a

GAO

United States Government Accountability Office

Report to Congressional Requesters

July 2005 GREAT LAKES 

INITIATIVE

EPA Needs to Better 

Ensure the Complete 

and Consistent 

Implementation of 

Water Quality 

Standards

GAO-05-829
www.gao.gov/cgi-bin/getrpt?GAO-05-829.

To view the full product, including the scope 

and methodology, click on the link above. 

For more information, contact John 

Stephenson at (202) 512-3841 or 

stephensonj@gao.gov. 

Highlights of GAO-05-829, a report to 

congressional requesters 

July 2005

GREAT LAKES INITIATIVE 

EPA Needs to Better Ensure the Complete 

and Consistent Implementation of Water 

Quality Standards 

GLI has limited potential to improve overall water quality in the Great Lakes 

Basin because it primarily focuses on regulated point sources of pollution, 

while nonpoint sources, such as air deposition and agricultural runoff, are 

greater sources of pollution. GLI’s potential impact is further limited 

because it allows the use of flexible implementation procedures, such as 

variances, whereby facilities can discharge pollutants at levels exceeding 

stringent GLI water quality standards. Finally, many of the chemical 

pollutants regulated by GLI have already been restricted or banned by EPA 

and have a limited presence in point source discharges. 

By 1998, the eight Great Lakes states had largely adopted GLI water quality 

standards and implementation procedures in their environmental regulations 

and NPDES programs. However, EPA determined that some states had 

failed to adopt some GLS provisions or had adopted provisions that were 

inconsistent with GLI and EPA promulgated rules imposing GLI standards. 

Wisconsin officials, however, believe that the state cannot implement 

standards that are not explicitly supported by state law, and disagreements 

with EPA over the rules remain unresolved. As a result, GLI has not been 

fully adopted or implemented in the state. Finally, a major challenge to fully 

achieving GLI’s goals remains because methods for measuring many 

pollutants at the low levels established in GLI do not exist. Consequently, 

some pollutants cannot be regulated at these levels. 

EPA has not ensured consistent GLI implementation by the states nor has 

the agency taken adequate steps toward measuring progress. For example, 

EPA did not issue a mercury permitting strategy to promote consistent 

approaches to the problems posed by mercury as it stated in GLI. In the 

absence of a strategy, states developed permits for mercury that vary from 

state to state. Attempts by EPA to assess GLI’s impact have been limited 

because of inadequate data or information that has not been gathered for 

determining progress on dischargers’ efforts to reduce pollutants. 

Great Lakes Basin Area in the United States and Canada 

The virtual elimination of toxic 

pollutants in the Great Lakes is a 

goal shared by the United States 

and Canada. While some progress 

has been made, pollution levels 

remain unacceptably high. The 

Great Lakes Initiative (GLI) 

requires stringent water quality 

standards for many pollutants in 

discharges regulated by states 

administering National Pollution 

Discharge Elimination System 

(NPDES) permit programs. 

As requested, this report examines 

the (1) GLI’s focus and potential 

impact on water quality in the 

Great Lakes Basin, (2) status of 

GLI’s adoption by the states and 

any challenges to achieving 

intended goals, and (3) steps taken 

by the Environmental Protection 

Agency (EPA) for ensuring full and 

consistent implementation of GLI 

and for assessing progress toward 

achieving its goals. 

GAO recommends that EPA take 

three actions to better ensure full 

and consistent implementation of 

GLI, including issuing a permitting 

strategy for a more consistent 

approach to controlling mercury 

and, resolve disagreements with 

the state of Wisconsin on GLI 

provisions. 

EPA generally agreed with GAO’s 

recommendations. It plans to work 

with the Great Lakes states in 

assessing approaches for reducing 

mercury in lieu of developing a 

mercury permitting strategy. 
Page i GAO-05-829 Great Lakes Initiative

Contents

Letter 1

Results in Brief 3

Background 6

Great Lakes Initiative Has Limited Potential to Impact Overall Water 

Quality 12

States Have Largely Completed Adopting GLI Standards in Their 

Regulatory Programs, but Measuring Some Pollutants at GLI 

Levels Is a Significant Challenge 20

EPA Has Not Ensured Consistent Implementation of GLI Standards 

or Taken Adequate Steps Toward Measuring Progress in 

Achieving GLI Goals 28

Conclusions 35

Recommendations for Executive Action 35

Appendixes

Appendix I: Scope and Methodology 40

Appendix II: Purpose and Status of Bioaccumulative Chemicals of 

Concern (BCC) Identified in GLI 42

Appendix III: Comments from the Environmental Protection Agency 44

Appendix IV: GAO Contact and Staff Acknowledgments 47

Tables Table 1: BCC Discharge Limits in Great Lakes States’ NPDES 

Permits 17

Table 2: State GLI Provisions Disapproved by EPA 23

Figures Figure 1: Area Comprising the Great Lakes Basin 7

Figure 2: Number of Facilities with NPDES Permits in the Great 

Lakes Basin by County 10

Figure 3: Illustration of Point and Nonpoint Sources of 

Pollution 13

Figure 4: Minnesota Mercury Emissions 15
Contents

Page ii GAO-05-829 Great Lakes Initiative

Abbreviations

BCC bioaccumulative chemicals of concern

EPA Environmental Protection Agency

GLI Great Lakes Initiative

GLWQA Great Lakes Water Quality Agreement

NPDES National Pollution Discharge Elimination System

PCS Permit Compliance System

PMP pollutant minimization program

PCB polychlorinated biphenyl

POTW publicly owned treatment works

TMDL total maximum daily load

TRI Toxics Release Inventory

WET whole effluent toxicity

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Page 1 GAO-05-829 Great Lakes Initiative

United States Government Accountability Office

Washington, D.C. 20548

A

July 27, 2005 Letr

Congressional Requesters:

Millions of people in the United States and Canada depend on the Great 

Lakes—the largest system of freshwater in the world—as a source of 

drinking water, recreation, and economic livelihood. Over the last several 

decades, the Great Lakes Basin—which includes the five Great 

Lakes—Superior, Michigan, Huron, Ontario, and Erie—and a large land 

area that extends beyond the lakes, including their watersheds, tributaries, 

and connecting channels, has proven vulnerable to the effects of toxic 

pollutants as a result of industrial, agricultural, and residential 

development. During the 1970s, it became apparent that certain toxic 

chemicals such as mercury and dioxin, can accumulate over time in aquatic 

species, such as fish, posing risks to those species as well as humans and 

wildlife that consume fish from the Great Lakes Basin. These chemicals, 

known as bioaccumulative chemicals of concern (BCC), are discharged 

into the basin from point sources, such as industrial or municipal facilities’ 

pipes and drains, or from nonpoint sources, which include air emissions 

mainly from coal-fired power plants, agricultural runoff, and sediments 

highly contaminated from past industrial practices. 

The United States and Canada have undertaken a variety of binational 

initiatives to improve environmental conditions in the Great Lakes Basin. 

In 1972, the two countries signed the first international Great Lakes Water 

Quality Agreement (GLWQA) to restore and enhance water quality in the 

lakes. In 1978, the parties signed a second GLWQA reaffirming the goals of 

the earlier agreement and calling for increased control over the discharge 

of toxic pollutants, such as BCCs, and their virtual elimination throughout 

the Great Lakes Basin. While progress has been made to control these toxic 

pollutants, inconsistencies developed in the way pollutants from point 

sources were controlled by the eight states bordering the Great Lakes. In 

1989, to promote consistency in Great Lakes states’ environmental 

regulatory programs, the eight states began developing a framework for 

coordinating regional action for controlling point sources of toxic 

pollution, based on the 1986 Great Lakes Toxic Substances Control 

Agreement or “the Governors’ Agreement.” Controlling point sources of 

pollution was already under way through the implementation of the 

National Pollution Discharge Elimination System (NPDES) program 

authorized in 1972 by the Clean Water Act. In most cases, states administer 

the NPDES program, which regulates the discharge of pollutants into 
Page 2 GAO-05-829 Great Lakes Initiative

surface waters of the United States from industrial, municipal, and other 

facilities through permits. 

In 1990, the Great Lakes Critical Programs Act amended the Clean Water 

Act to require the U.S. Environmental Protection Agency (EPA) to publish 

final guidance for the Great Lakes states, conforming to the objectives and 

provisions of the GLWQA, on minimum water quality standards, 

implementation procedures, and antidegradation policies for protecting 

existing water quality. The act required states to adopt provisions 

consistent with these standards, procedures, and policies.1

 In 1995, EPA 

issued the Final Water Quality Guidance for the Great Lakes System, also 

known as the Great Lakes Initiative (GLI). To control toxic substances and 

protect aquatic life, wildlife, and human health, GLI sets forth water quality 

criteria for 29 toxic substances, including BCCs and it primarily focused on 

22 BCC pollutants, such as mercury, polychlorinated biphenyls (PCB), and 

dioxin. Mercury is the most prevalent BCC in the Great Lakes Basin and 

poses a significant threat to human health. GLI also contains detailed 

methodologies for developing criteria for additional pollutants and 

implementation procedures for developing more consistent, enforceable 

water quality-based effluent limits in NPDES discharge permits for point 

sources of pollution. The eight Great Lakes states—Illinois, Indiana, 

Michigan, Minnesota, New York, Ohio, Pennsylvania, and Wisconsin—are 

responsible for implementing GLI, which provides them some flexibility in 

implementing water quality standards. EPA’s Regions 2, 3, and 5 are 

responsible for ensuring the adoption and implementation of GLI by the 

states. The NPDES program and the GLI are strictly U.S. efforts and do not 

apply to Canada, which follows a different approach to regulating point 

source pollution. 

You asked us to examine (1) the focus of GLI and its potential to impact 

water quality in the Great Lakes Basin; (2) the status of GLI’s adoption by 

the states and the challenges, if any, to achieving GLI’s intended goals; and 

(3) steps EPA has taken for ensuring the full and consistent implementation 

of GLI and for assessing progress toward achieving GLI’s goals. Because of 

the prevalence of mercury in the Great Lakes Basin, this report focuses on 

control of this pollutant. 

