Advisories or closings for recreational waters are issued 

based on standards for concentrations of Escherichia coli

(E. coli) or enterococci; these standards are based on criteria 
Goal 1 39

established in 1986 and include culture-based analytical methods that take too long to provide timely and accurate assessments. In 2012, the USEPA developed new recreational water 

quality criteria that include a rapid assessment method for 

Enterococcus spp., along with culture methods for E. coli and 

enterococci (USEPA, 2012a).

Research is being done by the USEPA and others to test 

and standardize rapid analytical methods using quantitative 

polymerase chain reaction (qPCR) technology for E. coli, 

enterococci, and Bacteroides (Bacteroides is a bacterium 

abundant in the gut of warm-blooded animals, and Bacteroides genes commonly are targeted for source-tracking 

purposes). The qPCR method is a molecular method that 

involves expensive start-up and equipment costs and many 

technology-transfer obstacles, all of which USEPA is working to address. Immunomagnetic separation/adenosine triphosphate (IMS/ATP) is an alternate rapid method that is less 

costly and easier to use (Bushon and others, 2009). USEPA 

and stakeholders at the state and local levels are interested in 

determining how well concentrations of indicator organisms 

Current (2003) secondary 

contact recreational criterion 

(single sample, illness rate of 

8 per 1,000 swimmers)

30-day moving 

geometric mean 

fecal coliform 

bacteria density

Current (2003) 

primary contact 

recreational criterion 

(geometric mean of five 

samples collected within a 

30-day period, illness rate of 

8 per 1,000 swimmers)

Measured density

Water-quality monitor

installed July 1, 1999

Estimated bacteria density

from interpolated turbidity Hourly estimated fecal

coliform bacteria density

Hourly estimates greater than 2,000

colonies per 100 milliliters of water 30-day geometric mean 

greater than 200 colonies 

per 100 milliliters of water

100,000

10,000

1,000

100

10

1

100

75

50

25

0

Fecal coliform bacteria density, in colonies per 100 milliliters of water Probability of exceedance,

in percent

May

June

July

Aug.

Sept.

Oct.

Nov.

Dec.

Jan.

Feb.

Mar.

Apr.

May

June

July

Aug.

Sept.

Oct.

Nov.

Dec.

Jan.

Feb.

Mar.

Apr.

May

June

July

Aug.

Sept.

Oct.

Nov.

Dec.

Jan.

Feb.

Mar.

Apr.

1999 2000 2001 2002

Figure 3.1

Figure 15. Comparison of measured and regression-estimated fecal coliform bacteria concentrations in the Kansas River at Desoto, 

Kansas, for May 1999 through April 2002 (upper plot) and the probability of exceeding recreational water-quality criteria established 

by the Kansas Department of Health and Environment (from Rasmussen and Ziegler, 2003). Such plots are updated on a near real-time 

basis and made available to the public through the USGS Water-Quality Watch Web site (http://waterwatch.usgs.gov/wqwatch/).
40 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

determined by rapid analytical methods compare to current 

culture methods as the transition to rapid methods is implemented over the next decade. 

Stakeholders also are interested in developing continuous surrogates for indicators and pathogens. These methods 

depend on concurrent collection of ancillary water-quality 

and hydrologic data at the time of collection of a fecal indicator bacteria sample. Typically, fecal indicator bacteria concentrations have been found to be correlated with turbidity 

and streamflow in streams (Rasmussen and Ziegler, 2003), 

and several states (Kansas, Georgia, Maryland) now use 

these relations to predict when water is safe for recreational 

uses (fig. 15; http://waterwatch.usgs.gov/wqwatch/faq?faq_

id=4). Routine NAWQA sampling of multiple water-quality 

constituents is an excellent foundation for developing surrogate relations and potentially establishing simple regression models that link one or more surrogate measures with 

indicator bacteria concentrations. 

The monitoring approach will involve sampling a 

subset of 75 NFSN sites for key indicator bacteria using both 

traditional culture and new rapid analytical methods. Siteselection criteria will include broad geographic coverage, a 

variety of land-use types and sources of fecal contamination, 

different climates and watershed sizes, and the capability of 

USGS personnel to perform the specialized sampling. NFSN 

sites that represent streams or rivers designated for recreational activities will be included in the monitoring design 

as well as sites not designated as formal recreational sites 

(because many of these sites, especially wadeable streams, 

are used for recreation). Twenty-five of the 75 sites selected 

will be sampled 14 times per year over a 3-yr period, 

followed by rotation to 25 new sites. Sites will be sampled 

on an approximately monthly schedule with more intensive 

sampling from May through September with collection of 

two additional storm samples. 

Contaminant Coverage

The indicator bacteria E. coli and enterococci will be 

determined by traditional membrane filtration culture techniques. E. coli and enterococci also will be determined by 

IMS/ATP and qPCR rapid methods, whereas Bacteroides will 

be done by qPCR only. 

Critical Requirements for Technical Support and Data 

Support

The qPCR method for enterococci (Method 1611) has 

been published and validated (USEPA, 2012b). Methods for 

Bacteroides (USEPA, 2010a) by qPCR and for E. coli by 

IMS/ATP have not been validated and will require USGS 

approval prior to the start of Cycle 3. Training of field crews 

on how to collect and process microbiological samples will 

also be needed. 

Objective 1d. Determine the Distributions and 

Trends of Contaminants of Concern in Aquifers 

Needed for Domestic and Public Supplies of 

Drinking Water

NAWQA Progress in Cycles 1 and 2

In Cycles 1 and 2, NAWQA analyzed groundwater 

samples for both regulated and unregulated contaminants of 

potential human-health concern using laboratory methods that 

provide low-level detections, commonly at concentrations one 

to three orders of magnitude below regulatory thresholds. To 

place observed concentrations in a human-health context, data 

were compared to human-health benchmarks: either USEPA 

Maximum Contaminant Levels (MCLs) for regulated contaminants or HBSLs for selected unregulated contaminants 

(mainly organic compounds). NAWQA also collected samples 

for various hydrologic tracers (stable isotopes), indicators of 

groundwater age (trace gases and radioisotopes), and indicators of geochemical conditions (pH and dissolved oxygen). 

These constituents provide a basis for interpreting the hydrologic and geochemical processes that affect groundwater 

quality and for tracing sources of contaminants derived from 

human activities.

NAWQA focused mostly on sampling shallow monitoring 

wells and domestic wells in Cycles 1 and 2, thus providing coverage for parts of the groundwater system (shallow) and user population (private domestic wells) that are not otherwise monitored (or 

regulated) on a systematic basis nationally. Both domestic wells 

and public-supply wells were sampled at the point of extraction 

and prior to treatment rather than sampling at the tap, thus providing a direct assessment of the ambient groundwater resource. 

Cycle 1 groundwater-monitoring networks were implemented at multiple scales within the context of study units 

(52 Study-Unit Investigations). MAS studies, which had areas 

of approximately 1,000 to greater than 100,000 km2

, were 

designed to provide a broad assessment of groundwater quality in areas with relatively similar geologic, hydrologic, and 

climatic conditions. Nationwide, groundwater samples were 

collected from about 3,000 wells (approximately 2,000 domestic, 500 public-supply, and 500 other well types, mostly irrigation) in about 100 MAS networks. LUS networks, which were 

approximately 100 to greater than 1,000 km2

, were nested 

within MAS study areas and were designed to assess relations 

between shallow groundwater quality and overlying land use. 

About 2,700 wells (primarily observation wells) were sampled 

in about 110 agricultural and urban land-use networks. FlowPath Study (FPS) assessments were designed to evaluate the 

hydrologic and geochemical processes affecting groundwater 

quality along a presumed flow path and were typically implemented at relatively short length scales (1–10 km). About 650 

observation wells, installed in shallow to moderate depth well 
Goal 1 41

clusters, were sampled in about 40 FPS networks, most of 

which were nested within LUS networks. Additional wells, 

including reference wells, were sampled by Study-Unit Investigation teams for various purposes to complement the MAS, 

LUS, and FPS networks.

In Cycle 2, 26 new MAS networks (with approximately 

780 wells) and 18 new LUS networks (with approximately 540 

wells) were sampled to fill spatial or specific land-use gaps, 

including a few areas outside of previously defined Study-Unit 

Investigation boundaries. Similar to surface-water studies, studies of ambient groundwater quality were augmented by Source 

Water-Quality Assessments (http://water.usgs.gov/nawqa/

swqa/) that involved sampling of selected groundwater supplies for about 280 organic contaminants (including analysis of 

both source and finished drinking water) to assess occurrence 

patterns in source water and to determine if these patterns also 

occurred in treated drinking water prior to distribution. For 

each groundwater system evaluated (about 30), samples were 

obtained from 15 high-volume supply wells. 

In contrast to the substantial reductions in the number of sites 

operated and samples collected that were incurred by the NAWQA 

surface-water network, the number of groundwater networks 

sampled in Cycle 2 for status and trends assessments largely 

adhered to the original implementation plan developed for Cycle 2 

by the NAWQA National Implementation Team and described by 

Gilliom and others (2001). However, synthesis of status and trends 

data in Cycle 2 is being done at the principal aquifer scale with 

synthesis efforts focused on 19 of 62 principal aquifers (Lapham 

and others, 2005). The principal aquifer-scale assessments are 

based mostly on analysis of data from Cycle 1 MAS, LUS, and 

FPS networks, and results from Cycle 2 Source Water-Quality 

Assessments (preceding paragraph) and Transport of Anthropogenic and Natural Contaminant (TANC) large-scale studies. 

With respect to groundwater trends, in Cycle 2, NAWQA 

resampled 33 MAS networks and 33 LUS networks (approximately 2,000 wells) for the purposes of monitoring trends on a 

decadal time scale. Results of the first round of decadal-scale 

resampling focused on trends in nitrate and pesticides and pesticide degradates. Findings show significant increases in nitrate 

concentrations over the last 10–15 yr, mainly in agricultural 

areas (Rupert, 2008). The detection frequencies of six frequently 

detected herbicides did not change; however, small but statistically significant decreases were observed in concentrations of 

two of the herbicides (atrazine and prometon) and one herbicide 

degradate (deethylatrazine) (Bexfield, 2008). Patterns in nutrient 

and pesticide concentrations over time generally reflect overall 

trends in fertilizer and pesticide use. Six Cycle 1 FPS networks 

also were resampled to assess changes in groundwater quality 

along a known flow path where rates of flow and contaminant 

loading to the local aquifer were known. Changes in rechargewater quality over the decadal time periods at the FPS sites 

generally reflected changes in land and chemical use at the local 

to regional scale (Rosen and others, 2008). 

A subset of 5 wells from each of the LUS and MAS 

trends networks were selected for quarterly and biennial trends 

sampling in Cycle 2. Quarterly sampling was conducted for 

1 yr at a subset of 100 biennial trend wells. Rosen and others 

(2008) found that quarterly sampling over a 1-yr period was 

ineffective for assessing seasonal effects on groundwater 

quality. Based on this finding, the decision was made in midCycle 2 to drop quarterly monitoring and devote the quarterly 

monitoring funds to increased groundwater age-dating and 

flow modeling. An evaluation of trends using the biennial data 

collected during the course of Cycle 2 has yet to be completed, 

and it is not known how much information will be provided 

by the six samples (four biennial samples collected between 

the two decadal samples) regarding intra-annual variability 

in groundwater quality caused by year-to-year changes in 

climate, human activities, and contaminant loading. 

Information Needs Not Addressed During Cycles 

1 and 2

The following information needs were not addressed for 

Objective 1d during Cycles 1 and 2:

• Spatial gaps exist from the perspective of principal 

aquifers because, with few exceptions, Cycle 1 and 

2 groundwater networks were located entirely within 

Study-Unit boundaries;

• Depth gaps exist in many areas; although NAWQA 

has adequately characterized water quality in shallow 

recharge areas and the depth zone used for domestic 

supply, the Program has not broadly assessed groundwater quality in the depth zone used for public supply; 

• Contaminant gaps exist for selected regulated and 

unregulated contaminants, including anthropogenic 

organic chemicals (for example, pharmaceuticals, 

wastewater and high production volume chemicals), 

radionuclides, and selected microbial pathogens;

• Ancillary data necessary to interpret changes in water 

quality at various scales (local, regional, national) is 

lacking, especially at the temporal scales needed to 

explain trends at the local and regional levels; 

• A weakness of the decadal-scale resampling approach 

to analyzing trends in groundwater quality is that the 

hydrogeologic position of the wells in the local or 

regional flow system often is unknown, especially 

in the MAS networks. Knowing where the wells and 

networks are located with respect to local and regional 

flow systems would allow for a more informed interpretation of trends, or the lack of trends; 

• Some insight into the relative hydrogeologic position 

of a well or network of wells is gained by age dating the groundwater. NAWQA collected a significant 

number of age-dating samples in Cycle 2; however, 

gaps in age-dating coverage in existing trend networks 

still exist; and 
42 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

• An evaluation of how variable groundwater quality 

is at shorter time scales, especially in response to 

seasonal or annual changes in recharge, discharge, or 

contaminant loading, is needed to determine the validity of statistically determined decadal-scale trends in 

groundwater quality

NAWQA’s Role in Cycle 3

Given the importance of groundwater as a source of 

drinking water, it is vital for NAWQA to continue assessing groundwater quality and changes in groundwater quality 

over time in the principal aquifers considered most critical 

for domestic and public supply. This includes evaluating the 

occurrence, concentration, and distribution of contaminants 

in groundwater using a monitoring design that captures the 

most relevant parts of the used resource. Cycle 3 groundwater assessments will focus on that part of the resource that is 

or potentially will be used for drinking-water supply, as the 

quality of groundwater used for drinking water is the highest 

priority from a human-health perspective.

With respect to changes in groundwater quality over 

time, NAWQA is the only national-scale program that is 

evaluating trends in groundwater quality. Because groundwater-residence times range from years to decades to millennia, changes in groundwater quality caused by either natural 

factors such as climate change, or human activities on the 

land surface, may not be reflected in changes in groundwater quality for years, decades, or longer. On the other hand, 

more rapid shifts in climate and human-induced changes in 

contaminant loading could accelerate changes in shallow 

groundwater quality, and it will be important to document 

those changes with data so models developed for extrapolation, forecasting, and scenario testing under Goals 2 and 4 

can be tested and validated. 

NAWQA’s role in Cycle 3 is to (1) collect enough data 

to support development of predictive models at a variety of 

temporal and spatial scales, (2) use flow models and other 

approaches to develop a better understanding of the hydrogeologic position of NAWQA wells and networks, (3) assess 

the range of expected groundwater-residence times and their 

relation to changes in key stressors that affect groundwater 

quality to better understand groundwater trends, and (4) 

selectively add new contaminants of potential human-health 

concern when resampling trend networks to better evaluate 

their distribution in key water-supply aquifers and establish a 

foundation for future trends monitoring. 

Planned Outcomes

The following are planned outcomes for Object 1d:

• Enhanced and updated occurrence and distribution 

assessments for present and potential groundwater 

sources of supply that (1) build on previous assessments by updating and expanding target contaminants 

(based on the NTAS work group recommendations 

described by Olsen and others, 2013), and (2) improve 

spatial and depth coverage of key contaminants at the 

local to national scale;

• Exceedance maps produced by combining data generated under Objective 1d with the modeling described 

in section on Goal 2 (see fig. 16); 

• Assessment of relations between groundwater quality, 

contaminant sources, and selected natural and human 

factors, such as climate and human activities at the 

land surface;

• Periodic national or regional reports on the status and 

trends of selected contaminants in groundwater from 

domestic and public-supply wells; 

• Regular, Web-based reporting of trends in groundwater 

quality at scales ranging from individual networks and 

principal aquifers to the Nation; 

• Development of an ETN whose purpose is to provide 

short and long-term groundwater-quality trend information to the Nation in key hydrologic settings; and

• Production of datasets that can be used to validate 

coupled groundwater flow and solute transport models 

used for extrapolation and forecasting. 

Approach

Overview

Within the context of a given principal aquifer, groundwater quality can vary as a function of position relative to the 

sources of recharge or relative to the areas of discharge; for the 

purposes of analysis, this can be referred to as hydrologic position. In turn, hydrologic position can be defined with respect to 

lateral location (for example, proximal, intermediate, or distal) 

and with respect to depth. From a depth and water-use perspective, the groundwater resource used for drinking water can 

be divided into two depth intervals: the depth zone pumped 

mostly for domestic supply and the zone primarily pumped 

for public supply. In some areas of the Nation, the two depth 

intervals overlap or coincide, and in other areas, the interval 

used for public supply is substantially deeper than the interval used for domestic supply. Two additional depth intervals 

can be defined: shallow groundwater (depth interval above 

the interval used for domestic supply) and deep groundwater 

(depth interval below the interval used for public supply. 

Existing NAWQA networks (MAS and LUS) and a new 

network type, PAS, will be used to characterize groundwater quality with respect to depth and hydrologic position in 

individual aquifers. The PAS network will consist primarily 

of public-supply wells screened at depths typical of the zone 

tapped for public supply. The PAS network design will follow 

the stratified random design used for MAS networks, but the 
Goal 1 43

Central

Valley

Sacramento

Valley

San Joaquin

Valley

120°

121°30’

120°

123°

121°30’

123°

39°

37°30’

36°

34°30’

EXPLANATION

2 or less

Greater than 2 to 10

Greater than 10

No data

Median nitrate concentration, 

in milligrams per liter

SIERRA NEVADA

0 50 100 KILOMETERS

0 50 100 MILES

0 50 100 KILOMETERS

0 50 100 MILES

CALIFORNIA

A B

Figure 3.2

Figure 16. Nitrate exceedance maps for California’s Central Valley principal aquifer based on nitrate samples collected in the 

1970s. The map on the left shows the nitrate exceedance distribution based on data from shallow (mostly domestic supply) wells 

screened at depths less than 73 meters (m) (240 feet) below land surface. The map on the right shows the nitrate exceedance 

distribution for deep (mostly public-supply) wells that are screened at depths greater than 73 m. Grid cells in red exceed the 

U.S. Environmental Protection Agency’s Maximum Contaminant Level (MCL) of 10 milligrams per liter for nitrate. The maps were 

created by using an equal area grid for the entire aquifer; compiling nitrate data from local, state, and Federal agency databases 

(approximately 21,000 wells); and by partitioning available data for wells in the grid cells by decade (Karen Burow, U.S. Geological 

Survey, written commun., September 2010).
44 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

size of the area covered and number of wells sampled will be 

larger than a typical MAS network depending on water-use 

patterns, the availability of non-USGS data to fill spatial and 

depth gaps, and the desire to increase coverage with respect to 

hydrologic position. 

Principal aquifers will remain the primary organizational 

and design unit for Cycle 3 groundwater assessments. As 

described earlier, the plan is to assess groundwater quality in 

24 of the 62 most important aquifer systems of the Nation 

based on water use for domestic and public supply, overall 

water use and population served, environmental setting, and 

relative vulnerability to contamination at varying levels of 

intensity. Where possible, NAWQA assessments will be done 

in collaboration with the USGS Groundwater Resources 

Program (GWRP; http://water.usgs.gov/ogw/gwrp/) where 

the GWRP has built or is building regional groundwater-flow 

models. The goal of the collaboration will be to produce wateravailability assessments that combine NAWQA information on 

the quality of groundwater for human use with GWRP information on the quantity of groundwater available in the aquifer. 

A major component of the Cycle 2 trends design that 

will be retained for Cycle 3 is decadal-scale resampling of 

FPS, LUS, and MAS networks (90 networks; see table 4 for 

breakdown by network type). This represents an increase of 9 

networks over the 81 trend networks resampled in Cycle 2; the 

increase in the number of trend networks reflects the addition 

of new networks during Cycle 2. However, existing groundwater-age information and flow-modeling results will be used 

to evaluate existing trend networks to determine if decadalscale resampling of entire networks is warranted or if a reduction in the number of resampled wells warrants consideration. 

Biennial-well sampling, which began in Cycle 2, will continue 

through Cycle 3 in order to obtain information on the magnitude of year-to-year variability in groundwater quality relative 

to observed decadal-scale trends. 

The ETN is a new monitoring component proposed for 

Cycle 3; it will consist of 100 wells distributed across 20 of 

the most important principal aquifers, with an approximate 

distribution of five wells per principal aquifer. These wells 

would be sampled bi-monthly over three 2-yr periods (this 

equates to 12 discrete samples over 2 yr—11 bimonthly 

samples plus one biennial sample). The wells would be 

equipped with data sondes capable of monitoring temperature, specific conductance, and water level; these sondes 

would be operated continuously during Cycle 3 to provide 

basic information on how the well is responding to human 

and natural factors. The continuous data also will be used 

to place the discrete bimonthly water-quality samples in a 

hydrologic context. 

Numbers of Networks and Wells 

A summary of the approximate number of networks, 

wells, and groundwater samples that would be included in the 

Cycle 3 assessment of the status and trends of the Nation’s 

groundwater resources is presented in table 4.

Contaminant Coverage

Proposed contaminant coverage for Objective 1d by 

network type is given in table 5 and is based on data needs for 

this and other Cycle 3 objectives. The proposed addition of 

Table 4. Approximate number of Cycle 3 groundwater networks and wells. (--, no data)

Network type

Number of 

new status 

networks

Number 

of trends 

networks

Average 

number of 

wells per 

network

Total 

number 

of wells 

sampled

Total 

number of 

decadal 

samples

Total number of 

trend (biennial 

or bimonthly) 

samples

Total 

number of 

samples

Flow-Path Study 15 20 20 700 700 400 a 1,100

Land-Use Study (agricultural, urban) 15 40 30 1,650 1,650 800a 2,450

Major Aquifer Survey 15 30 30 1,350 1,350 600a 1,950

Principal Aquifer Survey 55 0 50 2,750 2,750 -- 2,750

Finished water -- -- -- 450b 450 -- 450

Enhanced Trend Network -- 20c 5 100c -- 3,300d 3,300

Totals 100 90 -- 6,450 6,900e 5,100 12,000

a

 Biennial sampling: (5 wells per network) × (4 biennial samples) = 20 samples per trend network.

b

 Finished water samples are not included in column total; samples will be collected at wells that are within other networks: primarily new Major Aquifer 

Survey or Principal Aquifer Survey networks.

c

 Enhanced Trend Network wells are not included in column totals; they are a subset of trends networks/wells.

d

 Eleven bimonthly samples per 2-year cycle (plus one biennial sample); three 2-year cycles; 6 years of data per well.

e

 3,500 of the wells represent sampling of previously unsampled wells in new networks and the remaining 3,400 represent decadal-scale resampling of wells 

in Cycle 2 trend networks.
Goal 1 45

“new contaminants” to Cycle 3 monitoring for this objective 

is based on potential human-health concerns identified by the 

NTAS work group (Olsen and others, 2013) and is subject to 

having approved analytical methods and adequate funding. 

Continued development of HBSLs for unregulated contaminants that will be monitored in Cycle 3 is a key step in assessing which contaminants are of greatest potential concern. 

Samples from wells that are part of NAWQA MAS and 

LUS trend networks will be analyzed for the contaminant 

groups sampled in previous NAWQA Cycles to continue 

monitoring for changes in groundwater quality; additional 

contaminant groups may be analyzed to establish a baseline 

for previously unmonitored constituents or contaminant 

groups (table 5). Trend network wells that have not been 

sampled for groundwater-age tracers will be sampled for 

those tracers in Cycle 3. This strategy applies to biennial 

trend network wells although they will not be resampled for 

age tracers on a biennial basis. Bimonthly samples collected 

from wells in the ETN will be analyzed for major ions and 

nutrients. 

Expand Compilation and Analysis of Non-USGS Data

NAWQA will continue to selectively compile and analyze 

non-USGS water-quality data collected by the states and other 

organizations on contaminants in groundwater, especially for 

commonly measured contaminants of human-health concern 

such as nitrate, arsenic, and selected pesticides and volatile 

organic compounds. Such data will be critical for producing 

aquifer exceedance maps at various spatial and depth scales as 

Table 5. Water-quality constituents or contaminant groups to be monitored for characterizing groundwater quality for human health.

[P, indicates this contaminant group will potentially be included in this network depending on study objectives, environmental setting, and funding constraints]

Network type

Water-quality constituents to be monitored

Geochemical 

indicatorsa

Agedating 

tracersb

Major 

Ions

and 

nitrate

Trace

elements Pesticides

Volatile

organic 

compoundsc

Human

and

verterinary 

drugsd

Semivolatile 

organic 

chemicalse

Radionuclidesf Pathogensg

Flow-Path Study Yes Yes Yes P Yes P P P P P

Agricultural LandUse Study Yes Yes Yes P Yes No P No P P

Urban Land-Use 

Study Yes Yes Yes Yes Yes Yes Yes Yes P No

Major Aquifer 

Survey Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes

Principal Aquifer 

Survey Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes

Finished water No No No No Yes Yes Yes Yes No No

Enhanced Trend 

Network Yesh No Yes No No No No No No No

a

 Geochemical indictors include basic water-quality properties, such as temperature, specific conductance, and pH, and indicators of redox condition, such as 

dissolved oxygen.

b

 One or more potential age-dating tracers including tritium, tritium-helium-3, chlorofluorocarbons, and other trace atmospheric gases will be used to estimate 

the apparent recharge age of the water sample.

c

 Covers volatile organics, selected high-production volume chemicals, and disinfection by-products of potential human-health concern per findings of the 

NAWQA National Target Analyte Strategy (NTAS) work group.

d

 Covers pharmaceuticals, antimicrobials, and hormones of potential human-health concern per findings of the NTAS work group. 

e

 Covers a variety of trace organic chemicals including compounds found in personal-care products, detergents, flame retardants, and other organic contaminants of potential human-health concern per findings of the NTAS work group. Although some compounds may be of natural origin, most are associated with 

household, industrial, and agricultural waste sources. 

f

 Radionuclides of human-health concern including uranium, radon, radium, lead, and polonium. Selected radioisotopes would be assessed in aquifers where 

they were known or suspected to occur at concentrations approaching human-health benchmarks. 

g

 A subset of Principal Aquifer Survey supply wells (600 wells over the course of Cycle 3) will be sampled for key microbial indicator organisms in vulnerable 

aquifer systems. Indicator organisms to be analyzed include total coliforms, Escherichia coli, enterococci, somatic and F-specific coliphage, enteric viruses, and 

bacillus spores. 

h Enhanced Trend Network wells would be equipped with transducers/data sondes for continuous measurement of water level, temperature, and specific 

conductance.
46 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

well as filling gaps in hydrologic position analyses. Regularly 

updated ancillary data will be needed regarding land, chemical, and water-use information in the vicinity of the well and 

at larger scales. Some of this information can be collected by 

NAWQA but other information will require collaboration with 

state or local agencies to help explain short-term (seasonal, 

annual) trends in groundwater quality.

Continue Highly Selective and Targeted Comparisons of 

Source and Finished Water 

A subset of 450 wells from the PAA and MAS networks will be used to conduct source-water/finished-water 

comparisons. The goal of these comparisons is to provide a 

broad national coverage in a variety of hydrogeologic settings 

deemed vulnerable to anthropogenic organic contaminants. 

The objective of collecting finished water samples is to understand occurrence patterns in source water and determine (1) 

if these patterns also occur in finished water prior to distribution and (2) how those patterns vary as a function of different 

treatment types. 

Critical Requirements for Technical Support and Data 

Support

Ancillary hydrogeologic data regarding recharge and 

discharge rates (natural and human), hydrologic position 

(lateral and vertical), aquifer type, and mineralogy need to 

be compiled for each well sampled. Data on sources (and 

history) of contaminants or surrogates for those sources (land 

cover) in the vicinity of each well also will need to be compiled. Although NAWQA will compile much of these data at 

the national level, collaboration with other Federal, state, and 

local agencies (such as the Advisory Council on Water Information Subcommittee on Groundwater) will be important to 

gather key ancillary information. 

Objective 1e. Determine the Distributions and 

Trends for Contaminants, Nutrients, Sediment, 

and Streamflow Alteration that May Degrade 

Stream Ecosystems

NAWQA Progress During Cycles 1 and 2

Substantial progress was made during Cycles 1 and 2 on 

assessing the occurrence and distribution of a broad variety 

of contaminants and nutrients in stream water and relating 

time- or flow-weighted concentrations to (1) current biological 

condition as determined by evaluating the status of algae, macroinvertebrate, and fish communities; and (2) water-quality 

benchmarks for aquatic life. These data supported a variety of 

statistical analyses that related the degree of ecosystem impairment or frequency of exceeding benchmarks to concentrations 

of contaminants, nutrients, and suspended sediment. Findings indicate variable degrees of correlation, with aspects of 

some stressors highly correlated with ecosystem impairment, 

albeit with substantial uncertainty because of the concurrent, 

unmeasured effects of other stressors, such as habitat degradation and streamflow alteration, as well as natural variability. 

Trends in flow-adjusted concentrations of selected constituents that can impair aquatic ecosystems, including dissolved 

solids, nutrients, suspended sediment, and pesticides, have been 

analyzed using data collected at NAWQA monitoring sites that 

are part of the surface-water trends network. Flow-adjusted 

trends in surface-water quality vary widely across the country as 

a function of land use and environmental setting, with upward 

or downward trends reflecting changes in source terms, regulatory actions, or management practices. 

