National Water Quality Inventory: 

 Report to Congress 

2004 Reporting Cycle 

January 2009 

United States Environmental Protection Agency 

Office of Water 

Washington, DC 20460 

EPA 841-R-08-001 
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National Water Quality Inventory: 2004 Report to Congress 

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Table of Contents 

Section Page 

List of Figures..............................................................................................................................................iv

List of Tables ...............................................................................................................................................iv

List of Acronyms ..........................................................................................................................................v

Executive Summary ......................................................................................................................................1

I. Background ............................................................................................................................................5

About the Water Quality Assessment and TMDL Information Database (ATTAINS) ..................5

Assessing Water Quality .................................................................................................................7

II. Findings................................................................................................................................................13

Rivers and Streams........................................................................................................................13

Lakes, Ponds, and Reservoirs........................................................................................................16

Bays and Estuaries.........................................................................................................................20

Other Waters .................................................................................................................................23

Coastal Resources .............................................................................................................23

Great Lakes.......................................................................................................................24

Wetlands ...........................................................................................................................24

III. Probability Surveys of Water Quality ..................................................................................................26

National Coastal Assessment ........................................................................................................26

The Wadeable Streams Assessment ..............................................................................................27

Survey of the Nation’s Lakes ........................................................................................................29

National Rivers and Streams Assessment .....................................................................................30

National Wetland Condition Assessment......................................................................................30

State-Scale Statistical Surveys ......................................................................................................31

South Carolina ..................................................................................................................32

Indiana ..............................................................................................................................33

Florida...............................................................................................................................34

IV. Future Reporting...................................................................................................................................36 

V. References...........................................................................................................37 
National Water Quality Inventory: 2004 Report to Congress 

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List of Figures 

Figure Page 

1 Water quality in assessed river and stream miles..............................................................................13

2 Top 10 causes of impairment in assessed rivers and streams............................................................15

3 Top 10 sources of impairment in assessed rivers and streams. .........................................................16

4 Water quality in assessed lake acres. ................................................................................................17

5 Top 10 causes of impairment in assessed lakes, ponds, and reservoirs. ...........................................18

6 Top 10 sources of impairment in assessed lakes, ponds, and reservoirs...........................................19

7 Water quality in assessed bay and estuary square miles ...................................................................20

8 Top 10 causes of impairment in assessed bays and estuaries............................................................22

9 Top 10 sources of impairment in assessed bays and estuaries. .........................................................23

10 Findings of the National Coastal Condition Report III. ...................................................................27

11 Biological quality of the nation’s streams.........................................................................................28

12 Extent of streams rated poor for aquatic stressors, and increase in risk of poor biology in 

streams rated poor over streams rated good for each stressor...........................................................28 

13 Sampling locations for the survey of the nation’s lakes....................................................................29

14 Sampling locations for the national rivers and streams assessment..................................................30

15 Summary of statewide condition for Florida rivers and streams (left) and large lakes (right) 

(source: Integrated Water Quality Assessment for Florida: 2004 (FL DEP). ...................................34

List of Tables 

Table Page 

1 Major Impairment Cause Categories Used in this Report...................................................................9

2 Major Pollutant Source Categories Used in this Report....................................................................10

3 Individual Use Support in Assessed River and Stream Miles...........................................................14

4 Individual Use Support in Assessed Lake, Reservoir, and Pond Acres ............................................17

5 Individual Use Support in Assessed Bay and Estuary Square Miles ................................................21

6 Traditional vs. Probability-based Assessment Results for Rivers and Streams in South 

Carolina.............................................................................................................................................33

7 Traditional vs. Probability-based Assessment Results for Estuaries in South Carolina ...................33
National Water Quality Inventory: 2004 Report to Congress 

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List of Acronyms 

ATTAINS Assessment TMDL Tracking And ImplementatioN System (Water Quality 

Assessment and TMDL Information) 

BEACH Act Beaches Environmental Assessment and Coastal Health Act of 2000 

DIN dissolved inorganic nitrogen 

DIP dissolved inorganic phosphorus 

EPA U.S. Environmental Protection Agency 

FWS U.S. Fish and Wildlife Service 

IBI Index of Biotic Integrity 

NOAA National Oceanic and Atmospheric Administration 

NPS National Park Service 

PAHs polycyclic aromatic hydrocarbons 

PCBs polychlorinated biphenyls 

TMDL total maximum daily load 

USGS U.S. Geological Survey 
National Water Quality Inventory: 2004 Report to Congress 

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National Water Quality Inventory: 2004 Report to Congress 

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Executive Summary 

This National Water Quality Inventory: 2004 Report to Congress, prepared under section 

305(b) of the Clean Water Act, summarizes water quality reports submitted electronically by 44 

states, 2 territories, and the District of Columbia to the U.S. Environmental Protection Agency 

(EPA) for the 2004 reporting cycle. These state water quality assessment findings are contained 

in EPA’s Water Quality Assessment 

and Total Maximum Daily Load 

(TMDL) Information database and 

website, known as ATTAINS 

(Assessment TMDL Tracking And 

ImplementatioN System), for the 

2004 reporting cycle. The ATTAINS 

database is available online at the 

website http://www.epa.gov/waters/ir. 

Summary findings of the 2004 

state water quality reports are 

presented below. It is important to 

note that this information is for a 

relatively small subset of the nation’s 

total waters which may not be 

representative of the waters that were 

not assessed. Because many states 

target their limited monitoring 

resources to waters that they suspect are impaired, there may be a lower percentage of impaired 

waters among the non-assessed (and total) waters than among the assessed waters. Information 

about specific sources and causes of impairment is incomplete because the states do not always 

report the cause or source of pollution affecting every impaired waterbody. In some cases, states 

may recognize that water quality does not fully support a designated use; however, they may not 

have adequate data to document the specific pollutant or source responsible for the impairment. 

EPA also made changes in how specific causes and sources are categorized for 2004, and these 

changes in some cases affect how the findings of causes and sources of impairment compare to 

findings of previous years. Readers are urged to consult the ATTAINS website for detailed 

listings of the causes and sources of impairment reported by states. 

Rivers and Streams 

This report includes states’ assessments of 16% of the nation’s 3.5 million miles of rivers 

and streams for the 2004 reporting cycle. Of these waterbodies, 44% were reported as impaired 

or not clean enough to support their designated uses, such as fishing and swimming. States found 

the remaining 56% to be fully supporting all assessed uses. Pathogens, habitat alterations, and 

organic enrichment/oxygen depletion were cited as the leading causes of impairment in rivers 

and streams, and top sources of impairment included agricultural activities, hydrologic 

modifications (such as water diversions and channelization), and unknown/unspecified sources. 

EPA developed the Assessment TMDL Tracking And 

ImplementatioN System (ATTAINS) database and website 

to combine two formerly separate sites — the National 

Assessment Database (for 305(b) water quality 

assessment information) and the National Total Maximum 

Daily Loads (TMDL) Tracking System (for 303(d) impaired 

waters information). The ATTAINS database/website 

includes state-reported assessment decisions on the 

support of designated uses (such as recreation) in 

assessed waters; the waters that are impaired; the causes 

of impairment (such as pathogens); the sources of 

impairment (such as agriculture); and the status of actions 

(TMDLs) to help restore impaired waters. 

ATTAINS contains this information for each waterbody 

assessed by the states and summarizes key waterbody 

information by state, by region, and nationally. If a state 

did not provide waterbody-specific information 

electronically to EPA by the reporting deadline, it was not 

included in this report. EPA worked extensively with the 

states to assist in data submittal. 
National Water Quality Inventory: 2004 Report to Congress 

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Lakes and Reservoirs 

This report includes states’ assessments of 39% of the nation’s 41.7 million acres of 

lakes, ponds, and reservoirs during the 2004 reporting cycle. Of these waterbodies, 64% were 

reported as impaired and 36% were fully supporting all assessed uses. Mercury, polychlorinated 

biphenyls (PCBs), and nutrients were cited as the leading causes of impairment in lakes. Top 

sources of pollutants to lakes, ponds, and reservoirs included atmospheric deposition, 

unknown/unspecified sources, and agriculture. 

Bays and Estuaries 

This report includes states’ assessments of 29% of the nation’s 87,791 square miles of 

bays and estuaries for the 2004 reporting cycle. Of these assessed waterbodies, 30% were 

reported as impaired, and the remaining 70% fully supported all assessed uses. Pathogens, 

organic enrichment/oxygen depletion, and mercury were reported as the leading causes of 

impairment in bays and estuaries. Top sources of impairment to bays and estuaries included 

atmospheric deposition, unknown/unspecified sources, and municipal discharges/sewage. 

Probability Studies of Water Quality 

EPA and states have embarked on a series of probability-based surveys that are discussed 

later in this report. Probability-based surveys complement more traditional targeted monitoring 

and assessment programs and add substantially to our understanding of state, regional, and 

national water quality conditions. These studies select sites at random to provide estimates of the 

condition of a population of waters throughout a state, region, or the nation. They describe the 

percent of waters in a state or region supporting Clean Water Act goals and the percent of waters 

affected by the stressors that are included in the study design, which can inform protection and 

restoration priorities. Probabilistic surveys are a cost-effective approach for tracking changes in 

condition and stressors across the population of waters of the United States. As more states 

adopt probabilistic monitoring, EPA will be able to more accurately report on water quality 

trends. This effort will also help inform water quality policy and ensure resources are 

appropriately targeted. As of 2008, 30 states were participating in probabilistic water quality 

surveys, and EPA has set a goal of having participation by all 50 states by 2011. To date, EPA 

has provided $65 million in additional section 106 grant monitoring funds to help states improve 

water quality monitoring programs and implement probabilistic survey designs. 