1

EPA has interpreted the term “consistent with GLI” to mean as environmentally protective 

as GLI. The Court of Appeals for the D.C. Circuit has upheld this interpretation as 

reasonable under the Clean Water Act. American Iron and Steel Inst. v. EPA, 115 F.3d 979 

(D.C. Cir. 1997).
Page 3 GAO-05-829 Great Lakes Initiative

To determine the focus of GLI and its potential to affect water quality in the 

Great Lakes Basin, we reviewed the finalized GLI requirements and 

available data on the major sources of toxic pollutants in the Great Lakes 

Basin. We obtained information on the impact of GLI from officials of 

several state and other environmental organizations, including officials that 

were involved in developing GLI. To determine the status of GLI’s adoption 

by the states, we examined EPA regulations and analyzed documents 

pertaining to EPA’s review of state submissions under GLI to identify any 

remaining unresolved matters. To identify challenges that might exist to 

achieve GLI’s intended goals, we reviewed the water quality criteria 

established for individual pollutants in GLI, particularly BCCs, and 

analyzed information provided by EPA and state officials to determine if 

any challenges existed. To identify the steps EPA has taken for ensuring the 

full and consistent implementation of GLI, we reviewed GLI to identify the 

activities EPA committed to undertake and obtained information from EPA 

and Great Lakes state officials on the status of implementation, including 

any consequences resulting from delays in implementation. To determine 

the steps taken by EPA for assessing progress toward achieving GLI’s goals, 

we reviewed efforts by EPA Region 5 officials to determine progress made 

under GLI for improving water quality, including the agency’s analysis of 

available databases, and its efforts in monitoring of the states’ 

implementation of GLI. We performed our work from October 2004 to June 

2005 in accordance with generally accepted government auditing 

standards. A more detailed discussion of our scope and methodology is 

outlined in appendix I. 

Results in Brief GLI has limited potential to improve overall water quality in the Great 

Lakes Basin because it focuses primarily on point sources of pollution 

regulated by state NPDES programs rather than nonpoint sources, such as 

air deposition and agricultural runoff, which are a greater source of 

pollution. While the importance of nonpoint sources of pollution was 

mentioned in GLI, they were not specifically addressed. GLI’s ability to 

impact overall water quality is further limited because under certain 

circumstances it lets states use flexible implementation procedures, such 

as variances, when issuing permits for facilities, allowing them to discharge 

pollutants at levels exceeding stringent GLI water quality standards. Thus, 

while mercury is the only BCC with a significant number of permit limits 

established as a result of GLI, the discharger is often allowed to exceed 

mercury water quality standards in GLI because states have granted them 

variances, limiting GLI’s ability to impact water quality. GLI’s incremental 

impact is also limited by the fact that many of the BCCs regulated by GLI 
Page 4 GAO-05-829 Great Lakes Initiative

had already been previously restricted or banned by EPA. For example, 

certain pesticides targeted by GLI were banned in the 1970s and 1980s. 

Consequently, many of these chemicals are not present or are present only 

at low levels in Great Lakes point source discharges. While these factors 

limit GLI’s incremental ability to impact overall water quality in the Great 

Lakes, its effective implementation is still important because the virtual 

elimination of toxic pollutants remains a goal and controls on point source 

discharges are still needed to meet this goal. 

While EPA has concluded that the Great Lakes states have largely 

completed adopting GLI provisions in their regulatory programs, 

measuring some pollutants at GLI levels is a significant challenge to 

implementing the stringent water quality standards called for in GLI. By 

1998, the eight Great Lakes states had generally incorporated provisions 

consistent with GLI—including water quality criteria and implementation 

procedures—into their environmental regulations and NPDES permit 

programs. However, in 2000, EPA determined that six states had either 

failed to adopt some GLI provisions or had adopted some provisions that 

were inconsistent with GLI guidance. EPA promulgated rules disapproving 

these elements of the six states’ submissions and imposing the GLI 

standards. In Wisconsin, however, officials believe that the state cannot 

implement standards that are not explicitly supported by state law, and 

disagreements over certain GLI provisions between state and EPA officials 

have continued since 2000. As a result, GLI is not fully adopted or 

implemented in the state. While provisions consistent with GLI have largely 

been adopted in other state programs, a significant obstacle exists to 

achieving GLI’s intended goals. Specifically, many of the BCCs cannot be 

measured at the low level of GLI water quality criteria because sufficiently 

sensitive measurement methods do not exist. It is difficult to accurately 

assess the need for, or implement a permit limit for a pollutant when its 

presence in a facility’s discharge cannot be measured at the level 

established by the water quality standard. For example, when GLI was 

issued, mercury could only be measured at levels many times greater than 

its GLI water quality criteria. With the development of a new measurement 

method, a much more widespread and pervasive problem with mercury 

levels was found, resulting in many more facilities being required to have 

mercury discharge limits and monitoring requirements in their permits. In 

the case of other BCCs, such as PCBs, methods to measure at low levels 

have not been developed. 

EPA has not ensured the consistent implementation of GLI across the Great 

Lakes states or taken adequate steps to measure progress toward achieving 
Page 5 GAO-05-829 Great Lakes Initiative

GLI’s goals. Of particular note, to promote a uniform and consistent 

approach to the problems posed by mercury, EPA stated in GLI that it was 

committed to issuing a mercury permitting strategy for the Great Lakes 

Basin no later than 2 years after publishing GLI. Although EPA drafted a 

strategy, it was never issued because the agency perceived a general lack of 

public interest, and agency resources were directed to other GLI activities, 

according to EPA officials. In the absence of an EPA strategy, individual 

states developed permits for mercury that vary from state to state. For 

example, in Michigan, variances for dischargers allowing them to exceed 

mercury water quality standards are based on discharge levels that the 

state regulatory agency considers achievable by most dischargers in the 

state, while in Ohio, discharge levels are based on the level currently 

achievable by the individual facility. Such different approaches fail to 

promote the consistent implementation of water quality standards as 

envisioned by GLI. In addition, GLI stated that EPA Region 5, in 

cooperation with EPA Regions 2 and 3 and headquarters would establish a 

GLI Clearinghouse—a database that would allow states to share 

information for developing and updating consistent water quality 

standards. While development of the Clearinghouse was initiated in 1996, 

because of other agency priorities it was not made available to the states 

until 2005. In the absence of the Clearinghouse, some states developed 

their own water quality standards without the benefits of this shared 

information. As a result, EPA cannot be assured the Great Lakes states 

have adequate information to develop and update water quality standards 

in a consistent manner, which is a guiding GLI principle. Finally, EPA has 

been unable to sufficiently assess the impact of GLI with existing data 

sources and has not gathered additional information to monitor progress. 

The automated system that tracks NPDES permits does not provide 

accurate information that can be used to determine whether pollutant 

discharges have decreased under GLI. EPA Region 5 officials are 

attempting to assess the impact of GLI by comparing individual permits 

before and after GLI requirements, but this effort has yet to yield even 

preliminary results. EPA has also not assessed the impact of programs 

required by permits for minimizing pollutants that might exceed GLI 

standards. 

To better ensure the full and consistent implementation of GLI and improve 

measures for monitoring progress toward achieving GLI’s goals, we are 

making a number of recommendations to EPA aimed at issuing a mercury 

permitting strategy, fully developing a GLI Clearinghouse, and collecting 

information on the impact of discharger plans to minimize pollutants, 

among other actions. 
Page 6 GAO-05-829 Great Lakes Initiative

In commenting on this report, EPA believes that we did not effectively 

consider other benefits from GLI and that differences in how states address 

mercury in NPDES permits does not result in an unacceptable level of 

inconsistency. EPA plans to assist and work with the Great Lakes states in 

assessing the most effective approaches for reducing mercury loadings by 

dischargers. It will continue efforts to develop the Clearinghouse, collect 

information on pollutant minimization programs, and work with the state 

of Wisconsin to resolve outstanding issues. 

Background The Great Lakes and their connecting channels form the largest system of 

freshwater on earth. Covering more than 94,000 square miles, they contain 

about 84 percent of North America’s surface freshwater and 21 percent of 

the world’s supply. The lakes provide water for a multitude of activities and 

occupations, including drinking, fishing, swimming, boating, agriculture, 

industry, and shipping for more than 30 million people who live in the Great 

Lakes Basin—which encompasses nearly all of the state of Michigan and 

parts of Illinois, Indiana, Minnesota, New York, Ohio, Pennsylvania, 

Wisconsin, and the Canadian province of Ontario. 
Page 7 GAO-05-829 Great Lakes Initiative

Figure 1: Area Comprising the Great Lakes Basin

During the 1970s, it became apparent that pollution caused by persistent 

toxic substances, such as BCCs, was harming the Great Lakes and posing 

risks to human health and wildlife. On average, less than 1 percent of the 

Great Lakes’ water recycles or turns over each year, and many pollutants 

stay in place, settling in sediments or bioaccumulating in organisms. As a 

result, under the GLWQA of 1978, the United States and Canada agreed to a 

policy of prohibiting the discharge of harmful pollutants in toxic amounts 

and virtually eliminating the discharge of such pollutants. The two parties 

also pledged to develop programs and measures to control inputs of 

persistent toxic substances, including control programs for their 

production, use, distribution, and disposal. The concept of virtual 

elimination recognizes that it may not be possible to achieve total 

elimination of all persistent toxic substances. Some toxic substances may 

be produced by or as a result of natural processes, persist at background or 

natural levels, or cannot be eliminated for technological or economic 

reasons. 

Lake Superior

Lake

Michigan

Lake

Huron

Lake

Ontario

Lake

Erie

Chicago

Milwaukee

Cleveland

Detroit

Toronto

IL

IN

MI

NY

OH

PA

WI

MN

Ontario

Quebec

Great Lakes Basin

Sources: GAO, MapArt. 
Page 8 GAO-05-829 Great Lakes Initiative

In addition to agreeing to a policy calling for the virtual elimination of toxic 

pollutants, the 1978 GLWQA, as amended, also established a process and 

set of commitments to address the pollutant problem. Other joint United 

States and Canada toxic reduction efforts were initiated in subsequent 

years, in keeping with the objectives of the agreement. These included the 

1991 Binational Program to Restore and Protect the Lake Superior 

Basin—which, among other things, established a goal of achieving zero 

discharge of designated persistent and bioaccumulative toxic substances 

from point sources in the Lake Superior Basin. In addition, recognizing the 

long-term need to address virtual elimination, the EPA Administrator and 

Canada’s Minister of the Environment signed the Great Lakes Binational 

Toxics Strategy in 1997, which provides a framework for actions to reduce 

or eliminate persistent toxic substances, especially those that 

bioaccumulate in the Great Lakes Basin. 

Agreements within the two countries also addressed the problem of toxic 

pollutants and the implementation of the GLWQA. In the United States, the 

Governors’ Agreement in 1986 developed by the Council of Great Lakes 

Governors recognized that the problem of persistent toxic substances was 

the foremost environmental issue confronting the Great Lakes, and they 

were committed to managing the Great Lakes as an integrated ecosystem. 