The collection of suspended-sediment data by NAWQA 

in Cycles 1 and 2 has been secondary to data on other potential 

stressors and has primarily been for the purpose of characterizing trends in suspended-sediment concentrations at NAWQA 

fixed sites or loads at NASQAN and NMN sites. Streambedsediment samples were collected at approximately 500 sites 

across the country in Cycle 1 to characterize the occurrence 

and distribution of sediment-associated contaminants relative 

to land-use setting and sediment-quality guidelines. Streambed sediment data collected by NAWQA were compared with 

USGS and other agency data, and the results indicate continued declines in the concentration of bioaccumulative and toxic 

contaminants that were banned by USEPA in the 1970s and 

1980s such as organochlorine pesticides like DDT (Gilliom 

and others, 2006). However, repeat sampling at streambedsediment monitoring sites was not conducted in Cycle 2. More 

detailed information on trends in sediment quality is obtained 

from sediment cores collected at lakes and reservoirs in urban, 

agricultural, and reference-condition watersheds (see http://

tx.usgs.gov/coring/). 

Although the coring studies confirmed declining trends in 

most metals and several banned organic contaminants, they also 

showed that concentrations of other contaminants of concern to 

aquatic ecosystems, principally polycyclic aromatic hydrocarbons (PAHs), have increased in recent decades and frequently 

are found at concentrations that exceed sediment-quality guidelines in the youngest parts of the cores (Van Metre and Mahler, 

2005). In Cycle 2, NAWQA scientists, in collaboration with 

scientists working with the City of Austin, Texas, identified a 

major, previously unrecognized urban source of PAHs: coaltar-based pavement sealants. The importance of these sealants 

as a PAH source was recently confirmed by source-receptor 

modeling to 40 lakes, which identified coal-tar sealants as the 

largest PAH source (Van Metre and Mahler, 2010).

Evaluating the effect of streamflow alteration on aquatic 

ecosystems was not a major component of Cycle 1 or Cycle 2 

studies. In Cycle 2, the effect of altered streamflow and related 

physical properties was partially addressed by two of the five 

NAWQA topical studies and as part of a national analysis of 

ecological data collected during Cycles 1 and 2. In the first 

topical study, the effects of urbanization on physical habitat 

and biota (fish, macroinvertebrates, and algae) were studied 

in multiple urban areas across the conterminous United States 

(EUSE study; Coles and others, 2012). The EUSE study 

found that streamflow, temperature, and physical habitat were 
Goal 1 47

altered by urbanization and that changes in biological condition of urban streams were correlated with changes in various 

streamflow metrics. In the second study, the effects of nutrient 

enrichment on stream were studied in multiple agricultural 

areas across the conterminous United States ecosystems 

(NEET study; http://wa.water.usgs.gov/neet/). The NEET 

study showed that stream temperature and channel substrate 

have substantial effects on macroinvertebrate community 

response and that groundwater discharge, as measured by a 

base-flow index, was inversely correlated with stream temperature in the agricultural streams studied (Riseng and others, 

2011). Also, Carlisle and others (2010b) found that high flow, 

low flow, and flow variability in streams are altered compared to reference conditions and that alteration of these flow 

characteristics is associated with impaired aquatic ecosystem 

condition.

Information Needs Not Addressed During Cycles 

1 and 2

The following information needs for Objective 1e were 

not addressed during Cycles 1 and 2: 

• Potentially important contaminants not measured in 

water during Cycles 1 and 2 including some pesticides (especially those that are new or have recently 

increased in use), pesticide degradates and adjuvants, 

and other organic contaminants that are potentially 

toxic or hormonally active, such as those used in 

personal-care products, various dyes, surfactants, and 

other industrial chemicals (Olsen and others, 2013); 

• Potentially important contaminants not analyzed in 

streambed sediment or lake sediment cores during 

Cycles 1 and 2 including hydrophobic organic compounds that are toxic, bioaccumulative, or hormonally 

active and are potential endocrine disruptors. Examples 

include synthetic hormones; new pesticide compounds 

and their degradates; and various phenols, plasticizers, dyes, flame retardants, and other industrial and 

personal-care products (Olsen and others, 2013);

• Suspended-sediment sampling generally has been 

inadequate to describe how sediment concentrations 

vary spatially and temporally, especially at time scales 

relevant to aquatic ecosystems. The sampling also has 

been inadequate to identify trends and describe how 

these trends are related to changes in upstream landuse or land management practices;

• An assessment of the extent, severity, and types of 

streamflow and temperature alterations and an evaluation of how dominant types of streamflow and temperature alteration vary among regions; and 

• Documentation of historical temporal changes in 

streamflow and temperature alteration and an evaluation of how human activities and natural factors affect 

spatial and temporal variability in observed streamflow 

and temperature. 

NAWQA’s Role in Cycle 3

There is a continuing need for NAWQA in Cycle 3 to 

monitor contaminants and nutrients in the Nation’s streams 

and rivers to determine if concentrations are exceeding 

available aquatic-health benchmarks for water and sediment. 

Because of the overall importance of suspended sediment 

as a source of aquatic-ecosystem impairment, there is a 

longstanding unmet need to improve monitoring of this 

stressor in terms of the number of locations monitored and 

to improve the reliability of measurements of suspendedsediment concentration over time. 

The USGS and NAWQA also are well positioned 

to provide information to government agencies and nongovernmental organizations regarding the effects of streamflow and temperature alteration on aquatic ecosystems. The 

USGS has been collecting consistent streamflow and water 

temperature information at a national scale for more than a 

century, although the data are sparse in the early historical 

record (particularly for water temperature). National-scale 

data on aquatic ecosystem condition has been collected by 

NAWQA since the early 1990s. The NAWQA Program can 

leverage this historical information, together with new data 

collection and studies, to assess and better understand the 

direct and indirect effects of streamflow and temperature 

alteration on aquatic ecosystems. 

Data collected as part of Objective 1e will support 

evaluation of short-term variability in each of the key stressors across a range of environmental settings and help define 

long-term trends caused by changes in climate and land use 

(Goal 2). The data also will be critical for developing an 

improved understanding of how contaminants, excess nutrients, suspended sediment, and sediment-associated contaminants are affecting aquatic ecosystems (Goal 3).

Planned Outcomes

The following are planned outcomes for Objective 1e:

• Enhanced and updated occurrence and distribution 

assessments of contaminant, nutrient, and suspendedsediment concentrations in streams and rivers that 

(1) build on previous assessments of water-quality by 

updating and expanding target contaminants based on 

guidance from the NTAS work group as described in 

Olsen and others (2013); (2) improve geographic coverage of contaminant, nutrient, and sediment monitoring in streams and rivers to increase the reliability of 

assessments examining the effects of these stressors 

on aquatic-ecosystem condition; and (3) improve statistical models that extrapolate contaminant, nutrient, 

and suspended-sediment concentrations in streams, 

rivers, lakes, and reservoirs used for public supply 
48 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

based on watershed characteristics, chemical use, and 

other relevant ancillary data;

• Comparison of observed contaminant, nutrient, and 

suspended-sediment concentrations to existing aquaticlife guidelines, nutrient criteria, and related waterquality standards;

• Enhanced and updated occurrence and distribution 

assessment of new and emerging contaminants of concern in streambed sediment;

• Assessment of decadal-scale trends in new and emerging sediment-borne contaminants in urban, agricultural, and reference-condition watersheds;

• Assessment of flow and temperature metrics for all 

USGS streamgages with sufficient periods of record. 

The statistics will include a variety of metrics that 

characterize the flow and temperature regime and will 

be calculated for the period of record and on a yearby-year basis;

• Identification of a subset of all streamgages that, from 

a flow perspective, represent least-disturbed watersheds. The hydrologic regime at reference sites and 

non-reference sites can be compared to determine the 

severity of streamflow alteration;

• Classification of river types. All reference sites in the 

conterminous United States will be classified into river 

types, such as snowmelt dominated, intermittent flashy, 

or stable groundwater. The classification also will be 

done on a regional basis by ecoregion;

• Assessment of the severity of flow and temperature 

alteration will be determined for non-reference USGS 

streamgages that have sufficient streamflow record;

• Empirical models that can be used to estimate the 

reference flow regime and the degree of streamflow 

alteration at any location in the conterminous United 

States; and

• Web-based tools that allow users to view, query, and 

analyze streamflow alteration datasets. 

Approach

Overview

The status and trends of contaminant, nutrient, and 

suspended-sediment concentrations in water will be characterized by monitoring ambient water-quality conditions through 

the enhanced NFSN. Concentrations and decadal-scale 

change in sediment-associated contaminants will be characterized by resampling selected Cycle-1 streambed-sediment 

locations and lake coring sites and by sampling additional 

sites in high-priority settings (for example, downstream from 

wastewater discharges). 

Surface-Water Quality

Basic data regarding concentrations of contaminants, 

nutrients, and suspended sediment will be collected as 

part of the enhanced NFSN. Short- and long-term information on how concentrations of these constituents vary 

through time also will be provided by the NFSN through 

a combination of fixed-interval sampling conducted at a 

frequency sufficient to characterize contaminant, nutrient, 

and suspended-sediment concentrations over the seasonal 

and annual hydrograph combined with continuous monitoring of key water-quality properties like water temperature, 

specific conductance, dissolved oxygen, and turbidity. 

Increased monitoring associated with an enhanced NFSN 

will improve coverage of the concentrations of ecologically important contaminants, along with concentrations 

of nutrients and suspended sediment both spatially and 

temporally. Coverage also will be enhanced with respect to 

different environmental settings. 

Sediment Quality

Given the current lack of knowledge regarding the 

occurrence and distribution of many emerging contaminants of concern in sediment, the preferred approach will 

be to conduct a reconnaissance study of streambed sediment, lake-bottom sediment, and possibly stormwater pond 

sediments, for analysis of as large a set of ecologically 

important compounds as possible. Ideally, this sampling 

will include toxicity screening at all sites and an assessment of the benthic community, followed by toxicity 

identification and evaluation studies where toxicity is 

indicated. The survey and subsequent toxicity identification and evaluation studies would be done in collaboration with the USGS Toxic Substances Hydrology Program 

(http://toxics.usgs.gov/), the USGS Contaminant Biology Program, or both. The reconnaissance study will be 

conducted early in Cycle 3 with the goals of (1) providing 

findings that are relevant to resource managers in a timely 

manner and (2) of improving and focusing Cycle 3 studies 

of the health of aquatic ecosystems on the most important 

contaminant-related stressors. 

Site selection will be based on an analysis of existing 

NAWQA, Toxic Substances Hydrology Program, and other 

sediment-quality data to determine predominant mixtures of 

sediment-associated contaminants that pose a threat to human 

health or ecosystem condition and their relation to predominant land-use and source types. Approximately 100–200 sites, 

primarily in urban and agricultural settings associated with key 

types of contaminant sources, will be selected for sampling. A 

subset of the sites (10 percent) would be reference sites and an 

additional subset (10 percent) of the sites would be paired with 

lake or reservoir core sites for trend analysis. All sites would 

be sampled once and samples would be analyzed for the highpriority sediment-associated contaminants identified by the the 

NTAS work group (see following subsection “Contaminant 

Coverage”). 
Goal 1 49

Streamflow Alteration

Initial characterization of the current and historical degree 

of streamflow and water temperature alteration will be done 

by analyzing retrospective datasets for USGS streamgages that 

have sufficient periods of flow and temperature data (typically 10 yr of continuous data). Based on an assessment done 

in 2011, approximately 8,000 streamgages have sufficient 

flow data and 5,000 streamgages have adequate temperature 

data for a retrospective analysis. Following compilation of 

the available data, a set of least-disturbed references sites for 

both flow and temperature will be identified. Then, a set of 

empirical models that predict components of the natural flow 

regime and another set that estimates metrics describing the 

altered flow or temperature regimes will be constructed. 

The degree of alteration is determined by comparing 

observed flow and temperature metrics at altered sites against 

those estimated for reference or “least-disturbed” sites within a 

geographic region (for example, a USEPA Level 2 Ecoregion). 

Explanatory variables in the reference-condition models are 

restricted to natural (climate, geology, soils, terrain) watershed characteristics, whereas those used for altered flow or 

temperature regime models would include both human and 

natural characteristics that affect flow or temperature. Only 

explanatory variables that are available across the conterminous United States will be used in model development. 

Once degrees of streamflow or temperature alteration have 

been assessed, the results will be analyzed for spatial patterns 

among regions. Trends in the degree of flow or temperature 

alteration would then be developed by estimating the degree 

of alteration over time for selected time intervals (for example, 

annual to decadal) for sites that have multi-year or multidecadal periods of record. 

Contaminant Coverage

Proposed contaminant coverage for the sampling of 

ambient streams and rivers included in the NFSN is given 

in table 3. Target contaminant groups for Regional Synoptic 

Study (RSS) assessments will vary per individual RSS objectives. The addition of new contaminants to Cycle 3 monitoring for this objective is based on potential aquatic-ecosystem 

health concerns identified by the NTAS work group (Olsen 

and others, 2013) and is subject to having approved analytical 

methods and adequate funding. Contaminants that are considered a high priority from an ecosystem health perspective 

include trace elements, pesticides (including pyrethroids and 

organophosphates), and several important subclasses of hydrophobic organic compounds including PAHs, nonylphenols, 

alkyphenol ethoxylates, brominated flame retardants, and 

perfluorinated surfactants. For the reconnaissance study of 

sediment-associated contaminants described in the previous 

subsection “Sediment Quality,” a mix of approved analytical 

methods, custom methods (developed by USGS but not yet 

approved), and non-USGS methods and laboratories will be 

used. Information from the reconnaissance study will be used 

to guide sediment methods development in the future.

Expand Compilation and Analysis of Non-USGS Data

NAWQA will continue to selectively compile and analyze 

non-USGS water- and sediment-quality data collected by 

USEPA, the states, and other organizations to improve spatial 

and temporal coverage of the NAWQA data. 

Critical Requirements for Technical Support and Data 

Support

Critical requirements for technical support and data support include upgrading or replacing existing analytical methods 

for contaminants of potential aquatic-health concern in water 

and sediment per findings of the NTAS work group (Olsen and 

others, 2013). Historical datasets of land cover and land use, 

datasets describing stream channel modifications, and information regarding water withdrawals and use also will be needed.

Objective 1f. Determine Contaminant, Nutrient, 

and Suspended-Sediment Loads to Coastal 

Estuaries and Other Receiving Waters

NAWQA Progress During Cycles 1 and 2

Monitoring nutrient and sediment loads to estuaries 

and other large water bodies has not been a primary focus 

of the NAWQA Program for several reasons. First, most of 

the nutrients and suspended sediment delivered to estuaries 

is transported by large rivers such as the Mississippi River, 

whereas NAWQA monitoring and assessment in Cycles 1 

and 2 have emphasized smaller tributary rivers and wadeable streams; large-river monitoring has been covered by 

other USGS programs such as NASQAN (http://water.usgs.

gov/nasqan/). Second, the surface-water sampling strategy 

for nutrients used in Cycles 1 and 2 was designed to produce 

accurate estimates of mean annual concentration rather 

than mean annual loading. Finally, efforts to accurately 

characterize either the mean annual concentration or mean 

annual loading of suspended sediment were abandoned early 

in Cycle 1 because of a lack of funding. 

Despite these limitations, NAWQA monitoring and 

assessment activities in Cycles 1 and 2 produced a large 

body of nutrient data that has dramatically improved understanding of the factors that control transport and delivery of 

nutrients to streams, reservoirs, and estuaries (Dubrovsky and 

others, 2010). NAWQA scientists combined monitoring data 

from Cycles 1 and 2 with monitoring data from NASQAN 

and other state and Federal agencies to develop regression/

geospatial models that can be used to extrapolate nutrient 

and suspended-sediment loads to unmonitored locations 

throughout the Nation. The most relevant example of this 

approach is the SPARROW model (Smith and others, 1997; 

Schwarz and others, 2006), which has been applied at national 

and regional scales to estimate mean annual nutrient and 

suspended-sediment loads for any reach in the national stream 

network based on watershed characteristics and to provide 
50 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

source-allocation estimates for modeled watersheds (Alexander and others, 2008; Schwarz, 2008). 

In Cycle 2, NAWQA determined trends in nutrient 

concentrations and loads since 1993 at a national set of stream 

monitoring sites and related trend results to changes in watershed characteristics and nutrient inputs (Sprague and others, 

2009). At most sites, nutrient concentrations and loads did not 

change significantly between 1993 and 2003; where significant changes did occur, the trends were generally upward for 

total nutrient and total phosphorus concentrations and generally downward for nitrate concentrations. NAWQA regional 

assessments of suspended-sediment concentrations and loads 

indicate no significant change at most sites, despite documented reductions in field-scale erosion from improved soil 

controls. As noted previously, sites in NAWQA’s trend assessments have not included many of the large rivers that deliver 

the majority of nutrient and sediment directly to the coast but 

instead focus on the smaller tributary streams and rivers. 

Information Needs Not Addressed During Cycles 

1 and 2

Documenting, understanding, and predicting how nutrient 

and suspended-sediment loading to lakes, reservoirs, estuaries 

and other coastal waters changes over time is a critical 

national need as identified by NAWQA stakeholders. The following specific needs have been identified for Objective 1f:

• Coordination of nutrient and suspended-sediment 

monitoring across USGS programs at large river and 

tributary sites across the country; 

• Enhancing spatial coverage for assessing annual loads 

and trends of nutrients and suspended sediment in the 

Mississippi River Basin and several important estuaries; 

• Enhancing temporal coverage for determining how 

nutrient and sediment loading responds to short (days 

to seasons) and long-term (years to decades) variations 

in climate; and

• A better understanding of whether management practices designed to control nutrient and sediment loading 

to adjacent streams and rivers are effective in reducing 

downstream loading to lakes, reservoirs, estuaries, and 

other coastal waters.

NAWQA’s Role in Cycle 3

NAWQA’s role under Objective 1f is to assess seasonal 

and annual loading of nutrients and suspended sediment to 

downstream aquatic ecosystems in lakes, reservoirs, estuaries, 

and other coastal waters at national and regional scales. 

NAWQA’s contribution to these assessments is unique and 

builds on the models and analyses developed in Goal 2 to link 

spatial and temporal patterns in nutrient and sediment transport to the human and natural factors that affect water quality, 

and to evaluate if, when, and how changes in human activities 

and natural factors such as climate have affected downstream 

transport. The regional and national scales of assessing spatial 

and temporal patterns in nutrient and sediment loading used 

by NAWQA are necessary to help evaluate whether the large 

amount of funds spent on nutrient management and soil conservation have been effective in reducing downstream transport. Information on nutrient and sediment loads will be used 

to support and enhance source and transport models such as 

SPARROW and to transform current steady-state versions of 

these models to transient versions that can be used to forecast 

and predict nutrient and sediment loads over different time 

periods (Goals 2 and 4). 

Planned Outcomes

The following are planned outcomes of Objective 1f:

• Annual publication of nutrient and suspended-sediment 

loads delivered to reservoirs and estuaries monitored 

by the NFSN;

• Assessment at regular intervals (for example, 5 yr) of 

trends in loads of nutrients and suspended sediment 

to reservoirs and estuaries that can be linked to the 

NFSN, and relation of observed trends to changes in 

watershed conditions; and

• Assessment at regular intervals (for example, 5 yr), 

based on monitoring and modeling, of nutrient and 

sediment loads delivered to the 141 catalogued 

estuary systems in the Nation. The estimates would 

include nutrient and sediment loads to the estuary 

and estimates of loads and source shares from major 

tributaries that flow into the estuary. 

Approach

Overview

As described previously, a substantial increase in 

the number of large river NFSN sites where nutrients and 

suspended sediment would be monitored is proposed for 

Cycle 3. This includes reactivation of many of the NASQAN 

and NAWQA sites that were discontinued. Selection of 

sites to be reactivated would be done in collaboration with 

resource management and regulatory agencies including 

USEPA, NOAA, and the states to maximize coverage of 

important reservoirs, estuaries, and other coastal waters. 

The minimum sampling frequency at most NFSN sites will 

be increased to 18 samples per year to better characterize 

inter-annual and seasonal variability of nutrient and sediment 

loading (table 2). To further increase the accuracy of load 

estimates of sediment and sediment-associated constituents, 
Goal 1 51

continuous monitoring of turbidity or other suspendedsediment surrogates will be done at 50 percent of the NFSN 

sites. At a subset of NFSN sites, continuous monitoring of 

nitrate may also be done using new nitrate sensor technology 

(Pellerin and others, 2012). 

To better characterize the spatial distribution and 

occurrence of suspended sediment in streams and rivers, an 

important retrospective data compilation and analysis will be 

undertaken at the start of Cycle 3. This analysis of historical 

USGS sediment data is necessary to (1) determine how historical suspended sediment data vary with respect to sampling 

and analytical methods, (2) understand how biases/uncertainty 

associated with different methods affect computations of 

suspended sediment concentrations and loads, (3) characterize which sites and what data should be used to estimate 

suspended sediment loads and analyze trends, and (4) use 

available data to conduct regional/national assessments of how 

different environmental settings and human activities affect 

suspended sediment loads in streams and rivers and resulting 

sediment delivery to estuaries. 

Contaminant Coverage

Proposed contaminant coverage includes nitrogen constituents (nitrate plus nitrate, ammonia, and total nitrogen), 

phosphorus constituents (total and dissolved phosphorus, 

dissolved orthophosphate), carbon constituents (total and 

dissolved organic carbon), and suspended sediment. Grainsize analysis of suspended-sediment samples will be done to 

improve correlations with surrogate measures of suspendedsediment concentration determined by turbidity sensors or 

other continuous techniques. 

Expand Compilation and Analysis of Non-USGS Data

NAWQA will continue to selectively compile and analyze non-USGS water-quality data collected by the states and 

other organizations on nutrients and suspended sediment in 

the Nation’s streams and rivers. Substantial progress on this 

task has been completed for nutrients, and to a lesser extent 

for suspended sediment, as part of the efforts to build regional 

SPARROW models. However, continued tracking of ongoing 

monitoring by other Federal, state, and local agencies, and 

subsequent compilation of data will be needed to augment 

NAWQA and USGS data collection efforts. 

Critical Requirements for Technical Support and Data 

Support

The need to evaluate the use of surrogate technology 

for continuous measurement of suspended sediment or nutrient concentrations for load estimation is ongoing. Evaluation of the utility of continuous nitrate sensors and other 

potential surrogates to estimate nutrient loads is needed. 

Although continuous turbidity measurement has proven 

effective at estimating fine-grained suspended-sediment concentrations, other measurement techniques, such as optical 

backscatter or hydroacoustic methods, may be used at sites 

with predominantly sand-sized sediment transport (Gray and 

Gartner, 2010). Load-calculation software will need to be 

updated to better handle conversion of continuous surrogate 

data into sediment-load estimates. Additionally, retrospective analysis of historical sediment data is needed to determine where and when sampling was adequate to compute 

historical loads.

Objective 1g. Determine Trends in Biological 

Condition at Selected Sites and Relate Observed 

Trends to Changes in Contaminants, Nutrients, 

Sediment, and Streamflow Alteration

NAWQA Progress During Cycles 1 and 2

NAWQA biological assessments conducted at streams 

and rivers for trends assessment include collection of fish, 

macroinvertebrate, and algae community data, and in-stream 

and riparian habitat data. In the original Cycle 1 design, the 

primary focus of ecological sampling at NAWQA fixed sites 

was to compile a baseline assessment of the current biological condition in the study units, not an assessment of trends. 

Assessment of ecological trends under the Cycle 1 model was 

to be based on successive 3-yr intensive phases as the study 

units were resampled in subsequent decadal cycles. A decision 

was made to begin annual sampling of all ecological trend 

sites in 1998. 

At the start of Cycle 2, 129 of the 145 sites in the 

surface-water status and trend network were deemed suitable 

for ecology sampling on an annual basis. However, as funding declined, the number of surface-water status and trend 

network sites was reduced from 145 to 84, and the number 

of sites designated for ecological trends sampling decreased 

to 58 sites. At this time, the NAWQA Program abandoned its 

goal of providing a national assessment of the “status” of the 

Nation’s stream ecosystems, recognizing that biological data 

collected by the USEPA and the states would be better suited 

to address this objective at the national scale. With respect to 

trends, the NAWQA Ad Hoc Surface Water Status and Trends 

Redesign Committee noted that the 58-site network only 

allows a limited number of site-specific trend stories to be 

told and that extrapolation of trends observed in the network 

to regional or national scales would be in inappropriate. As a 

result, only limited trends analysis had been conducted as of 

2011 on the NAWQA ecological data. 

Information Needs Not Addressed During Cycles 

1 and 2

The following bullets describe information needs for 

Objective 1g that were not addressed during Cycles 1 and 2:

• Sustained ecological trends monitoring at reference or 

“least-disturbed” sites, because these sites will be critical for assessing the effects of natural factors such as 

climate change on aquatic-ecosystem condition; and
52 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

• Sustained ecological trends monitoring at “transitional 

sites” or sites where changes in land, water, or chemical use are occurring or where management practices 

are actively being implemented.

NAWQA’s Role in Cycle 3

In Cycle 3, NAWQA will focus on assessing ecological 

trends at a few sites where consistent, long-term monitoring 

of stream ecosystems is combined with monitoring of physical, chemical, and biological aspects of water quality to gain 

a better understanding of how stream ecosystems change in 

response to changes in key environmental drivers and stressors. Such long-term monitoring will provide temporal context 

for the more spatially extensive monitoring done by USEPA 

and the states and for assessing the effects of changing climate 

and land use on stream ecosystems.

Planned Outcomes

The following are planned outcomes for Objective 1g:

• A description of ecological trends in watersheds where 

human activities at the land surface are causing substantial changes; 

• A description of ecological trends associated with natural factors such as climate change (based on referencecondition watershed monitoring); and

• Incorporation of NAWQA trend sites in probabilistic 

surveys of ecosystem condition conducted by USEPA 

and the states to put results of the probabilistic survey 

results in a temporal context. 

Approach

Overview

A consistent set of ecologic data on important taxonomic 

groups (algae, macroinvertebrates, fish) will be collected 

at all NFSN ecology trend sites to provide a framework of 

information that is consistent in terms of ecological variables, 

methods, and sampling frequency. The framework serves multiple purposes that integrate with other stressor-related monitoring being performed at these sites and provides the response 

data on which to address objectives listed under Goals 2 and 3. 

A subset of NFSN sites where contaminant monitoring 

is being done will be selected for continued ecological monitoring to assess long-term ecological trends. These sites will 

support intensive studies with a core of high-quality, timeseries observations of biological conditions and stressors to 

support objectives laid out in Goals 2 and 3. All NFSN sites 

with ecological monitoring will be wadeable streams. The 

three major types of fixed sites for ecological trends monitoring follow:

• Trends in Streams in Transitional or Developing 

Watersheds: Assess long-term trends in biological conditions in relation to contaminants and other stressors 

for selected “example” streams distributed among a 

variety of the most important environmental settings 

of the Nation where ecological impairment is related 

to agricultural, urban, or other transitional land-use 

categories. 

• Reference Sites: Assess the current status and longterm trends in biological conditions at least-disturbed 

reference sites to evaluate the effects of natural factors 

(such as climate change) at a range of environmental settings. These sites would represent NAWQA’s 

contribution towards a proposed national reference 

watershed and monitoring site network. 

• Intensive Study Sites: Provide temporal assessment 

of biological conditions, as well as contaminants and 

other stressors, at sites included in the Intensive Study 

(IS) network (described in detail in section on Goal 2). 

The IS sites are expected to be primarily a subset of the 

transitional trend sites described above, although some 

new sites may be required to meet the design requirements of the intensive studies. 

It will be necessary to evaluate characteristics of the 58 

current NFSN ecology trend sites including the extent and 

quality of historical water-quality and ecological data and their 

distribution relative to the locations of selected IWS areas 

and related Intensive Studies. The relative importance of the 

four stressors selected for emphasis in Cycle 3 (contaminants, 

excess nutrients, sediment, and streamflow alteration) also 

will be factored into the evaluation, and it may be necessary 

to include some new sites to address specific stressors or 

combinations of stressors. The NFSN ecology sites also will 

be evaluated relative to sites included in recent (2008) USEPA 

NARS (http://water.epa.gov/type/watersheds/monitoring/

aquaticsurvey_index.cfm) Wadeable Streams Assessment to 

better understand how NAWQA long-term monitoring sites 

relate to sites sampled by USEPA. Per Table 1 the NFSN 

would add 30 new reference sites; the remaining sites would 

be a mix of 48 existing NAWQA trend sites in developing 

watersheds and 10 long-term NAWQA reference sites.

The 30 new reference sites will be selected in collaboration with the USGS Hydrologic Benchmark Network (http://

ny.cf.er.usgs.gov/hbn/), the USGS Global Change Program 

(http://www.usgs.gov/global_change/), the USEPA Office of 

Water, the U.S. Fish and Wildlife Service, and the National 

Park Service as part of an effort sponsored by the Advisory 

Committee on Water Information’s National Water-Quality 

Monitoring Council to support development of a collaborative 

and multipurpose national network of reference watersheds 

and monitoring sites for freshwater streams in the United 

States (http://acwi.gov/monitoring/workgroups/wis/National_

Reference_Network_for_Streams_rev2.pdf). 
Goal 1 53

Ecology sites will be sampled annually (no rotation) to 

ensure that monitoring of aquatic community status, contaminant exposure, and other stressors are sufficient to support 

analysis of trends in biological conditions and their relation to 

key stressors. Biological data will include annual sampling for 

in-stream and riparian habitat, algae, and macroinvertebrates; 

fish will be sampled biennially. Transitional and Intensive 

Study (IS) sites would be sampled for contaminants, nutrients, 

and suspended sediment per table 3. Reference sites will be 

monitored less intensively for contaminants, but basic waterquality properties (flow, temperature, specific conductance, 

and turbidity) will be monitored continuously and major ion 

and nutrient samples will be collected monthly. 

Critical Requirements for Technical Support and Data 

Support

Critical requirements for technical support and data support for Objective 1g include the review and update of biological and habitat protocols to optimize the scientific utility and 

cost effectiveness of NAWQA ecologic assessments.