Future Reporting 

States are working to strengthen their water monitoring and assessment programs by 

developing long-term monitoring strategies that identify the specific actions needed to move 

toward more comprehensive and consistent reporting of water quality conditions. These actions 

include implementing probability-based surveys in combination with more traditional monitoring 

targeted to waters of interest. In addition, states and EPA have streamlined water quality 

assessment and reporting by integrating various Clean Water Act reporting requirements and 

facilitating and improving electronic reporting of water data. The results of these efforts will be 
National Water Quality Inventory: 2004 Report to Congress 

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more comprehensive and valid information that can be easily accessed by water quality 

managers and the public in a timely fashion and used to describe water quality on a state, 

regional, or national scale. 
National Water Quality Inventory: 2004 Report to Congress 

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National Water Quality Inventory: 2004 Report to Congress 

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I. Background 

Under section 305(b)(1)(A) of the Clean Water Act, states, territories, and other 

jurisdictions of the United States are required to submit reports on the quality of their waters to 

the U.S. Environmental Protection Agency (EPA) every 2 years. Historically, states submitted 

these reports in hardcopy format, and EPA prepared a national hardcopy report that summarized 

their findings (see http://www.epa.gov/305b/). Under section 303(d) of the Clean Water Act, 

states also biennially provide a separate prioritized list of those waters that are impaired and 

require the development of pollution controls (to learn more about section 303(d) reporting, visit 

http://www.epa.gov/owow/tmdl/). 

Beginning with the 2002 reporting cycle, EPA urged states to combine sections 305(b) 

and 303(d) reporting requirements into one integrated report and to submit these reports 

electronically. EPA has encouraged states to combine these reports for several reasons. 

Integrating these reports merges environmental data from a variety of water quality programs, 

increases the consistency of this information, benefits the public by providing a more informed 

summary of the quality of assessed state waters, and provides decision makers with better 

information on the actions necessary to protect and restore these waterbodies. The integrated 

report also streamlines state reporting burdens by eliminating the need for two separate reports. 

For the 2004 reporting cycle, 16 of the 44 water quality reports submitted by the states 

were fully integrated. Progress toward full integration is expected in coming years. Data for both 

integrated and non-integrated state reports are available on EPA’s new Water Quality 

Assessment and Total Maximum Daily Load (TMDL) Information database and website, known 

as ATTAINS (Assessment TMDL Tracking and ImplementatioN System). To facilitate the 

states’ efforts to improve integrated reporting, EPA published reporting guidance in 2005 and a 

series of clarifying memoranda in subsequent years. For more information on integrated 

reporting, visit http://www.epa.gov/owow/tmdl/guidance.html#tmdl. 

About the Water Quality Assessment and TMDL Information Database 

(ATTAINS) 

 The Water Quality Assessment and TMDL Information database, known as ATTAINS 

(for Assessment TMDL Tracking and ImplementatioN System), presents electronic water 

quality information submitted since 2002 by the states, territories, and the District of Columbia. 

ATTAINS allows the user to view, via the Internet, dynamic tables and charts that summarize 

state-reported data for the nation as a whole, for individual states, for individual waters, and for 

the ten EPA regions. It shows which waters have been assessed, which are impaired, and which 

have plans (e.g., TMDLs) completed to help restore them. By displaying data in one location, 

ATTAINS allows for a more informed summary of the quality of state waters that have been 

assessed and provides decision makers with better information on the actions necessary to 

protect and restore assessed waters of the U.S. 
National Water Quality Inventory: 2004 Report to Congress 

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 To view ATTAINS, go to http://www.epa.gov/waters/ir and click on the map to find 

summary information and assessment results for specific states, EPA regions, watersheds, and 

waterbodies of interest. You can select information for a specific biennial reporting cycle (e.g., 

2002, 2004, etc) or the most recent available information across multiple cycles. A series of 

tables and charts also summarize the status of assessed waters across the nation. 

 For this report, EPA has included ATTAINS data from 44 states, the District of 

Columbia, the U.S. Virgin Islands and Puerto Rico. Pennsylvania, Maryland, Florida, Oregon, 

Idaho, Hawaii, the tribal nations, and the island territories of the Pacific did not provide data 

electronically that could be used for the 2004 reporting cycle. Although Pennsylvania, Florida, 

and Oregon did publish hard copy section 305(b) water quality reports, EPA relies on the 

electronic submittal by states of assessment information as the source of the water quality 

findings in this report. Maryland and Hawaii submitted only impaired waters lists under section 

303(d) in 2004 and did not provide information on assessed waters that were not impaired. 

Idaho is submitting a combined 2004/2006/2008 integrated report in 2008. Although only 2004 

reporting cycle data were used for this report, it is important to note that the ATTAINS database 

contains all available waterbody-specific data reported by the states and territories from 2002 on. 

 

 About half the states conduct their own probability-based surveys (based on statistical 

random sampling design) to complement this information and to draw state-wide conclusions 

about the state’s water resources. EPA fully supports these state efforts to provide more complete 

assessments of their waters and to increase their percentage of assessed waters. Because statelevel probabilistic monitoring efforts are in their initial stages in many states, the results of these 

state-scale probability surveys for the most part are not included in the 2004 ATTAINS database. 

We expect that the 2008 version of the database will begin to do so, and that we will be able to 

move toward water quality reports that assess all the states’ waters, providing a valuable 

complement to current knowledge on the subset of waters with targeted monitoring. 
National Water Quality Inventory: 2004 Report to Congress 

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Assessing Water Quality 

States assess the quality of their waters based on water quality standards they develop in 

accordance with the Clean Water Act. Water quality standards may differ from state to state, but 

must meet minimum requirements. EPA must approve these standards before they become 

effective under the Clean Water Act. 

Comparability of Water Quality Data 

Although the information in ATTAINS provides a picture of state assessment results, these data should 

not be used to compare water quality conditions between states, identify trends in statewide or national 

water quality, or compare the impacts of specific causes or sources of impairment over time. The 

following are reasons for this lack of comparability: 

 The methods states use to monitor and assess their waters, including what and how they monitor 

and how they report their findings to EPA, vary from state to state and within individual states 

over time. Many states target their limited monitoring resources to waters they suspect are 

impaired, or to address local priorities and concerns; therefore, the small percentage of waters 

assessed may not reflect statewide conditions. States may monitor a different set of waters from 

one reporting cycle to another, or may monitor fewer waters when state budgets are limited. It is 

also important to note that six states did not provide electronic data for the 2004 reporting cycle, 

and that the lack of data from these states affects the summary statistics. 

 The science of monitoring and assessment varies over time, and many states are better able to 

identify problems as their monitoring and analytical methods improve. For example, states are 

conducting more fish tissue sampling than in previous years. The use of improved assessment 

methods to collect better information may result in more extensive and protective fish 

consumption advisories, even though water quality conditions themselves may not have changed. 

 For the 2004 reporting cycle, EPA re-evaluated how it grouped sources and causes reported by 

the states into larger overall categories (such as municipal discharges/sewage or metals other 

than mercury) for national reporting purposes. The purpose of this re-evaluation was to more 

accurately categorize the source and cause information reported by the states. Some overall 

source and cause categories were renamed, and some state-reported sub-categories were 

moved into different overall categories compared to the 2002 reporting cycle. (See the section 

Sources of Impairment in this report for more information.) 

 Under the Clean Water Act, each state has the authority to set its own water quality standards; 

therefore, a state’s definition of its designated uses (for example, Warm Water Fishery or 

Livestock Watering) may differ from definitions used by other states, along with the criteria 

against which states determine impairments. (See the section Assessing Water Quality, below, 

for more information.) 
National Water Quality Inventory: 2004 Report to Congress 

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Water quality standards consist of three elements: the designated uses assigned to waters 

(e.g., recreation, public water supply, the protection and propagation of aquatic life); the criteria

or thresholds (expressed as numeric pollutant concentrations or narrative requirements) that are 

necessary to protect the designated uses; and the anti-degradation policy intended to prevent 

waters from deteriorating from their current condition. Waters may be designated for more than 

one use. To learn more about water quality standards, visit 

http://www.epa.gov/waterscience/standards/. 

After setting water quality standards, states assess their waters to determine the degree to 

which the standards are being met. State water quality assessments are normally based on six 

broad types of monitoring data: biological integrity, chemical, physical, microbiological, habitat, 

and toxicity. (Examples of the different types of data used to determine a state’s water quality are 

shown in the box below.) Each type of monitoring data yields an assessment that must be 

integrated with other data types for an overall assessment. Depending on the designated use, one 

data type may be more informative than others for making the final assessment. 