At that time, inconsistencies in state standards and implementation 

procedures became an increasing concern to EPA and state environmental 

managers. The Governors agreed to work together to, among other things, 

establish a framework for coordinating regional action in controlling toxic 

pollutants entering the Great Lakes Basin, increase federal emphasis on 

controlling toxic pollution, and expedite the development of additional 

national criteria or standards for toxic substances to protect both the 

ecosystem and human health. In Canada, the Canadian and Ontario 

governments entered into several agreements with each other over the last 

30 years to address environmental problems in the Great Lakes. These 

agreements, each referred to as the Canada-Ontario Agreement 

Respecting the Great Lakes Basin Ecosystem, included a focus on the 

control of toxic chemical pollution and runoff. In addition, a 2002 

agreement outlines how these two governments will continue to work 

together to focus efforts to help clean up the Great Lakes Basin ecosystem. 

Several priority projects are planned under the agreement, including 

reducing the amount of harmful pollutants, such as mercury, that find their 

way into the Great Lakes.

To further control toxic substances in the United States, efforts on the GLI 

began in the late 1980s to establish a consistent level of environmental 
Page 9 GAO-05-829 Great Lakes Initiative

protection for the Great Lakes ecosystem, particularly in the area of state 

water quality standards and NPDES programs for controlling point sources 

of pollution. As authorized by the Clean Water Act, the NPDES permit 

program controls water pollution by regulating point sources that 

discharge pollutants into U.S. surface waters. Under NPDES, all facilities 

that discharge pollutants from any point source into U.S. waters are 

required to obtain a permit that provides two levels of control: (1) 

technology based limits (discharge limits attainable under current 

technologies for treating water pollution) and (2) water quality-based 

effluent limits (based on state water quality standards). Point sources are 

discrete conveyances such as pipes or constructed ditches. Individual 

homes that are connected to a municipal system, use a septic system, or do 

not have a surface discharge, do not need an NPDES permit; however, 

industrial, municipal, and other facilities must obtain permits if their 

discharges go directly to surface waters. As of May 2005, there were nearly 

5,000 facilities in the Great Lakes Basin that had NPDES permits, and over 

500 of these were considered major facilities.2

2

Major dischargers include municipalities with capability to discharge greater than one 

million gallons per day and certain industrial facilities based on ratings by EPA and the 

states.
Page 10 GAO-05-829 Great Lakes Initiative

Figure 2: Number of Facilities with NPDES Permits in the Great Lakes Basin by 

County 

Note: Data provided by state officials, from February through May 2005.

In 1989, the Council of Great Lakes Governors agreed to join EPA in 

developing GLI because it supported the goal of consistent regulations 

among the Great Lakes states. The effort to develop GLI was under way 

when Congress amended the Clean Water Act with the passage of the Great 

Lakes Critical Programs Act of 1990. This act required EPA to publish by 

June 1992, final water quality guidance for the Great Lakes System that 

conformed to the objectives and provisions of the GLWQA. It further 

required the states to adopt water quality standards, antidegradation 

policies, and implementation procedures consistent with the guidance no 

later than 2 years after it was published. If the states failed to adopt such 

water quality standards, policies, and procedures consistent with the 

guidance, EPA was to promulgate them not later than the end of the 2-year 

period. In making such a determination, EPA reviewed the states water 

quality standards, antidegradation policies, and implementation 

procedures for consistency with the guidance. 

To control toxic substances and protect aquatic life, wildlife, and human 

health, GLI sets forth water quality criteria for 29 toxic substances, such as 

PCBs, mercury, dioxin, and chlordane. These criteria include standards for 

Sources: State NPDES program officials, GAO, MapArt.

Permitted facilities by county

1 to 25

26 to 50

51 to 75

More than 75

MI

MN WI

IL

IN OH

PA

NY
Page 11 GAO-05-829 Great Lakes Initiative

9 of 22 BCCs. GLI also contains detailed methodologies for developing 

criteria for additional pollutants and implementation procedures for 

developing more consistent, enforceable water quality-based effluent limits 

in discharge permits for point sources of pollution. The most common of 

the 22 BCCs currently being discharged from point sources in the Great 

Lakes Basin is mercury. Because mercury can be highly toxic and travel 

great distances in the atmosphere, it has long been recognized to have a 

wide range of detrimental effects for ecosystems and human health. When 

mercury is deposited within a water body, microorganisms can transform it 

into a very toxic substance known as methyl mercury. Methyl mercury 

tends to remain dissolved in water and can bioaccumulate in the tissues of 

fish to concentrations much higher than in the surrounding water. The 

primary way people are exposed to mercury is by eating fish containing 

methyl mercury. Poisoning can result from eating fish contaminated with 

bioaccumulated methyl mercury, which is dangerous to certain adults, 

children, and developing fetuses. 

Three general principles guided the development of GLI: (1) to incorporate 

the best science available to protect the Great Lakes Basin ecosystem; (2) 

to promote consistency in standards and implementation procedures in 

Great Lakes states’ water quality standards while allowing appropriate 

flexibility; and (3) to reflect the unique nature of the Great Lakes Basin 

ecosystem by establishing special provisions for toxic substances, such as 

BCCs. Although improved consistency in Great Lakes states’ water quality 

standards and NPDES programs was a primary goal of GLI, implementing 

and supplemental regulations published by EPA provided flexibility to 

states in adopting and implementing GLI provisions in several areas.3

 These 

regulations included relief from GLI provisions for point source 

dischargers through the use of existing NPDES program provisions such as 

variances, mixing zones, and compliance schedules. For example, 

provisions in GLI allow the states to grant dischargers variances for up to 5 

years from GLI water quality standards, which are the basis of a water 

quality based effluent limitation included in NPDES permits. According to 

GLI, variances are to apply to individual dischargers requesting permits and 

apply only to the pollutant or pollutants specified in the variance. 

3

60 Fed. Reg. 15366 (Mar. 23, 1995). 
Page 12 GAO-05-829 Great Lakes Initiative

Great Lakes Initiative 

Has Limited Potential 

to Impact Overall 

Water Quality

GLI has limited potential to incrementally improve water quality in the 

Great Lakes Basin because first, it primarily focuses on point sources, 

which are not the major source of certain toxic pollutants that currently 

affect the Great Lakes Basin. Moreover, once GLI was implemented, few 

NPDES permits included limits for BCCs because they were not in 

discharges, and many of these BCCs were already regulated or banned 

before the GLI guidance was issued. Finally, for mercury, which is the BCC 

that is most frequently controlled in NPDES permits, GLI provisions 

provide flexible implementation procedures, including variances, that 

under certain circumstances are used by states to allow dischargers relief 

from the more stringent water quality standards. The stringent water 

quality standards may be either technically or economically unattainable by 

dischargers. 

GLI’s Primary Focus Is on 

Point Sources Which Are 

Not the Major Source of 

Many Toxic Pollutants

A primary focus of GLI is to establish consistent water quality standards 

within the Great Lakes Basin, which apply to all sources of pollutants but 

mainly to point sources. Thirty-three years ago, point sources of pollution 

were the basis for the establishment of the NPDES program and the major 

cause of poor water quality in the Great Lakes Basin. In implementing this 

program, it was recognized that controlling point sources was an important 

means of reducing pollutants discharged into waterways by requiring 

permits that specified allowable levels of pollutants. Since the introduction 

of the NPDES program there have been significant water quality 

improvements in the Great Lakes Basin. Currently, however, nonpoint 

sources of certain toxic pollutants are a significant threat to overall water 

quality in the Great Lakes Basin and other areas within the United States 

and Canada. Nonpoint sources of pollutants often impact overall water 

quality through runoff from agricultural processes or releases into the air 

from industrial facilities, which are then deposited into the Great Lakes. 

For example, major sources of mercury released into the air include 

coal-fired power plants, industrial boilers, and waste incinerators that burn 

materials containing mercury. Much, if not most, of the mercury entering 

the Great Lakes is from atmospheric deposition. EPA Great Lakes National 

Program Office officials stated that air deposition is likely responsible for 

more than 80 percent of mercury loadings into the Great Lakes.4

 Currently, 

4

The Clean Water Act established the Great Lakes National Program Office within EPA, 

charging it to, among other things, develop and implement specific action plans to carry out 

responsibilities under the GLWQA.
Page 13 GAO-05-829 Great Lakes Initiative

nonpoint sources of pollution are more difficult to regulate than point 

sources because it is more difficult to determine the specific sources of 

pollutants. The dynamic nature of various source pollution is illustrated 

below. 

Figure 3: Illustration of Point and Nonpoint Sources of Pollution

Contaminated

sediment

Agricultural

runoff

Runoff

Urban and

ground water

runoff

Source: GAO depiction of EPA data.

Rain or snow

Atmospheric deposition

Point source discharge
Page 14 GAO-05-829 Great Lakes Initiative

Several state and environmental officials commented that while GLI 

resulted in states becoming more aware of the need to attain water quality 

standards for BCCs from point sources, it did not specifically address the 

larger problem of nonpoint sources of pollution. For example, Minnesota 

officials stated that they do not anticipate any water quality improvements 

from GLI for mercury, the most prevalent BCC in the Lake Superior Basin, 

because GLI does not specifically address nonpoint sources, such as 

atmospheric deposition. A 2004 state study estimated that 99 percent of 

mercury in Minnesota lakes and rivers comes from atmospheric deposition. 

The study concluded that although 30 percent of mercury atmospheric 

deposition in Minnesota is the result of natural cycling of mercury, 70 

percent is the result of human activities, such as the release of trace 

concentrations that are naturally present in the coal used by power plants, 

and in the mining and processing of taconite ore, which is used to produce 

iron and steel. Of the mercury atmospheric deposition in Minnesota, it is 

estimated that 10 percent of this is from emissions within Minnesota. The 

sources of mercury atmospheric deposition from within Minnesota are 

shown in figure 4.
Page 15 GAO-05-829 Great Lakes Initiative

Figure 4: Minnesota Mercury Emissions 

Note: The “other” category includes sources such as natural gas, wood, and fluorescent lamp 

breakage, which each, individually, make up less than 1 percent of the total. Due to rounding total 

percentage of individual categories exceeds 100 percent.