Partnerships for Goal 1

Monitoring the status and trends of the Nation’s water 

resources is done by other USGS Programs and many local, 

state, and Federal agencies. The goal of partnership with these 

entities is to coordinate and leverage assessment activities for 

the benefit of the country. The following subsection highlights 

current or desired partnerships that are critical to achieving 

Goal 1 objectives for Cycle 3. These partnerships involve 

other USGS Programs, agencies, and organizations where 

initial discussions regarding collaborative activities have been 

initiated or are planned with prospective partners. 

USGS Mission Areas and Programs

The following USGS mission areas and programs are 

potential partners for Goal 1 of Cycle 3:

• Climate and Land Use Change Mission Area: Data 

and assessment activities conducted under Goal 1 

objectives support goals listed for the USGS Global 

Change Science Strategy (Burkett and others, 2011) 

in assessing how climate change and land use affect 

streamflow, sediment transport, surface and groundwater quality, and freshwater availability. The information 

also will support efforts to understand how climate and 

land-use change affect aquatic ecosystems, particularly 

through Cycle 3 efforts to expand monitoring at reference watersheds. 

• Energy and Minerals, and Environmental Health 

Mission Area: Discussions with the Toxic Substances 

Hydrology Program have primarily focused on assessments of contaminant occurrence in source waters and 

finished drinking water and on joint methods development activities to increase USGS capabilities for 

analyzing new contaminants in water, sediment, and 

fish tissue samples. The Toxic Substances Hydrology 

and Contaminant Biology Programs also are important 

collaborators for evaluating the occurrence of contaminants in aquatic biota. 

• Ecosystems Mission Area: The NFSN provides a platform for long-term monitoring of aquatic-ecosystem 

condition that includes evaluation of aquatic ecosystem 

structure and function and related ecosystem services 

and how stream ecosystem condition is changing over 

time.

• Water Mission Area: NAWQA, through its data collection and statistical models, is envisioned to be the primary source of water-quality information for regional 

and national-scale assessments of water availability 

from a water quantity and quality perspective. This 

includes assessments of watersheds to be conducted by 

the USGS WaterSMART Program (http://water.usgs.

gov/watercensus/WaterSMART.html) and assessments 

of groundwater availability in principal aquifers being 

conducted by the Groundwater Resources Program 

(http://water.usgs.gov/ogw/gwrp/). 

External Partnerships

The following external agencies and organizations are 

potential partners for Goal 1 of Cycle 3:

• National Water Quality Monitoring Council:

• Support implementation of the National Monitoring Network (NMN; http://acwi.gov/monitoring/) 

by collaborating with the National Water Quality Monitoring Council and its member agencies 

and organizations to track water-quality conditions from headwater streams to coastal estuaries 

by monitoring physical, chemical, and biological 

characteristics of various hydrologic components. 

The NMN is composed of a “network of networks” 

and represents an integrated, multidisciplinary, 

and multi-organizational approach that leverages 

diverse sources of data and information, augments 

existing monitoring programs, and links observational capabilities in nine crucial environmental 

compartments from terrestrial to oceans: estuaries, 

the near shore, offshore and the exclusive economic 

zone, Great Lakes, coastal beaches, rivers and 

coastal streams, wetlands, groundwater, and the 

atmosphere. Network data—including observations 

on biological, chemical, and physical features—

help document inputs, sources, amounts, timing, 

and severity of natural and man-made stressors of 

coastal ecosystems such as freshwater, sediment, 

nutrients, and contaminants. 
54 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

• U.S. Environmental Protection Agency: Collaboration 

with the USEPA could involve the following areas:

• Assess status and trends of aquatic ecosystem 

condition: The USEPA Office of Water’s NARS 

(http://water.epa.gov/type/watersheds/monitoring/

aquaticsurvey_index.cfm) uses a probabilistic 

approach to characterize current water-quality and 

biological conditions of wadeable streams, lakes 

and reservoirs, large rivers, wetlands, and coastal 

estuaries. Identified areas of mutual interest for 

NARS and NAWQA include development of a 

national reference watershed and monitoring site 

network, monitoring of ecological trends in streams 

and rivers, and identification of causes of waterquality impairment.

• Assess risk of pesticides in the environment: The 

USEPA Office of Pesticide Programs (http://www.

epa.gov/pesticides/index.htm) is responsible for 

registration and re-registration of pesticide products and has frequently cited NAWQA information 

in its registration decisions. Identified areas of 

potential collaboration include characterization of 

new pesticide compounds and their degradates in 

drinking-water sources and supplies, development 

of methods to extrapolate pesticide concentrations 

to unmonitored areas, and evaluating the effects 

of individual pesticides or mixtures of pesticides 

on aquatic organisms (Goal 3). A key partner in 

this effort is the State FIFRA (Federal Insecticide, 

Fungicide, and Rodenticide Act) Issues Research 

and Evaluation Group, or SFIREG, which is a 

state-level group that advises USEPA on pesticide 

regulation issues. 

• Assess microbiological contamination in recreational 

waters: The USEPA Office of Research and Development (http://www.epa.gov/ord/) is developing 

recommendations for the USEPA Office of Water 

and the states regarding application of rapid analytical methods for recreational water-quality monitoring. There is a shared interest in testing these new 

methods in a variety of environmental conditions 

and in assessing their efficacy compared to traditional culture-based methods. 

• American Water Works Association, Administration 

of State Drinking Water Administrators, Centers for 

Disease Control and Prevention, National Institute 

of Environmental Health Sciences, Agency for Toxic 

Substances and Disease Registry:

• Coordinate USGS monitoring of drinking-water supplies by collaborating with these organizations. These 

organizations, along with USEPA, have a shared interest in evaluating contaminant occurrence and exposure 

in source and finished drinking water as it relates to 

drinking-water quality and human health. Individual 

water-supply systems and their professional associations, such as the American Water Works Association 

and Administration of State Drinking Water Administrators, would be asked to collaborate on site selection, 

identify suppliers willing to participate in source- and 

finished-water comparison studies, and facilitate 

retrieval of information regarding treatment processes. Agencies such as Centers for Disease Control 

and Prevention, National Institute of Environmental 

Health Sciences, and Agency for Toxic Substances and 

Disease Registry are potential partners for developing 

contaminant exposure estimates via modeling or addon data collection. They would also be contacted about 

coordinating NAWQA water-quality monitoring with 

state or Federal epidemiologic studies.

• National Oceanic and Atmospheric Administration, 

Integrated Ocean Observing System, and National 

Federation of Regional Associations:

• Develop an integrated approach to watershed and 

coastal protection and management of sustainable 

ecosystems through collaboration with these agencies and organizations. The Office of Ocean and 

Coastal Resource Management at NOAA (http://

coastalmanagement.noaa.gov/) manages the biological integrity of estuaries and coasts. Through partnerships with governmental and non-governmental organizations, the Nation’s Integrated Ocean Observing 

System (http://www.ioos.gov/) supports a coordinated 

national and international network of observations 

and data transmission; data management and communication; and data analyses and modeling for coastal 

waters. Associated with the Integrated Ocean Observing System are 11 regional associations that make 

up a broad community of data providers and users, 

including coastal states, Federal agencies, tribes, 

researchers, and non-governmental organizations 

(http://www.usnfra.org/). Data from the NAWQA and 

NASQAN Programs and SPARROW modeling of 

nutrient loads are used by and are directly relevant to 

these partners in protecting and managing key estuaries. Collaborative efforts are ongoing in selected 

regions, including Chesapeake and Delaware Bays, 

the Great Lakes, and the Gulf of Mexico.
Goal 2 55

Goal 2—Evaluate How Human 

Activities and Natural Factors, Such 

as Land Use, Water Use, and Climate 

Change, are Affecting the Quality of 

Surface Water and Groundwater

Goal 2 Outcome: An explanation of the causes of observed 

spatial patterns and temporal trends in water quality that leads 

to an understanding of the factors affecting the response of 

watersheds and aquifers to changes in hydrology, contaminant 

sources, transport mechanisms, natural factors, and past and 

current human activities.

Products

The following are planned products for Goal 2:

1. Surface-water and groundwater models that relate 

observed contaminant, nutrient, sediment, and 

streamflow concentrations, fluxes, and trends to 

human activities and natural factors that can be used 

to assess the potential for degradation of surfacewater and groundwater quality.

2. Dynamic watershed-scale models that explain the 

combined factors that affect observed seasonal and 

annual concentrations and fluxes of water, contaminants, nutrients, and sediment as they move through 

a large, complex watershed or aquifer system.

3. Models that can be used to assess the effects and 

effectiveness of urban and agricultural management 

practices on water quality.

4. Updated Web tools to access and visualize contaminant, nutrient, sediment, and streamflow distributions and trends and their relation to human activities 

and natural factors. 

5. Exceedance maps for selected contaminants of 

human or natural origin that impair the use of 

groundwater for drinking supply. 

Connections to other NAWQA Cycle 3 Goals

Data from NAWQA’s ongoing, long-term monitoring of 

water quality at multiple scales will be used in assessments 

of spatial patterns and temporal trends in water quality across 

the Nation, as described in the section on Goal 1 activities. 

A second vital role of NAWQA in assessing national water 

quality is to link the nature and distribution of water-quality 

conditions (status assessment) and changes and trends in 

water-quality conditions (trend assessment) to the human and 

natural factors that affect water quality. Goal 2 is focused on 

the development of explanations for, and the understanding 

of, observed patterns and trends in water quality identified by 

Goal 1 assessment activities. This understanding is critical 

for evaluating the effectiveness of management practices in 

reducing contaminant concentrations or loads and for evaluating the susceptibility of water quality to degradation. Modeling tools developed as part of this effort will be used in Goal 1 

to extrapolate findings to unmonitored areas and in Goal 4 

to explore improved management strategies and to evaluate 

the effects of potential changes in land use or climate. Waterquality properties and environmental conditions that lead to 

degradation of stream ecosystems will be identified in Goal 3. 

Strategies to remediate and minimize adverse water-quality 

effects on steam ecosystems will rely heavily on the understanding achieved by Goal 2 monitoring and modeling studies. 

Background

Evaluating the causes of broad-scale water-quality problems requires an understanding of processes occurring at multiple scales, from small watersheds and contributing areas for 

individual supply wells to major river basins and principal aquifers. The multi-scale, interdisciplinary approach of NAWQA is 

well-suited for incorporating the optimal mix of investigations 

for each problem. For example, the recent effort by USEPA to 

develop nutrient criteria, combined with concerns about the 

ecological status of inland and coastal waters, underscores the 

need to better understand the effects of watershed disturbance 

on the transport and effects of nutrients at the scale of major 

river basins, such as the Mississippi River Basin. However, it is 

understood that small headwater streams are important in reducing nutrient loading to surface waters due to in-stream processing and transformation, and therefore warrant consideration 

when evaluating large-scale transport of nutrients. It also is 

understood that nitrate currently stored in the unsaturated zone 

and shallow groundwater may be a source of nitrogen loading to surface-water bodies for years or decades into the future 

Dubrovsky and others (2010).

Explaining observed water-quality conditions and trends 

and understanding their connection to human activities and 

natural factors will be achieved through analyses that integrate 

information regarding source loading with flow and transport 

studies, including identification of specific biogeochemical 

or abiotic transformation processes. These studies of stressor 

source, transport, and transformation will make use of simulation and statistical models to help explain historical and 

current water-quality conditions, to estimate the susceptibility 

of water resources to degradation, and to evaluate how the 

effectiveness of management practices is related to flow and 

transport. These models will rely on historical data collected 

by the NAWQA Program and other agencies, as well as data 

to be collected during Cycle 3. Models and studies will be 

done at scales ranging from the national scale, to the major 

river basin and principal aquifer scale, to the intermediate 

scale (integrated watershed and regional aquifer analysis), 

and ultimately to the Intensive Study scale (reach and local 
56 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

flow-path scales). Studies will be nested within each other and 

designed to provide relevant results that can be used to benefit 

models and studies conducted at other scales. The complexity 

of models will range from simple statistical representations to 

detailed process-oriented models, and will vary by issue and 

across scales of study.

Ecosystem services are the benefits that people obtain 

from ecosystems (Millennium Ecosystem Assessment, 2005), 

with services categorized into provisioning (for example, 

involving food and water), regulating (involving regulation of floods, drought, land degradation, and water quality), supporting (involving soil formation, nutrient cycling, 

and primary production), and cultural (involving recreation 

and education). Increasing demands for ecosystem services 

means that trade-offs must be made among services; for 

example, conversion of forest to agriculture increases the 

service of food supply but diminishes the service of regulating floods and water quality. Increasing demand on water 

resources, including both quantity and quality, requires 

scientifically defensible information to make sound resource 

management decisions. Since its inception, the NAWQA Program has addressed multiple water-quality issues in surface 

water and groundwater across the United States, many of 

which overlap with several specific ecosystem services. In 

Cycle 3, however, NAWQA is organized for the first time to 

evaluate and quantify the factors—including indirect factors 

(for example, climate and land use) and direct factors (for 

example, nutrients and sediment)—that control the capacity 

of ecosystems to provide services related to water quantity 

and quality. Studies that support this and subsequent goals 

will inform USGS and other agency efforts to better understand the factors that affect ecosystem services, particularly 

those performed by stream ecosystems. 

Evaluating how surface water and groundwater quality responds to human activities and natural factors will be 

achieved through a Goal 2 study design that will integrate 

the regional and national scale data collected as part of 

Goal 1 with multi-scale analyses and models of flow, sources, 

transport, and transformation processes. These studies will 

be supplemented with spatially and temporally intensive data 

collection, to address the five objectives described in the 

following sections.

Objective 2a. Determine How Hydrologic 

Systems—Including Water Budgets, Flow Paths, 

Travel-times and Streamflow Alterations—are 

Affected by Land Use, Water Use, Climate, and 

Natural Factors.

As water moves through the hydrologic cycle, its 

suitability for human use and aquatic ecosystems changes. 

These changes occur at the land surface, where water 

interacts with the landscape, and in the subsurface, as 

water moves through shallow and deep aquifers. The magnitude and timing of changes in water quality will depend 

on how long it takes for the water to flow from one point 

to another and on the interactions that occur along flow 

paths. Thus, a critical step in understanding water-quality 

responses to human activities and natural factors is to gain 

a better understanding of the hydrologic system, as characterized by water budgets, flow paths, traveltimes, and 

streamflow alteration.

Objective 2b. Determine How Sources, 

Transport, and Fluxes of Contaminants, 

Nutrients, and Sediment are Affected by Land 

Use, Hydrologic System Characteristics, 

Climate, and Natural Factors.

Understanding how the combined effects of hydrologic 

setting, land use, climate, and natural factors affect water quality requires identifying sources of contaminants, nutrients, and 

sediment; how they are introduced to the environment; and 

how they are transported and transformed within the hydrologic 

system. Sources can be categorized as nonpoint sources, such 

as precipitation, pesticide use, fertilizer use, and runoff from 

urban land, or as point sources, such as (1) discharges from 

wastewater-treatment plants or confined feeding operations and 

(2) leaking waste storage facilities. Combining knowledge of 

the hydrologic characteristics of different parts of the country 

and sources of contaminants with observed concentrations 

and ecosystem processing will allow a better understanding of 

how and why loads of contaminants, nutrients, and sediment 

change, both temporally and spatially in response human and 

natural factors. 

Objective 2c. Determine How Nutrient Transport 

Through Streams and Rivers is Affected by 

Stream Ecosystem Processes

Nutrient transport in surface water is a complex issue 

that requires evaluating the interactions and feedback 

mechanisms between the stream ecosystem and nutrient 

concentrations and loads. The key to understanding the 

factors affecting nutrient enrichment in streams is to use 

a systems approach where the simultaneous effects of the 

various controlling factors and how these interactions 

change over time and space are examined. For example, 

stream-habitat modification can affect nutrient transport 

and processing, and nutrient transport and ecosystem function may change over time in response to changes in landuse practices and climate. 
Goal 2 57

Objective 2d. Apply Understanding of How 

Land Use, Climate, and Natural Factors Affect 

Water Quality to Determine the Susceptibility of 

Surface-Water and Groundwater Resources to 

Degradation

Sustaining water quality for human use and aquatic 

ecosystems requires that water-quality conditions and flows 

in current and potential sources of water meet designated 

standards and criteria. Understanding the distribution of waterquality and flow conditions in relation to land use and other 

factors is a critical step in developing strategies for protecting 

and improving water supplies. Furthermore, knowledge of 

sources, transport, and transformation processes will be used 

to evaluate the susceptibility of water resources to degradation 

caused by land use, climate, and natural factors.

Objective 2e. Evaluate How the Effectiveness of 

Current and Historical Management Practices 

and Policy is Related to Hydrologic Systems, 

Sources, Transport and Transformation 

Processes

The effectiveness of management practices is determined, 

in part, by characteristics of the hydrologic system where the 

practice is implemented. Scientific findings will be compiled 

into outcomes and products that demonstrate the connections 

between changing water quality, hydrologic setting, and 

regional and national management practices and policy.

Policy and Stakeholder Concerns Driving Key 

Management Questions

Continuing population growth will cause increases in 

urbanization, agricultural activity, natural resource development, and water demand. Large-scale changes in land use and 

associated activities—affected by increased population, changing economic conditions, and management strategies implemented to mitigate water quality problems—lead to changes 

in the quality of water for aquatic ecosystems and humans by 

alteration of flow conditions and changes in the sources and 

transport of contaminants, nutrients, and sediment. The magnitude and timing of flow and water-quality responses to these 

modifications will vary with climate, landscape, geology, geochemistry, and hydrology. Surface-water systems dominated 

by overland or tile-drain flows are expected to respond rapidly 

to these perturbations, whereas groundwater systems are 

expected to respond more slowly. Evaluating the effectiveness 

of policy and management strategies to sustain and improve 

water quality is dependent on understanding the effect of these 

factors on contaminants, nutrients, sediment, streamflow, and 

groundwater recharge and discharge as well as on understanding the varying sensitivities of different regions, watersheds, 

and aquifers to such changes. Understanding the causes of 

patterns and trends in water-quality degradation is essential 

for improving management of resources. Selected examples of 

management-relevant questions illustrate the broad range of 

applications:

• Are the most important point and nonpoint sources of 

contaminants being addressed by current management 

strategies?

• Are protection, conservation, and remediation programs working effectively to control sources and 

transport of contaminants?

• What strategies are needed to protect sources of 

drinking-water?

• What areas should be targeted for more intensive monitoring, protection, or remediation?

• What are the sources and transport processes controlling nutrients, contaminants, and sediment delivery 

to estuarine ecosystems, the Great Lakes, and other 

receiving waters? 

NAWQA Progress During Cycles 1 and 2

Cycle 1 of NAWQA was organized into Study-Unit 

Investigations to identify water-quality problems and relate 

them to local conditions and management practices. Analyses were based on a mixture of quantitative and descriptive approaches, depending on available data. Cycle 2 of 

NAWQA moved towards integration of findings across broad 

regions of the Nation, with models being a key tool in this 

effort. The following modeling approaches were included in 

Cycle 2:

• Broad-scale national and regional SPARROW 

models of regression/geospatial source and transport 

(Schwarz and others, 2006) for nutrients (nitrogen, 

phosphorus, and carbon), salinity, and sediment (Preston and others, 2009; Schwarz, 2008). These models 

incorporated steady-state accounting of nutrient and 

sediment loads to estimate a mass balance based on 

average hydrologic conditions and spatially variable 

inputs from difference sources.

• National regression/geospatial models, based on 

watershed properties and chemical use estimates 

without mass-balance accounting, were developed to 

predict pesticide concentrations in water and fish tissue (WARP models; Stone and Gilliom, 2009). 

• Process-simulation watershed models, such as TOPMODEL (Topography-based Model; Beven and 

others, 1995) and SWAT (Soil and Water Assessment 

Tool; Neitsch and others, 2005), were developed for 

small watersheds in some topical studies to improve 

understanding of the importance of flow paths in 

contaminant transport.
58 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

• Groundwater flow and particle-tracking models were 

developed at scales ranging from individual supply 

wells (1–10 km2) to regional aquifer systems (hundreds to thousands of square kilometers) (Paschke, 

2007).

• National regression/geospatial models were developed 

to estimate groundwater vulnerability to nitrate and 

pesticide contamination in shallow groundwater 

(Nolan and Hitt, 2006; Stackelberg and others, 2005).

Cycle 2 also initiated small-scale detailed topical studies, to complement these large-scale studies, geared towards 

making the connection between the effects of human activities 

and water quality. These studies have led to increased understanding of the processes and factors that control water-quality 

responses to agricultural practices, urbanization, and mercury 

bioaccumulation in stream ecosystems in selected areas representative of major settings in the Nation.

An illustration of complementary large- and small-scale 

studies in Cycle 2 is provided by (1) NAWQA’s activities 

aimed at understanding the factors that control transport and 

delivery of nutrients to streams, reservoirs, and estuaries, 

and (2) evaluating the response of in-stream nutrient loads 

to changes in land use, source inputs, and land-management 

practices. At the national scale, trends in nutrient concentrations and loads since 1993 at stream monitoring sites were 

related to changes in watershed characteristics and nutrient inputs (Sprague and others, 2009). NAWQA also integrated monitoring data collected during Cycles 1 and 2 with 

monitoring data from other agencies into statistical models 

to extrapolate water-quality conditions in unmonitored parts 

of the country. The results of simulations made with SPARROW models have been used to prioritize watersheds for 

implementation of conservation and management practices 

as part of the Mississippi River Basin Healthy Watershed 

Initiative (U.S. Department of Agriculture, 2009). Estimates 

of mean loading of nitrogen to estuaries throughout the 

Nation derived from SPARROW models (Smith and others, 

1997) were used in NOAA’s 1999 assessment of effects of 

terrestrial nutrient sources on estuarine ecosystem condition 

(Bricker and others, 1999). 

Detailed stream-reach studies conducted as part of the 

Effects of Nutrient Enrichment on Stream Ecosystems (NEET; 

http://wa.water.usgs.gov/neet/) topical study examining 

nutrients in agricultural streams found that (1) concentrations 

of nitrogen and phosphorus in agricultural streams commonly 

exceed proposed USEPA Regional Nutrient Criteria although 

algal biomass commonly was less than expected due to habitat 

alterations; (2) benthic algae showed a more rapid response 

to initial increases of nutrients than did macroinvertebrates or 

fish, and overall may be a better indicator of nutrient conditions; (3) agricultural streams commonly were heterotrophic 

and may have limited nutrient processing capacity, resulting in 

high nutrient export; (4) denitrification rates in surface water 

were less than 5 percent of surface-water nitrate loading rates 

and were unable to substantially reduce downstream transport 

of nitrate; and (5) legacy nitrate from fertilizer applied years or 

decades ago in groundwater that discharged to streams can be 

a source of nitrogen to streams for an extended period (years 

to decades).

In Cycle 1, NAWQA groundwater-quality studies 

were implemented at multiple scales within the context of 

study units. About 100 MAS assessments (with study areas 

of approximately 1,000 to greater than 100,000 km2

) were 

designed to provide a broad assessment of water quality 

in areas with relatively similar geologic, hydrologic, and 

climatic conditions. About 110 LUS networks were sampled 

in agricultural and urban settings and were designed to 

evaluate the relation between shallow groundwater quality 

and overlying land use; LUS networks were, with few 

exceptions, nested within MAS networks. About 40 FPSs 

were conducted; these studies generally were nested within 

LUS networks and were designed to evaluate the hydrologic 

and geochemical processes affecting groundwater quality. 

In Cycle 2, NAWQA groundwater data and interpretative 

investigations were organized, in part, by principal aquifers 

(or groups of principal aquifers) into 11 regional areas 

(approximately 200,000 to 3,000,000 km2

) to assess groundwater quality from a regional geologic, hydrologic, and 

climatic perspective. 

Two topical studies completed in Cycle 2 had a large 

groundwater focus. The Transport of Anthropogenic and 

Natural Contaminants (TANC) study (http://oh.water.usgs.

gov/tanc/NAWQATANC.htm) examined contaminant transport to public-supply wells at the scale of the contributing 

area and at the scale of the larger groundwater flow system 

(approximately 100 to 5,000 km2

). TANC studies were 

implemented in 10 representative areas distributed across 

the Nation. The Agricultural Chemicals Transport (ACT) 

topical study (http://in.water.usgs.gov/NAWQA_ACT/) 

examined transport of contaminants through the entire 

hydrologic cycle from a watershed perspective and was 

implemented using a nested design in seven small watersheds each approximately 10 to 1,000 km2

. The TANC and 

ACT studies were field intensive, made use of quantitative 

groundwater-flow modeling, and were designed to facilitate understanding of the hydrologic and chemical processes affecting water quality.

NAWQA’S Role in Cycle 3

Evaluating the effects of human activities and natural factors on water-quality patterns and trends will be 

achieved in Cycle 3 by integrating findings from studies 

conducted across multiple and nested spatial scales, as 

described in the section on Cycle 3 design elements and 

shown in fig. 17. Modeling will be a key component of all 

analyses of source and transport processes, with the complexity of the models being tailored to the scale and scope 

of the analysis. For example, complex process-simulation 

models will be applied at the most detailed scale of study, 
Goal 2 59

with the goal of providing information that can be used 

in more simplified, broader-scale models, and with the 

relation reversed. A key advance for modeling in Cycle 3 

will be to develop dynamic models that include temporal 

variability caused by time-varying source and water inputs, 

climate variability, and hydrology. The construction and 

calibration of these models will require the collection of 

data at a sufficient frequency and coverage to fulfill these 

modeling goals. Data-collection strategies and design 

components outlined in the section on Goal 1 assessment 

activities also are designed to support these process and 

modeling studies. In addition, these models will rely heavily on water-quality and ancillary data collected by other 

agencies. The models and understanding developed in this 

effort provide the basis of forecasting studies for Goal 4. 

General Approach

Goal 2 studies are designed to evaluate how ongoing human 

activities and natural factors result in observed distributions and 

trends in surface-water and groundwater quality identified through 

Goal 1 efforts. Although meeting the objectives of Cycle 3 will 

require integrated multidisciplinary studies, each different stressor, 

as well as surface water and groundwater, has unique characteristics that affect study approaches. For simplicity, the description 

of Goal 2 approaches is organized into (1) surface-water studies 

described by stressor, (2) an example of an IWS, (3) an example of 

an IS, and (4) groundwater studies. The studies described within 

each of these categories examine connections across scales, and 

between surface water and groundwater, as described by the explanations of each individual design and approach.

Locations of hypothetical National Fixed Site Network monitoring stations

Locations of hypothetical Regional Synoptic Study monitoring stations

Intensive study targeted watershed that features specific land use or set of

 management practices being evaluated as part of a paired-watershed study

Intensive study control or reference watershed for the paired-watershed study

study-unit boundaries from Cycles 1 and 2

Integrated watershed study area. 

Intensive studies 

Regional synoptic studies

National Fixed Site Network (NFSN)

FIGURE 41

EXPLANATION 0

0 500 KILOMETERS

500 MILES

0

10 KILOMETERS

10 MILES

0

0 500 KILOMETERS

500 MILES

Figure 17. Schematic diagram illustrating nested spatial scales for Cycle 3 surface-water studies. The national map shows 

hypothetical monitoring stations for the National Fixed Site network (red dots), the middle inset shows a close up of the southeastern 

U.S. showing location of NFSN monitoring sites with the geographic extent of a Regional Synoptic Study indicated by hypothetical RSS 

sampling locations (yellow dots). The area encompassed by a typical Integrated Watershed Study is shown by the oval outline. In the 

last inset, two watersheds that would be monitored as part of a paired watershed Intensive Study are shown. The shaded areas in the 

national map indicate Cycle 1 and Cycle 2 study unit areas (http://water.usgs.gov/nawqa/studies/study_units.html).
60 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Surface-Water Studies

Goal 2 surface-water studies will be used to continue 

to refine and improve regional and national modeling tools 

developed using the National Fixed-Site Network (NFSN) 

and other agency datasets to extrapolate water-quality information to unmonitored areas; evaluate delivery of contaminants, nutrients, and sediment to downstream areas; and 

determine the relative contributions of different contaminant 

sources to downstream receiving waters. Regional Synoptic 

Study (RSS) assessments will be done in conjunction with 

model development when more data are needed to improve 

existing water-quality models. The general direction of 

model enhancement will be towards dynamic models that can 

account for storage and loss of water, contaminants, nutrients, and sediment over time. Such models can be used to 

simulate seasonal and annual trends in contaminant concentrations and loads. Collection of NFSN data is designed to 

support these modeling efforts. Likewise, smaller-scale IWS 

and IS assessments will be done to provide process-level 

understanding that can be used to improve model accuracy 

and predictive capabilities. 

The IWS assessments are designed to provide information at the intermediate scale, nested between the much larger 

national and regional analyses and the much smaller scale IS 

assessments (fig. 17). The IWS assessments will integrate surface water and groundwater hydrology with source, transport, 

and transformation analyses for the stressors of concern in the 

watershed. These studies aim to provide a holistic scientific 

understanding of the fate of nutrients, sediment, and other 

contaminants as they are transported through the watershed, 

and of the human activities and natural factors that affect these 

constituents as they move through the watershed or aquifer. 

Concentrations and fluxes at critical locations within the 

watershed and at the basin outlet will be related to urban and 

agricultural management practices, as well as to watershed 

characteristics. Dynamic models developed at this scale will 

be the first modeling products and represent the foundation for 

larger regional- and national-scale models that will be released 

later in Cycle 3. 