Designated Use Categories in this Report 

The states have different names for the various uses they have designated for their waters. For 

example, one state might designate as Class A those waters that are capable of supporting fish 

species of commercial and recreational value (e.g., salmon, trout), whereas another state might 

classify similar waters as Cold Water Fishery waters. The ATTAINS database groups state-reported 

uses according to the following overall categories: 

 Fish, Shellfish, and Wildlife Protection and Propagation – Is water quality good enough to 

support a healthy, balanced community of aquatic organisms? 

 Recreation – Can people safely swim or enjoy other recreational activities in and on the water? 

 Public Water Supply – Does the waterbody safely supply water for drinking after standard 

treatment? 

 Aquatic Life Harvesting – Can people safely eat fish caught in the waterbody? 

 Agricultural – Can the waterbody be used for irrigating fields and watering livestock? 

 Industrial – Can the water be used for industrial processes? 

 Aesthetic Value – Is the waterbody aesthetically appealing? 

 Exceptional Recreational or Ecological Significance – Does the waterbody qualify as an 

outstanding natural resource or support rare or endangered species? 

You can find out which state classifications fit under each of these categories by clicking on the 

individual use category name in the ATTAINS database. 
National Water Quality Inventory: 2004 Report to Congress 

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States, tribes, and other jurisdictions monitor for a variety of pollutants, or causes of 

impairment. Table 1 provides a list of major causes of impairment cited in this report. 

Table 1. Major Impairment Cause Categories Used in this Report 

Category Examples 

Cause Unknown – 

Impaired Biota 

Impairment or degradation of the biological community (e.g. fish, 

macroinvertebrates) due to unknown/unidentified cause 

Dioxins Highly toxic, carcinogenic, petroleum-derived chemicals that are persistent in the 

environment and may be found in fish tissue, water column, or sediments 

Flow Alterations Changes in stream flow due to 

such as irrigation 

human activity; includes water diversions for purposes 

Habitat Alterations Modifications to substrate, streambanks, fish habitat; barriers 

Metals Substances identified only as “metals;” also, selenium, lead, copper, arsenic, 

manganese, others (Note: may, in some cases, include mercury) 

Mercury A toxic metal with neurological and developmental impacts; found in 

water column, or sediments 

fish tissue, 

Nuisance Exotic Species Non-native fish, animals, or plants such as Eurasian milfoil, Hydrilla, or zebra 

mussels, which choke out native species and alter the ecological balance of waters 

Nutrients Primarily nitrogen and phosphorus; in excess amounts, these nutrients overstimulate 

the growth of weeds and algae and can lead to oxygen depletion 

Organic Enrichment/ 

Oxygen Depletion 

Low levels of dissolved oxygen; high levels of biochemical oxygen demanding 

substances (e.g., organic materials such as plant matter, food processing waste, 

sewage) that use up dissolved oxygen in water when they degrade 

Types of Monitoring Data 

 Biological integrity data: Objective measurements of aquatic biological communities (usually 

aquatic insects, fish, or algae) used to evaluate the condition of an aquatic ecosystem. Biological 

data are best used when deciding whether waters support aquatic life uses. 

 Chemical data: Measurements of key chemical constituents in water, sediments, and fish tissue. 

Examples of these constituents include metals, oils, pesticides, and nutrients such as nitrogen 

and phosphorus. Monitoring for specific chemicals helps states assess waters against numerical 

criteria, as well as identify and trace the source of the impairment. 

 Physical data: Characteristics of water, such as temperature, flow, suspended solids, sediment, 

dissolved oxygen, and pH. These physical attributes are often useful indicators of potential 

problems and can have an effect on the impacts of pollution. 

 Microbiological data: Measurements of pathogen indicators such as fecal and total coliform 

bacteria, E.coli and Enterococci. Monitoring of these indicators helps determine possible 

contamination by such things as untreated sewage, septic systems, and livestock or pet wastes, 

and is often used to determine if waters are safe for recreation and shellfish harvesting. 

 Habitat assessments: Descriptions of sites and surrounding land uses; condition of streamside 

vegetation; and measurement of features, such as stream width, depth, flow, and substrate. 

These assessments are used to supplement and interpret other kinds of data. 

 Toxicity testing: Measurements of mortality of a test population of selected organisms, such as 

fathead minnows or Daphnia (“water fleas”). These organisms are exposed to known dilutions of 

water taken from the sampling location. The resulting toxicity data indicate whether an aquatic life 

use is being attained. These tests can help determine whether poor water quality results from 

toxins or from habitat degradation. 
National Water Quality Inventory: 2004 Report to Congress 

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Category Examples 

Pathogens Bacteria and pathogen indicators E.coli, total coliforms, fecal coliforms, Enterococci; 

used as indicators of possible contamination by sewage, livestock runoff, and septic 

tanks 

Polychlorinated A toxic mixture of chlorinated chemicals that are no longer used, but are persistent in 

biphenyls (PCBs) the environment; used originally in industry and electrical equipment; primarily 

found in fish tissue or sediments 

Pesticides Substances identified only as “pesticides;” also, chlordane, atrazine, carbofuran, and 

others; many older pesticides are persistent in the environment 

Sediment Excess sediments, siltation; affects aquatic communities by altering and suffocating 

habitat and clogging fish gills 

Toxic Organics Chemicals identified only as “toxic organics;” also, priority organic compounds, nonpriority organic compounds, polycyclic aromatic hydrocarbons (PAH), and others; 

often persistent in the environment 

Where possible, states, tribes, and other jurisdictions identify the sources of those 

pollutants associated with water quality impairment. Point sources discharge pollutants directly 

into surface waters from a conveyance, such as a pipe. Point sources include industrial facilities, 

municipal sewage treatment plants, combined sewer overflows, and storm sewers. Nonpoint 

sources deliver pollutants to surface waters from diffuse origins, such as fields and streets. 

Nonpoint sources include urban runoff that is not captured in a storm sewer; agricultural runoff 

from cropland and grazing areas; leaking septic tanks; and deposition of contaminants in the 

atmosphere due to air pollution. Habitat alterations, dams, channelization, dredging, and stream 

bank destabilization are also significant sources of water quality degradation. See Table 2 for 

more information on source categories used in this report. 

For 2004 reporting, EPA reorganized many source categories compared to previous 

reporting cycles; therefore, apparent significant increases or decreases in individual categories 

(e.g., Municipal Discharges/Sewage) may be attributable to these reporting changes rather than 

to actual changes in the impact of an individual source category. 

Table 2. Major Pollutant Source Categories Used in this Report 

Category Examples 

Agriculture Crop production, feedlots (including concentrated animal feeding operations), 

grazing, manure runoff 

Atmospheric Deposition Airborne pollution from many diverse sources (such as factory and automobile 

emissions and pesticide applications) that settles to land or water 

Construction Residential development, bridge and road construction, land development 

Habitat Alterations (Not Riparian and in-stream habitat modification and loss, filling and draining of 

Directly Related to wetlands, removal of riparian vegetation, streambank erosion 

Hydromodification) 

Hydromodification Pond construction, channelization, dam construction, dredging, flow alterations 

from water diversions, flow regulation, hydropower generation, streambank 

destabilization and modification, upstream impoundments 

Industrial Factories, industrial and commercial areas, cooling water intake structures, mill 

tailings 
National Water Quality Inventory: 2004 Report to Congress 

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Category Examples 

Land Application/Waste Salt storage piles, land application of biosolids, land disposal, landfills, leaking 

Sites/Tanks underground storage tanks 

Legacy/Historical Pollutants Brownfield sites, contaminated sediments, in-place contaminants 

Municipal Septic systems, sewage treatment plants, domestic sewage lagoons, sanitary 

Discharges/Sewage sewer overflows, municipal dry and wet weather discharges, unpermitted 

discharges of domestic wastes, combined sewer overflows, septage disposal 

Natural/Wildlife Flooding, drought-related impacts, waterfowl 

Recreation and Tourism Golf courses, marinas, turf management, boat maintenance 

Resource Extraction Abandoned mining, acid mine drainage, coal mining, dredge mining, 

mountaintop mining, petroleum/natural gas activities, surface mining 

Silviculture (Forestry) Forest management, forest fire suppression, forest roads, reforestation, woodlot 

site clearance 

Spills/Dumping Accidental releases/spills, pipeline breaks 

Unknown Source of impairment is unknown 

Unspecified Nonpoint Source Source of impairment is identified as nonpoint, but no further information 

available 

Urban-Related Discharges from municipal separate storm sewers (MS4), parking lot and 

Runoff/Stormwater impervious surfaces runoff, highway and road runoff, storm sewers, urban 

runoff, permitted stormwater discharges 

Hundreds of organizations in the United States conduct water quality monitoring. 

Monitoring organizations include state, interstate, tribal, and local water quality agencies; 

research organizations such as universities; industries and sewage and water treatment plants; 

and citizen volunteer programs. EPA, the U.S. Geological Survey (USGS), the National Park 

Service (NPS), and the National Oceanic and Atmospheric Administration (NOAA) are among 

the many federal agencies that collect water quality monitoring data. Monitoring organizations 

collect water quality data for their specific purposes, and many share their data with other users, 

including government decision makers. States evaluate and use much of these data when 

preparing their water quality reports. 