While the focus of GLI is on point sources, the importance of controlling 

nonpoint sources of pollution to improve overall water quality in the Great 

Lakes is recognized in GLI guidance. The guidance states that once GLI is 

implemented by the states, water quality criteria for pollutants and other 

provisions that are included in the guidance would be applied to nonpoint 

sources. However, according to the guidance, to be implemented, nonpoint 

source provisions would need to be enforced through the states’ own 

regulatory programs. GLI also promotes the use of total maximum daily 

loads (TMDL) as the best approach for equitably addressing both point

Coal

Taconite processing

Waste incineration

Volatization of disposed products

Smelters that recycle cars and appliances

Petroleum

3%

Dental preparations

2%

Crematories

1.6%

Other

1.4%

Recycling mercury from products

5%

5%

7%

10.2%

21%

46%

Sources: GAO and Minnesota Pollution Control Agency.
Page 16 GAO-05-829 Great Lakes Initiative

and nonpoint sources.5 TMDLs for the Great Lakes are also addressed in 

the Great Lakes Strategy 2002, which was developed by the U.S. Policy 

Committee for the Great Lakes.6

 The strategy has an objective that TMDLs 

for each of the Great Lakes and impaired tributaries will be completed by 

2013; but according to EPA officials, TMDLs for BCCs have not been 

established for any of the Great Lakes, and only two TMDLs for BCCs have 

been completed for tributaries. 

Few Permits Contain Limits 

for Toxic Pollutants, and 

Many Toxic Pollutants Are 

Already Restricted or 

Banned 

While GLI identified many toxic pollutants, few NPDES permits currently 

limit the discharge of these pollutants, particularly BCCs, because they are 

either not present in discharge water or the pollutants are already 

restricted or banned. BCCs are still present in some facilities’ discharges 

and are regulated by NPDES permits, but while there are nearly 5,000 

permits for facilities in the Great Lakes Basin, there are only about 250 

discharge limits for BCCs, according to Great Lake states’ officials. Five of 

the eight states reported that they had discharge limits for BCCs in the 

Great Lakes Basin.7

 Further, not only are there relatively few BCC 

discharge limits in permits, but most, 185, are for mercury—with Michigan 

issuing the most discharge limits of the five states. The number of BCC 

discharge limits by state and pollutant is shown in table 1. 

5

TMDLs are limits for identified pollutants in impaired water bodies identified by the states 

as required by the Clean Water Act.

6

The U.S. Policy Committee is a group of senior level representatives from federal, state, and 

tribal government agencies with environmental protection or natural resource 

responsibilities in the Great Lakes Basin. 

7

The information presented is based on data reported from Great Lakes states’ permit 

officials. The states of Illinois, Pennsylvania, and Wisconsin reported that none of their 

permits in the Great Lakes Basin establish discharge limits for BCCs. 
Page 17 GAO-05-829 Great Lakes Initiative

Table 1: BCC Discharge Limits in Great Lakes States’ NPDES Permits

Sources: GAO and state NPDES program officials.

Note: Data provided by state officials, from February through May 2005.

a

Ohio officials provided an estimate of 1-5 PCB discharge limits in Great Lakes Basin permits. The 

number “3” is used as an approximation.

Several of the pollutants addressed by GLI had their use restricted or 

banned by EPA in the 1970s and 1980s and therefore are not used by 

facilities or found in their discharges. Of the 22 BCCs covered by GLI, at 

least 12 are either banned or are no longer produced in the United States. 

Some of the banned BCCs, such as toxaphene and dieldrin, are pesticides 

and insecticides that are likely to be present in the Great Lakes Basin water 

bodies as contaminated sediments from prior agricultural runoff rather 

than municipal and industrial point source discharges. Other BCCs, such as 

lindane, are no longer produced in the United States, while others, such as 

mirex and hexachloracyclohexane, are no longer produced or used in the 

United States. See appendix II for BCCs identified in GLI and whether they 

have been banned, restricted, or are still in use. 

While the preceding factors limit GLI’s potential to improve overall water 

quality in the Great Lakes, its effective implementation is still important 

because the virtual elimination of toxic pollutants in the Great Lakes Basin 

remains a goal for the United States and Canada. Controlling point source 

pollution is still needed to meet this objective. Although point source 

discharges of toxic pollutants are not as widespread as nonpoint sources, 

point source discharges may create localized “hot spots” of elevated 

concentrations of BCCs. These areas can have potentially adverse effects 

on aquatic life, wildlife, and humans. For example, while the major sources 

of mercury are nonpoint sources, it is still the most prevalent BCC found in 

Illinois Indiana Michigan Minnesota New York Ohio Pennsylvania Wisconsin Total

Mercury 0 20 83 2 37 43 0 0 185

PCBs 0 1 10 1 10 3a 0 0 25

Dioxin 0 0 2 1 0 0 0 0 3

Lindane 0 0 2 0 2 0 0 0 4

Hexachlorobenzene 0 0 2 0 4 0 0 0 6

Hexachlorobutadiene 0 0 2 0 3 0 0 0 5

Other 0 0 2 0 16 0 0 0 18

Total 0 21 103 4 72 46 0 0 246

Great Lakes Basin 

Permitted Facilities 12 150 1753 89 1275 1041 84 319 4723
Page 18 GAO-05-829 Great Lakes Initiative

point source discharges overall in the Great Lakes, and heavy 

concentrations of mercury in these hot spots may result in its 

bioaccumulation in fish to levels that are dangerous to both humans and 

wildlife that consume them. Achieving GLI’s objective to have consistent 

water quality standards for controlling point sources of toxic pollutants 

may prove difficult, however, because of flexible implementation 

procedures that allow discharge of pollutants at levels greater than GLI 

water quality standards. 

Many NPDES Permits Allow 

for Dischargers’ Mercury 

Pollutant Levels to Exceed 

GLI Standards

Many NPDES permits for facilities in the Great Lakes Basin allow the 

discharge of mercury at levels greater than the GLI water quality standard. 

Flexible implementation procedures such as variances are widely used to 

allow dischargers to exceed the strict GLI mercury water quality standard 

of 1.3 nanograms per liter of water (ng/L). GLI allows states to grant 

variances for complying with the mercury and other water quality 

standards under certain circumstances, such as if the imposition of water 

quality standards would result in substantial and widespread harmful 

economic and social impact. Variances are applicable only to the permit 

holder requesting the variance for up to 5 years and are only available for 

dischargers that were in existence as of March 23, 1997.8

 New facilities are 

not eligible for variances and must comply with the water quality standard 

for mercury established under GLI. Officials in two states—Minnesota and 

Michigan—expressed concerns that new industrial facilities that discharge 

mercury may not locate in the state because of their inability to comply 

with the mercury standard. 

The use of variances for mercury became a more critical concern when 

new methods to measure the pollutant were approved by EPA in 1999, 

allowing mercury to be measured at a quantification level of 0.5 ng/L, below 

the GLI water quality standard of 1.3 ng/L.9

 This method was 400 times 

more sensitive than the one previously used by EPA and allowed the very 

low GLI limits to be quantified for the first time, causing potentially 

widespread problems for Great Lakes Basin dischargers that discovered for 

the first time that they were exceeding the mercury water quality criteria, 

8

Variances may be renewed along with the renewal of a NPDES permit, which may be issued 

for up to 5 years. 

9

A quantification level is the lowest concentration of a contaminant that can be 

quantitatively measured using a specific laboratory procedure.
Page 19 GAO-05-829 Great Lakes Initiative

according to state NPDES program officials. Using the more sensitive 

method, many more facilities were found to have levels of mercury in their 

effluent that exceeded water quality standards. State and EPA officials also 

determined that no economically feasible treatment technologies existed to 

reduce mercury to the lower level, and states were unwilling to issue 

permits that placed facilities in noncompliance. Michigan officials stated 

that they knew of only one permitted facility that was able to comply with 

the lower standard. As a result, states issued variances under their GLI 

regulations that provide for the most efficient short-term relief to 

“ubiquitous” pollutants, and EPA encouraged states to consider variances 

for multiple dischargers on a watershed basis, where appropriate.10 EPA 

wanted to provide the states appropriate flexibility in adopting and 

implementing GLI’s requirements, while also maintaining a minimum level 

of consistency. To facilitate granting variances for numerous facilities 

exceeding the mercury standard, three states—Indiana, Ohio, and 

Michigan—adopted procedures that expedited and simplified the variance 

application and granting process. 

While variances are widely used under GLI, mixing zones and compliance 

schedules are also options that states may use under GLI. Mixing zones are 

areas around a facility’s discharge pipe where pollutants are mixed with 

cleaner receiving waters to dilute their concentration. Within the mixing 

zone, concentrations of toxic pollutants, such as mercury, are generally 

allowed to exceed water quality criteria as long as standards are met at the 

boundary of the mixing zone. Several Great Lakes states no longer allow 

the use of mixing zones for BCCs in their permits, and GLI authorization for 

their use by all existing BCC dischargers expires in November 2010.11

Mixing zones, as with variances, are not authorized for new dischargers. 

Compliance schedules are another option and grant dischargers a grace 

period of up to 5 years before they must comply with certain new or more 

restrictive permit limits. Similar to mixing zones, compliance schedules are 

also not available to new dischargers in the Great Lakes Basin and are only 

available for existing permits reissued or modified on or after March 23, 

1997. According to state officials, Minnesota uses compliance schedules for 

10Final Water Quality Guidance for the Great Lakes System: Supplementary Information 

Document (SID), EPA, 1995, 820-B-95-001.

11EPA’s initial 1995 mixing zone provision under the GLI was vacated by the U.S. Court of 

Appeals for the District of Columbia Circuit in American Iron & Steel Institute v. EPA, 115 

F.3d 979 (D.C. Cir. 1997) and was remanded to EPA for further consideration. EPA 

promulgated a final rule in 2000 in response. 65 Fed. Reg. 67638 (Nov. 13, 2000).
Page 20 GAO-05-829 Great Lakes Initiative

existing dischargers to issue permits for facilities that have mercury levels 

above GLI water quality criteria. These schedules extend no later than 

March 2007, and then the GLI water quality standard of 1.3 ng/L must be 

met, unless a variance is granted, according to a state official. 

States Have Largely 

Completed Adopting 

GLI Standards in Their 

Regulatory Programs, 

but Measuring Some 

Pollutants at GLI 

Levels Is a Significant 

Challenge 

By 1998, the Great Lakes states largely completed adopting GLI provisions 

in their regulatory programs by incorporating GLI standards in their 

environmental regulations and NPDES permit programs. Upon reviewing 

state regulations, however, EPA found that several states had either failed 

to adopt some GLI provisions or adopted provisions that were inconsistent 

with GLI guidance. As a result, EPA promulgated regulations applying 

certain GLI provisions to some states, but issues surrounding the 

implementation of these provisions, particularly in Wisconsin, have not 

been fully resolved. Further, while GLI provisions have been adopted in 

most state programs, a significant obstacle exists to achieving GLI’s 

intended goals, in that many BCCs targeted by GLI cannot be measured at 

the low level of GLI water quality criteria because sufficiently sensitive 

measurement methods do not exist. Without the ability to measure to the 

water quality criteria, it is difficult to accurately determine whether there is 

a need for a pollutant permit limit for a facility’s discharge. 