Embedded within each IWS area will be one or more 

detailed IS areas that address specific scientific questions, the 

answer to which will improve NAWQA’s ability to simulate 

contaminant, nutrient, and sediment transport at the IWS scale 

(fig. 18). One goal of the IWS design is to better understand 

the effects of watershed disturbance on sources, transport, 

and transformation of important constituents at the watershed scale. The IWS analysis will provide an opportunity to 

scale-up IS findings and determine the relative importance of 

IS-scale processes within the larger watershed. IS assessments 

will initially focus on nutrient and sediment transport and fate. 

As Cycle 3 studies progress, other priority contaminants and 

(or) the effects of streamflow alteration on aquatic biota may 

be integrated into the nutrient and sediment design or added 

through additional IS assessments.

Planned study approaches and outcomes are described in 

the following subsections for each type of stressor: contaminants, nutrients, sediment, and streamflow alteration.

Groundwater flow path study

National Fixed-Site Network (NFSN) monitoring site

Integrated Watershed Study (IWS) monitoring site

Intensive Study (IS) monitoring site

EXPLANATION

watershed

watershed

Integrated Watershed Study boundary

Figure 18. Example of an Integrated Watershed Study 

(IWS) design with an embedded Intensive Study (IS) that 

uses a paired-watershed design for comparing sediment 

and nutrient sources, transport, and transformations. The 

IS will be conducted in a small reference or least-disturbed 

watershed and in an agricultural or urban watershed and 

related to the downstream effects observed in the IWS. For 

example, periodic geomorphic assessments (along with 

the collection of sediment data and analysis of sediment 

flux and explanatory ancillary data) will be conducted to 

characterize sediment sources and sinks from headwater 

to downstream channels. Local-scale groundwater 

flow-path studies will be nested within the IS and IWS 

watersheds to examine surface-water/groundwater 

interactions. A National Fixed-Site Network monitoring site 

at the outlet of the basin anchors the IWS.
Goal 2 61

Contaminants

Contaminants that will be considered for Goal 2 studies include constituents or chemicals that are commonly 

detected in streams and rivers and, if present at high enough 

concentrations, can degrade drinking water-quality or affect 

ecosystem health. Example constituents include selected 

high-use pesticides, dissolved solids (salinity), and mercury. 

These constituents contain well-defined sources, are commonly detected in the environment, and can be tracked as 

they move through a watershed and in and out of shallow 

groundwater systems. The following sections describe the 

approach and planned outcomes for contaminants in surfacewater studies. 

Approach

Broad-scale national and regional models of contaminant concentration distributions will be developed for 

surface-water systems using Goal 1 data from the expanded 

NFSN as well as retrospective data where available. Surfacewater-quality regression/geospatial models developed in 

Cycle 2 such as WARP (Stone and Gilliom, 2009) will be 

expanded to include additional contaminants or contaminant mixtures of concern, refined regional models that are 

based on all regional data sources (even when these data are 

not available nationally), improved representation of critical sources and processes, and development of temporally 

dynamic (seasonal and annual) models that simulate the 

effects of time-varying sources and transport processes at 

the time periods of greatest relevance. Also, a mechanistic 

understanding of transport pathways and transformation 

processes developed from process-based watershed and 

reach-scale transport models will be used to improve the 

broad-scale hybrid models. National and regional contaminant studies will focus on those contaminants of widespread 

human and ecosystem concern (for example, atrazine in 

agricultural areas, insecticides and wastewater compounds in 

urban areas, salinity in arid areas, and mercury nationwide, 

including reference areas). 

Planned Outcomes

The modeling tools developed to explain observed 

contaminant distributions and trends in surface water will be 

used to: 

• Identify primary sources of priority contaminants found 

in surface water and their relation to human activities 

and natural factors;

• Understand the factors that limit or enhance the 

seasonal and annual fluxes of critical contaminants to 

downstream receiving waters;

• Analyze and interpret the transport pathways and transformation processes for selected contaminants in river 

and stream networks and how they affect implemented 

management practices; and

• Evaluate national and regional vulnerability of drinking-water resources to water-quality degradation and 

the relation of vulnerability to human activities and 

natural factors.

Nutrients

Nutrients to be monitored in Cycle 3 include nitrogen, 

phosphorus, and carbon. The following subsections describe 

the approach and planned outcomes for nutrients in surfacewater studies.

Approach

Considerable effort was devoted to monitoring and 

modeling sources of nutrients and how they move through 

the environment in Cycle 2, with the greatest emphasis on 

nitrogen and phosphorous. Cycle 3 modeling and analysis 

efforts will be geared towards shifting from the steady-state 

source and transport models of Cycle 2 to dynamic models 

that can represent seasonal and year-to-year variability in 

nutrient transport. Additional emphasis will be given to carbon transport in watersheds to complement ongoing studies 

of carbon sequestration and carbon cycling being conducted 

by the USGS Global Change Program (http://www.usgs.gov/

global_change/) and to complement goals laid out by the 

USGS Climate and Land Use Change Strategic Science Planning Team (Burkett and others, 2011).

Existing nutrient models will be refined to include 

temporal variability (seasonal and annual) and improved 

representations of water-quality management practices. For 

example, answering questions such as “Are regulatory and 

non-regulatory actions in the Mississippi River Basin making a difference in riverine nutrient loading to the Gulf of 

Mexico?” requires an improved understanding and prediction 

of how fluxes of nutrients and the timing of their delivery to 

downstream water bodies (including reservoirs and estuaries) 

responds to implemented practices. A major obstacle is the 

challenge of discerning whether changes observed in nutrient 

delivery are due to implemented management practices or to 

natural climatic variation (or even human-induced climate 

change). 

To address this challenge, water-quality models such as 

SPARROW (Smith and others, 1997) that were developed in 

Cycles 1 and 2 will need to be modified or coupled with other 

models to simulate the effect of specific conservation practices 

as well as annual and seasonal variations in nutrient loading. 

This will require assembly of ancillary data characterizing 

nutrient source inputs at seasonal and annual time steps, and 

adapting the models to account for nutrient storage and sinks. 

The development of realistic, dynamic models of regional 

nutrient transport can progress only if our understanding of 

nutrient processing at smaller scales is improved. This will be 

achieved through model development and testing at the IWS 

scale and improved representation of important processes 

identified from IS results.
62 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Planned Outcomes

The modeling tools developed to explain observed nutrient loads and concentration distributions and trends in surface 

water will be used to:

• Relate trends in concentrations and loads of nutrients 

to changes in watershed conditions and to distinguish 

trends related to human activities from those related to 

natural factors;

• Improve estimates of nutrient delivery to critical water 

bodies, including year-to-year and seasonal variability, which includes (1) periodic assessment, based 

on combined monitoring and modeling, of nutrient 

loads (annual, seasonal) for important estuaries in the 

Nation; (2) maps for each estuary of tributary watersheds which show estimated nutrient loads delivered 

to the estuary; and (3) estimates of the relative contribution of nutrients from different sources for specific 

time periods (seasonal, annual); and 

• Evaluate the effect of specific ecological resources, 

such as wetlands and forested riparian areas, on nutrient loads delivered to downstream targets, which in 

turn supports valuation of ecosystem services in relation to nutrient processing.

Sediment

Suspended sediment and selected surrogates will be monitored in Cycle 3 to assess sediment concentrations, loads, and 

transport. The following subsections describe the approach 

and planned outcomes for sediment in surface-water studies.

Approach

NAWQA has a unique capability to conduct broad-scale 

evaluations of how changes in land use and land management have affected sediment transport in streams and rivers. 

Although attention to sediment transport was minimal in 

Cycles 1 and 2, the USGS is the only agency with the infrastructure (that is, streamgages, nationally consistent sampling 

and analytical methods, and historical data) with which to 

conduct regional and national assessments of sediment concentrations, loads, and transport. Development and improvements in use of continuous sensor technology that can measure 

suspended-sediment surrogates such as turbidity in real time 

over the past decade afford NAWQA an opportunity to more 

accurately quantify sediment concentrations and loads at fine 

temporal resolutions and across multiple spatial scales. 

Watershed-scale analysis of factors affecting the erosion, transport, and deposition of sediment is needed to better 

understand the time scales at which climate, land use, and 

land management affect suspended-sediment concentrations 

and loads in streams and rivers. NAWQA data and assessments will be used to improve existing SPARROW models 

and also to test watershed models currently used by state 

and Federal agencies, such as the SWAT (Neitsch and others, 

2005) or the Hydrological Simulation Program—Fortran 

(HSPF; Bicknell and others, 1997). The models will be 

used to analyze how various factors affect sediment movement in streams and rivers. Knowledge of the extent to 

which in-stream sediment transport has been altered from 

its natural condition is necessary to help governmental and 

non-governmental agencies identify and manage the effects 

of altered sediment transport on aquatic ecosystems. These 

goals will be achieved as follows:

• Continuous suspended sediment surrogates (that is, 

turbidity, optical backscatter, or acoustic sensors) 

will be installed, and periodic suspended-sediment 

and stream-habitat data will be collected at selected 

stream and river sites in the NFSN. Sites will include 

many reference sites to better quantify sediment flux 

from relatively pristine, small watersheds in different 

geographic regions; 

• Suspended sediment loads will be computed at each site 

using statistical software that can incorporate hourly 

sediment surrogate data to compute loads and uncertainty (USGS LOADEST (Load Estimator) model or 

adaptation; http://water.usgs.gov/software/loadest). 

Sediment loads and differences in the magnitude, frequency, and duration of historical and current sediment 

concentrations will be evaluated across regions and 

land-use settings, and through time to assess how climate, environmental setting, and human activities affect 

the movement of sediment in streams and rivers;

• Geomorphic assessments and analyses derived from 

GIS datasets for channel stability will be conducted to 

characterize in-channel sediment erosion and deposition from headwater to downstream reaches;

• Sediment sources can be characterized through comparison of chemical and radiochemical signatures of 

end-member sediment sources (such as surface and 

channel-bank soils) to signatures in suspended sediments (Gellis and Walling, 2011); and

• National/regional SPARROW models will be improved 

using surrogate-derived sediment loads and updated 

ancillary data.

Planned Outcomes

The following are planned tools to explain sediment concentrations, loads, and transport in surface water:

• Updated Web tools to access and visualize historical 

suspended-sediment and ancillary data;

• Databases and Web tools derived from geographic 

information systems and geomorphic surveys that 

characterize river types based on factors affecting 

stream stability and sediment transport (such as segment slope, valley type, geologic setting, streambed 

substrate, historical land use, and channel change);
Goal 2 63

• Long-term, continuous sediment-surrogate and ancillary data that improve our ability to identify current and 

future changes in sediment transport and streamflow 

pathways;

• Assessment of trends and spatial patterns in sediment 

concentrations and loads relative to environmental setting, human disturbance, and erosion controls;

• Assessment of how human disturbance and natural factors 

affect the sources, transport, and deposition of suspended 

sediment in specific environmental settings; and

• Improved national/regional SPARROWsediment models based on existing and future data collection that 

characterizes variability in sediment transport relative 

to human disturbance and natural factors.

Streamflow Alteration

Streamflow alteration will be evaluated in Cycle 3. The 

following subsections describe the approach and planned 

outcomes for streamflow alteration in surface-water studies.

Approach

Natural patterns in the magnitude and timing of streamflow are major controlling factors of water quality and ecosystem integrity (Postel and Richter, 2003) and have been extensively altered by human activities throughout the United States 

(Graf, 1999; Carlisle and others, 2010a). Scientific expertise 

in hydrologic and geospatial analysis will enable NAWQA 

scientists to clarify how human activities and natural factors 

affect the flow regime. This effort will rely on characterization of major patterns in streamflow alteration at streamgages 

determined for Goal 1. For example, major differences in 

streamflow alteration are expected among different climatic 

regions, land uses, and water-management activities. Using 

this characterization, empirical models that predict components of the natural flow regime and another set of models that 

estimates metrics that describe the altered flow regime will 

be developed. Predictive models will be used to extrapolate 

estimates of streamflow alteration to ungaged river segments 

across each region. Observed annual flow regime metrics will 

be compared to the streamflow metric values estimated for reference conditions by calculating the ratio of the observed value 

to the estimated reference condition value (O/E) to summarize 

the frequency distribution of O/E values by region and time 

period and to identify sites with abrupt or gradually changing 

O/E values. These patterns and trends will be explained in relation to changing human activities and natural factors, and will 

be related in Goal 3 to aquatic-ecosystem habitat and health.

Planned Outcomes

NAWQA will produce datasets, models, analysis tools, 

maps, and reports that will assist the agencies and organizations responsible for maintaining the integrity of aquatic 

ecosystems. 

Example of an Integrated Watershed Study

Integrated Watershed Study assessments are a critical 

design component for furthering our understanding of the 

effects of human activities and natural factors on water-quality 

conditions. IWS assessments will incorporate small-scale 

IS assessments that facilitate understanding of water-quality 

processes, but will focus on improving our understanding of 

fate and transport processes at a scale much larger than that 

typically assessed by traditional research studies. IWS areas 

will be nested within nationally important regional watersheds 

(such as the Mississippi River Basin or Chesapeake Bay) to 

leverage ongoing data collection and modeling activities; for 

example, USDA’s Mississippi River Basin Healthy Watersheds 

Initiative areas (U.S. Department of Agriculture, 2009), the 

National Ecological Observatory Network (NEON; http://

neoninc.org/), the Chesapeake Bay Program (http://www.

chesapeakebay.net/), and WaterSMART Program (http://water.

usgs.gov/watercensus/WaterSMART.html) focus area watersheds such as the Colorado and Delaware River Basins. 

Approach

Each IWS will build on Cycle 1 and 2 studies, will 

incorporate local information collected by other agencies and 

entities, and will be supplemented by additional data collection during Cycle 3. An example watershed where considerable work has already been conducted, the White River Basin, 

Indiana, is used to illustrate the approach and objectives of an 

IWS (fig. 19). The goal of the IWS assessments is to combine previous data and analyses with additional monitoring 

in critical locations into a comprehensive hydrologic-systems 

understanding of how human activities and natural factors 

have affected sources, transport pathways, and transformation 

processes and resulted in observed water-quality distributions 

and trends. The first steps in an IWS analysis will include: 

• Aggregating historical NAWQA findings from Cycle 

1 study-unit analyses, regional SPARROW models, 

PAA studies, Cycle 2 topical studies, and studies by 

other agencies and organizations to develop a broad 

conceptual understanding of the watershed system. 

An illustration of the kind of information available 

from previous NAWQA work in the White River Basin 

includes estimates of nitrogen and atrazine loads across 

the watershed produced by national SPARROW and 

WARP models (respectively figs. 19A and B) (Smith 

and others, 1997; Stone and Gilliom, 2009). 

• Cataloging existing monitoring infrastruction including 

stream gages (fig. 19E), locations of NAWQA monitoring sites or studies (figs. 19I and 19J), and locations 

where other long-term nutrient or sediment datasets 

were collected (respectively figs 19F and 19L).

• Compiling detailed current and past land-use, wateruse, climate, contaminant-source, and managementpractice information. For example, land use, nitrogen 
64 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

fertilizer applications, and wastewater discharge 

points for the White River Basin are shown in figures 

19C and 19K. This illustrates that the IWS scale will 

encompass a variety of land-use categories and source 

inputs. This is important for analyzing how water quality changes in response to changing land use; and

• Characterizing watershed and aquifer characteristics 

that affect flow, transport, time lags, and transformations. For example, spatially detailed hydrologic analysis of the surface-water system is now possible with 

the National Hydrography Dataset-Plus dataset (http://

nhd.usgs.gov/; fig. 19G).

A key element of the IWS is the analysis of fluxes of contaminants, nutrients, and sediment across important interfaces 

within the watershed (for example, surface-water/groundwater 

interface, interior sub-basins, and watersheds with drinkingwater intakes (fig. 19D) and relating fluxes to sources, specific 

land uses, and natural factors). A comparison of watershed 

source loading and export predicted by water-quality models 

will be conducted at multiple nested spatial scales using a 

longitudinal design to discern how these processes change as 

stream size increases and water moves through the watershed 

(fig. 20). Time-varying load estimates also will be compared to 

changing sources and changing human activities and climate 

for both short-term seasonal effects and long-term trends. The 

percentage of streamflow derived from groundwater discharge 

to the stream will be determined by either groundwater-flow 

modeling or by base-flow separation analysis. These estimates 

can be coupled with estimates of the average age and contaminant concentration of discharging groundwater to provide an 

estimate of contaminant loading from the aquifer to the watershed. IWS assessments will rely on a subset of NFSN sites for 

long-term monitoring, with the addition of several short-term 

monitoring sites that will be needed to complete the longitudinal design. This enhanced monitoring network will be needed 

to measure and analyze water budgets, and contaminant, nutrient, and sediment mass budgets. Selection criteria for these 

additional monitoring sites will include considerations for the 

flow system, land use, active streamgages, and sites where 

other programs are collecting water-quality data.

Enhanced IWS monitoring will provide the opportunity to: 

• Compile water budgets, and contaminant, nutrient, and 

sediment mass budgets along the river corridor;

• Examine how the fluxes of selected contaminants, 

nutrients, and suspended sediment differ with varying 

land use and natural factors;

• Evaluate how the flow regime changes in response to 

human activities and natural factors;

• Evaluate how changes in the flow regime affect transport and fluxes of contaminants, nutrients, and sediment; and

• Compile regularly updated (monthly, seasonal, annual) 

data on chemical or nutrient application rates, water 

use, and other human activities or natural factors that 

change on a regular basis.

Applying and developing modeling tools will be a key 

element of the IWS analysis. Modeling efforts will include the 

following:

• Examining the reliability of national and regional scale 

NAWQA regression/geospatial models such as SPARROW and WARP, as well as USDA watershed models 

such as SWAT and the Agricultural Nonpoint Source 

Pollution Model (AGNPS; Bingner and Theurer, 2001) 

that have been developed to track sources of contaminants, their relation to land use and natural factors, and 

the relative contributions of watersheds to contaminant and nutrient processing, and sediment erosion 

and deposition. As illustrated in figures 19A and 19B, 

predictions of nitrogen flux and atrazine concentrations 

for detailed river networks are available from national 

and regional-scale regression/geospatial models. These 

predictions represent average values based on many 

years of monitoring data at sparse sites across the 

Nation. Enhanced data collection within the IWS areas 

will make it possible to examine the local uncertainty 

in these average predictions, the causes of uncertainty, 

and the deviation of annual and seasonal variability 

from average predictions. This analysis will identify 

the enhancements needed to reduce uncertainty in 

model predictions, and also identify the factors that 

warrant incorporation into the models to provide 

dynamic predictions of annual and seasonal variations 

in fluxes and concentrations; 

• Improving representations of groundwater contributions, management practices, and watershed storage 

and transformation processes in regression/geospatial 

models, based on results of analysis described in 

the previous bullet, to develop the ability to predict 

annual and seasonal trends in water quality. NAWQA 

has been successful in estimating average fluxes of 

nutrients through large-scale river networks and in 

identifying the sources of these nutrients using the 

SPARROW model. A goal of Cycle 3 is to develop 

SPARROW-like dynamic regression/geospatial 

models that have the capability to estimate annual and 

seasonal fluxes and to identify the factors controlling 

the temporal variability in fluxes and concentrations. 

The data collection and conceptual understanding 

resulting from the IWS will be used to develop and 

test these models. Ultimately, the goal is to take these 

models that have been tested in the IWS assessments and apply them across the Nation. Estimates 

of groundwater flows and fluxes to streams and rivers 

within the IWS will be determined using a variety of 

techniques including base-flow separation and output 

from regional groundwater flow models;
Goal 2 65

• Applying and testing the ability of watershed-scale 

process models such as the Precipitation Runoff Modeling System (PRMS; Leavesley and others, 1983) and 

the Coupled Ground-Water and Surface-Water FLOW 

model (GSFLOW; Markstrom and others, 2008) to 

reproduce system responses at multiple-scales within 

the IWS (including the IS as explained in the following 

section “Example of an Intensive Study for Sediment 

and Nutrient Transport”). These models will be used to 

help identify the important hydrologic processes and 

factors that affect watershed water-quality responses 

at multiple scales that warrant incorporation into the 

dynamic regression/geospatial models. The importance 

of surface-water/groundwater interactions on watershed water quality will be examined as part of these 

modeling efforts; and

• Using regression/geospatial and watershed process 

models to improve understanding of how human 

activities and natural factors affect observed patterns 

and trends within the IWS. These models will be tools 

for integrating knowledge of flow systems, sources, 

transport, and transformation processes into a conceptual and quantitative understanding of how land use, 

water use, management practices, climate, and watershed characteristics are related to historical and current 

water-quality patterns and trends observed in the IWS.

Planned Outcomes

The following are planned outcomes from the IWS 

assessments:

• An understanding of the fate of contaminants, nutrients, and sediment as they move through a large, 

complex watershed;

• An understanding of the watershed characteristics that 

determine the water-quality response of a watershed to 

applied stressors;

• Dynamic watershed-scale models that explain the combined factors that affect observed seasonal and annual 

concentrations and fluxes for sub-basins within the 

watershed, and the aggregate at the outlet;

• Assessment of the effects and effectiveness of urban 

and agricultural management practices on water quality 

(using models); and

• Annual reports summarizing data collected, progress 

made, and any publications released.

Example of an Intensive Study for Sediment and 

Nutrient Transport

Previous studies have shown that headwater streams are 

important in reducing nutrients through in-stream processing 

and transformation. Thus, a detailed understanding of the 

factors controlling contributions of headwater streams to 

downstream nutrient and sediment transport will be part of the 

planned watershed studies. The Intensive Study (IS) assessments for sediment and nutrients is designed to answer the 

following questions:

• What are the dominant pathways responsible for the 

transport of nutrients to streams, and how have landuse practices affected these pathways?

• How do stream habitat and riparian modifications 

affect nutrient and sediment transport and nutrient 

processing? 

• How are nutrient and sediment transport and ecosystem processes affected by management practices, and 

can the outcomes of changes in management practices 

that either increase or decrease landscape alteration be 

predicted? 

• What watershed characteristics affect nutrient pathways and processes, and are these characteristics 

effective predictors of the susceptibility of streams to 

nutrient enrichment? 

• What watershed characteristics affect the erosion, 

transport, and deposition of suspended sediment?

Questions will be addressed using a combination of 

paired IS watersheds in small watersheds (50–150 km2

) that 

are nested within a larger IWS watershed (fig. 18). The paired 

IS watersheds will include one small reference watershed that 

is relatively undisturbed and one in which landscape practices have altered nutrient and sediment loading. Due to the 

complexity and time required to address this question, these 

paired IS assessments will be done in only three IWS areas but 

for an extended period of time (5–10 yr). The advantages of 

focusing on a few long-term sites are to (1) maximize use of 

sites because substantial investment in monitoring infrastructure occurs at startup; (2) facilitate compilation and analysis 

of retrospective, current, and future data on chemical use, 

fertilizer and manure application, sedimentation, and landuse practices through long-term site operation; (3) maintain 

a long-term focus on a particular watershed, which will 

facilitate partnering with other USGS Programs (for example, 

National Research Program and Toxic Substances Hydrology 

Program) and external partners (for example, USEPA, USDA, 

NEON, and universities) on collaborative studies; and (4) gain 

additional data from such sites that could be useful in assessing gradual, longer-term trends, such as climate change or 

sustained development.

Three pairs of IS watersheds will be established in three 

IWS areas that span a variety of physiographic areas with 

varying levels of landscape development. The IS assessments 

will include evaluating antecedent conditions in the watershed 

and determining how land use, flow, and sediment and nutrient loading have potentially changed ecosystem condition. 
66 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

A — Total nitrogen concentration, in milligrams 

 per liter

0 to 0.5

0.6 to 0.9

1.0 to 1.5

1.6 to 3.3

Greater than 3.3

B — Atrazine concentration, in micrograms per liter

D — Drinking water intakes and basins

0

0.1 to 0.5

0.6 to 1.0

1.1 to 3.0

Greater than 3.0

Basin

Intake location

E — Active streamgages

Streamgage location

F — Nutrient monitoring

Nutrient monitoring site

All maps — White River watershed

Watershed boundary 

EXPLANATION

Agriculture

Urban land

Undeveloped land

Mixed land use

A, B, D, E, F — Land use

E F

C D

A B

C — Farm nitrogen fertilizer, in kilograms per 

 square kilometer

0

1 to 1,055

1,056 to 2,461

2,462 to 4,921

4,922 to 89,633

Figure 4.3 A-F

Figure 19 (facing pages). Examples of geospatial information available for the White River Basin in Indiana that would be of use 

in an Integrated Watershed Study: A, estimates of total nitrogen flux in streams from national SPARROW model (Smith and others, 

1997); B, estimates of atrazine concentration from national WARP model; (Stone and Gilliom, 2009) C, farm fertilizer inputs of nitrogen 

(Gronberg and Spahr, 2012); D, locations of drinking-water intakes and associated contributing watersheds (Curtis Price, U.S. 

Geological Survey, written communication, 2012); E, locations of active streamgages; F, locations of nutrient monitoring sites (U.S. 

Geological Survey and other agency sites); 
Goal 2 67

G — National Hydrography Dataset 

 (NHD-Plus) streams

NHD stream

H — Mississippi River Basin Initiative areas

J — Prior National Water-Quality Assessment 

 (NAWQA) studies 

Initiative label

Agricultural chemical transport (ACT) 

 study location

Effects of nutrient enrichment on 

 streams (NEET) study location

Groundwater study location

K — Wastewater discharge

Wastewater discharge location

L — Historical sediment monitoring

Sediment monitoring site

All maps — White River watershed

EXPLANATION

Agriculture

Urban land

Undeveloped land

Mixed land use

G, H, J, K — Land use

K L

I J

G H

I — Fixed and trend monitoring sites

Fixed site

Trend site

Watershed boundary 

Figure 4.3 G-L

Figure 19 (facing pages)—Continued. G, high-resolution National Hydrography Dataset-Plus stream network that can be 

used to enhance models; H, location of the U.S. Department of Agriculture Mississippi River Basin Initiative (U.S. Department of 

Agriculture, 2009) areas within and adjacent to the White River Basin IWS area; I, locations of National Water-Quality Assessment 

Program surface-water-quality monitoring sites; J, locations of previous National Water Quality Assessment studies including 

Agricultural Chemicals Transport study (ACT, http://in.water.usgs.gov/NAWQA_ACT/), Effects of Nutrient Enrichment on Stream 

Ecosystems (NEET, http://wa.water.usgs.gov/neet/), topical study sites, and groundwater studies; K, location of wastewater 

discharges; and L, historical sediment monitoring sites.
68 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Although specific IWS areas have not yet been identified, 

there will be a western, central, and eastern IWS in settings 

that capture a representative range of climatic conditions and 

land-use practices and that have high transfer value. Intensive 

Studies will have high- and low-intensity phases and will be 

implemented on a rotational basis. 

Approach

The paired IS watersheds for the sediment and nutrient 

transport assessments will have reaches that extend for 2–5 km 

and will be gaged near the upper end of the watershed and 

at the mouth (fig. 18). A longitudinal design will also be 

incorporated to discern how these processes change as water 

moves from small headwater systems into larger river systems. 

Due to the complexity of the sediment and nutrient-transport 

assessments, more detailed studies will be done in the smaller 

IS watersheds, and lower levels of data collection will be collected at downstream sites.

The IS assessments in the small watersheds will characterize the hydrology, sediment sources and transport, surface-water 

and groundwater nutrient transport, nutrient transformations, 

assessments of stream-channel form and stability, and ecological interactions with nutrient processing. The IS assessments 

will be repeated periodically at a site to identify temporal patterns and better understand changing conditions and processes. 

Data collection will be maintained at a lower level in between 

individual IS assessments. Continuous data collected at the 

streamgages will include flow, turbidity, conductivity, and dissolved oxygen, whereas samples for analysis of nutrients (nitrogen, phosphorus, and carbon) and suspended-sediment concentrations will be collected approximately monthly to calculate 

nutrient and suspended-sediment mass balances in each of the 

paired IS watersheds. The amount and type of data collection 

may vary according to region-specific factors affecting nutrient 

and sediment transport and ecosystem processes. 

The effect of groundwater on nutrient transport and transformations will be characterized by data from a network of FPS 

wells in each IS watershed that will be used to determine the 

quantity and age of groundwater and the quantity and rate of 

nutrient transport from groundwater to surface water. The FPS 

will be complemented by in-stream piezometer studies to determine nutrient exchange with shallow groundwater. The fraction 

of nutrients derived from groundwater will be determined by 

coupling estimates of base flow with measured nutrient concentrations in groundwater. Water levels will be measured at 

wells throughout the IS watersheds nested within the IWS area 

as input for the development of local groundwater-flow models. 

In-stream studies to address nutrient transformations and 

ecological processes include sediment denitrification experiments; biogeochemical cycling of nitrogen, phosphorus, and 

carbon; stream metabolism; and other process-related measures. Several methods will be used to study the interactions 

of nutrient processes and biota, including methods to assess 

primary and secondary production, trophic interactions, and 

the food quality of primary producers. The effect of nutrients 

on biological condition will be assessed using natural and artificial substrates. Although nutrients in the water column are an 

important part of this study of sediment and nutrient transport, 

nutrients in sediment also will be assessed because of their 

effect on macrophyte growth. 