The states, territories, and tribes maintain monitoring programs to support several 

objectives, including assessing whether water is safe for drinking, swimming, and fishing. States 

also use monitoring data to review and revise water quality standards, identify impaired and 

threatened waters under Clean Water Act section 303(d), develop pollutant-specific TMDLs, 

determine the effectiveness of control programs, adjust drinking water treatment requirements, 

measure progress toward clean-water goals, and respond to citizen complaints or events such as 

spills and fish kills. 

Nationally consistent probability surveys are an efficient way to get a good understanding 

of national water quality conditions and trends. Probability surveys are scientifically based 

studies designed to sample water quality conditions at randomly selected sites that are 

statistically representative of the population of waters across the United States. EPA and its 

monitoring partners have used this methodology to develop a series of National Coastal 

Condition Reports (http://www.epa.gov/nccr/). These reports summarize the findings of the 

National Coastal Assessment, a probability-based study. Another probability-based project 
National Water Quality Inventory: 2004 Report to Congress 

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currently underway is the National Study of Chemical Residues in Lake Fish Tissue 

(www.epa.gov/waterscience/fishstudy), which is the first national freshwater fish contamination 

survey to have statistically selected sampling sites. EPA also partnered with states to conduct a 

probability-based Wadeable Streams Assessment (www.epa.gov/owow/streamsurvey) to 

determine the biological condition of small streams in the United States. The Wadeable Streams 

Assessment was completed in 2006. 

To learn more about the water quality monitoring, assessment, and reporting practices of a specific 

state, visit the state’s water quality Internet site and read the explanatory and programmatic 

information included in most reports. 
National Water Quality Inventory: 2004 Report to Congress 

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II. Findings 

Rivers and Streams 

The 2004 ATTAINS database summarizes river and stream designated use support 

information reported by the states by overall use support and by individual categories of uses. 

Waters are rated for overall use support as follows: 

 Good if they fully support all their designated uses 

 Threatened if they fully support all uses, but exhibit a deteriorating trend 

 Impaired if they are not supporting one or more designated uses. 

This report includes states’ 2004 assessments of 563,955 miles of rivers and streams, or 

16% of the nation’s 3.5 million stream miles (Figure 1). Because six states did not provide 

specific waterbody data electronically in 2004, the findings of this report address about 130,000 

fewer stream miles than were reported in 2002. States identified 44% of the assessed miles as 

being impaired, or not supporting one or more of their designated uses. The remaining 56% of 

assessed miles fully supported all uses, and of these, 3% were considered threatened (i.e., water 

quality supported uses, but exhibited a deteriorating trend). 

*Total U.S. river and stream miles based on state 2004 Integrated Reports. 

Percents may not add up to 100 because of rounding. 

Figure 1. Water quality in assessed river and stream miles. 

Individual use support assessments also provide important details about the nature of 

water quality problems in rivers and streams. Table 3 shows the top five assessed uses in rivers 

and streams. States evaluated support of the Fish, Shellfish, and Wildlife Protection and 

Propagation use most frequently, assessing a total of 466,617 stream miles (or 13% of U.S. 
National Water Quality Inventory: 2004 Report to Congress 

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stream miles) and reporting that 36% of assessed stream miles were impaired for this use. States 

assessed 303,317 stream miles for Recreation uses (primary and secondary contact) and found 

recreation to be impaired in 28% of these waters. 

Table 3. Individual Use Support in Assessed River and Stream Milesa

Designated Use 

Miles 

Assessed 

Percentage 

of Total U.S. 

River Miles 

Percentage of Waters Assessed 

Good Threatened Impaired 

Fish, Shellfish, and Wildlife 

Protection/Propagation 

466,617 13 61 3 36

Recreation 303,317 9 69 3 28

Agricultural 200,817 6 90 <1 10

Aquatic Life Harvesting 154,746 4 56 4 40 

Public Water Supply 144,245 4 79 3 18

a

 Waterbodies can have multiple designated uses, resulting in an overlap of river and stream miles assessed. 

The ATTAINS database provides more detailed information about the sources and causes 

of impairments in rivers and streams, but it is important to note that the information about 

specific sources and causes of impairment is incomplete. States do not always report the 

pollutant or source of pollutants affecting every impaired river and stream. Although states may 

recognize that water quality does not fully support a designated use, they may not have adequate 

data in some cases to document the specific pollutant or source responsible for the impairment. 

It is also important to note that— in an effort to provide clearer and more specific 

information— the actual categories of causes of impairment have changed since previous 

reporting cycles. For example, the cause of impairment category previously identified as Metals 

has now been divided into two cause categories: Metals and Mercury; however, some states may 

continue to report mercury under the Metals category. 

Similar changes have occurred to the source categories used in this report. For example, a 

new source category —Unspecified Nonpoint Source— was created in 2004 to capture sources 

previously part of the Unspecified/Unknown category, but for which some information (i.e., their 

nonpoint source origins) had been identified; therefore, the Unknown/Unspecified category is 

somewhat smaller in 2004 than it was in 2002. Similarly, the 2002 source category Municipal 

Permitted Discharges has been renamed Municipal Discharges/Sewage and now captures 

combined and sanitary sewer overflows; therefore, it is larger than it was in 2002. 

Figure 2 shows the top 10 reported causes of impairment in assessed rivers and streams. 

According to the states, the top causes of river and stream impairment regardless of designated 

use were the following: 

 Pathogens (bacteria), which indicate possible fecal contamination that may cause illness 

in people; 

 Habitat alteration, such as disruption of stream beds and riparian areas; and 

 Organic enrichment/oxygen depletion, or low levels of dissolved oxygen, often due to 

the decomposition of organic materials.
National Water Quality Inventory: 2004 Report to Congress 

15 

Note: Percents do not add up to 100% because more than one cause may impair a waterbody. 

Figure 2. Top 10 causes of impairment in assessed rivers and streams. 

The listed top 10 causes of impairment (above) differ from those reported in 2002. This 

difference is more likely attributable to reporting changes (e.g., fewer river and stream miles 

assessed; improved reporting of the results of 

fish tissue monitoring; and administrative 

changes in cause category definitions, 

described above) than to actual changes in 

water quality. 

Figure 3 shows the top reported sources 

of impairment in assessed rivers and streams. According to the states, the top sources of river and 

stream impairment included the following: 

 Agricultural activities, such as crop production, grazing, and animal feeding operations; 

 Hydromodifications, such as water diversions, channelization, and dam construction; 

and 

 Unknown or unspecified sources (i.e., the states could not identify specific sources). 

Other leading sources of impairment in streams included habitat alteration (e.g., loss of 

streamside habitat), natural sources (e.g., floods, droughts, wildlife), municipal 

discharges/sewage (which includes sewage treatment plant discharges and combined sewer 

overflows), and unspecified nonpoint sources. 

More detailed information on state-reported 

causes and sources of impairment is available 

from the ATTAINS Water Quality Assessment and 

TMDL Information database at 

http://www.epa.gov/ir. 
National Water Quality Inventory: 2004 Report to Congress 

16 

Note: Percents do not add up to 100% because more than one source may impair a waterbody. 

Figure 3. Top 10 sources of impairment in assessed rivers and streams. 

Lakes, Ponds, and Reservoirs 

The 2004 ATTAINS Water Quality Assessment and TMDL Information database 

summarizes designated use support information reported by the states for lakes, ponds, and 

reservoirs (referred to hereafter as lakes) by overall use support and by individual categories of 

uses. 

This report includes states’ assessments of 16.2 million acres of lakes (excluding the 

Great Lakes), or 39% of the nation’s total 41.7 million lake acres, for the 2004 reporting cycle 

(Figure 4). States identified 64% of assessed acres as impaired, or not supporting one or more of 

their designated uses (such as fishing or swimming). The remaining 36% of assessed acres fully 

supported all uses, and of these, 1% were considered threatened. It should be noted that 3.7 

million impaired lake acres—about a third of all impaired lake acres— were reported by one 

state, Minnesota, due to increased fish tissue and water monitoring activities addressing mercury. 
National Water Quality Inventory: 2004 Report to Congress 

17 

*Total U.S. lake acreage estimate based on 2004 state Integrated Reports. 

Figure 4. Water quality in assessed lake acres. 

Individual use support assessments provide important details about the nature of water 

quality problems in lakes and reservoirs. Table 4 shows the top five uses assessed in lakes, 

ponds, and reservoirs. States assessed 11.8 million lake acres for support of the Fish, Shellfish, 

and Wildlife Protection and Propagation use, of which 30% were found to be impaired. The 

Aquatic Life Harvesting use (primarily fish consumption) was assessed in 9.4 million acres; of 

these, 73% were impaired and 1% were considered threatened (i.e., water quality is 

deteriorating). This high percentage of lake, pond, and reservoir waters impaired for fish 

consumption is most likely related to changes in how states report on waters with statewide fish 

consumption advisories. For example, in previous cycles, some states may not have reported 

waters with fishing advisories as impaired. Recreational use (e.g., swimming, boating) was 

assessed in 8.1 million acres of lakes and found to be impaired in 26%. 

 Table 4. Individual Use Support in Assessed Lake, Reservoir, and Pond Acresa

Designated Use 

Acres 

Assessed 

Percentage 

of Total U.S. 