Great Lakes States Have 

Generally Incorporated GLI 

Provisions into Their 

Regulations and NPDES 

Programs 

GLI provisions have generally been incorporated into state regulations and 

NPDES programs, but this did not occur within the statutory time frame; 

and, as a result, two lawsuits were filed against EPA to implement the 

requirements of the Great Lakes Critical Programs Act of 1990. This act, 

which amended the Clean Water Act, required the Great Lakes states to 

adopt standards, policies, and procedures consistent with GLI within 2 

years of its publication. The act further required EPA to issue GLI 

standards by the end of that 2-year period for any state that had failed to do 

so. EPA, however, did not issue GLI standards by the required date for 

those states that had failed to develop standards. Consequently, in July 

1997, the National Wildlife Federation filed a lawsuit to force EPA to take 

action. In response, EPA negotiated a consent decree providing that it must 

make GLI provisions effective in any state that failed to make a submission 

by February 1998. EPA was never forced to take action, however, because 

all of the Great Lakes states adopted GLI standards into their regulations 

and submitted them to EPA for approval by the February deadline. For 

example, in July 1997, Michigan modified its administrative rules for water 

quality standards and added implementing procedures to the state’s 
Page 21 GAO-05-829 Great Lakes Initiative

administrative rules. Other states adopted GLI into their regulations for the 

Great Lakes Basin area of their states, and they later adopted aspects of the 

GLI provisions, or all of them, for the entire state. For example, according 

to state officials, when GLI was originally adopted by Ohio, most of its 

provisions only applied to the Lake Erie Basin, but in 2002, Ohio adopted 

GLI aquatic life criteria statewide. Further, Ohio applied GLI criteria for 

human health only to the Lake Erie Basin and based human health criteria 

for the remainder of the state on EPA national guidance. However, 

according to Ohio environmental officials, the two health criteria have 

been converging since the adoption of GLI. 

In addition to the requirements of the Great Lakes Critical Programs Act 

and the consent decree provisions, EPA’s GLI regulations bound the agency 

to publish a notice approving the submission within 90 days or to notify the 

state that all or part of their submission was disapproved and to identify 

changes required for EPA’s approval. Because EPA did not take the 

required actions on every state’s submission, in November 1999, the 

National Wildlife Federation and the Lake Michigan Federation filed a 

lawsuit to force EPA to take action on all Great Lakes states’ GLI 

submissions.12 EPA negotiated another consent decree providing that EPA 

would take the required actions by July 31, 2000, for six states—Illinois, 

Indiana, Michigan, Minnesota, Ohio, and Pennsylvania—and by September 

29, 2000 and October 31, 2000, for New York and Wisconsin, respectively. 

EPA ultimately issued its final determinations for Michigan, Ohio, Indiana, 

Minnesota, Pennsylvania, and Illinois in August 2000. Determinations for 

New York and Wisconsin followed in October and November 2000, 

respectively. Although a few exceptions were identified, EPA determined 

that all the Great Lakes states had generally adopted requirements 

consistent with GLI; however, certain matters relating to the state 

submissions remained unresolved. 

Unresolved Matters 

Affecting Full GLI Adoption 

Remain in Several Great 

Lakes States

While EPA determined that all the Great Lakes states had generally adopted 

requirements consistent with GLI, it disapproved certain elements of six 

states’ submissions as less protective than GLI. EPA promulgated final 

rules applying the relevant GLI provisions to the disapproved elements. For 

example, EPA disapproved four states’ rules relating to determining the 

need for permit limits on the aggregate toxicity of facility’s 

12The Lake Michigan Federation changed its name to the Alliance for the Great Lakes, 

effective April 14, 2005.
Page 22 GAO-05-829 Great Lakes Initiative

discharge—termed whole effluent toxicity (WET) reasonable potential. 

EPA disapproved certain elements of the state rules because they were 

deemed inconsistent with GLI provisions. In determining whether the 

states adopted policies, procedures, and standards consistent with GLI, 

EPA evaluated whether the states’ provisions provided at least as stringent 

a level of environmental protection as the corresponding provisions of the 

guidance. In 12 instances, EPA determined that state provisions were not as 

stringent or were absent. EPA then promulgated final rules specifying 

which state provisions it was disapproving as being inconsistent with GLI 

and applying the relevant GLI provisions. If the state later adopted 

requirements that EPA approved as being consistent with the GLI 

provisions, then EPA indicated that it would amend its regulations so that 

they would no longer apply for the state. 

The individual provisions disapproved by EPA vary from state to state, 

although the WET provisions were disapproved for four of the six states 

with disapproved elements. For Michigan and Ohio, the WET reasonable 

potential procedure was the only GLI provision that was disapproved. For 

Indiana, EPA disapproved its WET reasonable potential procedure and two 

additional provisions. Specifically disapproved were Indiana’s criteria for 

granting of variances from water quality standards and provisions 

preventing the inclusion of discharge limits in permits when a facility has 

applied for a variance. Illinois’ sole disapproved provision related to TMDL 

development while New York’s disapproved provisions related to chronic 

aquatic life criteria and mercury criterion for the protection of wildlife. GLI 

provisions disapproved by EPA are summarized in table 2. 
Page 23 GAO-05-829 Great Lakes Initiative

Table 2: State GLI Provisions Disapproved by EPA

Source: EPA.

 Note: Pennsylvania and Minnesota had no disapproved elements in their adoption of GLI.

The Great Lakes states now have requirements, consistent with GLI, to 

follow that are either fully incorporated into their rules or that have been 

promulgated by EPA.13 However, in Wisconsin, the GLI provisions 

promulgated by EPA have not been implemented because state officials 

believe provisions that are not explicitly supported by Wisconsin law 

cannot be implemented and because material disagreements exist between 

state officials and EPA over the GLI provisions. This situation has resulted 

in delays in issuing renewals of some NPDES permits or issuing permits 

under state provisions that are inconsistent with GLI, according to state 

officials. 

Of the four requirements EPA found inconsistent for Wisconsin, one 

significant disagreement involved certain technical and scientific details 

relating to the consideration of intake pollutants and another involved the 

determination of WET reasonable potential under GLI. For the WET 

Illinois TMDL development

Indiana WET reasonable potential

Criteria for granting variances

Inclusion of discharge limits in permits with a pending variance 

application 

Michigan WET reasonable potential

New York Chronic aquatic life criteria

Mercury wildlife criterion

Ohio WET reasonable potential

Wisconsin WET reasonable potential

Consideration of intake pollutants in establishing discharge limits

Aquatic life criteria for copper and nickel; chronic aquatic life criteria 

for endrin and selenium

TMDL development

13None of the states with rules promulgated by EPA have amended their rules and 

regulations to resolve inconsistencies; and there is no requirement that they do so, as long 

as they are following the EPA promulgated rules. However, Michigan and New York are 

attempting to change their rules and regulations to have the federally imposed GLI 

requirements withdrawn.
Page 24 GAO-05-829 Great Lakes Initiative

determination, Wisconsin Department of Natural Resources officials stated 

that the GLI requirements are a misapplication of statistical procedures and 

overly burdensome. Because of these differences in determining WET 

reasonable potential, Wisconsin uses both state and GLI procedures. If the 

Wisconsin procedures result in the need for a WET limit, but the GLI 

procedures do not, then the permit is issued with the WET limit. However, 

if GLI procedures result in the need for a WET limit, but the state 

procedures do not, the permit is backlogged until a solution can be 

negotiated. As a possible resolution to this issue, EPA has recently 

provided the state with a small grant to reevaluate their WET procedure 

and identify possible changes that would be as protective as the GLI and 

acceptable to Wisconsin officials. While the state has not implemented 

WET reasonable potential provisions that are consistent with GLI, it has 

only impacted a relatively small number of permits in the Great Lakes 

Basin.

The disagreement involving Wisconsin’s provisions for intake pollutants 

that are inconsistent with GLI have a potentially greater impact and, 

according to state officials, they do not have the resources to use the more 

complex GLI approach. The GLI provisions for intake pollutants are 

important because, according to state officials, the most prevalent BCC, 

mercury, exists at levels exceeding its water quality criteria throughout the 

Great Lakes Basin. GLI provisions address the condition where pollutant 

levels in a water body contain “background” levels that exceed the water 

quality criteria for that pollutant. Specifically, provisions address the 

discharge of pollutants that are taken in through a facility’s source or intake 

water and are then returned to the same water body. GLI allows facilities to 

discharge the same mass and concentration of pollutants that are present 

in its intake water—a concept of “no net addition”—provided the discharge 

is to the same body of water and certain other conditions are met. EPA 

considers this practice to be environmentally protective and consistent 

with the requirements of the Clean Water Act when a pollutant is simply 

moved from one part of a water body to another that it would have reached 

regardless of its use by a facility. 

However, EPA determined that Wisconsin’s procedures allow pollutant 

discharges at background levels, regardless of whether the pollutant 

originated from the same body of water, a different body of water, or the 

facility generated the pollutant itself. Further, EPA found that the state’s 

procedures would allow granting of a permit without discharge limits in 

situations where one would be required by GLI. EPA therefore determined 

that the state’s procedure was inconsistent with GLI because it would allow 
Page 25 GAO-05-829 Great Lakes Initiative

facilities to discharge pollutants that were not previously in the water body 

at levels greater than the applicable water quality criteria, which EPA 

believed was inconsistent with the fundamental principles of GLI 

permitting procedures. Although the procedures were disapproved, state 

officials continue to disagree with EPA’s determination. The disagreement 

has remained unresolved since 2000, and EPA’s rule applying the GLI 

provisions to Wisconsin have not been followed by the state. EPA Region 5 

officials stated that they have had some contacts with the Wisconsin 

officials, but these contacts have not resulted in resolving the differences. 

GLI Has Provided Benefits 

but the Inability to Measure 

Pollutants at Low Levels Is a 

Significant Challenge

The introduction of GLI in the Great Lakes states has produced several 

benefits. GLI introduced new standards and methodologies that are based 

on the best science available for protecting wildlife, deriving numeric 

criteria for additional pollutants, developing techniques to provide 

additional protection for mixtures of toxic pollutants, and determining the 

bioaccumulative properties of individual pollutants. GLI also formalized a 

set of practices and procedures for states to use in administering their 

NPDES permit programs and resolved legal challenges to provisions 

similar to GLI in at least one state. Through its emphasis on BCCs, GLI 

played a large role in stimulating efforts to address these particularly 

harmful and problematic toxic chemicals. GLI’s impact on state water 

quality programs has also extended beyond the Great Lakes Basin, as a 

number of states have adopted GLI standards and procedures statewide. 