Studies to address sediment transport through IS and 

IWS watersheds will use retrospective data compilation and 

collection of new data on suspended-sediment concentrations 

and loads, stream stability and flood-plain deposition, and 

analysis of sediment sources. Retrospective and geographic 

information-system data will be used to categorize stream 

segments in relation to natural factors that affect sediment 

transport processes (for example, slope, valley type, sinuosity, soils, and geology). Historical aerial photography and 

EXPLANATION

Nested streamgage

Groundwater study

Active streamgage

Watershed boundary

Agriculture River corridor

Urban land

Undeveloped land

Mixed land use

Land use

Figure 20. The White River Basin in Indiana showing nested 

streamgages that could be added to the water-quality monitoring 

network and used to track fluxes along a river corridor and deduce 

the effects of varying land uses, management practices, and 

watershed characteristics on the fate of contaminants, nutrients, 

sediment, and streamflow. Local groundwater studies and regional 

model results will be used to determine the effect of groundwater 

processes and fluxes on surface-water quality.
Goal 2 69

changes in stream geometry (at existing USGS streamgages 

or other historical survey locations) will be analyzed to better understand how historical land-use practices and climate 

may have affected sediment loading and stream-channel 

migration. Concentrations of suspended sediment in water 

samples collected periodically at streamgages will be related 

to continuous measurements of turbidity to produce hourly (or 

more frequent) estimates of suspended-sediment concentration 

and load and will be compared to concentrations in historical 

sediment samples to identify potential trends. Periodic stream 

geomorphic surveys will be conducted to characterize areas 

of sediment erosion and deposition in relation to hydrologic 

condition. Predominant sediment sources can be characterized 

at headwater and downstream locations by comparing chemical and radiochemical signatures of suspended sediments to 

hypothesized sediment sources, such as surface and channelbank soils (Gellis and Walling, 2011) . 

A longitudinal design will be used to integrate the smallscale IS watersheds with the larger-scale IWS watershed. 

This will enable a better understanding of how nutrient and 

sediment transport and transformations change as stream 

size increases. The longitudinal approach also will enable an 

assessment of how riparian and near-stream land uses affect 

nutrient and sediment transport along the stream system. Studies at larger streams will rely more heavily on models of water 

chemistry and stream discharge (for example, LOADEST, 

metabolism, and base-flow index). 

Planned Outcomes

The following are planned outcomes from the Intensive 

Study (IS) assessments:

• Develop coupled groundwater and surface-water 

models to predict the effect of climate and land-use 

changes on the stream and groundwater quality;

• Assist SPARROW modeling efforts by determining 

rates of nutrient transport and retention. These rates 

will be used to improve parameter estimates used in 

SPARROW models for headwater basins;

• Assess the effectiveness of management practices on 

the processing and export of nutrients and sediments 

along a river corridor;

• Determine the age distribution of nitrate in streams and 

how it varies as a function of stream order (longitudinally) and land-use change; and

• Develop a methodology for assessing the vulnerability 

of streams to legacy sources using the process-based 

understanding of nutrient transport.

Groundwater Studies

In Cycle 3, NAWQA will focus on groundwater resources 

needed for public and domestic drinking supply and on 

groundwater contributions to surface water. Evaluating the 

vulnerability of aquifers used for drinking-water supply to 

water-quality degradation caused by human activities and 

natural factors requires an understanding of the groundwaterflow system; the loading history of man-made contaminants; 

the mineralogy, redox state, and pH within the aquifer system; 

and the distribution of groundwater residence times. Additional 

complications can arise because supply wells can draw water 

from different parts of the aquifer system, thereby producing 

a mixture of waters that may not reflect a linear combination 

of the sources. Given these complexities, Cycle 3 studies will 

be conducted from a hydrogeologic-systems perspective that 

considers the three-dimensional and temporal characteristics of 

groundwater-flow systems over a range of nested, spatial scales 

(local to regional to principal aquifer scales; fig. 21). These 

studies will incorporate data previously collected by NAWQA 

and others, provide for collection of new data as needed, use 

quantitative groundwater flow and transport modeling, and use 

statistical relations between groundwater quality and hydrogeologic characteristics. Groundwater-flow models developed 

at regional scales and statistical-regression/geospatial models 

developed at national scales in Cycle 2 will provide the basis 

for modeling contaminant distributions in Cycle 3. 

In Cycle 3, NAWQA groundwater studies will address 

key scientific questions in five topical areas: 

• Trends in groundwater quality: How is groundwater 

quality changing in the depth interval used for domestic supply? How is groundwater quality changing in 

the depth interval used for public supply? What are the 

hydrologic and geochemical processes responsible for 

attenuating or exacerbating these changes?

• Legacy contamination: To what extent will legacy 

contaminants, such as nitrate and solvents, impair the 

continued use of groundwater at depth intervals used 

for domestic and public supply?

• Vulnerability of groundwater to degradation: What 

is the vulnerability of aquifers used for domestic 

and public supply to contaminant sources introduced at the land surface? What is the vulnerability 

of these aquifers to natural contaminants? (Vulnerability is defined as the likelihood of detecting a 

contaminant at a concentration greater than humanhealth benchmarks or at some ratio deemed protective of human health from a monitoring perspective, 

such as one tenth or one hundredth of a humanhealth benchmark).

• Effects of hydrologic changes: How does groundwater 

quality change in response to changes in the hydrologic 

cycle, and over what times scales do those changes 

occur? Hydrologic changes can include increases in 

recharge due to the use of imported surface water, 

acceleration of the movement of water through the 

hydrologic cycle resulting from groundwater pumping 

and irrigation, artificial recharge, aquifer storage and 

recovery, and water reclamation and reuse.
70 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

• Interactions of groundwater and surface water: 

How do groundwater contributions to surface water 

affect stream-water quality? Groundwater can be a 

substantial source of water to streams, particularly 

during base-flow conditions, and can be a source of 

contaminants to those streams. In general, the volume 

of water in the groundwater system is large relative to 

the volume of water in streams, and therefore groundwater can be a long-term source of contaminants to 

surface-water systems. For example, in many areas of 

the Nation, nitrate has accumulated in groundwater 

over a period of several decades, and the contaminated 

groundwater may contribute nitrate to streams over a 

period of decades to centuries. 

The above questions will be addressed by developing a 

hydrogeologic-systems approach for evaluating groundwater 

quality that will account for the three-dimensional and temporal variability of groundwater flow in aquifers, the external 

factors affecting aquifers, and the internal characteristics of 

studied aquifers. External factors include hydrologic and 

contaminant inputs. Internal characteristics include physical 

properties, aqueous-phase chemical properties, and mineral 

composition. Models are a key part of this approach. Four 

levels of model sophistication will be used. For each level of 

sophistication, field data will be used to develop and calibrate 

the model(s):

• Regression/geospatial models: NAWQA has successfully used regression/geospatial models for evaluating the distribution of contaminant concentrations in 

groundwater at regional and national scales. An important aspect of those models is incorporation of spatially 

distributed explanatory factors. In Cycle 3, regression/

geospatial models also will include hydrologic position 

and groundwater residence time as explanatory factors 

for groundwater quality and as surrogates for other factors that can affect groundwater quality, such as redox 

state. This in turn will require development of straightforward methods for estimating hydrologic position 

and residence time.

• Groundwater-flow and particle-tracking models:

These models will be based, to a large extent, on 

models previously developed by NAWQA and the 

USGS Groundwater Resources Program. The models 

will provide estimates of hydrologic position and 

residence time.

• Groundwater-flow and solute-transport models: These 

models can directly simulate the transport and transformation of contaminants of concern, such as salinity, or 

simulate factors that affect groundwater quality such as 

redox conditions.

• Simulation models of groundwater flow and reactive 

transport: The reactive-transport component could be 

simplistic, whereby sets of reactions are treated as if 

they followed simple rate laws, or the reactive transport component could be fully simulated.

Approach

In Cycle 3, NAWQA will implement multi-scale studies that use monitoring data, process-simulation models, and 

regression/geospatial models to develop an understanding 

of the relation between contaminant concentrations and the 

sources and processes affecting groundwater quality. 

Monitoring data will include contaminant concentrations, indicators of geochemical condition (for example, 

redox state and pH), tracers of groundwater age (residence 

time), and surrogates for contaminant source (for example, 

land use and fertilizer application history). Process-simulation models will include one-dimensional vadose zone 

transport using the Process-based Groundwater Vulnerability Assessment model (P-GWAVA; Nolan and Hitt, 2006), 

groundwater flow with particle tracking using the Modular 

Groundwater Flow Model (MODFLOW) and the related 

particle-tracking model MODPATH (Harbaugh, 2005; and 

Pollock, 2012), solute-transport using the Method of Characteristics Solute Transport Model (MOC3D; Konikow and 

others, 1996) and the Modular 3-D Groundwater Solute 

Transport Model (MT3D; Zheng, 1990), dual-domain transport using the MT3DMS model (Zheng and Wang, 1999), 

which is the successor to MT3D, and coupled models of flow 

and reactive transport.

Multi-scale groundwater investigations will be conducted 

as follows:

Principal aquifer assessment—

Approximately 10,000 to greater than 

100,000 square kilometers

Regional groundwater study—

Approximately 1,000 to 

10,000 square kilometers

Local groundwater study—

Approximately 10 to 100 square 

kilometers

EXPLANATION

Figure 21. Nested spatial scales for Cycle 3 groundwater 

studies. Principal aquifers (or groupings of principal 

aquifers) will be the primary organizational unit, with regional 

groundwater studies and local groundwater studies conducted 

within the principal aquifers.
Goal 2 71

• Implement multi-scale studies at a sufficient number of 

locations that are representative of important watersupply aquifers found throughout the Nation. At each 

location, the scale will range from local (approximately 

10–100 km2) to regional (MAS assessments; approximately 1,000–10,000 km2

) to principal aquifer and 

groupings of principal aquifers (PAS assessements 

and PAA studies, approximately 10,000 to greater than 

100,000 km2) (fig. 21); 

• Develop regression/geospatial and process-simulation 

models at local, regional, and principal aquifer scales. 

The level of model sophistication will depend on 

scale; it is anticipated that coupled flow and reactivetransport models will be developed only at local scales, 

whereas flow and particle tracking will be developed 

at all scales except national. Information gained from 

process-simulation at a given scale will be used in the 

development of regression models at larger scales;

• Develop exceedance maps for selected contaminants 

of human and (or) natural origin at the depth interval 

used for domestic supply and at the depth interval used 

for public supply. The maps will be developed using 

regression/geospatial and process-simulation models 

at local, regional, and principal-aquifer scales. Multiple maps will be produced for each depth interval of 

interest at each of the multi-scale study areas. In some 

areas, the depth interval for domestic wells corresponds to the depth interval for public-supply wells; 

• For a given modeling approach (regression or process 

simulation), compare exceedance maps produced at the 

different scales of spatial resolution. These comparisons can provide a measure of the uncertainty introduced with representing groundwater-flow systems 

at decreasing levels of resolution and can be used to 

evaluate the limitations of using regression/geospatial 

models for exceedance mapping while also providing 

more quantitative estimates of error and the reliability 

of predicted exceedance values. 

• For a given spatial scale (local, regional, principal 

aquifer), compare exceedance maps produced by the 

different modeling approaches. These comparisons 

would provide insight into the relative benefits of using 

more sophisticated modeling approaches; and

• For the study areas where flow and reactive-transport 

models are developed, the comparative evaluations would 

include this third modeling approach. Comparisons of 

flow and transport model results with water-quality data 

and estimates of groundwater age could be used to evaluate the limitations of using regression/geospatial models.

In addition, NAWQA will use local and regional scale 

models in Cycle 3 to address the issue of how groundwater 

contamination affects surface-water quality. Local Groundwater 

Study (LGS) assessments will be implemented along groundwater flow paths that terminate at streams; the scale of these studies likely will range from 1 to 10 km. The primary goal of these 

LGS assessments will be to identify the physical and chemical 

processes affecting the subsurface transport of contaminants, 

including nitrate. A secondary goal would be the development of simplified models that account for the major processes 

affecting contaminant transport and transformation. Regional 

Groundwater Study (RGS) assessments and models will include 

the streamflow network, and output from these models will 

include the location and quantities of groundwater that flows 

into (or out of) streams. Model-derived groundwater volumes 

can be combined with estimated contaminant concentrations to 

estimate contaminant loads. Resulting estimates of groundwater-derived contributions to streams at local or regional scales 

can be input into other watershed regression/geospatial and 

process models being developed to examine contaminant loads 

in streams and rivers, such as SPARROW. 

Planned Outcomes

In Cycle 3, NAWQA groundwater studies will provide: 

• Exceedance maps (fig. 16) for selected human and natural contaminants that impair the use of groundwater for 

drinking supply at the depth interval tapped by domestic 

wells and at the depth interval tapped by public-supply 

wells (fig. 22). Exceedance maps will indicate the likelihood of detecting concentrations relative to humanhealth benchmarks such as MCLs or HBSLs. The 

maps would be developed at a coarse resolution for the 

Nation and at finer scales of resolution for selected local 

areas and principal aquifers. The maps will incorporate 

existing and newly acquired water-quality data and will 

be generated by models developed for this purpose. 

Resource managers and planners will be provided with 

(1) information on the extent to which groundwater 

might or might not be available to meet the demands of 

current and growing populations and (2) a context for 

understanding how groundwater quality in their area 

compares to water quality in other areas;

• Systematic approaches and modeling tools for evaluating groundwater quality from a hydrogeologic-systems 

perspective. These approaches and tools will be 

applicable at multiple scales; will use hydrogeologic, 

climate, land-use, contaminant, and water-use data; 

and will be calibrated with available chemical data. 

NAWQA will evaluate groundwater quality, not only 

from a time and space perspective, but also from a 

“parameter-space” perspective in which variation in key 

groundwater system properties (“parameters”) along a 

flow system (such as lateral hydrologic position, depth, 

groundwater age, mineralogy, redox, or pH) would 

be related to groundwater quality. Local and regional 

agencies will be able to use these approaches and tools 

to develop exceedance maps within their areas; and
72 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

• For representative areas and depths within important 

principal aquifers, evaluation of the magnitude of seasonal and annual variability as compared to long-term 

trends in groundwater quality. Resolving the magnitude of water-quality responses on different time scales 

is important for assessing the effectiveness of management decisions and policies.

Critical Requirements for Technical Support and 

Data Support

All activities in Goal 2 have the objective of understanding the relation between water-quality and current and 

historical human activities and natural factors that determine the observed water-quality. This can be achieved only 

A

׳A

~150 meters

~150 meters

~10 kilometers

~ 50 meters

A A׳

~2 kilometers

~20 meters

EXPLANATION

Monitoring well

Domestic well

Public-supply well

Groundwater-flow path

Proximal

Distal

Distal

10 years

50 years

100 years

Figure 4.6

Figure 22. Three-dimensional representation of a groundwater-flow system illustrating the depth intervals sampled by 

monitoring, domestic, and public-supply wells; flow-path studies, and groundwater ages; and proximal and distal regions of 

the aquifer. The hydrologic systems approach described in the text involves sampling the aquifer at key locations along the 

flow system, from recharge to discharge areas (proximal to distal) and with depth (shallow to deep) to better characterize how 

groundwater quality changes with flow and increased residence time. Inset at lower right illustrates small-scale flow-path 

study along transect A-A’. (~, approximately)
Goal 2 73

if the spatial and temporal datasets describing the effects 

of human activities and natural factors can be assembled. 

These include (1) historical and current land use, (2) 

historical and current source inputs, (3) historical and current water budgets, (4) historical and current agricultural 

and urban practices, (5) historical and current climate, (6) 

watershed characteristics, (7) aquifer characteristics, and 

(8) geochemical conditions. 

Partnerships for Goal 2

The objectives of Goal 2 for assessing sources, transport, 

and transformation of key stressors in surface water and contaminants in groundwater and how water quality is affected by 

human activities and climate change offer important opportunities for scientific collaboration on study design, sampling 

and analytical methods, advances in data analysis, and modeling applications. The following section highlights current or 

desired partnerships that are important to achieving the Goal 2 

objectives outlined for Cycle 3. 

USGS Mission Areas and Programs

The following USGS mission areas and programs are 

potential partners for Goal 2 of Cycle 3:

• Climate and Land Use Change Mission Area: 

Research studies conducted under Goal 2 objectives 

support the USGS Global Change Science Strategy 

(Burkett and others, 2011) in assessing how climate 

change and land use affect the four stressors. Findings 

regarding how climate and land use affect hydrologic 

processes, which in turn directly affect stressors, also 

support efforts to develop mechanistic and processbased models and understand how climate and landuse change affect aquatic ecosystems, particularly 

through Cycle 3 efforts to expand monitoring at reference watersheds. 

• Energy and Minerals, and Environmental Health 

Mission Area: RSS, IWS, IS, and LGS assessments 

will be conducted at scales conducive for partnering 

with the Toxic Substances Hydrology Program, in 

order to improve understanding of contaminant transport and transformation in watersheds and aquifers. 

• Ecosystems Mission Area: The IWS and IS assessments will provide scientific infrastructure for 

leveraging additional research on how aquatic 

ecosystems respond to important stressors with the 

following Ecosystem Mission Area Programs (http://

www.usgs.gov/ecosystems/): (1) Status and Trends of 

Biological Resources, (2) Terrestrial, Freshwater, and 

Marine Ecosystems, and (3) Fisheries: Aquatic and 

Endangered Resources. Mass-balance and hydrologic 

studies that examine nutrient transport and processing 

have implications for assessing how climate and 

human activities affect ecosystem services in different watersheds.

• Water Mission Area: Goal 2 studies represent the 

logical intersection of NAWQA and National Research 

Program (NRP) research that is conducted at a variety 

of scales and in various hydrologic settings built on the 

foundation of extensive NRP involvement in Cycle 2 

topical studies. Considerable expertise exists within 

NRP that can be leveraged in Cycle 3 of NAWQA. 

This expertise includes the development and application of new analytical techniques, field methods, 

modeling tools, and data-analysis approaches.

• WaterSMART Program: The “follow-the-water” 

design of the IWS assessments also is compatible with 

the “focus area study” concept of the WaterSMART 

Program. Opportunities also exist for NAWQA and 

WaterSMART to conduct joint collaborative work on 

ecologic flow requirements. 

• Groundwater Resource Program: One goal of the 

GWRP is to provide information regarding the quantity 

of groundwater available in the Nation’s major aquifer 

systems. This complements NAWQA objectives of 

characterizing the Nation’s groundwater quality. Plans 

are being developed to couple GWRP flow models 

with NAWQA water-quality data to develop groundwater-availability estimates that combine information 

on groundwater quantity and quality. Coupling waterquality models with flow models can be used to evaluate how groundwater quality may change in response 

to natural and human stresses. 

External Partnerships

The following external agencies and organizations are 

potential partners for Goal 2 of Cycle 3:

• U.S. Environmental Protection Agency, U.S. Department of Agriculture, and National Oceanic and 

Atmospheric Administration: Coordinate modeling 

of nutrient and sediment transport from source areas 

to receiving waters. A common goal expressed by 

strategic plans of all three agencies is to develop 

models that can identify the sources of nutrients and 

sediment delivered to receiving waters and predict 

temporal or spatial changes in nutrient or sediment 

delivery in response to changing environmental conditions. A secondary goal is to link models that have 

been constructed at different scales. The focus of 

collaboration would be to link other agency data and 

models to NAWQA models developed as part of the 

IWS assessments, as well as to larger-scale regional 

and national models; 

• U.S. Department of Agriculture: Evaluate the effects 

of agricultural management practices on water quality.
74 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Through its Conservation Effects Assessment Project 

(CEAP; http://www.nrcs.usda.gov/wps/portal/nrcs/

main/national/technical/nra/ceap), the USDA has 

developed large-scale models to quantify the effects 

of historical and current conservation practices and 

programs on the environmental quality of agricultural 

landscapes. Evaluation of the uncertainty in USDA and 

NAWQA model estimates will benefit from the comprehensive data-collection efforts of the IWS assessments. The goal of partnering would be to compare 

modeling approaches, reduce uncertainty in model 

results, and provide improved estimates of the effectiveness of past and current management practices at a 

range of scales; and 

• National Science Foundation National Ecological 

Observatory Network Program: Assess how biological processes affect the transport of nutrients to stream 

ecosystems. The STReam Experimental and Observatory Network (STREON; http://www.neoninc.org/

science/experiments) component of NEON is designed 

to study how stream ecosystems respond to eutrophication and features long-term dosing experiments 

that complement proposed Cycle 3 nutrient transport 

studies. The desired outcome of this partnership is colocation of STREON and NAWQA nutrient studies in 

one or more IWS watersheds. 

Goal 3—Determine the Relative 

Effects, Mechanisms of Activity, and 

Management Implications of Multiple 

Stressors in Aquatic Ecosystems

Goal 3 Outcome: Improve understanding of the effects of (1) 

multiple stressors on stream ecosystems and how stressors 

act, alone or in combination, interact to cause degradation 

and (2) how management practices can be used to reduce the 

effects of stressors. 

Products

The following are planned products for Goal 3:

1. Journal articles on individual stressors, combined 

effects of stressors, and the effect of management 

practices; 

2. Regional- or national-scale map products that show 

where predicted contaminant, nutrient, or sediment 

concentrations (or the degree of streamflow alteration) are at levels capable of adversely affecting 

aquatic biota or stream ecosystems (for example, 

fig. 8);

3. Water-quality indicators that can be used to predict 

the initiation of ecological impairment in response to 

specific stressors or combinations of stressors;

4. Regional predictive models that incorporate the 

effects of land use and management practices on the 

interaction of key environmental stressors and how 

these stressors affect stream ecosystem condition.

Connections to other NAWQA Cycle 3 Goals

Goal 3 builds on Goals 1 and 2 by incorporating ecosystem processes and condition into water-quality assessment, 

understanding, and management. Goal 1 provides the national 

network for assessing status and trends of water quality that 

primarily focus on stressor conditions, and Goal 2 builds on 

Goal 1 by linking water-quality stressors to the human and 

natural factors that affect water quality. Goals 1 and 2 provide 

the foundation for understanding the complex interactions of 

land use, climate, management practices, and major stressors 

(contaminants, nutrients, sediment, and streamflow alteration) and the water-quality or biological measures (indicators) 

that are best correlated with degraded stream ecosystems. 

The development of regional-scale predictive models in 

Goal 3, which predict the effects of stressors and management 

practices on ecosystem condition, will be applied in Goal 4 

to predict the effects of future land use, climate change, and 

management strategies on stream ecosystem condition.

Background

Incorporating knowledge of an ecosystem’s condition 

into water-quality assessments is important for two primary 

reasons. First, the Clean Water Act lists biological integrity as a 

key part of water quality, and therefore regulatory agencies and 

resource managers incorporate biological endpoints into their 

water-quality programs to assess current condition and to track 

changes due to management practices. Second, biological processes are key determinants of water-quality conditions in that 

they can affect both the chemical and physical quality of surface 

waters. For example, initial increases of nutrients commonly 

cause an increase in plant production; however, as plant biomass 

increases it begins to reduce nutrient concentrations and loads 

due to uptake, while also affecting in-stream habitat (Munn 

and others, 2010). When stream habitat is altered such that the 

ecosystem doesn’t function normally, nutrients will remain 

elevated in the water column and be transported to downstream 

receiving waters (Duff and others, 2008). Therefore, in order to 

effectively manage water quality, it is important to understand 

the interactions of the biological system within the physical and 

chemical environment and how management practices affect 

these interactions. Regional-scale models that can describe and 

predict the effect of these interactions are needed by agencies 

tasked with managing local water resources. However, accurately simulating interactions among multiple factors, stressors, 
Goal 3 75

and ecosystem endpoints represent a substantial challenge to the 

development of reliable models in Cycle 3. 

Several unique challenges are faced when assessing the 

relative importance of stressors—contaminants, nutrients, sediment, and streamflow alteration—in affecting aquatic ecosystems. 

Sediment, streamflow variation, and nutrients are essential parts 

of a natural, healthy stream ecosystem and therefore are not, in 

and of themselves, detrimental to ecosystem condition. However, 

when any of these stressors are altered due to human or natural 

perturbations and deviate from their natural condition, degradation 

of the stream ecosystem may result. Contaminants differ from the 

other stressors in that although some are natural contaminants (for 

example, trace elements), most are derived from human activities 

and have the potential to directly affect aquatic life through toxic 

or endocrine-disrupting effects. Hence it is important to know 

when an individual stressor or combination of stressors causes the 

initial decrease in biological condition (for example, threshold) 

and at what point ecosystem condition moves through identified 

categories of concern (fig. 23). These types of analyses are currently common within specific regions and stressors, but have not 

been addressed at larger spatial scales or with multiple stressors. 

Predictive models will be developed at regional scales because 

of regional differences in stressors, management practices, and 

biogeography. Model development and validation will require that 

stressors be examined through both individual and multi-stressor 

approaches to address the five objectives described in the following sections for Goal 3. 

Objective 3a. Determine the Effects of 

Contaminants on Degradation of Stream 

Ecosystems, Determine which Contaminants 

Have the Greatest Effects in Different 

Environmental Settings and Seasons, and 

Evaluate Which Measures of Contaminant 

Exposure are the Most Useful for Assessing 

Potential Effects

Understanding the effects of contaminants on ecosystem condition is a major challenge in Cycle 3. Contaminants, either individually or as mixtures, are known 

to occur in streams at concentrations that pose a threat to 

aquatic ecosystems. However, the complexity of contaminant mixtures and variable spatial and temporal exposure 

patterns has resulted in an insufficient understanding of 

their actual ecological effects, particularly in combination with other stressors. Cycle 3 activities will focus on 

identifying the appropriate tools for measuring exposure to 

contaminant mixtures and determining what the ecological thresholds are for early detection of effects. Studies to 

address this objective will rely primarily on field-based 

studies, but will use some laboratory testing to select the 

appropriate measure of contaminant exposure and to guide 

model development. 

Ecological condition

Identified thresholds

Increase in stressors 

Excellent

Good

Fair

Poor

Figure 23. Schematic diagram showing the decrease in biological condition as stressors increase. 
76 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Objective 3b. Determine the Levels of Nutrient 

Enrichment that Initiate Ecological Impairment, 

What Ecological Properties are Affected, and 

Which Environmental Indicators Best Identify 

the Effects of Nutrient Enrichment on Aquatic 

Ecosystems

Nutrients continue to be a major concern for waterresource managers due to the scale of the problem and the 

complexity of nutrient cycling and effects. The severity of 

the problem has led the USEPA to begin developing regionalbased nutrient criteria. It is well documented that excess 

nutrients can lead to eutrophication, with its associated effects 

of low dissolved oxygen, increased macrophyte plant growth, 

and harmful algal blooms. However, general information 

is lacking on what indicators provide an early warning of 

nutrient enrichment and on how nutrients affect ecosystems 

through interactions with other stressors. In Cycle 3, NAWQA 

will focus on determining what measures are most appropriate for use as early warning indicators and how responses 

differ among regions and their interaction with other stressors. 

Results from this objective also will be integrated with the 

nutrient process component of Goal 2, which evaluates how 

biological processes affect nutrient cycling and loads. Nutrient-enrichment indicators also will be included in the predictive models as response variables to enrichment. 

Objective 3c. Determine How Changes to 

Suspended and Depositional Sediment 

Impair Stream Ecosystems, Which Ecological 

Properties are Affected, and What Measures are 

Most Appropriate to Identify Impairment

Sediment has long been cited as an important and widespread cause of stream ecosystem degradation. Changes in the 

amount of sediment supplied to streams can alter critical streambed habitat and reduce light penetration to benthic communities, 

thereby affecting primary and secondary production. What is not 

well understood is (1) if, where, and how streams are impaired 

with regard to sediment, (2) what measures of suspended or depositional sediment are optimal for quantifying sediment-related 

impairments on ecosystems, and (3) at what point of sediment 

disturbance are ecosystems first affected (for example, doseresponse). Monitoring and studies for Goals 1 and 2 will be used 

to characterize how legacy and ongoing activities have altered 

the movement of sediment in streams, but additional work is 

needed to identify indicators of sediment impairment that can be 

consistently applied and to characterize how these impairments 

affect various measures of ecosystem condition. 

Objective 3d. Determine the Effects of 

Streamflow Alteration on Stream Ecosystems 

and the Physical and Chemical Mechanisms 

by Which Streamflow Alteration Causes 

Degradation. 

Assessment of streamflow conditions has always been 

an important part of the NAWQA Program, particularly in 

relation to contaminant and nutrient transport. The effect of 

streamflow alteration on biological condition at a regional 

and national scale will be assessed in Cycle 3 by analyzing 

data from USGS streamgages across the Nation and data from 

multiple programs, including NAWQA, USEPA, and states. 

Objective 3d will be addressed using a multi-regional implementation of an established framework for evaluating the 

Ecological Limits of Hydrologic Alteration (ELOHA; Poff and 

others, 2010). The ELOHA framework provides a consistent 

and scientifically recognized approach to understanding the 

relations between altered streamflow and biological condition. 

The NAWQA study is unique in its application of the ELOHA 

approach, in a uniform manner, on a national level at thousands of sites.

Objective 3e. Evaluate the Relative Effects of 

Multiple Stressors on Stream Ecosystems in 

Different Regions that are Under Varying Land 

Uses and Management Practices. 

The four individual stressor objectives (Obejctives 3a–3d) 

provide the building blocks for assessing multiple stressors 

and developing regional-scale predictive models. Addressing this multiple stressor objective will be accomplished by 

collecting key measures of the four stressors and biological 

response measures. Quantifying how the four stressors vary 

spatially and temporally at key locations (such as through 

paired IS assessments and at land-use change thresholds), at 

multiple spatial scales, and in different environmental settings 

will allow NAWQA to characterize the relative importance of 

the various stressors on ecosystem condition. This will help 

managers better understand how the stressors interact, which 

stressors are most important in causing degradation in different hydrologic or land-use settings, and which management 

practices may help in reducing the effects of the stressors. The 

primary approach for addressing Objective 3e will be by use of 

statistical modeling; several different approaches will be used 

to identify the relative effects of different stressors on specific 

measures of ecosystem condition and to relate the magnitude of 

the stressor effect on ecosystem condition to land use, management practices, or natural factors. 
Goal 3 77

Policy and Stakeholder Concerns Driving Key 

Management Questions

Although the ultimate motivation guiding management 

questions is to protect and improve the quality of aquatic 

ecosystems, management strategies focus on the control of 

stressors, Thus, stakeholder concerns are commonly expressed 

in terms of specific stressors. Contaminants in water and 

sediment can result in lethal toxicity, potentially causing fish 

kills, elimination of sensitive species, or reduced diversity. 