Lake Acres 

Percentage of Waters Assessed 

Good Threatened Impaired 

Fish, Shellfish, and Wildlife 

Protection/Propagation 

11,770,370 28% 66% 4% 30%

Aquatic Life Harvesting 9,390,396 23% 26% 1% 73% 

Recreation 8,069,018 19% 70% 4% 26%

Public Water Supply 6,427,687 15% 78% 1% 20%

Industrial 2,848,335 7% 82% <1% 17%

a

 Waterbodies can have multiple designated uses, resulting in an overlap of acres assessed. 
National Water Quality Inventory: 2004 Report to Congress 

18 

The ATTAINS database provides more detailed information on the sources and causes of 

impairments in lakes, but it is important to note that the information about specific sources and 

causes of impairment is incomplete. The states do not always report the pollutant or source of 

pollutants affecting every impaired lake, pond, and reservoir. In some cases, states may 

recognize that water quality does not fully support a designated use; however, they may not have 

adequate data to document the specific pollutant or source responsible for the impairment. The 

states may then simply report the cause or source of impairment as “unknown” or “unspecified.”

It is also important to note that, in some cases, groupings of causes and sources may have 

changed since previous reporting cycles. These changes were made to more accurately 

categorize the source and cause information reported by the states. 

Figure 5 shows the top causes of impairment in assessed lakes, ponds, and reservoirs. 

According to the states, the top causes of lake impairment were the following: 

 Mercury, which has been widely detected in fish tissue, where it may pose a health risk 

to people and animals who eat fish; 

 PCBs, which are hazardous chemicals released via industrial and municipal waste 

disposal, spills, and leaks; and 

 Nutrients, such as phosphorus and nitrogen, which disrupt lake ecosystems by 

stimulating growth of undesirable algae and aquatic weeds. 

Note: Percents do not add up to 100% because more than one cause may impair a waterbody. 

Figure 5. Top 10 causes of impairment in assessed lakes, ponds, and reservoirs. 

Heightened reporting of mercury, PCBs, and metals is largely the result of the reporting 

of broad-based fish consumption advisories due to these substances in fish tissue; some states 

have begun reporting the extent of waters affected by such advisories and bans. For example, 
National Water Quality Inventory: 2004 Report to Congress 

19 

Minnesota reported 3.7 million acres impaired by mercury (representing 63% of the lake acres 

impaired by mercury in the United States) and 1.6 million acres impaired by PCBs (representing 

70% of the lake acres impaired by PCBs in the 

United States). Other leading causes of 

impairments in lakes include organic 

enrichment/low dissolved oxygen, fish 

consumption advisory/pollutant unspecified, 

nuisance exotic species, sediment, turbidity, 

and pathogens. 

Figure 6 shows the top sources of impairment in assessed lakes, ponds, and reservoirs. 

According to the states, the top sources of lake impairment were the following: 

 Atmospheric (or air) deposition, primarily of toxic substances such as mercury, PCBs, 

and other metals, from both local and long-range sources; 

 Unknown or unspecified sources (i.e., the states could not identify specific sources); 

and 

 Agricultural activities, such as crop production and grazing. 

Note: Percents do not add up to 100% because more than one source may impair a waterbody. 

Figure 6. Top 10 sources of impairment in assessed lakes, ponds, and reservoirs.

It should be noted that about one fourth (485,376 acres) of lake acres impaired by 

atmospheric deposition were reported by one state, Wisconsin. This is because Wisconsin 

reported that all its lake acres are under a fish consumption advisory due to mercury from 

atmospheric deposition sources. However, the total does not include lake acres that may be 

impaired by atmospheric deposition in Minnesota, which reported the largest number of impaired 

lake acres for mercury and PCBs, because Minnesota did not identify the source of these 

More information on state-reported causes and 

sources of impairment is available from the 

ATTAINS Water Quality Assessment and TMDL 

Information database at 

http://www.epa.gov/waters/ir. 
National Water Quality Inventory: 2004 Report to Congress 

20 

impairments. It is likely that the majority of impairment by mercury and PCBs in Minnesota is 

from atmospheric deposition. Other leading sources of impairment include natural/wildlife 

sources (e.g., droughts, flooding, waterfowl), hydromodification, urban-related 

runoff/stormwater, municipal discharges/sewage, and legacy/historical pollutants (primarily in 

sediments). 

Bays and Estuaries 

The ATTAINS database summarizes state-reported designated use support information 

for bays and estuaries by overall use support and by individual categories of uses. 

 This report includes states’ assessments of 25,399 square miles of bays and estuaries, or 

29% of the nation’s total estimated 87,791 square miles, for the 2004 reporting cycle (Figure 7). 

About 5,000 fewer estuarine square miles were assessed in 2004 than in 2002, at least in part 

because several coastal states did not provide electronic data in 2004. States identified 30% of 

assessed square miles as impaired, or not supporting one or more of their designated uses (e.g., 

swimming, fishing, shellfishing). The remaining 70% of assessed estuarine square miles were 

fully supporting all uses. 

*Total U.S. estuarine square miles estimate based on 2004 state Integrated Reports. 

Figure 7. Water quality in assessed bay and estuary square miles 

Individual use support assessments provide important details about the nature of water 

quality problems in bays and estuaries. Table 5 shows the top three uses assessed in bays and 

estuaries. States assessed 24,338 estuarine square miles for support of the Fish, Shellfish, and 

Wildlife Protection and Propagation use and found that 27% were impaired; the Aquatic Life 

Harvesting use was assessed in 11,004 square miles and found to be impaired in 19% of assessed 
National Water Quality Inventory: 2004 Report to Congress 

21 

waters; and 13% of the 9,322 square miles assessed for Recreation uses (e.g., swimming, 

boating) were reported as impaired. 

Table 5. Individual Use Support in Assessed Bay and Estuary Square Miles a

Designated Use 

Square Miles 

Assessed 

Percentage 

of Total U.S. 

Estuarine 

Miles 

Percentage of Waters Assessed 

Good Threatened Impaired 

Fish, Shellfish, and Wildlife 

Protection/Propagation 

24,338 28% 73% <1% 27% 

Aquatic Life Harvesting 11,004 13% 81% <1% 19% 

Recreation 9,322 11% 87% <1% 13% 

a

 Waterbodies can have multiple designated uses, resulting in an overlap of square miles assessed. 

State-reported information about specific sources and causes of impairment may be 

incomplete because the states do not always report the pollutant or source of pollutants affecting 

every impaired bay and estuary. In some cases, states may recognize that water quality does not 

fully support a designated use; however, they may not have adequate data to document the 

specific pollutant or source responsible for the impairment and report the cause or source as 

“unknown.” 

Figure 8 shows the top causes of impairment in assessed bays and estuaries. According to 

the states, the top causes of estuarine impairment were the following: 

 Pathogens, i.e., bacteria used as indicators of possible contamination by sewage, 

livestock runoff, and other sources;

 Organic enrichment/oxygen depletion, i.e., low levels of dissolved oxygen and/or high 

levels of oxygen-demanding substances such as organic waste; and

 Mercury, a toxic metal found in fish tissue, and, to a lesser extent, in the water column, 

often entering the aquatic environment via atmospheric deposition.
National Water Quality Inventory: 2004 Report to Congress 

22 

Note: Percents do not add up to 100% because more than one cause may affect a waterbody. 

Figure 8. Top 10 causes of impairment in assessed bays and estuaries.

Toxic organics, nutrients, pesticides, and metals are also reported as top causes of 

impairment for estuarine waters. 

Figure 9 shows the top sources of impairment in assessed bays and estuaries. According 

to the states, the top sources of estuarine impairment included the following: 

 Atmospheric (or air) deposition, which can bring pollutants such as mercury from 

distant locations such as industrial centers; 

 Unknown/unspecified sources, or sources 

that cannot be further identified by the 

states; and 

 Municipal discharges/sewage, which 

includes septic systems, sewage treatment 

plants, and sanitary and combined sewer 

overflows. 

Other leading sources of impairment in bays and estuaries were unspecified nonpoint 

sources, other sources (such as sources outside state waters), and industrial sources. 

More information on state-reported causes 

and sources of impairment is available from 

the ATTAINS Water Quality Assessment and 

TMDL Information database at 

http://www.epa.gov/waters/ir. 
National Water Quality Inventory: 2004 Report to Congress 

23 

Note: Percents do not add up to 100% because more than one source may impair a waterbody. 

Figure 9. Top 10 sources of impairment in assessed bays and estuaries.

Other Waters

The 2004 ATTAINS database also contains state-reported information on conditions in 

coastal shoreline waters, ocean waters, Great Lakes, and wetlands, although, in some cases, only 

a small percentage of these resources were assessed in the 2004 reporting cycle. These waters are 

discussed below. 

Coastal Resources 

Coastal resources are identified in the ATTAINS database in two categories: coastal 

shorelines (the water immediately offshore, reported in miles) and ocean/near-coastal waters 

(i.e., the area of water extending into the ocean or gulf, range not specified, in square miles). 