Also, according to EPA officials, parts of GLI have been used nationally and 

in other states, including implementation methods in California, wildlife 

criteria in New Jersey, and bioaccumulation factors in EPA’s revised 

national guidance for deriving human health water quality criteria. 

While GLI has provided benefits, developing the ability to measure 

pollutants at GLI water quality criteria levels remains a challenge to fully 

achieving GLI goals in the Great Lakes Basin. Several GLI pollutants cannot 

be measured near their water quality criteria, and without this ability it is 

difficult to determine whether a discharge limit is needed and to assess 

compliance. For example, if a pollutant has a water quality criteria of 4 ng/L 

but can only be measured at 40 ng/L, it cannot be determined if the 

pollutant is exceeding the criteria unless it is at or above the measurement 

level, which is about 10 times greater than the criteria level. Therefore, the 

ability to accurately and reliably measure pollutant concentrations is vital 

to the successful implementation of GLI water quality standards. Michigan 

and Ohio officials identified 23 GLI pollutants where the water quality 

criteria is lower than the level at which the pollutant’s concentration in 
Page 26 GAO-05-829 Great Lakes Initiative

water can be reliably measured. In addition, for Ohio, 11 of the 22 BCCs 

that are the central focus of GLI cannot be measured to the level of their 

water quality criteria. These include two of the more prevalent 

BCCs—PCBs and dioxin. Currently, using EPA approved methods, PCBs 

can be detected only at levels around 65,000 times greater than the levels 

established by their water quality criteria. Minnesota officials stated that, if 

methods existed to measure PCBs at low levels, it might be revealed that 

PCBs are as much of a problem as mercury. At the time GLI was developed, 

it was envisioned that more sensitive analytical methods would eventually 

be developed to allow measurement of pollutant concentrations at or 

below the level established by GLI water quality criteria, which would 

allow for the implementation of enforceable permit limits based on GLI 

criteria. Until this could be realized, EPA provided a provision in GLI 

requiring dischargers to implement a pollutant minimization program 

(PMP) to increase the likelihood that the discharger is reducing all 

potential sources of a pollutant to get as close as possible to the water 

quality criteria. A PMP sets forth a series of actions by the discharger to 

improve water quality when the pollutant concentration cannot be 

measured down to the water quality criteria. 

The Great Lakes states’ experience with mercury illustrates the impact that 

having sufficiently sensitive measurement methods can have on identifying 

pollutant discharges from point sources. Until 1999, methods to measure 

mercury at low levels were generally not available. Few mercury permit 

limits existed, and measurement sensitivity using EPA approved methods 

was about 400 times less sensitive than the currently used method. Then, in 

1999, EPA issued a newly approved analytical method with the capability to 

reliably measure mercury concentrations down to 0.5 ng/L, well below the 

lowest GLI mercury water quality criteria of 1.3 ng/L. This development had 

a significant impact on discharging facilities and permitting authorities as 

the more sensitive measurement methods disclosed a more pervasive 

problem of high mercury levels in Great Lakes Basin waterbodies than 

previously recognized. Likewise, the new measurement methods showed 

that many facilities had mercury levels in their discharges exceeding water 

quality criteria; and, for the first time, permits could include enforceable 

discharge limits, based on these low criteria. The result was a significant 

increase in the number of permits needing mercury limits and monitoring 

requirements. The enhanced measurement capability also resulted in the 

development of statewide mercury strategies, including variances, to assist 

facilities in implementing the new measurement methods and eventually 

attaining the GLI water quality criteria. In conjunction with the use of 

variances for mercury, EPA encouraged the use of PMPs so that facilities 
Page 27 GAO-05-829 Great Lakes Initiative

could reduce potential sources of mercury and thus move closer to meeting 

the GLI water quality standards. While the development of more sensitive 

methods for measuring other BCCs may not have as significant an impact 

as it did with mercury, such a development would provide for a more 

meaningful assessment of comparing pollutant levels with GLI water 

quality criteria. 

When GLI was developed, EPA recognized that the relatively low water 

quality criteria levels for many pollutants would result in instances where 

limits were set below levels that could be reliably measured. Water quality 

criteria levels were based on the best science available for protecting 

wildlife, aquatic species, and human health whether or not methods were 

available for measuring pollutants at those levels. While EPA officials 

involved in developing GLI believed that measurement methods would 

eventually be available, developing EPA approved methods can be a 

time-consuming and costly process. EPA officials involved in the 

development of measurement methods explained that the development 

process is based on needs and priorities as well as development costs and 

resources. EPA is currently involved in developing a more sensitive 

analytical method for measuring PCBs, but EPA officials believe it will take 

4 to 5 more years before it will be used because of the nature of the 

agency’s approval process and potential legal challenges. One class of 

pollutant that has not yet been included as a BCC under GLI is 

polybrominated diphenyl ethers or PBDEs—a flame retardant containing 

toxic chemicals with bioaccumulative characteristics. The agency has 

allocated $60,000 to develop an analytical method for this class of 

pollutant. EPA officials did not know when a method for this class of 

pollutant will be approved but may have a better idea at the end of 2005. At 

that point, if results are promising and funding is available, EPA would 

validate the method. 
Page 28 GAO-05-829 Great Lakes Initiative

EPA Has Not Ensured 

Consistent 

Implementation of GLI 

Standards or Taken 

Adequate Steps 

Toward Measuring 

Progress in Achieving 

GLI Goals

To ensure the eight Great Lakes states implement GLI consistently, EPA 

stated in GLI that it would undertake certain activities, including issuing a 

mercury permitting strategy and developing and operating a Clearinghouse 

for the sharing of information by states to facilitate the development and 

implementation of GLI water quality standards. EPA began work on the 

mercury strategy but abandoned efforts because of a perceived lack of 

interest and other agency priorities. Further, EPA has yet to fully develop 

the Clearinghouse. Additionally, because EPA has not collected sufficient 

data, the agency cannot determine whether GLI is reducing pollutant 

discharges into the Great Lakes, whether GLI is improving water quality, or 

assess overall progress toward achieving GLI goals. 

EPA Has Not Developed the 

Mercury Permitting Strategy 

Envisioned in GLI

To promote a uniform and consistent approach to the problems posed by 

mercury from point sources, EPA stated in GLI that it was committed to 

issuing a mercury permitting strategy for use by the Great Lakes states no 

later than 2 years after GLI’s publication. Although EPA believed that there 

was sufficient flexibility in GLI to handle the unique problems posed by 

mercury, such as variances and TMDLs, it intended to develop a mercury 

permitting strategy to provide a holistic, comprehensive approach by the 

states for addressing this pollutant. In June 1997, EPA published a draft of 

this strategy for public comment. The strategy described the flexibility in 

developing requirements for controls on the discharge of mercury. 

However, the strategy was not implemented because, according to EPA 

officials, few substantive comments were submitted on the draft strategy, 

and agency resources were directed to other GLI activities. Three 

states—New York, Michigan, and Wisconsin—that provided comments 

generally supporting the effort each provided additional observations. For 

example, New York noted that the strategy offered only administrative 

solutions rather than tangible technical solutions to the mercury problem. 

Wisconsin suggested that the strategy conformed to the basic framework 

and principles of a previously developed state strategy and therefore 

thought it unnecessary to substitute EPA’s strategy for their own. 

In lieu of a formal strategy, EPA participated in meetings with state officials 

and has approved mercury permitting strategies submitted by some of the 

Great Lakes states. However, in the absence of an EPA strategy on 

implementing water quality standards for mercury, most of the Great Lakes 

states developed their own approaches to ensuring that facilities meet the 

water quality criteria established in GLI, but these approaches have been 

inconsistent and create the potential for states to have different mercury 
Page 29 GAO-05-829 Great Lakes Initiative

discharge requirements. A major goal of GLI was to ensure that water 

quality standards of Great Lakes states were consistent within this shared 

ecosystem, however, the mercury permitting approaches adopted by the 

Great Lakes states contained different requirements for mercury. For 

example, limits in Ohio were set at 12 ng/L based on state standards 

existing before adoption of GLI, and limits established in Michigan were 

initially set at 30 ng/L primarily based on data from the state of Maine. EPA 

officials stated that while disparities exist, the overall limits are being 

lowered. 

Further, differences in states’ strategies for reducing mercury from point 

sources have emerged in states’ use of variances for existing facilities.14

Each state followed their own approach for mercury based on their needs 

and a consideration of the approaches taken by other Great Lakes states. 

While Ohio, Michigan, and Indiana based their mercury strategies on the 

use of streamlined processes for obtaining mercury variances, each state’s 

approach varies in significant ways. For example, Michigan uses a mercury 

permitting strategy where all existing facilities in the state are granted a 

variance in their NPDES permits if there is reasonable potential for the 

mercury standard to be exceeded. The variance exempts a facility from 

meeting the GLI water quality standard of 1.3 ng/L and establishes this 

water quality standard as a goal for a PMP. The variance establishes a 

universal discharge limit, based on all the facilities in the state, rather than 

on a facilities’ current discharge level or discharge level it could achieve 

individually. Michigan chose this approach after the new measurement 

method was approved in 1999, substantially increasing sensitivity for 

mercury in water, and most facilities found they could not meet the GLI 

water quality standard. As a result, Michigan established an interim 

discharge level of 30 ng/L, based on what could be achieved by the majority 

of the facilities in the state, and dischargers are considered to be in 

compliance with the mercury limit if they do not exceed the level in their 

permit and are implementing a PMP. Michigan has recently lowered this 

discharge level to 10 ng/L for permits issued or renewed in 2005. 

Conversely, Ohio’s mercury strategy requires dischargers to apply for a 

variance and submit detailed studies and action plans to identify and 

eliminate known sources of mercury. According to state officials, Ohio’s 

mercury permitting strategy allows dischargers to operate for 19 months 

using the new mercury measurement method to determine their discharge 

14New facilities constructed after 1997 are not eligible for variances under GLI.
Page 30 GAO-05-829 Great Lakes Initiative

levels and evaluate whether they are able to comply with the water quality 

standard. If the discharger can comply with the GLI water quality standard, 

then the limit is included in their permit. If the discharger cannot comply 

they may request a variance. A variance establishes a monthly permit limit, 

based on the level currently achievable for that individual facility, and 

includes a required PMP. An annual permit limit of 12 ng/L is included as an 

annual discharge requirement for all facilities with a variance. According to 

state officials, Indiana’s NPDES permits for major facilities may contain 

monitoring requirements for mercury, and some will contain effluent limits 

that must be achieved after a 3 to 5 year compliance schedule. Additionally, 

Indiana developed a streamlined mercury variance rule. This rule 

establishes a process for dischargers to obtain temporary effluent limits, 

based on the level of mercury currently in their effluent, and requires 

dischargers to develop and implement a PMP in conjunction with a 

mercury variance. 