Alternatively, contaminants may cause sub-lethal effects, such 

as endocrine disruption, reproductive impairment, growth 

inhibition, or increased susceptibility to disease. Both lethal 

and sub-lethal effects can cause impairment of ecosystems 

compared to natural conditions. Yet lack of suitable data on 

contaminants in USEPA and state 305(b) surveys has prevented examination of the same kinds of linkages to biological effects as has been possible with other, more commonly 

measured stressors such as nutrients, sediment, or metals. 

In streams and rivers, adverse ecological effects of 

nutrient enrichment include increased algal and macrophyte 

biomass, which can result in periodic reductions in dissolved 

oxygen (hypoxia), loss of fish habitat, release of toxic metals 

from sediments, and increases in the availability of substances like ammonia. Nutrients also are associated with the 

occurrence of harmful algal blooms, which can produce toxins that negatively affect fish and human health. As nutrients 

move downstream, they create problems for coastal waters, 

resulting in hypoxia and toxic algal blooms. The spread of 

dead zones (areas of low dissolved oxygen) in coastal estuaries is considered a key stressor on marine ecosystems and 

thus an issue of global concern; formation of these areas is 

directly linked to increased fluxes of nutrients from rivers 

(Bricker and others, 1999; Diaz and Rosenberg, 2008; Rockstrom and others, 2009). 

The 2004 Clean Water Act 305(b) report (http://water.

epa.gov/lawsregs/guidance/cwa/305b/2004report_index.cfm) 

lists sediment as the seventh leading cause of impairment to 

streams and rivers in the United States. Sediment is related to 

the six other leading causes of stream impairment in that (1) 

sediment transports pathogens, organic matter, nutrients, and 

metals (the first, third, fifth, and sixth most reported impairments, respectively), and (2) sediment is a principal cause of 

habitat alteration and biological impairments (the second and 

fourth most reported impairments). In addition to the physical effects of sediment transport, suspended sediments are a 

primary transport mechanism for phosphorus, trace elements, 

and a variety of hydrophobic organic contaminants (Horowitz, 

1991; Rasmussen and Ziegler; 2003, VanMetre and Mahler, 

2005). Altered sediment transport also is a known or suspected 

cause of habitat degradation to endangered mussel, fish, and 

bird species. 

A national assessment of streamflow alteration found that 

about 86 percent of monitored sites experienced altered magnitudes of minimum flows, maximum flows, or flow variability (Carlisle and others, 2010b). Abundant indirect evidence 

indicates that physical habitat alteration is commonly the ultimate cause of ecological impairment. Indeed, at least one-third 

of ecologically impaired rivers and streams (as designated by 

state assessments) across the Nation are affected by modified 

physical habitat, water temperature, and streamflow (U.S. 

Environmental Protection Agency, 2008). In addition, more 

than one-half of impaired rivers and streams are affected by 

excessive sediment and nutrients and oxygen depletion (U.S. 

Environmental Protection Agency, 2008), which are commonly caused or exacerbated by altered streamflows (Bunn 

and Arthington, 2002).

With a backdrop of clear-cut documentation of widespread biological impairment of streams but uncertain 

assignment of specific causes in many situations, each type 

of stressor needs to be characterized and understood in relation to its relative importance in affecting aquatic ecosystems. Without an understanding of the effects of each type of 

stressor, their relative importance compared to each other, and 

their interactions, management strategies aimed at improving 

aquatic ecosystems cannot be reliably and efficiently devised 

or implemented.

Understanding the relative importance of different stressors on ecosystem condition, understanding related ecosystem 

services, and developing predictive models that relate stressors 

to effects are essential for improving management. Selected 

examples of management-relevant questions illustrate the 

broad range of applications:

• What is the importance of various physical and chemical stressors on stream ecosystem condition, and which 

are most important to control?

• Which management strategies will most effectively 

improve and protect stream ecosystem condition? 

• What ecological measures are most appropriate as early 

warning indicators for assessing stream ecosystem 

degradation due to physical or chemical stressors and 

for monitoring recovery after changes in management 

practices? 

• What levels of stressors can be tolerated by stream 

ecosystems, and how can this information be used to 

develop regional thresholds for use in management 

issues such as nutrient criteria? 

NAWQA Progress in Cycles 1 and 2

Most of work in Cycle 1 focused on characterizing the 

occurrence and distribution of nutrients and contaminants 

(mainly pesticides) in the Nation’s streams. Ecological studies 

included assessment of the condition of algae, macroinvertebrate, and fish communities at ecological status and trend sites; 

these data provided insight regarding current stream condition 

and how aquatic communities change over time in relation 

to habitat or chemical measures. Synoptic studies targeting 

various ecological questions were done within individual 
78 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

study units to provide broader spatial or temporal information 

on a specific stressor or hydrologic condition (for example, 

spring runoff). The degree to which a specific biological study 

integrated water chemistry varied greatly; however, these 

studies provide important insight into the response of algae, 

macroinvertebrate, and fish assemblages to varying land 

uses, in-stream habitat, and some chemical measures, such as 

nutrients or pesticides. Cycle 1 provided the ecological data 

for the beginning of modeling efforts that greatly expanded in 

Cycle 2. 

New ecological efforts in Cycle 2 included two topical 

studies on urban and agricultural streams, along with a major 

effort to develop regional and national statistical models. The 

first topical study, called Effects of Urbanization on Stream 

Ecosystems (EUSE, http://water.usgs.gov/nawqa/urban/), 

examined urbanization and the quality of aquatic ecosystems 

in metropolitan areas. This study showed that urban impairment is the result of a suite of co-occurring stressors that 

change over the urban gradient but in different ways among 

various regions of the country (Coles and others, 2012). 

The Effects of Nutrient Enrichment on Stream Ecosystems topical study, examined the effects of nutrients on the 

aquatic communities in agricultural streams (http://wa.water.

usgs.gov/neet/). This study found that (1) concentrations of 

nitrogen and phosphorus in agricultural streams commonly 

exceed proposed USEPA Regional Nutrient Criteria (U.S. 

Environmental Protection Agency, 2002) and thus indicate 

potential eutrophication, yet algal biomass commonly is less 

than expected due to habitat alterations; (2) benthic algae show 

a more rapid initial response to increases of nutrients than do 

macroinvertebrates or fish, and overall benthic algae may be 

a better indicator of nutrient conditions; (3) denitrification 

rates in surface water were less than 5 percent of surface-water 

nitrate loading rates and were unable to substantially reduce 

downstream transport of nitrate; and (4) legacy groundwater 

inflow can continue to be a source of nitrogen to streams years 

after nutrient applications to cropland is stopped.

Large-scale modeling efforts were included as part of 

the two ecological topical studies, as part of the surface-water 

status and trends program within Major River Basins (see 

MRB in fig. 3), and at the national scale as part of ecological 

synthesis. A brief summary of each effort is presented below. 

• Urban modeling: The EUSE topical study (http://water.

usgs.gov/nawqa/urban/) has been involved in several 

ecological modeling activities. Bryant and Carlisle 

(2012) used regression approaches to identify multiple 

stressor models for predicting condition of algae, invertebrates, and fish communities and how responses differ 

among varying urban areas (fig. 24). Qian and others 

(2010), Cuffney and others (2011), and Kashuba and 

others (2010) used hierarchical modeling to examine 

the effect of regional-scale processes on the relation 

between watershed-scale urbanization and stream macroinvertebrates. Last, Kashuba and others (2012) used a 

Bayesian network modeling approach to link watershed 

and reach-scale stressors with biological condition. 

• Nutrients in agricultural streams: The NEET topical study focused on the use of structural equation 

modeling for examining the relations between landuse activities, riparian characteristics, nutrients, and 

in-stream biological conditions. Structural equation 

modeling was used to develop a set of causal models and examine the direct, indirect, and total effects 

of agriculture on biological integrity acting through 

different nutrient and habitat pathways (Riseng 

and others, 2011). The structural equation modeling was done using 226 sites distributed across 

eight NAWQA study units (fig. 25A). The national 

model (fig. 25B) provided an integrated view of the 

relations between crop cover (basin percent cropland), riparian cover (buffer percent of wetland), 

and biological integrity (invertebrate community 

quality). Cropland primarily affects benthic communities by altering stream habitat and secondarily 

by imposing water-quality stresses, particularly 

nutrients. This national model provides managers 

with a better understanding of the relations between 

land use, nutrients and biota, as well as a tool for 

assessing the effects of land use/riparian management on water quality and biological integrity. 

Regional models (West, Midwest, and East) were 

also developed that provide more specific interactions and management implications. These models 

can be used to predict how changes in land use/

riparian practices or in-stream conditions can affect 

biological conditions.

• Major river basins/regional studies: Ecological modeling in major river basins is diverse due to the differences among the regions and the variety of ecological 

questions being addressed. Two recent papers illustrate 

this diversity. Kennen and others (2010) used a variety 

of multivariate statistical analyses to assess the effects 

of landscape and streamflow alteration on stream 

macroinvertebrates in northeastern streams. Results 

indicated that urbanization patterns alter streamflow 

sufficiently to negatively affect stream biota. Waite and 

others (2010) compared several watershed disturbance 

predictive models for stream invertebrates in the 

western United States. The study concluded that only a 

few explanatory variables were required to develop the 

“best” multiple linear regression models for a region 

and that all models required a combination of land use 

and natural explanatory variables. 

• National-scale streamflow: A recent study by Carlisle and others (2010b) found that human effects 

on hydrology are widespread, with as much as 

86 percent of streams having altered flow patterns 

(fig. 26). Results showed that diminished flow magnitudes were the primary predictors of macroinvertebrate and fish condition with the streams. Annual and 

seasonal cycles of water flows—particularly the low 
Goal 3 79

Factor Metropolitan Study Area

High flow duration

High flow magnitude

High flow frequency

Water temperature

Width:depth ratio

Sand/silt in streambed

Chloride

Phosphorus

Nitrogen

Dissolved pesticides1

HOC toxicity2

Portland Atlanta Raleigh Denver Dallas Milwaukee

1

Pesticide Toxicity Index for cladocerans, which combines information on exposure of aquatic biota to pesticides (measured 

 concentrations of pesticides in streamwater) with toxicity estimates (results from laboratory toxicity studies) to produce a

 relative index value for a sample.

2

Toxicity of hydrophobic organic compounds (HOC) based on the p450 bioassay, which is a measure of the activity of an 

 enzyme system important in detoxifying some contaminants.

EXPLANATION

Effects of Urbanization on Stream

 Ecosystems study area

0 250 500 MILES

0 250 500 KILOMETERS

B

Algae

Invertebrates

Fish

EXPLANATION

Figure 5.2

A

Dallas

Boston

Denver

Raleigh

Atlanta

Portland

Milwaukee

Birmingham

Salt Lake City

Figure 24. A, Location of Effects of Urbanization on Stream Ecosystems study areas and B, results of multiple regression 

modeling for identifying effects of multiple stressors on algae, invertebrate, and fish communities in six metropolitan study 

areas (Bryant and Carlisle, 2012). This figure indicates which of the three taxa (algae, invertebrates, or fish) respond to varying 

stressors in different urban settings. 
80 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

EXPLANATION

Ozarks

WhiteMiami

Delmarva

Peninsula

Georgia

Coastal

Plains

Columbia

Plateau

Snake 

River

Central

Nebraska

Upper

Mississippi

Agricultural land, in percent 

(National Land Cover Database 2001;

http://www.mrlc.gov/nlcd01_data.php)

0

0.01 to 14

14.01 to 48

48.01 to 84

84.01 to 100

Study area

Western Region

Central Region

Eastern Region

0 250 500 MILES

0 250 500 KILOMETERS

-0.15

-0.49

-0.10

-0.49

-0.30 -0.35

-0.29 -0.63

-0.22

-0.22

Invertebrate

community 

quality

Temperature,

degrees Celsius 

Hydraulic

habitat

n = 226

Water quality,

dissolved Coarse

substrate

Base-flow

index 

Buffer percent

for wetland

Water quality,

particulate

Basin percent

cropland

0.54 0.19

-0.15

0.42

0.72

0.72

n

EXPLANATION

Negative correlation

Positive correlation

Number of sites

A

B

Figure 5.3

Figure 25. A, Location of the eight agriculturally dominated NAWQA study units included in the Effects of Nutrient Enrichment on 

Stream Ecosystems (NEET) topical study, and B, the national structural equation model developed from data collected at the eight 

study sites. Values between environmental variables are calculated correlations.
Goal 3 81

and high flows—affect ecological processes in rivers 

and streams. An adequate minimum flow is important 

to maintain suitable water conditions and habitat for 

fish and other aquatic life. High flows are important 

because they replenish flood plains and flush out 

accumulated sediment that can degrade habitat.

NAWQA’s Role in Cycle 3

Although NAWQA, USEPA, States, and universities 

have made large gains in understanding the effects of individual stressors on ecological systems, they continue to lack 

understanding of which stressors are most detrimental under 

different conditions, the interactions and effect mechanisms 

of the stressors, and the effectiveness of various management 

practices in reducing the impacts of stressors on aquatic ecosystems. Therefore, Goal 3 studies will focus on research that 

will result in the development of ecologically-based predictive 

models that will assess the interactions of different stressors 

in various environmental settings and predict how specific 

management practices will affect ecosystem condition. 

Approach

Goal 3 objectives will be addressed using a combination 

of IS, IWS, and RSS assessments. Findings from Goal 3 will 

provide the needed information for explaining the ecological 

status and trends in Goal 1 and the effect of the four stressors 

on ecological processing in Goal 2. In combination, the IS 

and RSS assessments will provide the data and understanding 

needed to develop models for predicting the effect of the four 

stressors on ecosystem condition, the mechanisms by which 

they function, and what management practices are most likely 

to improve stream ecosystem condition. 

Design Features

Previous studies have demonstrated that the most appropriate scale for developing ecological models is at the regional 

scale due to a combination of biogeography and differences 

in human and natural factors. Therefore, Goal 3 will have a 

regional-based design using the five design elements described 

in the following subsections. 

Severity of reduction in annual high streamflows 

Percentage of sites biologically altered 

None Low Medium High 

10 

0 

100 

50 

90 

80 

70 

60 

40 

20 

30 

Figure 5.4

Figure 26. Relation between percent reduction in in-stream flow and the 

percentage of stream sites with impaired fish communities (from Carlisle and others, 

2010b). The graph shows a positive correlation between increases in percent 

reduction of flow and the number of streams with impaired fish communities. This 

study provides an example of the many efforts that have either been published or are 

presently in progress. These efforts are the building blocks for the development of 

predictive models in Cycle 3.
82 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

1. Identify Geographic Regions for Assessment and 

Modeling

Numerous strategies are available for dividing the 

United States into geographically distinct regions. The 

first step in Goal 3 will be to identify the most appropriate 

regional scale to use for the development of predictive models. Having 10–20 regions subdividing the conterminuous 

United States will be considered optimal. The process will 

start by examining the USEPA Level 2 Ecoregions (USEPA,

2010b; fig. 27) because those ecoregions encompass major 

geographic regions and because the Level 2 ecoregions have 

been shown to be one of the better geographic-based classification systems at larger scales. The regions will then be 

ranked based on several criteria, including representation of 

a variety of stressor conditions, number of reference sites, 

and containing a sufficient number of NFSN sites and having 

some overlap with IWS areas. Where possible, regions will 

be selected to take advantage of collaborative opportunities 

with other USGS programs and Federal, state, or academic 

studies (such as the STREON Program).

2. Develop Conceptual Model

Although it is common to develop a conceptual model 

as part of an ecological study, this step is particularly critical 

to Goal 3. A conceptual model (fig. 28) will be developed 

for each region selected for study based on a combination 

of NAWQA findings from Cycles 1 and 2 and consultation 

with USEPA, state, and local experts. The conceptual model 

will incorporate factors (land use) and associated stressors 

(e.g., nutrient enrichment, temperatures, hydrologic regime), 

their interactions, and how they affect selected measures 

of biological condition. The actual measures of biological 

condition will vary depending on the stressors examined. 

The development of a conceptual model is critical to the 

refinement of stressor-related questions specifically for the 

selected region, to assist in prioritizing information gaps, and 

in evaluating what study approaches are most appropriate. In 

addition to being important for the overall design of a study, 

the conceptual model also will be used as the starting place 

for the development and testing of a predictive model. For 

example, some modeling approaches, like structural equation 

modeling, require that a conceptual model be developed in 

order to test the hypothesis on which the model is based. 

3. Intensive Studies

Once a region is selected and a conceptual model is 

developed, the next step will be select an IS watershed. The 

IS assessments are the smallest scale study in Cycle 3 (figs. 17 

and 18) and will be nested within an IWS watershed, which is 

the primary scale for studies addressing Goal 2. The primary 

purpose of the IS assessments is to fill critical knowledge gaps 

about specific stressors, refine the conceptual model, and assist 

in the selection of the best measures of stressor and ecological endpoints. Therefore, the IS assessments are a critical first 

step in designing regional-based studies for the development 

of predictive models. The time period for IS assessments may 

vary depending on the specific questions being addressed. 

For Goal 3, some of these IS assessments will continue for 

1–3 years to address specific stressor and methods questions, 

whereas for other questions, as in Goal 2, the IS assessment 

may continue for longer periods (5–10 yr). The IS sites for 

Goal 3 will be selected to represent a variety of stressor conditions. The types of IS assessments may differ among regions 

and stressors. For example, in some areas it may be important 

to focus more on identifying useful metrics of contaminant 

effects due to a lack of information on contaminant conditions 

and what endpoints are most relevant to biological systems. The IS assessments have two critical roles that are not 

addressed by other design components: 

• The level of study intensity and use of multiple methods will enable a more refined and complete answer to 

questions than is possible using more general-purpose 

monitoring data; and

• IS assessments serve to test and determine the most 

effective new methods and approaches for evaluating 

stressor effects that may be adapted to fixed-site monitoring or Regional Synoptic Studies.

4. Regional Synoptic Studies

The RSS assessments, which are the third largest study 

scale in Cycle 3 (fig. 17), are the scale at which data will be 

collected for the development and application of predictive 

ecological models. Once an IS is completed, the original 

conceptual model will be updated to reflect study findings, 

and the knowledge gained from the IS will be used to select 

key measures of individual stressors and biological endpoints 

that will be incorporated into a larger, regional-based study. 

The selection of a few key measures for the regional assessment is important because regional-based ecological models 

commonly will require a large number of sites (50–150). 

The actual number of sites selected is an important part of 

the statistical design of the RSS assessments prior to the 

collection of data and will vary depending on the region and 

modeling approach selected. Although the RSS assessments 

likely will be based on short-term synoptic studies, these 

assessments also may include some temporal sampling in 

order to assess how stressors affect biological endpoints over 

time. This will provide insight into how and to what extent 

individual stressors affect ecosystem condition and will also 

provide a more complete understanding about the relative 

and combined effect of the four stressors. Sites selected also 

will include a gradient of watershed management practices 

within a region, so that models developed can address the 

effects of various management practices on both stressor and 

ecosystem conditions. 

5. Develop Ecologically-Based Predictive Models

Ultimately, a primary purpose of studies addressing 

Goal 3 objectives is to develop and test regional models for 
Goal 3 83

Figure 27. Map showing U.S. Environmental Protection Agency Level 2 Ecoregions (Commission for Environmental Cooperation, 

2008). Ecoregion definitions are available at http://www.epa.gov/wed/pages/ecoregions/na_eco.htm.

Fig. 5.5 (Note to author: Add reference to References section of report: U.S. Environmental Protection Agency, 2010, Level 2 ecoregions: 

accessed April 29, 2013, at http://www.epa.gov/wed/pages/ecoregions/na_eco.htm.)

100° 90° 80°

70°

120°

110°

40°

30°

Ecoregion

EXPLANATION

Western Cordillera

Marine West Coast Forest

Mixed Wood Plains

Cold Deserts

Warm Deserts

Mediterranean California

Western Sierra Madre Piedmont

Upper Gila Mountains

Everglades

Water

Central U.S. Plains

Southeastern U.S. Plains

Temperate Prairies

West-Central Semiarid Prairies

South-Central Semiarid Prairies

Texas-Louisiana Coastal Plain

Tamaulipas-Texas Semiarid Plain

Mixed Wood Shield

Atlantic Highlands

Ozark/Ouachita-Appalachian Forests

Mississippi Alluvial And Southeast U.S. Coastal Plains

0 500

0 250 750 KILOMETERS

250 750 MILES

500

Base from U.S. Geological Survey, 2006, 1:2,000,000

Albers Equal-Area Conic projection

Standard parallels 45°30’N and 29°30’N, 

central meridian 96°W

Ecoregions from U.S. Environmental Protection Agency, 2010b

predicting the effects of various stressors on ecosystem condition and to test scenarios of how changes in stressors, land 

use, climate, and management practices may affect ecosystem 

condition. One of the tasks for Cycle 3 will be to assess what 

types of models will be most appropriate for the regional-scale 

assessments. During Cycle 2, NAWQA made substantial progress using a variety of ecologically-based statistical models, 

including Bayesian network models in the EUSE topical study 

and structural equation models in the NEET topical study. 

These models improved understanding of ecological interactions in both urban and agricultural streams, and enhanced 

predictions of how biological communities are affected by 

land use and in-stream factors. The development and testing of 

ecological models is a planned outcome of Goal 3, and will be 

a critical part of Goal 4 efforts to develop forecasting models 

for prediction of ecosystem response. 
84 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Study Designs and Outcomes for Each Individual 

Stressor

Study designs and outcomes for Goal 3 are described 

relative to the four stressors affecting stream ecosystems: 

contaminants, nutrients, sediment, and streamflow alteration.

Contaminants

NAWQA has completed numerous studies on the occurrence and distribution of contaminants, including specialized studies of source, transport, and transformations in both 

Cycles 1 and 2. Contaminant studies have included trend 

assessments; transport to agricultural, urban, and reference 

streams; transport to groundwater; and transport to individual supply wells. Contaminant concentrations have been 

compared to concentration benchmarks to assess potential 

toxicity, with results indicating concentrations of potential 

concern are frequently exceeded in the environment, but no 

direct information suitable for evaluating cause-and-effect 

relations has been collected to date. In Cycle 3, NAWQA 

will more directly address the effects of contaminants on 

ecosystem condition. 

Approach

Contaminants differ from other stressors in that they 

consist of a diverse array of inorganic and organic compounds 

of natural (trace elements) and human (pesticides and PAHs) 

origin that occur in various combinations depending on the 

environmental setting and time period. Furthermore, contaminants can cause a variety of ecological effects, some of which 

are severe and easily measured (acute toxicity), whereas others 

produce long-term chronic effects that are very difficult to 

measure and assess. It is this vast array of chemical mixtures 

and potential effects that make assessing contaminant effects a 

challenge at larger scales. 

The use of a combination of IS and RSS assessments, 

each described previously in this section, is an ideal approach 

for addressing several contaminant-related stressor issues. 

Potential causes of contaminant effects include a variety of 

factors, such as contaminants from different sources, mixtures 

of contaminants, or effects caused by a specific individual 

contaminant. Effects of these factors can be shown through a 

variety of indicators, such as reduced species diversity or differences between reference and observed conditions. The use 

of several sites along a gradient of contaminant effects within 

an IS is a practical way to improve understanding of contaminant stressor effects relations. 

The use of the IS assessments will aid clarification of 

several key elements of contaminant effects. First, IS assessments will provide an assessment of the types, concentrations, and timing of the various contaminants in each region. 

Second, based on improved understanding of the contaminants 

of concern, in-stream ecosystem condition can be compared 

with various laboratory toxicity tests to determine if contaminants in water or sediment are toxic to aquatic life and if 

these contaminants actually affect natural communities. This 

information is needed before designing a RSS, because it will 

be important to know what contaminant-related measures are 

most appropriate for assessing biological condition. Contaminant indicator measures selected may vary depending on the 

specific features of the region. Once the contaminants effects 

indicators are selected, then an RSS assessment can be completed in order to develop a predictive model. 

Planned Outcomes

The following are planned outcomes of Goal 3 studies of 

contaminants:

• Integrated laboratory and field methods for assessing 

potential toxicity of contaminants to aquatic organisms. 

Ecological measures could include some traditional 

approaches (for example, species-specific measures) 

and non-traditional measures of ecosystem function (for 

example, stream metabolism); and

• Development of models for predicting potential 

toxicity of contaminants or mixtures of contaminants 

(for example, the pesticide toxicity index; Munn and 

others, 2006) to aquatic life under various land use or 

management scenarios. 

Nutrients

It is well documented that severe eutrophication causes 

ecological impairment, but three specific aspects of nutrient enrichment in streams require additional study. First, it is 

still common to address nutrient-related issues by measuring 

concentrations of nutrients, even though studies have shown a 

poor connection between ecosystem condition and concentrations due to biological activity. For example, the NEET topical 

study found that concentrations of nitrogen and phosphorus 

in agricultural streams commonly exceed proposed USEPA 

Figure 28. Example of a regional-scale conceptual model based 

on existing studies and expert knowledge that relates various 

environmental features and stressor characteristics to the 

condition of benthic stream communities.

Land use/cover

Nutrient

enrichment

Hydrologic

regime Temperature Water

quality

Substrate Productivity

Channel

hydraulics

Benthic stream

community
Goal 3 85

Regional Nutrient Criteria (U.S. Environmental Protection 

Agency, 2002) and thus indicate potential eutrophication, yet 

algal biomass commonly is less than expected due to habitat 

alterations. Studies are needed to provide a more accurate 

understanding of how stream ecosystems respond to various 

levels of nutrients in different regions and under different 

environmental conditions. Second, agencies are developing 

various monitoring programs to address USEPA-initiated 

nutrient criteria. Most state and local agencies are relying on 

existing methods; however, the need to determine what ecological endpoints are most appropriate for assessing the early 

onset of nutrient enrichment and for tracking improvements 

after changes in management practices is growing. Third, a 

general lack of knowledge remains on how various management practices affect the source, transport, and biological 

effects of nutrients in streams. 

Approach

The effects of nutrients (nitrogen, phosphorus, and carbon) on biological condition will be assessed primarily by the 

IS/RSS design presented previously in this section. Effects of 

nutrient enrichment are not tied directly to the concentrations 

of nutrients, but instead are a function of ecological changes 

within the stream. For example, an increase in nutrients commonly results in an increase in plant production, which can 

alter dissolved oxygen concentrations and habitat (for example, in-stream physical habitat and riparian), both of which can 

become major stressors to aquatic species. 

NAWQA historically has addressed specific aspects of 

nutrient effects using established protocols for assessing habitat 

and biological communities. Although habitat and biological 

assessments of nutrient effects may use components of the 

existing protocols, development/implementation of different 

methods for assessing habitat and ecosystem structure/function 

will be based on lessons learned from Cycles 1 and 2. Examples of new assessment techniques that may be used include (1) 

measures of primary and secondary production, (2) food web 

analysis, (3) food quality analysis, (4) importance of sedimentbound nutrients in community composition, and (5) effect 

of nutrient cycling on plant and animal communities. The IS 

assessments will be used to assess various measures of nutrient 

enrichment and how biological indicators respond to increased 

nutrients. Findings from the IS assessments will be used to 

select the most appropriate indicators of nutrient enrichment 

and biological endpoints for regional-based studies. 

Planned Outcomes

The following are planned outcomes of Goal 3 studies of 

nutrients:

• A habitat-based stream-classification system for predicting ecological response to nutrient enrichment;

• Determination of the timing and magnitude of elevated 

nutrient concentrations essential to initiate excessive 

plant or algal growth in streams;

• Environmental indicators for identifying early onset of 

ecological impairment due to nutrient enrichment; and

• Information on how specific management practices 

affect nutrient effects.

Sediment

Assessment of sediment-related impairments to ecosystems is challenging because suspended and streambed 

sediment varies naturally in different regions and through 

time. Sediment has been identified by the USEPA as one of 

the most widespread stressors to aquatic ecosystems (U.S. 

Environmental Protection Agency, 2006). Sediment-related 

effects can be divided into three categories: (1) those caused 

by changes in the concentrations of suspended sediment, 

(2) those caused by alteration of streambed substrates, and 

(3) those caused by bedload and suspended sediment which 

can alter the physical structure or morphology of the river. 

Suspended-sediment effects typically are related to changes in 

light penetration, which alter primary productivity and affect 

sight-feeding fish, but also include abrasion of macroinvertebrate communities. Alteration of streambed substrates can 

be caused by changes in upstream sediment supplies or by 

changes in shear stress related to alteration of streamflow or 

channel conditions. Fining or coarsening of streambeds can 

affect stream ecosystems in many ways, including burial or 

scour of macroinvertebrate habitat and fish spawning beds 

(Waters, 1995). In streams with undisturbed flow, channel 

morphology is in equilibrium with streamflow, sediment (bedload and suspended sediment), and channel slope. Alterations 

of any of these parameters can lead to changes in channel 

morphology, which in turn, can affect the habitat of aquatic 

organisms living in the stream. 