Eight states assessed 1,859 miles of coastal shorelines, or about 3% of the nation’s total 58,618 

shoreline miles. The majority of assessed shoreline miles (68%) fully support their designated 

uses, with 12% of these miles classified as supporting uses, but threatened (i.e., water quality is 

deteriorating). In the 32% of shoreline miles not fully supporting their uses, metals (which could 

in some cases include mercury) and pathogens were the leading causes of impairment, and 

municipal discharges/sewage and industrial sources were listed as top sources of impairment. 

To help protect the public at coastal recreation waters, Congress passed the Beaches 

Environmental Assessment and Coastal Health Act of 2000 (BEACH Act), requiring that coastal 

and Great Lakes states and territories report to EPA on beach monitoring and notifications to the 

public of potential health risks. Public notification may include issuing a beach advisory, 

warning people of possible risks of swimming due to water quality problems, or closing a beach 

to the public. The BEACH Act also requires EPA to maintain an electronic monitoring and 

notification database of those data. 
National Water Quality Inventory: 2004 Report to Congress 

24 

For the 2004 swimming season, 28 of 30 coastal states and Puerto Rico reported public 

notification actions to EPA. Of the 3,574 beaches that were monitored in 2004, 942 (26%) had at 

least one advisory or closing. A total of 4,907 beach notification actions were reported. EPA 

calculates “beach days” (number of beaches multiplied by number of days in the swimming 

season) to get a better sense of the extent of the advisory and closure information. For the 2004 

season, EPA determined that there were 584,150 beach days for all of the monitored beaches, 

and actions were reported about 4% of the time. EPA is continuing to work to improve the 

delivery of its beach advisory information to the public. Visit http://www.epa.gov/beaches/ for 

more information on beach monitoring and notification. 

A total of 5,544 square miles of oceans and near-coastal waters, or 10% of approximately 

54,120 square miles of oceans and near-coastal waters in the United States, were assessed by 5 

states in 2004. Of the assessed square miles, 88% were identified as impaired. Mercury was by 

far the most commonly reported cause of 

impairment, followed by organic 

enrichment/oxygen depletion. Atmospheric 

deposition was the predominant reported 

source of impairment in oceans and nearcoastal waters. (It is important to note that 

Texas alone assessed nearly 3,879 square 

miles of oceans and near-coastal waters and reported that 100% of its assessed square miles are 

impaired due to mercury in fish tissue from atmospheric deposition.) 

Detailed information on U.S. coastal condition trends is available in the EPA’s National 

Coastal Condition Report series, which presents the findings of a collaborative effort between 

the states, EPA, and other federal agencies to characterize the condition of 100% of the nation’s 

coastal resources. Section III of this report summarizes key findings of the draft National 

Coastal Condition Report III.

Great Lakes 

The Great Lakes—Superior, Michigan, Huron, Erie, and Ontario—are freshwater inland 

seas of vast importance for water consumption, recreation, fisheries, power, transportation, and 

many other uses. Of the eight states bordering the Great Lakes, six reported on the condition of 

their Great Lakes shoreline miles. 

About 1,070 of 5,521 total Great Lakes shoreline miles were assessed in 2004, and of 

these, 93% were reported as impaired. The leading causes of impairment included PCBs, toxic 

organics, pesticides, and dioxins. Legacy or historical pollution—primarily contaminated 

sediment—were the leading source of shoreline impairment reported by the states, followed by 

municipal discharges/sewage. 

Wetlands 

Wetlands occur where water and land come together for a prolonged period of time and 

where saturation of the land with water is the dominant factor determining soil types and the 

plant and animal communities living in the soil and on the surface. Wetlands vary widely 

More information on state-reported causes and 

sources of impairment is available from the 

ATTAINS database information website at 

http://www.epa.gov/waters/ir.. 
National Water Quality Inventory: 2004 Report to Congress 

25 

because of regional and local differences in soils, topography, climate, hydrology, water 

chemistry, vegetation, and other factors, including human disturbance. Included among the many 

types of U.S. wetlands are marshes, bogs, swamps, wet meadows, vernal pools, playas, pocosins, 

sloughs, peat lands, prairie potholes, and fens. 

Wetlands are a critically important resource due to the many benefits they provide to 

humans, aquatic life, wildlife, and the environment. Wetlands produce great quantities of food 

that attract a huge variety of animal species. They serve as nurseries and habitat for many game 

and commercial fish and wildlife species, and they help improve water quality by intercepting 

surface runoff and removing, retaining, or filtering out a broad range of substances (e.g., 

nutrients, sediments, organic wastes). By storing and slowly releasing water, wetlands help 

reduce the impacts of floods and erosion, as well as help replenish groundwater and stream flow 

during dry periods. Wetlands are also of great recreational value to bird watchers, hunters, 

fishermen, and nature lovers. 

Only 10 states provided information on the support of designated uses for 1.8 million 

acres of wetlands assessed in their 2004 reports—a tiny portion of the nation’s estimated 107 

million acres. States identified 30% of these assessed acres as impaired. Organic 

enrichment/oxygen depletion, sediment, and turbidity were the leading causes of wetland 

degradation in these six states. Agriculture, unknown/unspecified sources, and atmospheric 

deposition were listed by the states as top contributors to impairment. 

Section III of this report discusses plans for an upcoming National Wetland Condition 

Assessment. 
National Water Quality Inventory: 2004 Report to Congress 

26 

III. Probability Surveys of Water Quality 

EPA, other federal agencies, and the states have embarked on a cost-effective approach to 

assess status and track trends in the quality of the nation’s waters: probability-based surveys that 

complement existing monitoring and assessment programs and add to our understanding of 

national, regional, and local water quality conditions. Probability surveys are designed to yield 

unbiased estimates of the condition of a whole resource (such as lakes or rivers and streams) 

based on a representative sample of waters. These surveys are designed to answer key questions 

asked by Congress, the public, and decision makers, such as 

 Is water quality improving? 

 What is the extent of waters that support healthy ecosystems, recreation, and fish 

consumption? 

 How widespread are the most significant water quality problems? 

 Are we investing in restoration and protection wisely? 

Several national probability-based studies have already been completed, and several more 

are underway. 

National Coastal Assessment 

The National Coastal Assessment surveys the condition of the nation’s coastal resources. 

The results of these surveys have been compiled into the National Coastal Condition Report 

Understanding the Value of Probability-based Surveys and the National 305(b) Report 

Although some of the findings of the national 305(b) report appear similar to the findings of the 

national, probability-based coastal and streams surveys, there are many differences in the scope of 

these reports and how they are best used to inform water quality management. 

Probability surveys provide consistent environmental indicators of the condition of the nation’s water 

resources, much as economic indicators report on the health of the nation’s economy. Their design 

ensures that results represent the population of all waters of a certain type across the United States, 

and their consistent sampling methods ensure that results can be aggregated into regional and 

national indicators of the health of the resource. The survey results quantify, with documented 

confidence, how widespread water quality problems are across the country and estimate the extent of 

waters affected by key stressors. This helps set priorities for water resource protection and restoration. 

Nationally consistent surveys provide a standardized measure for tracking changes in the condition of 

the nation’s waters over time and for evaluating, at a broad scale, progress in investments to protect 

and restore water quality. 

In contrast to the probability surveys, this national 305(b) report summarizes information reported by 

states for only a portion of waters (approximately 16% of U.S. river and stream miles, 39% of lake 

acres, and 29% of bay and estuarine square miles). It tallies state findings based on data collected 

using a variety of sampling methods and parameters; water quality standards and interpretation 

methods; extrapolation methods; and time periods. The strength of the 305(b) report is that it provides 

useful information on the nature of water quality problems identified by state monitoring programs; 

documents the amount of waters assessed and unassessed; and supports the identification of specific 

waters not meeting water quality standards; therefore, it helps states set priorities for these waters. 
National Water Quality Inventory: 2004 Report to Congress 

27 

series. The states, EPA, and partner agencies — NOAA, USGS, and the U.S. Fish and Wildlife 

Service (FWS) — issued the first three reports of the National Coastal Condition Report series

in 2001, 2005, and 2008. These reports include evaluations of 100% of the nation’s estuaries in 

the contiguous 48 states and Puerto Rico. Federal, state, and local agencies collected samples 

using nationally consistent methods and a probability-based design to assess five key indices of 

coastal water health. 

The National Coastal Condition 

Report III finds that the overall 

condition of the nation’s coastal waters 

is generally fair and has improved 

slightly since the 1990s. This rating is 

based on five indices of ecological 

condition: a water quality index 

(calculated based on ratings for 

dissolved oxygen, chlorophyll a, 

dissolved inorganic nitrogen, dissolved 

inorganic phosphorus, and water 

clarity), a sediment quality index 

(calculated based on ratings for 

sediment toxicity, sediment 

contaminants, and sediment total 

organic carbon), a benthic index, a 

coastal habitat index, and a fish tissue 

contaminants index. For each of these 

indicators, a score of good, fair, or poor 

was assigned to each coastal region of 

the United States. Ratings were then averaged to create the overall regional and national scores 

illustrated in Figure 10, which uses “traffic light” color scoring. Based on the findings of this 

survey, fifty-seven percent of the area of the nation’s estuaries and coastal embayments are in 

good condition for the water quality index, 6% are in poor condition, and 35% are in fair 

condition. 