Other states have developed different mercury permitting approaches. 

Minnesota includes a discharge limit in permits, based on the standard of 

1.3 ng/L and implemented through a compliance schedule allowing the 

facility up to 5 years to meet the limit. According to state officials, if 

dischargers are unable to meet the limit at the expiration of the compliance 

schedule, they will be required to apply for a variance on an individual 

basis. State officials also reported that Minnesota recently developed a 

draft statewide TMDL for mercury as a response to the mercury problem. 

Wisconsin has not granted variances, but it has granted PMP’s for about 20 

facilities that are unable to comply with the mercury standard. According 

to a Wisconsin official, the state considers that granting PMPs without a 

limit is in essence a variance. However, it is referred to as an "alternative 

mercury limitation," and the state official explained that, if it were an 

official variance, the discharge limit would actually be in the permit, and 

the variance would be a part of that limit. New York and Pennsylvania only 

recently began using the more sensitive mercury testing method and 

therefore have yet to address how facilities will be granted variances. 

EPA’s Delayed Introduction 

of the GLI Clearinghouse 

Limited the Development of 

Consistent Water Quality 

Standards

To promote a more consistent and shared approach to developing water 

quality standards among the Great Lakes states, EPA stated in GLI that 

Region 5 would develop a GLI Clearinghouse. As envisioned in GLI, this 

Clearinghouse would be a database containing all the information on the 

criteria and data used by the Great Lakes states in developing water quality 

standards. The Clearinghouse was to be developed in cooperation with 

EPA Headquarters, Regions 2 and 3, and the Great Lakes states. As 
Page 31 GAO-05-829 Great Lakes Initiative

envisioned, data included in the Clearinghouse could be quickly shared 

between the states to assist them in developing or updating numeric water 

quality criteria for toxic chemicals for aquatic life, wildlife, and human 

health. It could also be used to share data on any new pollutants that might 

be designated a BCC. When EPA developed GLI, it assumed that more 

chemicals would emerge as BCCs in the future and require development of 

additional water quality standards. GLI allows the Great Lakes states to 

designate additional chemicals for BCC controls without EPA sponsoring a 

public review and comment process. EPA was concerned that 

inconsistencies could arise among states when they identified future BCCs 

and believed the Clearinghouse would minimize this possibility. As 

envisioned in GLI, EPA Region 5 would operate the Clearinghouse, and if 

new information indicated a pollutant was a potential BCC, this 

information would be reviewed by EPA and the states and placed in the 

Clearinghouse to alert all the other Great Lakes states. Once alerted, states 

could then notify the public of any revisions to their water quality 

standards or permit requirements. 

The development of the Clearinghouse did not proceed as envisioned in the 

GLI. The Clearinghouse development effort was initiated in 1996 and EPA 

began entering data into the database at that time. However, the database 

was not available for use by the states until recently, because of other EPA 

priorities. Meanwhile, states developed their own water quality criteria for 

some GLI pollutants without centralized access to information from other 

states, likely resulting in longer development time and potential for 

inconsistencies among states. According to Minnesota state officials, 

without a GLI Clearinghouse, developing numeric criteria has been a 

problem since information on toxic chemicals or criteria are not readily 

available from other Great Lakes states. Currently, Minnesota is not close 

to developing criteria for all GLI pollutants. Officials stated that the 

availability of the Clearinghouse will help them in developing these criteria. 

Ohio officials expressed disappointment that EPA had not developed the 

Clearinghouse so many years after the guidance was issued because of its 

importance as a resource for developing water quality criteria. EPA 

renewed its efforts to complete the development of the Clearinghouse in 

late 2004. In early 2005, EPA Region 5 officials held conference calls with 

officials from the eight Great Lakes states, resulting in an agreed approach 

for jointly populating and maintaining the Clearinghouse. It is unclear, 

however, whether the Clearinghouse was jointly developed as planned with 

the active participation of EPA Regions 2 and 3, headquarters, and the eight 

Great Lakes states. As of April 2005, the Clearinghouse was still in the 

testing stage and, according to EPA Region 5 officials, by July 2005, all 
Page 32 GAO-05-829 Great Lakes Initiative

states had access to its information. However, currently, the states are not 

able to make additions or modifications to the data in the Clearinghouse. 

States were also providing comments to EPA Region 5 on the 

Clearinghouse’s operation, and EPA planned to make modifications based 

on these comments. EPA has yet to determine the most efficient approach 

for maintaining and updating information in the database. Until the 

database is fully operational and utilized, however, EPA cannot be assured 

that the Great Lakes states have adequate information for developing and 

updating consistent water quality standards.

EPA Has Not Determined 

the Overall Impact of GLI or 

of PMPs in Reducing 

Pollutant Loadings 

While monitoring the impact of GLI on water quality and pollutant loadings 

may be difficult and not required by the Critical Programs Act or GLI, it is 

important to determine if progress is being made toward GLI goals and the 

virtual elimination of toxic substances in the Great Lakes Basin. Currently, 

the effect of GLI in improving water quality and reducing loadings of toxic 

pollutants is unclear because EPA has been unable to assess GLI’s impact 

with existing data sources and has not gathered additional information to 

monitor progress on plans to reduce future loadings. EPA’s primary data 

source for the NPDES permits program is the Permit Compliance System 

(PCS), an automated system used for tracking compliance with individual 

permits. Information is entered into the system by states administering the 

program, and the system tracks when a permit is issued and expires, how 

much a facility is allowed to discharge, and what a facility has discharged. 

The system is useful for identifying noncompliance with GLI-based effluent 

limits by major NPDES dischargers through quarterly noncompliance 

reports. However, the system is inadequate for determining whether GLI 

has reduced pollutant loadings. 

EPA Region 5 officials attempted to use PCS to estimate the trends of point 

source loadings for specific pollutants in the Great Lakes Basin, but 

frequent errors occurred because of system limitations. These errors 

resulted from missing or inaccurate data, which distorted a clear estimate 

of pollutant loadings by facilities. For example, discharge quantities for 

some pollutants were reported as zero in some instances when they do not 

require monitoring, resulting in lower estimated total discharges. In 

addition, PCS data are primarily for major facilities, so calculated pollutant 

loadings do not reflect the sizeable universe of minor facilities. 

Inconsistencies in PCS also occur from the way state discharge monitoring 

report data are entered into the system. Because of these data limitations, 

EPA’s attempt to identify trends in point source loadings did not produce 

firm conclusions, rather, it produced only speculation as to why actual 
Page 33 GAO-05-829 Great Lakes Initiative

loadings increased or decreased in certain states. In addition, loading data 

that compared the years 1999 through 2000 to the years 2000 through 2001 

was considered too short a time frame for comparative analysis since most 

of the permits had not been modified or reissued to reflect the new GLI 

standards during these time periods. Further hampering this effort was a 

lack of baseline data for loadings before GLI, which prevented 

comparisons between pollutant loadings before and after GLI 

implementation. The overall limitations of PCS to support the NPDES 

program were first recognized by EPA as an agency weakness in 1999. 

While EPA has attempted to modernize the system, the costs and time to 

complete the project have escalated significantly, as reported by the EPA 

Office of Inspector General.15 As of June 2005, the modernization project 

had not been completed. 

Officials from EPA Region 5 made two other attempts to determine GLI’s 

impact on Great Lakes water quality. One attempt involved using Toxics 

Release Inventory (TRI) data.16 However, EPA officials stated that for a 

number of reasons TRI did not lend itself to assessing the changes in water 

quality attributed to GLI. For example, TRI does not include information 

from publicly owned treatment works (POTW). Based on this effort, EPA 

concluded that any improvements in water quality resulting from GLI could 

not be isolated from the many other initiatives undertaken to improve 

water quality in the Great Lakes Basin. A second effort is currently under 

way and involves comparing a sample of individual permits before and 

after GLI implementation to determine its impact on permit limits. 

However, this effort has yet to yield preliminary results. Further, even when 

this effort is completed, EPA will only be able to make limited conclusions 

about how certain permit requirements have changed, and may incorrectly 

assume that the changes were a result of implementing GLI. This latest 

effort will not provide an ongoing monitoring of the impact of GLI, and EPA 

officials stated that in order to do a good analysis of GLI, all relevant data 

would have to be stored in a central database for analysis. Currently 

different types of information are stored in a variety of areas. 

15Memorandum Report: EPA Should Take Further Steps to Address Funding Shortfalls and 

Time Slippages in Permit Compliance System Modernization Effort, EPA, OIG Rpt. No. 

2003-M-00014, May 20, 2003.

16TRI is a database that contains information on releases and transfers of certain toxic 

chemicals from industrial facilities, and waste management and source reduction activities. 
Page 34 GAO-05-829 Great Lakes Initiative

In addition to attempts by EPA Region 5 to determine GLI’s impact, as part 

of its oversight of the NPDES program, regional staff review a sample of 

major NPDES permits issued by the six Great Lakes states in the region. 

The criteria for selecting permits for review varies from year to year and is 

typically based on issues that concern EPA staff. One factor in the selection 

of permits is whether the facility discharges within the Great Lakes Basin, 

thus requiring compliance with GLI. EPA officials stated that permits are 

reviewed in accordance with applicable federal rules and policies, 

including GLI implementation procedures. For selected permits issued by 

the state of Michigan, EPA specifically reviews the implementation of GLI 

requirements. For the other states, compliance reviews addressing GLI 

requirements are being phased in and will take significant time to fully 

implement, according to EPA officials. EPA’s reviews have not included a 

determination of whether GLI is being implemented consistently among 

states, but rather, focus on issues of compliance. 

Finally, EPA is not gathering information on how the implementation of 

PMPs or other GLI provisions is reducing pollutant discharges in the basin. 