Approach

Because ecosystems are adapted to natural sediment 

transport and streambed substrates, characterization of sediment impairments will rely on understanding developed in 

Goals 1 and 2 and local knowledge to develop hypotheses 

related to if and how sediment-related impairments may affect 

ecosystem condition. The IS assessments will focus on assessing and developing measurements of suspended and depositional sediment along with indicators of ecosystem condition 

that potentially are affected by sediment disturbance. The 

magnitude, frequency, and duration of suspended-sediment 

concentrations will be evaluated through time and across 

hydrologic conditions through periodic sample collection and 

computation of suspended-sediment concentrations at hourly 

or finer temporal scales using surrogate technologies (Pellerin 

and others, 2012). In regards to streambed sediment, aquatic 

community response can be evaluated using representative 

measures of habitat quality identified as important during 

Cycles 1 and 2, and measures used by regional or national 

agencies, such as the relative bed stability index developed 

by USEPA (Kaufmann and others, 2008; Kaufmann and 

others, 2009). The relative importance of sediment-related 
86 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

impairments to aquatic ecosystems will be evaluated with 

respect to both temporal and spatial variability in suspended 

and streambed sediments; an emphasis will be placed on 

reference sites and on sites in which ecosystem degradation 

from contaminants are hypothesized to be minor. Ecological 

variables to be considered include aquatic macrophyte beds, 

biological assemblages (algae, macroinvertebrates, and fish), 

primary production, and potentially other indicators. 

The IS results will be used to evaluate indicators of sediment-related impairments for incorporation into RSS assessments. These assessments will result in a predictive ecological 

model that will assess the relative importance of sedimentrelated impairments on stream ecosystems. This model also 

will provide insight into the importance of sediment-related 

management practices to the health of stream ecosystems. 

Planned Outcomes

The following are planned outcomes of Goal 3 studies of 

sediment:

• Identification of the predominant mechanisms by which 

changes to sediment transport affect stream habitat and 

aquatic ecosystems in different environmental settings;

• Evaluation of existing, and development of new environmental indicators of sediment-related impairments 

to aquatic ecosystems; and

• Regional assessments of the importance of sedimentrelated impairments to aquatic ecosystems.

Streamflow Alteration

Although streamflow alteration has been of concern for 

many years, it has recently become a major focus of many 

agencies and environmental groups because of its importance 

in sustaining a healthy stream ecosystem (from a physical 

habitat perspective) and its overall effect on stream quality. 

The recent concern regarding water withdrawals and competing needs for both human uses and biological condition has 

only intensified the need for a better understanding of how 

streamflow alteration affects biological condition. Information 

that quantifies relations between severity of streamflow alteration and degree of biological impairment is critically needed 

by environmental policy makers and managers. In addition, 

the scientific literature points out large gaps in our knowledge 

of the mechanisms by which streamflow alteration affects 

aquatic ecosystems (Carlisle and others, 2010a and 2010b). 

Filling these information gaps will improve our effectiveness 

in managing water resources to both satisfy human needs and 

maintain healthy ecosystems.

Approach

Streamflow alteration is unique among stressors because 

of the wealth of historical and current streamflow information collected and maintained by the USGS. More than 8,000 

streamgages across the Nation have at least 20 yr of flow 

record, and about the same number of real-time streamgages 

currently (2012) are in operation. Drainage basins for these 

streamgages have been delineated, which allows for characterization of many watershed features, whether natural or affected 

by humans. This rich dataset has enabled the development of 

statistical models that predict the expected baseline (that is, natural) and the altered streamflow condition for any stream in the 

Nation. The three complementary methods summarized below 

take advantage of this predictive capability to quantify relations 

between streamflow alteration and ecosystem condition:

1. Data from the existing streamgage network will 

be used to develop statistical models that estimate 

streamflow alteration at sites where biological condition data previously have been collected by Federal 

and state monitoring activities, but where streamflow 

data do not exist. The USEPA, for example, through 

its National Rivers and Streams Assessment (http://

water.epa.gov/type/rsl/monitoring/riverssurvey/

index.cfm), quantified physical and chemical habitat, 

along with biological condition, at almost 1,400 sites 

across the Nation. The assessment, however, did not 

include any aspects of streamflow alteration. The 

statistical models developed by NAWQA will be 

applied to the National Rivers and Streams Assessment sites to estimate streamflow-alteration metrics. 

These streamflow-alteration metrics will be combined with the data collected by the USEPA to assess 

relations among the habitat measures, streamflow 

alteration, and biological condition. Similar studies 

will be conducted at the state level where appropriate biological and habitat data have been collected 

by state agencies.

2. NAWQA will measure multiple potential stressors 

(contaminants, nutrients, sediment, habitat, and 

streamflow alteration) and biological condition 

over time at many long-term streamgages across 

the Nation. An analysis of the temporal variability 

among the stressors and biological condition will 

provide insight into covariance among the stressors 

and their effects on biological condition.

3. Statistical tools will be used to select streamflow 

sites within a region, such as a USEPA Level 2 

Ecoregion, to control for possible confounding 

effects of other stressors. Biological condition will 

be measured at these sites to determine the effects of 

specific types of streamflow alteration on the status 

of aquatic communities. Measurements of other 

stressors will be made to confirm that streamflow 

alteration effects have been isolated.

In addition to the three methods described above, which 

rely on statistical analyses, the effects of streamflow alteration 

on biological condition also will be addressed through intensive studies designed to assess the effects of contaminants, 

nutrients, and sediment. Including consideration of streamflow 
Goal 3 87

in IS will permit a better understanding of the mechanisms by 

which streamflow affects contaminants, nutrients, and sediment 

as stressors. Streamflow also can be assessed to determine what 

aspects of streamflow affect biological systems, including habitat features (for example, wetted perimeter), water temperature, 

and sediment effects (for example, scour). The IS assessments 

also will enable evaluation of how various streamflow metrics 

affect various biological endpoints. For example, it is important to understand the effects of streamflow alteration on plant 

biomass accrual and production, which form the overall types 

of communities that can reside in a stream. In the IS design, 

hydrodynamic and process-oriented watershed models will be 

used to improve predictions of stream channel hydraulic characteristics and daily streamflow at ungaged sites.

Planned Outcomes

The following are planned outcomes of Goal 3 studies of 

streamflow alteration:

• Predictions of the effects of streamflow alteration on 

biological condition; and 

• Mechanisms of how streamflow alteration affects biological systems at regional and national scales.

Example Designs for Integrated Intensive and 

Regional Studies Assessing Stressors in Urban 

and Agricultural Settings

This section presents example study designs for an urban 

and agricultural setting, with the urban example presenting 

all components of the study design from conceptual model 

to regional model and application. The agricultural example 

provides a second example of model development and 

application. 

Urban Example

In Cycle 2, the EUSE topical team reported that ecosystem condition generally became degraded with watershed 

urbanization, but the relations between degree of watershed 

urbanization and degree of degradation varied among different natural environmental settings (Coles and others, 2012). 

The EUSE study also yielded a multi-level hierarchical model 

that relates degree of urbanization and climatic variables to 

ecosystem condition (Kashuba and others, 2010). However, 

the EUSE study was not designed to assess the relative importance of different stressors as a function of land use, water use, 

chemical loading, or other natural factors. Therefore, Cycle 3 

will focus on assessing the effects of contaminants, nutrients, 

sediment, and streamflow alteration on biological condition 

and will develop a regional-scale predictive model for important landscape features, in this case, specifically for urban 

lands. The example described in this section focuses on urban 

settings; howerver, Cycle 3 also will feature stressor studies 

conducted in agricultural settings. 

Study Questions

The example urban study will address the following 

questions:

• Which stressors are causing ecosystem degradation as a 

watershed becomes urbanized?

• How do the relative effects of different stressors 

change with degree of urbanization?

• How do stressor-effect relations vary among different 

natural settings?

Approach

The example urban study will use the following 

approach:

Regional settings (10–20): Will be ranked according to 

the urban and agricultural settings of greatest interest. Urban 

regional environmental settings will be assessed on the basis 

of Cycle 2 EUSE findings to determine if major urban areas 

can be combined into a single region. One example would be 

to combine Raleigh, North Carolina (N.C.), and Atlanta, Georgia (Ga.), because they occur within the same USEPA Level 3 

Ecoregion. 

Conceptual model: Modeling efforts by EUSE combined 

with additional information from other NAWQA studies, 

studies by other agencies, and local expertise will be used to 

construct a conceptual model of how land use affects the four 

stressors identified and how these stressors likely would affect 

specific indicators on ecosystem condition (fig. 29). 

Intensive Study: Based on the conceptual model above, 

several Intensive Study (IS) sites could be selected; for 

example, within the Raleigh-Durham, N.C., urban area, where 

three streams draining low-, medium-, and high-density urban/

surburban watersheds could be selected (fig. 30). These sites 

would be gaged and studied over a 1–3 yr period to assess what 

stressors are most important and what endpoints and methods 

will be most useful for a regional synoptic study. With respect 

to toxic contaminants, the IS sites will monitor a suite of ecologically important contaminants known or suspected to occur 

at urban sites to determine their concentrations, seasonal exposure patterns, and the effects the contaminants have on biota. 

Measurements will be used to construct predictive indicators of 

potential toxicity, including the pesticide toxicity index (Munn 

and others, 2006) for water, and the Probable Effects Concentration Quotient (MacDonald and others, 2000) for sediment. 

Toxicity testing will be highly targeted and selective, using a 

variety of bioassay methods and other techniques based on the 

types of contaminants indicated to be most important. Methods 

will include a combination of field and laboratory measures, 

including both acute and chronic toxicity tests. 

Regional Synoptic Study: Results from the IS assessments will be used to design a RSS for which key variables 

of stressors and indicators of ecosystem condition will be 

collected. The RSS would include 50–100 sites across the 

identified metropolitan area(s) with data used to develop a 

regional-scale urban predictive model. Figure 31 shows an 
88 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

USEPA Level 3 Ecoregion that encompasses two urban areas 

previously studied by NAWQA (Raleigh, North Carolina, and 

Atlanta, Georgia). The RSS sites will be established to capture 

gradients ofurbanization and dominant stressors identified for 

that region. Data and findings from the RSS will then be used 

in the development of a regional-based model. 

Develop ecologically-based predictive models: The data 

collected as part of the RSS will be used to develop a regional 

model. For example, the Bayesian network model shows the 

probabilities that a stream would have properties associated 

with each of the categories for each model node (fig. 32). For 

example, if it is known with 100-percent certainty that a stream 

is located in a watershed with 31–100 percent urban land cover, 

this model predicts that stream will have a 50-percent chance 

of having high flashiness (greater than four streamflow rises 

above the median flow in a year), about a 48-percent chance 

of having low generic richness (less than 15 total taxa), and 

slightly more than a 1-percent chance of achieving Biological Condition Gradient Tier 1 (equivalent to natural biological 

condition). Managers can set the known or desired value of any 

node in the model, and the model can be used to predict the 

likely values of all other nodes in the system. 

This model can be used to evaluate the effects of various 

management actions on the probability of achieving desired 

levels of a biological condition standard. For example, managers could change the level of urban disturbance in the model 

to determine the degree to which a shift in urbanization affects 

key stressors and how biological condition is affected.

Agricultural Example

Along with urbanization, there is substantial interest in 

how agricultural management practices are affecting water quality and biological condition. This agricultural example focuses 

on agricultural lands and is based on ongoing NEET studies. 

Study Questions

The example agricultural study will address the following 

questions:

• Which stressors are causing ecosystem degradation in 

response to specific agricultural practices?

• How do the relative effects of different stressors 

change with agricultural intensity?

• How do stressor-effect relations vary among different 

agricultural settings?

Approach

Development of conceptual model: Once a regional 

setting is selected, a conceptual model will be developed 

that provides a hypothesis of how stressors and management 

practices affect stream biota. This model can incorporate both 

human and natural factors, along with specific management 

practices. For the conceptual model for agricultural lands, 

emphasis will be placed on how land use and cover affect flow 

(hydrologic regime), substrate, and water chemistry, primarily 

nutrient enrichment (fig. 33). Specific contaminants, such as 

pesticides, could be added to this example if necessary. 

Intensive and Regional Studies: As in the urban 

example, IS watersheds will be selected for assessment of the 

effects of the various stressors and to refine the selection of 

indicators for use in a regional study. Once this is completed, 

an RSS is initiated for which data are collected at multiple 

sites throughout the region. Data collected will include measures of key stressors and ecological endpoints that can be 

used for the development of a model. 

Development of regional model: In contrast to the urban 

example, which relies on a Bayesian network model, this 

agricultural example illustrates the use of a structural equation 

model, which is used to develop a set of causal models and 

to examine the direct, indirect, and total effects of agriculture 

on biological integrity acting through different nutrient and 

habitat pathways (Riseng and others, 2011). For example, in 

the Coastal Plains ecosystem, cropland tends to be located on 

well-drained upland areas separated from streams by undisturbed riparian flood plain and wetland habitats resulting in 

lower nutrient concentrations in many of its streams. In the 

Coastal Plain structural equation model developed by Riseng 

and others (2011), riparian forested wetland had substantial 

positive effects on the invertebrate community by reducing 

dissolved nitrate, total phosphorus, and suspended sediment 

Urban

disturbance

Streamflow

alteration

Habitat Sediment Nutrients Contaminants

EPT taxa

richness Richness-weighted

tolerance

Percent

intolerant taxa

Figure 29. Hypothetical conceptual model showing the primary 

stressors that determine ecosystem condition in an urban stream 

ecosystem [EPT, Ephemeroptera sp.(mayfly), Plecoptera sp. 

(stonefly), and Trichopera sp. (caddisfly)].

Figure 30 (facing page). Study sites included in the Cycle 2 

Effects of Urbanization on Stream Ecosystems (EUSE) study in the 

Raleigh-Durham metropolitan area in North Carolina. Hypothetical 

locations of three Intensive Study sites where detailed stressor 

studies would be conducted in watersheds with low, moderate, 

or high degrees of urbanization could include streams draining 

watersheds labeled numbers 1, 14, and 28, respectively.
Goal 3 89

36°

35°

80° 79°

9

5

1

11

20

27

4

28

22

23

19

8

21

24

2

7

26

3

29

6

15

14

12

18

10

25

16

13

30

17

Gulf of Mexico

Atlantic Ocean

Study area

Land use

EXPLANATION

Level III ecoregion boundary

Open water/wetlands

Developed

Bare rock/sand

Forest/shrub/scrubland

Agriculture/grassland/herbaceous

Cary

Durham

Raleigh

Danville

High Point

Greensboro

Burlington

Chapel Hill

Winston-Salem

VIRGINIA

NORTH CAROLINA

29

Watershed boundary

Study site and number

0 10 20 30 KILOMETERS

0 10 20 30 MILES

LEVEL III ECOREGION—

PIEDMONT

Figure 5.8
90 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

concentrations and providing a coarse substrate habitat (woody 

debris) that far outweighed the negative effects of agriculture. 

The results indicated the importance of intact riparian flood 

plains and wetlands for maintaining biotic integrity in the 

Coastal Plains ecosystem (fig. 34). 

This regional model can be used to evaluate the effects 

of various management actions on habitat, nutrients, and 

invertebrate community quality. For example, managers could 

determine to what degree increasing the percent of buffer that 

is wetland habitat affects biological condition. 

Critical Requirements for Technical Support and 

Data Support

The following critical requirements for technical support 

and datesets are needed for Goal 3:

• Existing biological data: Numerous local, state, and 

Federal agencies are collecting biological and habitat 

data as part of their existing monitoring and assessment 

programs. Obtaining and incorporating these data 

into a common database is important for addressing 

specific stressor objectives. For example, biological 

data collected near USGS streamgages are critical for 

addressing some of the streamflow alteration questions 

presented earlier in this Section. This activity will assist 

NAWQA in working with other agencies to address 

common questions on stressors and ecological effects. 

• Evaluate existing or newer assessment tools: NAWQA 

has existing protocols for the collection of habitat and 

stream biological assemblages (algae, macroinvertebrates, 

and fish). However, current (2012) protocols may need to 

be modified and updated for Cycle 3 (1) based on experience gained in Cycles 1 and 2 and (2) to facilitate the rapid 

collection of key variables from a large number of sites at 

the regional scale. Furthermore, some stressors, such as 

toxic contaminants, will require methods not previously 

used in the NAWQA Program. These include field and 

laboratory toxicological tools that are important for the 

assessment of contaminant effects. 

Figure 31. Regional Synoptic Study design for assessing key stressors and biological response.

VIRGINIA

OHIO

KENTUCKY

TENNESSEE

NORTH CAROLINA

INDIANA

WEST VIRGINIA

ILLINOIS MISSISSIPPI

MARYLAND

ALABAMA

GEORGIA

SOUTH CAROLINA

Birmingham

Atlanta

Raleigh

76°

38°

34°

88°

84°

80°

Level III ecoregion—

Piedmont (Eastern 

temperate forest)

Regional synoptic

study site

EXPLANATION

0 50 100 MILES

0 50 100 KILOMETERS

Figure 5.9
Goal 3 91

Figure 32. Example of a Bayesian network model showing the prior predictive probabilities that a stream would have 

properties associated with each of the categories for each model node under high urban development. Probabilities are 

represented as percentages, numerically and graphically (horizontal colored bars represent percent probability for each 

category, factor, or tier) (modified from Kashuba and others, 2012).

1

2

3

4

5

6

1.19

5.69

13.62

30.48

37.66

11.36

Hydrology

(flashiness) Water chemistry

(specific conductance)

Habitat

(substrate)

Generic richness

(number of taxa)

Filter feeder 

(relative abundance)

Plecoptera + Ephemeroptera

(P+E)(relative abundance)

Biological Condition

Gradient (BCG)

Likelihood of

attainment (%)

BCG

Tier

Probability of

occurring (%) Probability of

occurring (%)

Probability of

occurring (%)

Probability of

occurring (%)

Probability of

occurring (%)

Probability of

occurring (%)

Factor

level

Factor

level

Factor

level

Factor

level

Factor

level

Factor

level

Fine

Coarse

23.30

76.70

Low

Medium

High

7.20

20.60

72.20

Low

Medium

High

10.00

40.00

50.00

Low

Medium

High

47.59

38.23

14.17

Low

Medium

High

30.18

41.00

28.82

Low

Medium

High

49.01

44.12

6.86

Urban

development

Development in

watershed (%)

Urban

 category 

Percentage of

watersheds

0-7

7-31

> 31

0.00

0.00

100.00

Low

Medium

High

Figure 5.10
92 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Partnerships for Goal 3

Goal 3 offers substantial opportunities for collaboration 

with other USGS programs and agencies. These partnerships 

are critical for achieving Goal 3 objectives outlined above. 

The following sections provide some specific examples of current or desired partnerships. 

USGS Mission Areas

The following USGS mission areas and programs are 

potential partners for Goal 3 of Cycle 3:

• Energy and Minerals, and Environmental Health 

Mission Area: The Toxic Substances Hydrology and 

Land use/cover

Nutrient

enrichment

Hydrologic

regime Temperature Water

quality

Substrate Productivity

Channel

hydraulics

Biotic integrity

Figure 33. Conceptual model for testing the effects of land use, 

habitat, and nutrients on biological integrity in an agricultural 

setting.

Invertebrate

community 

quality

Temperature,

degrees Celsius 

Water-surface

gradient

n = 54

Water quality,

dissolved Coarse

substrate

Base-flow

index 

Buffer percent

for wetland

Water quality,

particulate

Basin percent

cropland

-0.38

-0.47

0.44

0.19

n

0.51

-0.28

-0.47

0.63

0.19 -0.60

EXPLANATION

Negative correlation

Positive correlation

Number of sites

0.22

Figure 34. Example of a structural equation model of a coastal 

plain agricultural setting showing relations between land use 

(cropland, wetland buffer), habitat (substrate), water quality, 

and invertebrate community quality. Values shown are similar to 

correlation coefficients (modified from Riseng and others, 2011).

Contaminant Biology Programs are important collaborators for evaluating the effects of contaminants 

on ecosystems. NAWQA has begun discussions on 

how the programs can work together on topics such 

as methods development and combined studies that 

examine the effects of chemical stressors on aquatic 

organisms using laboratory and field methods. 

• Ecosystems Mission Area: Three programs within 

the Ecosystems Mission Area have potential for 

collaborative work with the NAWQA Program in 

Cycle 3. These programs are (1) Status and Trends of 

Biological Resources, (2) Terrestrial, Freshwater and 

Marine Environments (http://ecosystems.usgs.gov/

ecosystems/), and (3) Fisheries: Aquatic and Endangered Resources. Additional discussions are planned to 

assess collaborative opportunities. 

• Water Mission Area: A specific goal of the WaterSMART Program is to develop models and tools to 

evaluate the effects of streamflow on aquatic biota 

and developing methods for estimating ecologic flow 

requirements for different hydrologic and climatic 

settings. Cycle 3 streamflow-alteration studies are 

designed to enhance and complement planned work 

by the WaterSMART Program on ecologic flow issues. 

The National Research Program (NRP; http://water.

usgs.gov/nrp/) also conducts studies evaluating the 

effects of various stressors on aquatic ecoystems and 

will continue to be an important part of the NAWQA 

program in Cycle 3. 

• Climate and Land Use Change Mission Area: Activities within the Climate and Land Use Change Program 

(http://www.usgs.gov/climate_landuse/) are directly 

related to Cycle 3 NAWQA activities, especially 

mutual goals of assessing relations between land-use 

change and water-quality and biological conditions. 

Goals listed in the Climate and Land Use Change strategic science plan (Burkett and others, 2011) address 

how climate change will affect various water-quality 

and ecosystem stressors, such as streamflow and temperature, which have strong connections to NAWQA 

plans for Cycle 3. 

U.S. Environmental Protection Agency 

The USEPA is a potential partner for Goal 3 as described 

in the following bullets:

• USEPA National Aquatic Resource Surveys and 

Office of Research and Development: NAWQA has 

a long history of working with the USEPA National 

River and Streams Assessment (http://water.epa.gov/

type/rsl/monitoring/riverssurvey/index.cfm) and has 

collaboratively published with the USEPA on the biological condition of surface waters. This collaborative 

effort will continue in Cycle 3 in regards to all four 
Goal 3 93

of the stressors. NAWQA and USEPA are currently 

(2012) working on streamflow alteration as a major 

stressor of biological condition and on collaborating on 

the next USEPA National Aquatic Resource Survey of 

the Nation’s streams and rivers scheduled for 2013.

• USEPA Causal Analysis/Diagnosis Decision Information System (CADDIS) Program: The CADDIS 

Program (http://www.epa.gov/caddis/) assists scientists and engineers in the regions, states, and tribes to 

conduct causal assessments in aquatic systems. The 

CADDIS Program is based on identifying the dominant stressors within a stream or watershed for taking 

management action. Scientists within the CADDIS 

Program are very interested in collaborative efforts 

with NAWQA because of joint interest in identifying 

and understanding stressors in stream environments. 

Goal 4—Predict the Effects of 

Human Activities, Climate Change, 

and Management Strategies on 

Future Water-Quality and Ecosystem 

Condition

Goal 4 Outcome: Improved understanding of how human 

activities, climate change, and management strategies might 

affect water-quality and ecosystem condition in the future 

under different environmental scenarios.

Products

The following are planned products for Goal 4:

1. Models that predict how the use and management 

of land and water, together with climate change, are 

likely to affect future water-quality and ecosystem 

conditions.

2. Model-based decision-support tools for managers 

and policy makers to evaluate the effects of changes 

in climate and human activities on water quality 

and ecosystems at watershed, state, regional, and 

National scales.

3. Reports describing studies at selected watersheds 

that assess the potential effects of future climate and 

land-use change on water quality and ecosystem 

condition.

Connections to other NAWQA Cycle 3 Goals

The objectives, approaches, and products described in 

this section are tightly integrated with, and dependent on, the 

studies and assessments associated with the other goals. In 

Goal 1, data from NAWQA’s ongoing, long-term, monitoring of water quality will be used in assessments of temporal 

trends in water quality across the Nation. These water-quality 

data will be used to develop and evaluate the models used to 

understand historical trends (in Goal 2) and forecast future 

changes in water quality (Goal 4). Goal 2 is focused on 

developing understanding of the observed spatial patterns and 

temporal trends in water quality. Modeling tools developed to 

explain historical trends will be applied in Goal 4 to predict 

the effects of potential future changes in land use, water 

management, and climate on water-quality conditions (that is, 

stressors). In Goal 3, water-quality and hydrologic conditions 

that lead to degradation of stream ecosystems are to be identified and incorporated into regional ecological models. These 

models, which predict the effects of stressors on ecosystem 

condition, will be applied in Goal 4 to predict the effects of 

future land use, climate change, and management strategies 

on stream ecosystem conditions.

Background

NAWQA has been addressing three broad questions since 

the program started: “What is the current condition of the Nation’s 

water quality?,” “Has the quality of water been getting better or 

worse?,” and “What human or natural factors are responsible 

for current water-quality conditions?”. A critical next question is 

“How do we expect water quality to change in the future?” 

An example forecasting question is “How will nitrate in 

streams and public-supply wells change in the future under 

different scenarios of fertilizer use?” This question was 

addressed during Cycle 1 in southern New Jersey by using the 

groundwater-flow model MODFLOW and NAWQA waterquality data for streams and supply wells in the area (Kauffman and others, 2001). Simulations indicated a slow response 

in nitrate concentrations of streams and groundwater to 

changes in fertilizer use, even for a scenario where a total ban 

in fertilizer application is implemented (fig. 35). The example 

illustrates the importance of understanding the hydrologic 

system that governs the transport of nitrogen in both surface 

water and groundwater when making science-based forecasts. 

Continued development of such understanding is an important 

component of Cycle 3 studies.

Policy and Stakeholder Concerns Driving Key 

Management Questions

Forecasts of future water-quality and ecosystem conditions 

are essential information for policy makers and water managers. 

The primary factors that might cause future changes in water 

quality include changes in climate; population; land, water, 

and energy use; changes in water-use patterns or wastewater 

treatment technologies; regulatory changes; and management 

practices. In some cases—such as agricultural and urban best 

management practices—changes or implementation of these 
94 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

practices may result in improvements in water quality (for 

example, decreasing concentrations of pesticides and nutrients 

in streams). In other cases, increased demands on agricultural 

land uses to support food and energy requirements may yield 

increases in the concentrations and fluxes of agricultural chemicals, nutrients, and sediment to streams and rivers, adversely 

affecting stream quality and ecosystem condition. 

Predicting the effects of climate change on future water 

quality is one of the highest priorities among NAWQA’s 

stakeholders and is directly aligned with goals outlined 

in the science plan for the USGS Climate and Land Use 

Change Mission Area (Burkett and others, 2011). Changes 

in air temperature will affect water temperature and, thereby, 

also affect algal blooms, eutrophication, microbiological 

processes, and overall ecosystem condition. Precipitation 

and temperature affect streamflow which, in turn, affects 

many factors related to water quality. Increases in streamflow in areas experiencing wetter climate could dilute point 

sources of contaminants but also could increase erosion and 

downstream flux of sediment and sediment-bound contaminants. Decreases in streamflow in areas that become drier 

also would affect contaminant fluxes and concentrations. In 

addition, streamflow and temperature conditions are crucial 

components of the aquatic-ecosystem habitat, and changes 

in these physical features of the environment would likely 

affect biological condition. 

Examples of management questions related to forecasting 

include: 

• How will projected changes in climate, population, 

land use, water use, management actions, and other 

human activities affect water quality for future beneficial uses?

• Which strategies will most effectively improve and 

protect biological communities and stream ecosystem 

condition?

• Which management strategies are most cost effective?

• What are the expected lag times between implementation 

of management practices and beneficial outcomes?

• Is water quality more sensitive to changes in land use 

or climate?

NAWQA Progress During Cycles 1 and 2

Forecasting future water-quality conditions was not a 

program goal in Cycles 1 and 2, but NAWQA monitoring and 

studies during the first two cycles provide a strong foundation for addressing this goal in Cycle 3. The work in assessing 

status and trends, together with focused topical studies and 

development of models across a range of scales, has led to an 

improved understanding of how human activities and natural 

factors affect water quality in streams and aquifers. Forecasting future water-quality conditions requires that this understanding be integrated with predictions of how these factors 

and activities might change in the future.

The increased emphasis in Cycle 2 on the integration of 

monitoring with modeling led to the development of modeling 

tools and required ancillary datasets that will form the basis 

of the Cycle 3 forecasting approaches. For example, spatialextrapolation models that provide estimates of water-quality 

conditions in both streams and groundwater throughout the 

conterminous United States were developed or enhanced. 

Statistical relations between spatial variability in environmental factors and water-quality conditions form the basis of 

these models; some of these models (table 6) can be adapted to 

evaluate temporal changes in water conditions as environmental drivers such as climate and land use change over time.

The objectives of model applications in Cycles 1 

and 2 can be viewed in the context of the driver/stressor/

receptor conceptual model (fig. 36). Cycle 1 and 2 studies 

1940 1960 2000 2040 2080 2100

0

5

1

2

3

4

Historical input

1980 2020 2060

A. Streams B. Public-supply wells

Nitrate concentration, in milligrams per liter 

Year Year

1940 1960 2000 2040 2080 2100

Historical input

1980 2020 2060

Immediate ban

Gradual reduction

Fixed input

Fixed input

Gradual reduction

Immediate ban

Figure 35. Simulated nitrate concentrations in A, streams, and B, public-supply wells (Kauffman and others, 2001).
Goal 4 95

used process-based models such as MODFLOW (Harbaugh, 

2005), hybrid conceptual/regression/geospatial models such 

as WARP and SPARROW (Stone and Gilliom, 2009; Schwarz 

and others, 2006), and more conventional statistical models to 

assess how land use (a driver) affects the fluxes and concentrations of contaminants and nutrients (stressors) to human uses 

and aquatic ecosystems (receptors). The relevance of pesticide concentrations to human uses and aquatic ecosystems 

was determined by comparison to water-quality benchmarks 

developed by the USEPA, the USGS, and others. In addition, 

the effect of streamflow alteration and land use (for example, 

urbanization) on aquatic-ecosystem health was quantified with 

regression models.