The indices that show the poorest condition are coastal habitat and benthic condition. 

Two of the individual component indicators of the water quality index generally show the best 

condition —dissolved oxygen and dissolved inorganic nitrogen. 

In 2010, EPA and its partners expect to undertake a new survey of coastal waters and 

expect to report survey results in 2012. For more information on the National Coastal Condition 

Report series, go to http://www.epa.gov/nccr/. 

The Wadeable Streams Assessment 

The Wadeable Streams Assessment, a survey of the biological health of the nation’s 

wadeable streams, was launched by EPA and the states to provide a national baseline of stream 

water quality based on conditions at approximately 1,300 randomly selected sites across the 

conterminous United States. With support from EPA, state water quality agencies sampled 

Figure 10. Findings of the National Coastal 

Condition Report III (U.S. EPA, 2008). 
National Water Quality Inventory: 2004 Report to Congress 

28 

streams using the same methods at all sites. Crews collected macroinvertebrates to determine the 

biological condition of streams. They also measured key chemical and physical indicators that 

reveal stress or degradation of streams. The Wadeable Streams Assessment reports on four 

chemical indicators (i.e., phosphorus, nitrogen, salinity, and acidity) and four physical condition 

indicators (i.e., streambed sediments, in-stream fish habitat, riparian vegetative cover, and 

riparian 

disturbance). 

The 

Wadeable Streams 

Assessment found 

that 42% of U.S. 

stream miles are in 

poor biological 

condition compared 

to best-available 

reference sites in 

their ecological 

regions, 25% are in 

fair condition, and 

28% are in good 

condition (Figure 

11). The confidence 

level for these key 

findings of 

biological quality is 

±2.8%. Five percent 

of U.S. stream miles 

were not assessed 

because the New 

England states did 

not include first 

order streams in the 

sample design. 

The study was 

designed to examine 

eight key stressors. 

The most widespread 

stressors observed 

across the country and 

in each of the three 

major regions are 

nitrogen, phosphorus, 

riparian disturbance, 

and streambed 

sediments (Figure 12). 

Figure 11. Biological quality of the nation’s streams 

(U.S. EPA, 2006). 

Figure 12. Extent of streams rated poor for aquatic stressors, and 

increase in risk of poor biology in streams rated poor over streams 

rated good for each stressor (U.S. EPA, 2006). 
National Water Quality Inventory: 2004 Report to Congress 

29 

These stressors can degrade stream conditions for fish and other aquatic life. Nitrogen and 

phosphorus are nutrients that, when present in excess amounts, can increase the growth of algae, 

decrease levels of dissolved oxygen and water clarity, and degrade stream habitat. Excess 

streambed sediments can smother habitat for aquatic organisms. Riparian disturbance is evidence 

of human activity alongside streams, such as pipes, pavement, and pastures. The survey found 

that increases in nutrients and streambed sediments have the highest impact on biological 

condition, i.e., streams scoring poor for these stressors are twice as likely to have poor biological 

condition as streams that score in the good range for the same stressors. For more information on 

the Wadeable Streams Assessment, go to http://www.epa.gov/owow/streamsurvey. 

Survey of the Nation’s Lakes 

 In 2007, EPA and 

its state partners completed 

the field sampling season 

for the Survey of the 

Nation’s Lakes, a baseline 

assessment of the condition

of the nation’s lakes, 

ponds, and reservoirs. Mor

than 900 lakes were 

sampled over the course of 

a summer for this survey 

(see Figure 13). The 

population of lakes to be 

sampled was comprised of 

natural and man-made 

freshwater lakes, ponds, 

and reservoirs that were 

greater than 10 acres, at 

least one meter in depth, 

and located in the conterminous United States. The survey does not include the Great Lakes, the 

Great Salt Lake, natural saline systems, or treatment and disposal ponds. In order to examine 

potential trends in water quality, a representative subset of lakes from EPA’s 1972 National 

Eutrophication Survey was included. 

Key indicators sampled for the Survey of the Nation’s Lakes included the following: 

 Trophic indicators, such as in situ temperature and dissolved oxygen profiles, water 

chemical quality, nutrient concentrations, chlorophyll a levels, transparency measured 

by Secchi disk, turbidity, and color 

 Ecological integrity indicators, such as sediment diatom abundance, diversity, and 

trends; phytoplankton abundance and diversity; zooplankton abundance and diversity; 

shoreline physical habitat conditions; and benthic macroinvertebrate abundance and 

diversity 

e

Figure 13. Sampling locations for the survey 

of the nation’s lakes. 
National Water Quality Inventory: 2004 Report to Congress 

30 

 Recreational indicators, such as pathogen (Enterococci) concentrations, algal toxin 

(microcystins) levels, and sediment mercury concentrations. 

Analysis of the survey’s data is underway in 2008, and a report on the condition of the 

nation’s lakes is planned for 2009. 

National Rivers and Streams Assessment 

EPA is undertaking a survey of the nation’s rivers—including the “Great Rivers” of the 

United States—and intends to combine it with a second Wadeable Streams Assessment. 

In 2008 and 2009, field crews expect to collect data on indicators of the following: 

 Ecological condition, such as the abundance and diversity of periphyton, 

phytoplankton, benthic macroinvertebrates, and fish 

 Recreational value, such, as fecal contaminant concentrations in water and 

contaminant residue in fish tissue 

 Physical habitat condition, such as bank stability, channel alterations, and invasive 

species 

 Water quality, such as 

basic water chemistry. 

The focus will be on 

wadeable streams in the first year 

of monitoring and non-wadeable 

systems (e.g., rivers) in the 

second. Figure 14 shows the 

locations of the 1,350 new sites 

that will be sampled and the 450 

sites from the 2006 Wadeable 

Streams Assessment will be resampled for this survey. A 

national report on rivers and 

streams is scheduled for 2011. 

For more information on the 

National River and Streams 

Assessment, visit 

http://www.epa.gov/owow/riverss

urvey/index.html. 

National Wetland Condition Assessment 

In 2011, EPA and the states plan to conduct a survey (National Wetlands Condition 

Assessment) of the condition of the nation’s wetlands, with a report planned for 2013. EPA and 

the states are working with the FWS to design the wetland assessment to ensure that it effectively 

Figure 14. Sampling locations for the 

national rivers and streams assessment. 
National Water Quality Inventory: 2004 Report to Congress 

31 

complements the FWS Status and Trends reports, which focus on the distribution of wetlands 

rather than their condition. 

EPA is currently in the research phase of the National Wetland Condition Assessment 

and has identified several significant challenges to designing and implementing a wetland 

assessment on a national scale. These include designing the best sample frame and methods to 

support a national report; selecting efficient, scientifically valid indicators; ensuring that 

adequate resources are available; maintaining the resultant data; and building partnerships to 

most effectively use the information gleaned from the National Wetlands Condition Assessment. 

EPA is coordinating a number of regional pilot projects with states, academics, and other 

federal agencies to test design approaches, field protocols, and indicators. EPA anticipates that in 

2009, the project team will be making initial decisions on condition indicators and assessment 

methods that can apply across the nation’s wide range of wetland types. For more information on 

the National Wetland Condition Assessment, visit http://www.epa.gov/owow/wetlands/survey. 

State-Scale Statistical Surveys 

More than half of the states have begun to implement state-scale statistical or 

probabilistic surveys to characterize the full population of a water resource type (e.g., streams, 

lakes). The majority of these surveys are of streams and rivers, although lakes, coastal waters, 

and wetlands are also surveyed. 

States use probabilistic monitoring designs to develop estimates of water quality across 

the entire state, based on a representative sample, and to examine trends in water quality over 

time statewide. Probability surveys can eliminate the risk of generating a biased picture of water 

quality conditions; they provide information on changes in water quality over time statewide, and 

serve as a cost-effective benchmark of the effectiveness of the state’s water quality program. 

Also as part of the probability assessment, a state can produce an estimate of the accuracy of its 

assessment results. The results also provide information on whether it would be useful to target 

certain waters for further assessment, or if limited resources for water quality assessment can be 

used more effectively in other ways. 

States use targeted monitoring, on the other hand, to meet state management objectives 

such as identifying specific waters that are not meeting water quality standards, setting priorities 

for impaired waters, and tracking the restoration of individual waters. The two approaches are 

not expected to provide the same results because they are designed to achieve different 

objectives. 

Comparing the results of the two monitoring designs is a useful evaluation tool for the 

state. For example, the statistical survey’s overall description of the full population of waters 

Through the institution of regular probability surveys of all waterbody types, EPA and its partners in the 

states and other federal agencies expect to be able to cost-effectively assess 100% of the water 

resources of the United States and track trends in water quality over time. This scientifically based 

data will assist in the evaluation of the effectiveness of pollution-control activities and will greatly 

improve our ability to manage the nation’s water resources. 
National Water Quality Inventory: 2004 Report to Congress 

32 

provides a useful benchmark for comparing the results of targeted monitoring activities and can 

help the state identify potential gaps in its targeted monitoring program. 

The following are examples of how some states use probability assessments for water 

quality assessment reporting in 2004. It is important to note that for the 2004 reporting cycle, 

statewide probability assessments are still a fairly new development, and most states are only 

beginning to report their findings. 

South Carolina 

South Carolina’s monitoring program includes a probability-based component to 

complement its targeted monitoring activities. Probability-based monitoring is conducted for 

streams, lakes/reservoirs, and estuaries. Each year, a new statewide set of probability-based 

random sites is selected for each waterbody type. These random sites are sampled on a monthly 

basis for one year. South Carolina’s 2004 Integrated Report (South Carolina DHEC, 2004) 

includes details on site selection. 

South Carolina provides tables comparing assessment results from its traditional 

monitoring program and its probability-based assessment results for rivers and streams and for 

estuaries, including a discussion of the findings. 

For rivers and streams, the traditional approach included data from 630 monitoring 

stations strategically located around the state, many of which include biological 

(macroinvertebrate) and chemistry data. Approximately 15,300 stream miles—or about half the 

state’s total 29,794 stream miles—were assessed using the traditional 305(b) assessment 

approach. 

South Carolina summarized data from a total of 58 randomly located stream sites for the 

probability-based assessment conclusions, 29 of which were sampled in 2001 and 29 of which 

were sampled in 2002 (Table 6). These sites represent the total stream miles in the state, 

weighted by stream size (i.e., based on the relative proportion of small headwater streams, 

second order or intermediate streams, and larger streams to the stream resource as a whole). 
National Water Quality Inventory: 2004 Report to Congress 

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Table 6. Traditional vs. Probability-based Assessment Results for Rivers and Streams in 

South Carolina (South Carolina DHEC, 2004) 

Estimated percent of 

Percent of assessed miles total resource in 

Use Support in category -- traditional category -- probabilityCategory Degree of Use Support 305(b) approach based approach 

Aquatic Life Use Fully supporting 65.3% 79.0% 

Partially supporting 12.1% 5.9% 

Not supporting 22.5% 15.0% 

Recreational Use Fully supporting 59.3% 49.9% 

Partially supporting 21.5% 14.6% 

Not supporting 19.2% 35.5% 

For its probability-based estuarine condition conclusions, the State summarized data from 

60 randomly located estuary sites—30 sampled in 2001 and 30 sampled in 2002. These sites 

represent the total estuarine area in the state. Probability-based approach results were compared 

to the traditional approach, under which 221 square miles of South Carolina’s total 401 square 

miles of estuaries were assessed (Table 7). 

Table 7. Traditional vs. Probability-based Assessment Results for Estuaries in South 

Carolina (South Carolina DHEC, 2004) 

Percent of assessed Estimated percent of 

Use Support 

Catgory Degree of Use Support 

square miles in category 

-- traditional 305(b) 

approach 

total resource in 

category -- probabilitybased approach 

Aquatic Life Use Fully supporting 68.0% 75.3% 

Partially supporting 14.4% 3.0% 

Not supporting 17.6% 21.7% 

Recreational Use Fully supporting 94.1% 100% 

Partially supporting 4.5% -- 

Not supporting 1.4% -- 

Indiana 

In Indiana, probability-based representative samples are used to determine overall aquatic 

life use support, as part of the state’s rotating basin approach (i.e., a plan for monitoring a subset 

of the state’s watersheds on a rotating 5-year cycle, such that in 5 years, all watersheds have been 

cumulatively monitored). A stratified random sampling design is used to generate sampling sites 

and provide a representative sample set for each basin. A fish community Index of Biotic 

Integrity (IBI) is determined for each sampling location, and the results of each year’s sample 

data are analyzed to estimate the percentage of stream miles supporting aquatic life use for each 

basin. This approach allows the state to make statistically valid estimates of aquatic life use 

support for a large geographic area (e.g., a basin) with a relatively small number of 

representative samples. For its 2004 Integrated Report (Indiana DEM, 2004), Indiana’s 

probability-based program found that 22,157 stream miles in the state’s major river basins 
National Water Quality Inventory: 2004 Report to Congress 

34 

supported aquatic life and 13,168 miles did not support uses, for a total of 35,325 river and 

stream miles covered by the probabilistic assessment. 

Indiana’s probability-based sampling design, known as the Watershed Monitoring 

Program, allows the state to predict with reasonable certainty what percentage of its rivers and 

streams are impaired. An individual stream or stream reach is considered assessed only when 

sufficiently detailed monitoring data representative of that stream are available. According to the 

state, the principal advantage of the probabilistic monitoring approach is that it allows the agency 

to meet the goals of assessing all the waters of the state (in terms of the overall quality of each 

basin) while providing data that can also be used to make waterbody-specific assessments. 

Florida 

Florida uses a three-tiered approach to monitor surface water quality, ranging from the 

general to the specific. Tier 1, or probability monitoring, addresses statewide and regional 

questions and is used to develop statistical estimates of statewide water quality based on a 

representative sample. It allows the state to assess 100% of the waters of the state over a 5-year 

period. Tier 2 addresses basin-specific and stream-specific questions (e.g., to verify waterbody 

impairment), and Tier 3 addresses site-specific questions, such as those associated with permits 

and the development of TMDLs. 

The first cycle of the statewide probability assessment through the Integrated Water 

Resource Monitoring Network began in 2000 and was completed in 2003. The results for each 

basin are aggregated by waterbody type and assessed against water quality targets to assess the 

overall health of that type of water in the basin. Florida assessed rivers and streams, large lakes, 

and small lakes using this approach (see Figure 15). 

Figure 15. Summary of statewide condition for Florida rivers and streams (left) 

and large lakes (right) (Florida DEP, 2004). 

Although the report (Florida DEP, 2004) presents preliminary results for the statewide 

probability assessment, it also notes the fundamental differences between this approach and the 

basin and stream assessments of Tier 2. Assessment targets, parameters monitored, and sample 
National Water Quality Inventory: 2004 Report to Congress 

35 

sizes are different between the two types of assessments. The results of the probability network 

should be more representative of statewide conditions and may be able to shed light on any 

biases in the basin and stream assessments due to, for example, the location of monitoring 

stations. The State plans to make comparisons between both types of monitoring approaches as 

its probability network continues to evolve. 
National Water Quality Inventory: 2004 Report to Congress 

36 

IV. Future Reporting 

In March 2003, EPA issued guidance describing the basic elements of a state monitoring 

and assessment program. In response to this guidance, states have prepared long-term strategies 

that address comprehensive monitoring of all water types, including those for which little data 

currently exist. Along with the traditional, targeted monitoring approach, which describes the 

condition of individual waters of concern, probability surveys are an important component of 

comprehensive water monitoring programs, providing a cost-effective means of assessing and 

reporting on status and trends in overall populations of waters (e.g., streams and rivers, lakes). 

In the future, 305(b) reports will be able to provide statistically valid water quality data that is 

comparable across states. 

The states and EPA are taking steps toward streamlining and improving water quality 

monitoring and assessment by integrating monitoring and reporting requirements under sections 

305(b) and 303(d) of the Clean Water Act (see the section Background, Integrated Water Quality 

Reporting of this report). EPA has issued guidance to the states to clarify reporting requirements 

for the 2008 reporting cycle and has established a goal that all 50 states and 6 territories and 

jurisdictions use the integrated reporting format by 2008. EPA continues to promote this 

comprehensive assessment approach to improve the states’ ability to track both programmatic 

and environmental goals of the Clean Water Act, and ideally, to increase the pace of achieving 

these important environmental goals. (See http://www.epa.gov/owow/tmdl/ for more information 

on EPA’s national water quality reporting guidance.) 

Electronic reporting of water quality information is a continuing EPA priority and 

involves a significant commitment at the state and national levels. EPA and the states are 

working to ensure that each assessed watershed and waterbody is identified using a consistent 

national surface water locational system, the National Hydrography Dataset (see 

http://nhd.usgs.gov/ for more information), and that electronic reporting continues to improve. 

EPA intends to continually adapt and improve the ATTAINS database to reflect new reporting 

requirements and the full range of state monitoring activities, including state-scale probabilitybased surveys, and will continue to fully support state efforts to adopt electronic reporting. This 

commitment to providing more comprehensive, easily shared water quality information will help 

managers and the public make more informed decisions about the future of our waters. 
National Water Quality Inventory: 2004 Report to Congress 

37 

V. References 

Florida DEP (Department of Environmental Protection). 2004. Integrated Water Quality 

Assessment for Florida: 2004 305(b) Report and 303(d) List Update. Florida Department of 

Environmental Protection, Division of Water Resource Management, Tallahassee, FL. 

Indiana DEM (Department of Environmental Management). 2004. Indiana Integrated 

Water Quality and Assessment Report. Indiana Department of Environmental Management, 

Indianapolis, IN. 

South Carolina DHEC (Department of Health and Environmental Control). 2004. The 

State of South Carolina’s 2004 Integrated Report. South Carolina Department of Health and 

Environmental Control, Columbia, SC. 

U.S. EPA (Environmental Protection Agency). 2006. Wadeable Streams Assessment.

EPA/841-B-06-002. U.S. Environmental Protection Agency, Office of Water, Washington, DC. 

U.S. EPA (Environmental Protection Agency). 2008. National Coastal Condition Report 

III. EPA/842-R-08-002. U.S. Environmental Protection Agency, Office of Research and 

Development and Office of Water, Washington, DC.