Substantial progress also was made in development of 

Web-based decision-support tools. A “view and query” tool 

was constructed to enable users to explore and download 

input data and atrazine concentration predictions from WARP 

models. Also, a decision-support system (DSS) for national 

and regional SPARROW nutrient models is available at http://

cida.usgs.gov/sparrow/. The SPARROW DSS (Booth and 

others, 2011) provides functionality for user-controlled predictions, scenario testing, and regulatory assessment. The only 

software requirements for the DSS are an Internet connection 

and a Web browser.

NAWQA’s Role in Cycle 3

In Cycle 3, NAWQA will develop tools for waterresource managers and policy makers to forecast the effects of 

future changes in land use, water use, and climate on stressors 

and the suitability of water for human and aquatic-ecosystem 

needs as outlined in the following sections for the three objectives for Goal 4. These tools will be based on models and 

decision-support systems that have already been developed 

in the NAWQA Program. An important role for NAWQA is 

to evaluate which of the existing models are most suitable 

for estimating, with quantified uncertainty, changes over time 

in water-quality and ecosystem conditions due to changes in 

climate, land and water use, and management practices. In 

addition to the development of modeling tools, NAWQA will 

assess and report on the effects of changes in climate, land 

use, and water use on water-quality and ecosystem conditions 

at selected study areas. 

Objective 4a. Evaluate the Suitability of 

Existing Water-Quality Models and Enhance as 

Necessary for Predicting the Effects of Changes 

in Climate and Land Use on Water-Quality and 

Ecosystem Conditions

Appropriate NAWQA models, other USGS models, and 

established models developed by others will be used “as is” 

or will be enhanced to improve their utility for forecasting. 

Most existing NAWQA models provide only steady-state 

predictions of stressor or aquatic-ecosystem conditions based 

on steady-state factors. Some of these models can be modified 

so that they vary with time and, therefore, estimate transient 

conditions. Such dynamic representation of processes can 

yield more realistic predictions as a function of time. In addition, models may need to be modified to include representation 

of the variables expected to change in the future. 

The SPARROW model, for example, is a steady-state 

model that predicts mean-annual stressor flux throughout 

a river network as a function of sources applied to the land 

surface, land-to-stream delivery factors, and in-stream attenuation factors. In the SPARROW model for nitrogen (table 6), 

mean-annual nitrogen flux is a function of sources (including 

land use, fertilizer, atmospheric deposition, wastewater discharge), land-to-water delivery factors (precipitation, temperature, soil permeability, extent of tile drainage), and attenuation 

factors (in-stream decay). Regression coefficients that represent the strength of the delivery and attenuation factors are 

determined through calibration of model-estimated fluxes to 

measured fluxes at or near streamgages. After the model has 

been calibrated, scenarios of changes in land use or management practices can be evaluated by increasing or decreasing 

specific sources or delivery factors. Results from this type of 

model application indicate the long-term, steady-state effect of 

a specified land-use or management change. This type of scenario application, however, does not provide any information 

about the lag time between a change in land-use management 

and its subsequent effect on water quality.

Many of the existing NAWQA models, including SPARROW and WARP (table 6), are calibrated to match the spatial 

pattern of water quality measured in a monitoring network 

across a broad geographic area. The calibrated model coefficients reflect the spatial pattern, not the temporal patterns, 

of the monitoring data and the explanatory variables. Using 

a spatial model to represent changes over time is valid only 

if temporal variations in the forcing variables have the same 

effect as spatial differences. This restriction does not apply to 

a dynamic model; therefore, one of the objectives in Goal 2 in 

Cycle 3 is to develop transient versions of SPARROW models. 

This would require adding storage compartments to the models that can “hold and release” target chemicals or constituents 

(such as nutrients or sediment) and also require specifying 

input time series, such as monthly or seasonal values, for 

fluxes of water and chemicals.

Certain non-transient models also may be used to evaluate temporal changes in water quality due to changes in land 

or water use. For example, the steady-state version of MODFLOW (table 6) predicts spatial patterns of flow paths and 

statistical distributions of traveltimes; these variables can be 

used to evaluate time lags required for a change at the land 

surface (such as fertilizer application) to propagate through 

the system and provides the capability to generate forecasts of 

future conditions (fig. 35). 

NAWQA models that will be used to forecast future 

stressor and aquatic-ecosystem conditions in response 
96 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Figure 36. Conceptual model of the connections between environmental drivers, stressors, and receptors.

Stressors Contaminants Nutrients Sediment

Receptors

Streamflow

alteration

Human

health

Aquatic

ecosystems

Climate and

other natural

factors

Population

growth, land

and water use

Drivers

Table 6. Water-quality models to be used in Cycle 3 for prediction and forecasting.

[Nutrients include nitrogen, phosphorous, and carbon]

Model Model type Factors Stressors Receptors Water resource

MODFLOW a Process Climate, land use Contaminants Human needs Groundwater

b SPARROW Geospatial/process/ Population growth, climate, 

statistical land and water use Nutrients, sediment Aquatic ecosystems Streams and rivers

WARP c Geospatial/statistical Climate, land use Contaminants Aquatic ecosystems, 

human needs Streams and rivers

d RZWQM2 Process Climate, land and water use Contaminants Human needs Shallow groundwater

Generic Population growth, climate, Statistical land and water use

Streamflow alteration, 

contaminants, nutrients

Aquatic ecosystems, 

human needs

Streams and rivers, 

shallow groundwater

a Harbaugh, 2005, (http://water.usgs.gov/nrp/gwsoftware/modflow.html).

b Schwarz and others, 2006, (http://water.usgs.gov/nawqa/sparrow/).

c

 Stone and Gilliom, 2009, (http://infotrek.er.usgs.gov/warp/).

d

 Ma and others, 2012, (http://www.ars.usda.gov/Main/docs.htm?docid=17740).

to changes in climate and land use require the following 

characteristics:

• Applicability at a regional and/or national scale;

• Explanatory or input variables that represent 

environmental drivers or stressors;

• Dependent variables that represent stressors or 

receptors; and

• Quantifiable uncertainty.

Descriptions of these models, the evaluation approach, and 

enhancements are given in the sections on Goals 2 and 3 of 

this report.
Goal 4 97

Objective 4b. Develop Decision-Support Tools 

for Managers, Policy Makers, and Scientists 

to Evaluate the Effects of Changes in Climate 

and Human Activities on Water Quality and 

Ecosystems at Watershed, State, Regional, and 

National Scales

One of the primary Goal 4 products is model-based, decision-support tools for scientists, managers, and policy makers. 

A Web-based DSS and the underlying software that supports 

it has been developed to provide access to NAWQA models 

of stream water-quality conditions and to offer sophisticated 

scenario-testing capabilities for research and water-quality 

planning through a graphical user interface (http://cida.usgs.

gov/sparrow/). The DSS (Booth and others, 2011) is provided 

through a Web browser over an Internet connection, making 

it widely accessible to the public in a format that allows users 

to easily display water-quality conditions and to describe, test, 

and share simulated scenarios of future conditions and to generate maps illustrating model predictions at various scales. 

The DSS and underlying software framework are intended 

to make running sophisticated model simulations easier by 

combining familiar Web site user interface controls with a 

powerful computer server infrastructure. This paradigm places 

new capabilities in the hands of decisionmakers and waterquality planners and managers in ways that previously were 

not available. The DSS takes advantage of innovations in the 

information technology field that allow for a flexible and robust 

Web-based decision-support framework for most NAWQA 

models. The DSS removes desktop software dependencies, 

simplifies scenario testing, and provides a map interface.

Some of the functionality of a DSS is illustrated by the 

preliminary SPARROW sediment model for the conterminous 

United States (Schwarz, 2008), which has been incorporated in 

a graphical system for viewing, querying, and scenario testing 

developed by the USGS Center for Integrated Data Analysis 

(http://cida.usgs.gov/) (figs 37–41). Through the user’s Web 

browser, maps of model results—such as the total suspended 

sediment load in streams and rivers (fig. 37) and the mass 

per unit area delivered to the stream from individual areas 

(fig. 38)—are displayed.

The SPARROW DSS can be used to generate tables summarizing the sources of stressor loads, for example, estimated 

sources of suspended sediment at the downstream end of the 

Kansas River (fig. 39). This specific river reach was selected 

by using the pan and zoom features of the DSS. The table 

can be viewed through the user’s Web browser and includes 

several tabs of information. The model results indicate that the 

primary source of sediment in the basin is agricultural (crop/

pasture) land (fig. 39).

User-controlled scenarios of changes in sources can be 

evaluated in the DSS. The Trinity River in Texas is displayed 

on the map with the Dallas metropolitan area and Lake Livingston (fig. 40). This lake is used for recreation and water 

supply for Houston.

Mean annual sediment load flowing into Lake Livingston 

estimated by using the SPARROW model is about 5 million 

tons per year. The model indicates that almost one-half of 

the load originates in urban areas (see the blue section of the 

upper pie chart in fig. 41).

The DSS can be used to evaluate scenarios of land-use 

change. For illustration, a prescribed scenario of a 50-percent 

decrease in sediment transported from urban land in the 

upper Trinity River Basin—assumed to result from sediment 

control measures—was evaluated in terms of its effect on 

sediment delivery to Lake Livingston. This scenario resulted 

in a 22-percent decrease in urban sources of sediment to Lake 

Livingston but only an 11-percent decrease in total sediment 

flux to the lake. It should be noted that this type of analysis 

does not consider the elapsed time between implementation 

of management practices and desired outcomes. The length of 

this lag time can be many years.

Currently, the DSS offered on the NAWQA website 

includes only steady-state river water-quality models: SPARROW nutrient and sediment models and the WARP atrazine 

model. The most crucial enhancements to the DSS for Cycle 3 

are (1) support of additional models, (2) explicit depiction of 

predictive reliability and uncertainty, and (3) seamless access 

to land-use and climate change scenarios.

Enhancements for the support of additional models 

include

• Models previously developed by NAWQA (table 6) 

with enhancements for prediction and forecasting;

• New SPARROW models for carbon, temperature, 

dissolved oxygen, pesticides, and salinity; and

• Models developed and supported outside of the 

NAWQA Program, such as PRMS (Leavesley and others, 1983) and SWAT (Neitsch and others, 2005), that 

provide functionality unavailable in NAWQA models.

Predictive reliability enhancements include quantification of model reliability, which is crucial for meaningful 

model predictions. Placing model predictions within a reliability/uncertainty context is essential to avoid overconfidence or misinterpretation by the DSS user. Approaches for 

quantifying predictive reliability are described in the sections 

on Goals 2 and 3.

Seamless access to climate and land-use change scenarios 

will involve two USGS projects (the Center for Integrated 

Data Analysis and the Modeling of Watershed Systems Project

that are collaborating to develop seamless access to a variety 

of climate and land-use change scenarios. The term “seamless” 

indicates that a user accessing the DSS website through the 

Internet would be able to choose, in an intuitive and straightforward way, both a change scenario and model to evaluate 

the effects of climate or land-use changes on water-quality and 

aquatic-ecosystem conditions. Climate and land-use change 

scenarios are constantly evolving, and several sources of scenarios that could provide the basis for transient water-quality 

or ecological models are listed in table 7.
98 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Figure 37. Total suspended sediment load estimated by using the SPARROW model from Schwarz (2008). (kg, kilograms; year –1, per 

year) 

Figure 38. Estimated yield of sediment transported to streams and rivers from catchments, expressed on a per unit area basis, by 

using the SPARROW model from Schwarz (2008). (kg, kilograms; km–2, square kilometers; year –1, per year) 

Figure 6.3

EXPLANATION

Total Load

kg-year –1 of Suspended Sediment

3×106 to 9×106

9×106

 to 28×106

28×106

 to 131×106

> 131×106

< 3×106

N

EXPLANATION

Incremental Yield

kg-km–1-yr –1 of Suspended Sediment

31×103 to 58×103

58×103

 to 103×103

103×103

 to 197×103

> 197×103

< 31×103

N
Goal 4 99

Figure 40. Total sediment load in streams and rivers in south-central Texas overlaid on land-use 

classes. The land-use categories shown are urban (red), agriculture (yellow), forest (green), and 

water (blue). Lake Livingston is used as a water supply for Houston. (kg, kilograms; year –1, per year)

Figure 39. Sources of sediment in the Kansas 

River Basin estimated using the SPARROW 

Decision Support System (http://cida.usgs.gov/

sparrow/). (kg, kilograms)

Sources

Total Load by Source (billions of kg/year)

Share of Total Suspended Sediment Load by Source

Urban land

Federal land

Other land

Forested land

Crop/pasture land

Reach length

0

1.0

2.0

3.0

4.0

5.0

48.2%

3.3%

0.2%

6.3%

15.7%

26.2%

Dallas

Lake

Livingston

EXPLANATION

Total Load

kg-year –1 of Suspended Sediment

3×106 to 9×106

9×106

 to 28×106

28×106

 to 131×106

> 131×106

< 3×106

N
100 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Sources

Total Suspended Sediment Load by Source (billions of kg/year)

Share of Total Suspended Sediment Load by Source − Original

Share of Total Suspended Sediment Load by Source − Adjusted

Urban land

Federal land

Other land

Forested land

Crop/pasture land

Reach length

0

0.25

0.50

0.75

1.25

1.50

1.75

2.00

2.25

2.50

2.75

31.4%

0.9%

0.5%

47.8%

6.8%

12.6%

35.2%

1%

0.5%

41.5%

7.7%

14.1%

Original Adjusted Original Adjusted

Figure 41. Sources of sediment in the Trinity River basin upstream 

of Livingston Lake estimated using the SPARROW Decision Support 

System (http://cida.usgs.gov/sparrow/). (kg, kilograms). Source loads 

for two scenarios are shown: Original (Orig.) indicating no adjustment to 

sediment transport and Adjusted (Adj.) in which sediment transport from 

urban land in the Upper Trinity River Basin is decreased by 50-percent. 

Comparison between the original and adjusted scenarios is depicted in 

two ways. The bar chart shows differences between the two scenarios 

in the estimated mass of sediment per year delivered to the lake. The 

pie charts show the same information expressed as percentages or 

“shares” of the total suspended sediment load.
Goal 4 101

The WARP web-mapper, (http://infotrek.er.usgs.gov/

warp/), illustrates how model reliability information can be 

included in a decision-support tool. Figure 42 shows WARP 

predictions of annual mean atrazine concentration estimated 

for rivers and streams in the conterminous United States. 

The regression analysis that WARP predictions are based on 

also estimates model reliability/uncertainty metrics for the 

pesticide concentration predictions. If a meaningful contaminant concentration threshold—such as a human-health 

benchmark—is available, then the probability of exceeding 

the threshold can be estimated. Figure 43 shows such a map 

of exceedance probabilities for WARP-estimates of annual 

mean atrazine concentrations in the context of a threshold 

of 3 micrograms per liter, which is the USEPA Maximum 

Contaminant Level for atrazine (http://water.epa.gov/drink/

contaminants/index.cfm). 

Objective 4c. Predict the Physical and Chemical 

Water-Quality and Ecosystem Conditions 

Expected to Result from Future Changes in 

Climate and Land Use for Selected Watersheds

In addition to providing models (Objective 4b) and associated decision-support systems (Objective 4c), NAWQA will 

complete selected studies in high priority areas (table 8) of the 

potential effects of climate, land-use, and water-use changes 

on water quality and ecosystems. Within each study area, the 

study will focus on a crucial issue that will be identified by 

one of NAWQA’s partners.

A brief hypothetical study is described in the following 

section to illustrate how NAWQA could forecast the effects of 

both climate and land-use change on water quality. 

Hypothetical Study in Chesapeake Bay

The objective of this hypothetical study is to evaluate the 

potential effects of climate and land-use change on the transport of nutrients to the Chesapeake Bay, which is the largest 

estuary in the United States. Chesapeake Bay borders Delaware, Maryland and Virginia. The general approach would 

be adapted to the individual study area. The brief description 

of the hypothetical study illustrates how NAWQA and its 

partners could forecast the effects of both climate and land-use 

change on water quality.

The Chesapeake Bay watershed SPARROW model would 

be used with climate and land-use change scenarios to estimate potential future nutrient loads to the bay. The following 

steps outline the approach for this hypothetical example:

1. The steady-state version of the Chesapeake 

SPARROW nutrient model serves as the baseline 

condition. 

Table 7. Scenarios for forecasting changes in land use and climate.

Climate-change scenarios

Global climate models (GCMs) have been constructed at many universities and agencies around the world; National Oceanic and 

Atmospheric Administration, (http://data1.gfdl.noaa.gov/) and National Aeronaturic and Space Administration, (http://www.giss.nasa.

gov/projects/gcm/) are examples of agencies actively producing GCM simulations. GCMs are downscaled (the spatial resolution of the 

climate predictions is enhanced) using approaches developed at the Bureau of Reclamation, U.S. Geological Survey (USGS), Texas Tech 

University, and Penn State University.

Paleoclimate reconstructions of decadal-to-multidecadal (D2M) ocean climate modes can be used to estimate probability distribution functions of future shifts in climate and streamflow. Examples of D2M climate indices are the Pacific Decadal Oscillation (PDO) and the 

Atlantic Multidecadal Oscillation (AMO). Measurement of current and recent climate indices enables a probabilistic forecast of future 

ocean climate regimes and associated continental climate and streamflow condition.

Land-cover change scenarios

Several Federal agencies and research institutions are developing methods to generate scenarios of future land-cover change. The USGS 

is supporting land-cover modeling projects including the National Land-Change Community Modeling System (http://egsc.usgs.gov/

currentscienceprojects.html), the National Ecosystem Assessment and Forecasting Consortium, the Land Cover Dynamics and Environmental Processes Project (http://egsc.usgs.gov/dynamicsandprocesses.html), the Land Cover Trends Project (http://landcovertrends.usgs.

gov/), and Project Gigalopolis (http://www.ncgia.ucsb.edu/projects/gig/). The U.S. Environmental Protection Agency is estimating future 

land cover in its Future Midwestern Landscapes Study (http://www.epa.gov/AMD/Research/Ecosystems/Exposure_Application_Studies/

fml.html), and the U.S. Department of Agriculture (USDA) is generating future agricultural land-use scenarios (http://www.srs.fs.usda.

gov/pubs/39404).

Economic (cost-benefit) considerations in forecasting

Economic analyses can be an important component of forecasting the effects of climate and land-use change on water resources for human 

and ecosystem needs. Examples of such analyses would include: an evaluation of the costs and benefits of implementing agricultural best 

management practices or an economic assessment of costs associated with water-quality degradation due to climate change. NAWQA will 

continue to collaborate with economists from the organization Resources for the Future (http://rff.org/Pages/default.aspx) and the USDA 

Economic Research Service (http://www.ers.usda.gov/) to obtain necessary technical support. 
102 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

Figure 42. Estimated annual mean atrazine concentration for conterminous U.S. streams based on 2007 atrazine use. The highest 

atrazine concentrations are shown in red and the lowest concentrations are dark blue. Only streams with substantial agriculture use in 

their drainage basins are shown.

Figure 43. Probability that the estimated annual mean atrazine concentration exceeds 3 micrograms per liter. This Maximum 

Contaminant Level is a water-quality benchmark established by the U.S. Environmental Protection Agency for public drinking-water 

supplies.

Figure 6.8

N

Model Estimate Unavailable

< 0.001

0.001–0.038

0.039–0.150

0.151–1.026

> 1.026

EXPLANATION

Based on estimated 2007 Atrazine use

N

Model Estimate Unavailable

< 0.001

0.001–0.038

0.039–0.150

0.151–1.026

EXPLANATION

Based on estimated 2007 Atrazine use
Goal 4 103

Table 8. Potential climate and land-use change effects study areas. Note that additional study areas are likely to be added.

Watershed study areas Primary partnerships

Chesapeake Bay U.S. Geological Survey Chesapeake Bay Program.

Mississippi River Gulf of Mexico Watershed Nutrient Task Force, Louisiana Universities Marine Consortium.

Delaware River WaterSMART

Colorado River WaterSMART

Apalachicola-Chattahoochee-Flint Rivers WaterSMART

Great Lakes Great Lakes Restoration Initiative, Great Lakes Commission

2. A land-cover change scenario for the Chesapeake 

Bay watershed, selected by the Chesapeake Bay 

Program, is used to alter the land-cover dependent 

inputs to the baseline model. The baseline model 

is then rerun to simulate stream nutrient loads for 

future land-cover conditions. 

3. A climate-change scenario also selected by the 

Chesapeake Bay Program is input to a water-balance 

model to estimate future streamflows throughout the 

watershed. The estimated flows are used to estimate 

future nutrient loads at existing monitoring sites, 

and the estimated future nutrient loads are used to 

calibrate a new steady-state SPARROW nutrient 

model. This model simulates stream nutrient loads 

for future climate conditions but present-day source 

conditions.

4. The land-cover change scenario is used to alter the 

land-cover dependent inputs to the model developed in step 3, and that model is rerun to simulate 

nutrient loads under future land-cover and climate 

conditions.

5. SPARROW results from the three change scenarios 

and the baseline condition are compared to infer the 

relative effects of climate and land-use change on 

nutrient loads to the Bay.

The approach described above uses a steady-state version 

of the SPARROW model, not a transient version. The results 

do not describe the lag time between changes in land use 

and changes in water quality; that lag time is expected to be 

on the order of a decade or so based on age-dating analyses 

indicating typical traveltimes of water from the land surface 

through subsurface flow paths to streams and rivers is about 

10 yr (Denver and others, 2010), or in the case of sediment or 

sediment-bound contaminants, possibly much longer. Thus, 

model simulations using land-cover and climate projections 

for the year 2030 may be predictive of stream-nutrient loads 

expected to occur in 2040 or later. 

Potential products for this hypothetical example would be 

determined by the Chesapeake Bay Program and would likely 

include a report and Web-accessible output from the model in 

the form of data and maps.

Partnerships for Goal 4

Activities related to forecasting future water-quality 

conditions are being conducted by several USGS programs 

and Federal agencies. Like the NAWQA Program, a few of 

these efforts involve developing the capability to predict the 

effects of climate and land-use change on water-quality and 

ecosystem conditions. To not be redundant it is crucial for 

Cycle 3 activities to complement and not duplicate these other 

efforts. This requires that NAWQA partner and plan with the 

programs and agencies listed below. 

USGS Mission Areas

The following USGS mission areas are potential partners 

for Goal 4 of Cycle 3:

• Climate and Land Use Change Mission Area: 

Forecasting the effects of climate and land-use 

change on water-quality and ecosystem conditions is 

clearly aligned with this mission area. Examples of 

complementary goals include carbon sequestration, 

monitoring water quality and quantity, understanding 

and simulating the effects of climate and land-cover 

changes on ecosystems and other natural resources, 

geographic analysis and monitoring, and science 

applications and decision support. These are further 

described in the following bullets:

• Model effects of climate change on water 

quality and aquatic ecosystems: The U.S. 

Climate Change Science Program oversees 

the U.S. Global Change Research Program 

(http://www.globalchange.gov/) and the 

President’s Climate Change Research Initiative 

(http://www.climatescience.gov/about/ccri.htm). 

These federally supported programs include a 

variety of activities related to forecasting changes 

in water quality. Some of the planned activities 

include long-term streamflow monitoring to detect 

effects of climate and land-use change on waterquality and aquatic-ecosystem conditions, integration of global climate models with ecological 
104 Design of Cycle 3 of the (NAWQA) Program, 2013–23: Part 2: Science Plan

habitat models to develop management response 

options in the context of a changing climate, and an 

assessment of the potential of carbon sequestration 

to mitigate climate change.

• Forecast effects of urban growth, future urban 

planning scenarios, and resulting land-cover 

change in urban areas on water quality and stream 

ecosystems: The long-term goal of the USGS Urban 

Dynamics Program /University of California at 

Santa Barbara’s Project Gigalopolis (http://www.

ncgia.ucsb.edu/projects/gig/) is to predict urban 

growth patterns on a regional and continental scale 

to guide both local and regional community planners in achieving sustainable urban growth. Recent 

modeling work incorporates land-conservation 

scenarios in the coupled models of urban growth and 

land-use change, creating a set of scenarios that can 

be used to experiment with alternative futures. The 

goal of the collaboration would be to link NAWQA 

models that relate urban land cover to stream ecological effects with Project Gigalopolis forecasts of 

land cover under different scenarios of urban growth 

and urban land planning and conservation. 

• Water Mission Area: NAWQA’s goal is to be a leading 

source of scientific information for the development 

of effective policies and management strategies by 

providing objective and reliable data, water-quality 

models, and scientific studies that characterize where, 

when, how, and why the Nation’s water quality is 

degraded, and what can be done to improve and protect 

it. The model-based decision-support tools developed 

in Goal 4 will deliver scientific information directly to 

the water-quality policy makers and managers and will 

aid in analysis and decisionmaking. This goal is clearly 

aligned with the Water Mission Area. Goals of other 

Water programs that complement Goal 4 include:

• Forecasting availability of water: A goal of the 

WaterSMART Program is to develop an improved 

ability to forecast the availability of water for future 

human, economic, and environmental uses. The program includes a systematic examination of the ecological effects of flow alteration and definition of the 

flow alteration (ecological response relations for the 

various types of streams). The goal of the collaboration with WaterSMART would be to link NAWQA 

models that predict the severity of flow alteration to 

Water Census studies that relate ecological effects to 

degree of flow alteration; and

• Couple water-quality models with USGS watershed 

models: The USGS National Research Program 

project Modeling of Watershed Systems (MOWS; 

http://wwwbrr.cr.usgs.gov/projects/SW_MoWS/index.

html) is designed to develop and support hydrologic simulation models at the watershed scale and 

currently is involved in simulating the effects of 

climate and land-use changes on flow in streams and 

groundwater. In addition, the MOWS project will 

serve as a central distribution point for climate and 

land-use change scenarios produced by the USGS 

and other agencies. Linking MOWS model output 

and NAWQA models of water-quality and ecosystem 

conditions will facilitate forecasting water-quality 

and ecosystem conditions for MOWS-generated 

scenarios.

External Partnerships

The external agencies and organizations described in 

the following subsections are potential partners for Goal 4 of 

Cycle 3.

U.S. Department of Agriculture

The following are potential areas of collaboration 

between NAWQA and the USDA:

• Assessing the effects of biofuel development on water 

quality: The USDA is estimating the effects of biofuel 

development in the Midwest by coupling scenarios 

of land use and cropping patterns with a watershed 

model. These forecasts will show how increasing corn 

acreage and associated agricultural chemical use could 

affect nutrient and pesticide concentrations in streams; 

and 

• Evaluating the effects of agricultural management 

practices on water quality: Through its Conservation 

Effects Assessment Project (http://www.nrcs.usda.gov/

wps/portal/nrcs/main/national/technical/nra/ceap), 

the USDA is quantifying the effects of conservation 

practices and programs on the environmental quality 

of agricultural landscapes. The Conservation Effects 

Assessment Project includes both monitoring and 

modeling projects at watershed and national scales. 

Recently (2012), the USDA released a description of a 

modeling study for the Upper Mississippi River Basin 

that focused on the effects of conservation practices 

on sediment, nutrient, and pesticide losses from farm 

fields (http://www.nrcs.usda.gov/wps/portal/nrcs/detail/

national/technical/nra/ceap/?cid=nrcs143_014161). 

U.S. Environmental Protection Agency

The following is a potential areas of collaboration 

between NAWQA and USEPA:

• Model response of water-quality to clean air 

regulation: The NAWQA Program and USEPA can 

potentially collaborate on a model of water-quality 

response to clean air regulation. Through ongoing 

development of secondary standards for nitrogen 

dioxide and sulfur dioxide, USEPA is assessing 
References Cited 105

the relation between regulatory emission control 

scenarios for nitric oxide and nitrogen dioxide, air 

quality, atmospheric nitrogen deposition, and nutrient 

enrichment of aquatic ecosystems. The Community 

Multiscale Air Quality modeling system (http://www.

epa.gov/AMD/Research/RIA/cmaq.html), developed 

by USEPA and NOAA, links emission-control scenarios to predictions of atmospheric nitrogen deposition. Identifying the levels of emission control that 

result in restoring healthy ecosystems in nitrogensensitive aquatic resources is of particular interest 

to the USEPA and the NAWQA Program. The goal 

of the collaboration would be to link the predictions 

from the Community Multiscale Air Quality modeling system with NAWQA models (SPARROW) that 

predict nitrogen inflows to nitrogen-sensitive aquatic 

resources to identify levels of emission control that 

result in restoring healthy ecosystems.

National Oceanic and Atmospheric Administration

The following are potential areas of collaboration 

between NAWQA and NOAA:

• Forecast water-quality at National Weather Service 

forecast sites: As part of NOAA’s Next Generation 

Strategic Plan (http://www.ppi.noaa.gov/ngsp/), 

NOAA proposes to pilot short-term (hours to days) 

water-quality forecasting at existing National Weather 

Service forecast sites. In this pilot program, the Office 

of Hydrologic Development (http://www.nws.noaa.

gov/oh/) will produce a system for forecasting temperature to assist fisheries management. 

• Forecast nutrient delivery to estuaries: Within 

NOAA’s Coastal Hypoxia Research Program (http://

www.cop.noaa.gov/stressors/pollution/current/chrp/

default.aspx), the USGS, Smithsonian Environmental 

Research Center, University of Michigan, and Cornell University have developed models to predict the 

effects of land-use and climate change on delivery of 

nutrients to estuaries.

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