EPA officials in Region 5 stated that GLI was intended to make the 

standards and goals of the Great Lakes states more consistent and 

implementing an elaborate monitoring scheme was not its intent. Without 

some type of monitoring, however, it is difficult to determine whether the 

standards and goals are having the desired environmental effect and 

whether GLI is being implemented consistently. This is particularly 

important because the use of flexible implementation procedures, such as 

variances and PMPs, adds uncertainty as to when facilities' discharge levels 

will ultimately attain GLI water quality standards. For PMPs, EPA Region 5 

and the states cooperatively developed mercury PMP guidance for 

POTWs.17 This guidance was finalized in November 2004 and provides 

information on what elements should be in PMPs, including reporting of 

progress by the facility to the state in achieving PMP goals. The reported 

information, however, is not reviewed by EPA, and, therefore, the agency 

cannot determine what overall progress is being achieved. When EPA 

reviews a state-issued permit under a compliance review the agency checks 

only to see if PMP requirements are recorded appropriately in the permits 

17POTWs collect wastewater from homes, commercial buildings, and industrial facilities and 

transport it via a series of pipes, known as a collection system, to the treatment plant. 

POTWs remove harmful organisms and other contaminants from the sewage so it can be 

discharged safely into the receiving stream. Generally, POTWs are designed to treat 

domestic sewage only. However, POTWs also receive wastewater from industrial 

(nondomestic) users.
Page 35 GAO-05-829 Great Lakes Initiative

and it does not determine if progress is being made to reduce pollutants 

under PMPs. EPA Region 5 officials stated that they could get a better 

understanding of GLI implementation if PMP data were collected and 

analyzed. Region 5 has not yet initiated a regional review process for these 

programs, but it will be developing a strategy to do so in its NPDES 

Program Branch. This strategy would involve working with the states on 

review criteria and compliance determination issues. Region 5 officials 

stated that their efforts are for the six states in their region. They do not 

have responsibility to gather information on PMPs or other activities 

regarding GLI implementation for New York or Pennsylvania, which are in 

EPA regions 2 and 3, respectively. 

Conclusions While GLI has limited potential to improve overall water quality in the 

Great Lakes Basin because of its focus on point source pollution, it is 

important that GLI’s goals be achieved because they assist in the virtual 

elimination of toxic pollutants called for in the GLWQA. Several factors, 

however, have undermined progress toward achieving GLI’s goal of 

implementing consistent water quality standards. First, EPA has taken 

steps to implement GLI by ensuring that states adopt GLI standards or by 

issuing federal rules in the absence of state standards but has yet to resolve 

long-standing issues with the state of Wisconsin regarding the state’s 

adoption and implementation of GLI provisions. Second, EPA chose not to 

issue a mercury permitting strategy that it committed to do in GLI, and 

subsequently mercury was addressed in NPDES permits in different ways. 

Third, EPA’s efforts to complete the development of the GLI Clearinghouse 

have only recently been renewed, reflecting a lethargic approach to 

implementing actions it committed to in GLI. Finally, while EPA has made 

efforts to assess GLI’s impact on water quality, we believe additional efforts 

are needed to obtain information on the progress in implementing GLI and 

on reducing pollutant discharges from point sources in the Great Lakes 

Basin. In particular, information is needed to gauge dischargers’ progress in 

using PMPs to address pollutants that are exceeding GLI standards.

Recommendations for 

Executive Action

To better ensure the full and consistent implementation of the Great Lakes 

Initiative and improve measures for monitoring progress toward achieving 

GLI’s goals, we are recommending that the EPA Administrator direct EPA 

Region 5, in coordination with Regions 2 and 3, to take the following three 

actions: 
Page 36 GAO-05-829 Great Lakes Initiative

• issue a permitting strategy that ensures a more consistent approach to 

controlling mercury by the states, 

• ensure the GLI Clearinghouse is fully developed, maintained, and made 

available to the Great Lakes states to assist them in developing water 

quality standards for pollutants covered by GLI, and 

• gather and track information that can be used to assess the progress of 

implementing GLI and the impact it has on reducing pollutant 

discharges from point sources in the Great Lakes Basin. In particular, 

EPA should consider collecting better information on the impact of 

discharger programs to minimize pollutants that are exceeding GLI 

standards. 

In addition, we recommend that the EPA Administrator direct EPA Region 

5 take the following action:

• increase efforts to resolve the disagreements with the State of 

Wisconsin over the implementation of provisions to ensure the equitable 

and timely implementation of GLI among all Great Lakes states. 

Agency Comments and Our 

Evaluation

GAO provided EPA with a draft of this report for its review and comment. 

The agency generally agreed with the findings and recommendations in the 

report, but stated that our draft report has overlooked significant results or 

benefits of GLI, such as establishing a consistent and scientifically sound 

method to derive point source permit limits for mixtures of toxicants. We 

acknowledge the many benefits of GLI in our report, however, our review 

focused on the potential impact of GLI on water quality, implementation of 

GLI, and the steps taken by EPA to ensure consistent implementation and 

assessing progress toward achieving GLI goals. EPA also stated that while 

our report recognizes that many of the Great Lakes water quality problems 

are due to nonpoint sources, the benefits from GLI point source 

implementation procedures are not fully recognized in the report. Further, 

EPA stated that it was never expected that GLI would address nonpoint 

source discharges, and it is not authorized to develop and implement 

programs for nonpoint discharges. However, our report recognizes the 

importance of controlling point source pollution and that under the 

GLWQA of 1978, the United States and Canada agreed to a policy of 

prohibiting harmful pollutants in toxic amounts and virtually eliminating 

the discharge of such pollutants. GLI was an effort by the United States to 

further control these substances. Moreover, as we note above, our review 
Page 37 GAO-05-829 Great Lakes Initiative

focused on the potential impact of GLI on water quality and therefore, we 

note as a factual matter in our report that nonpoint sources are not 

addressed.

Regarding the differences in the Great Lakes states approaches to mercury 

and our recommendation for EPA to develop a mercury permitting strategy, 

the agency stated that some differences exist in mercury requirements for 

individual facilities. However, EPA did not believe these differences 

represented an unacceptable level of inconsistency and believed that state 

approaches were similar. Further, EPA compares pre-GLI standards to 

post-GLI standards to illustrate the consistency in addressing mercury. 

While consistent standards are an expected outcome of GLI, the guidance 

does not ensure consistent implementation, particularly with the use of 

variances and PMPs by states in lieu of compliance with the stringent GLI 

water quality standards. EPA Region 5 has issued guidance for consistency 

in development of PMPs by the states for publicly owned treatment works, 

but states are not required to follow the guidance, and the regional 

guidance does not apply to the two Great Lakes states that are outside of 

the geographic boundaries of Region 5. EPA further states that mercury 

variances are temporary measures allowing time to transition to the 

stringent GLI standards. However, facilities with NPDES permits can apply 

to have a variance renewed with a permit renewal and, therefore, variances 

can be approved by the states for a 5-year period, which may be in addition 

to a previous 5-year variance. It is also not evident that time frames exist 

for when facilities are to meet these stringent GLI standards. EPA stated 

that a mercury permitting strategy would not improve consistency and, 

rather than focusing on a strategy, it would work with the states and 

provide assistance on the most effective approaches for reducing mercury 

loadings by point source dischargers. The agency, however, committed 

itself in the GLI to developing a strategy. An overall goal of GLI is to have 

consistency among the Great Lakes states, and mercury is clearly the most 

important pollutant regulated in NPDES permits. 

Regarding our recommendation on the GLI Clearinghouse, EPA stated that 

the Clearinghouse has a vital role to play in the GLI implementation. In 

early 2005, Region 5 and the eight Great Lakes states reached agreement 

for populating and maintaining the Clearinghouse. After further 

information updates and revisions by EPA, the states will review the 

Clearinghouse for accuracy and thoroughness, and then it will be 

functional, according to EPA. 
Page 38 GAO-05-829 Great Lakes Initiative

Regarding our recommendation on the need to gather and track 

information to assess the implementation of GLI, EPA stated that it will be 

working with the states to develop PMP oversight tools, and it will be 

tracking the permits issued for mercury requirements and biosolids data 

regarding trends in mercury levels. For resolving its differences with the 

state of Wisconsin regarding GLI, EPA stated that Region 5 is working with 

the state to resolve outstanding issues. Further, the state is evaluating its 

whole effluent toxicity reasonable potential procedures, and then EPA will 

work with the state to ensure that its procedures are at least as protective 

as EPA’s. EPA also provided specific comments on the draft report, and we 

have made changes in our report to reflect many of these comments. The 

full text of EPA’s comments is included in appendix III. 

As agreed with your offices, unless you publicly announce the contents of 

this report earlier, we plan no further distribution until 30 days from the 

report date. At that time, we will send copies of this report to appropriate 

Congressional Committees, the EPA Administrator, various other federal 

and state departments and agencies. We also will make copies available to 

others upon request. In addition, the report will be available at no charge 

on the GAO Web site at http://www.gao.gov.

If you or your staff have any questions, please call me at (202) 512-3841. 

Contact points for our Offices of Congressional Relations and Public 

Affairs may be found on the last page of this report. GAO staff who made 

major contributions to this report are listed in appendix IV.

John B. Stephenson

Director, Natural Resources

 and Environment
Page 39 GAO-05-829 Great Lakes Initiative

List of Congressional Requesters

The Honorable Mike DeWine

The Honorable Russell D. Feingold 

The Honorable Carl Levin

The Honorable Debbie Stabenow

The Honorable George V. Voinovich

United States Senate 

The Honorable John Conyers, Jr. 

The Honorable John D. Dingell

The Honorable Rahm Emanuel

The Honorable Vernon J. Ehlers

The Honorable Marcy Kaptur

The Honorable Dale Kildee

The Honorable Ron Kind

The Honorable Mark Kirk

The Honorable Dennis Kucinich

The Honorable Steven C. LaTourette

The Honorable Sander M. Levin

The Honorable Candice S. Miller

The Honorable James Oberstar

The Honorable Bart T. Stupak

House of Representatives
Page 40 GAO-05-829 Great Lakes Initiative

Appendix I

Scope and Methodology ApApenednxidexiIs

To determine the focus and its potential to affect water quality in the Great 

Lakes Basin we analyzed the published final rule on the Great Lakes 

Initiative (GLI), including its methodologies, policies, and procedures. 

Specifically, we reviewed the flexible implementation procedures allowed 

under GLI, such as those allowed for mercury, the most common 

bioaccumulative chemical of concern (BCC) regulated in permits for point 

sources of pollution. We also obtained opinions on GLI’s impact from 

officials representing environmental organizations that were involved in 

the formulation of GLI, such as the Lake Michigan Federation and the Great 

Lakes Water Quality Coalition. We also gathered and analyzed available 

data on the major sources of toxic pollutants in the Great Lakes Basin from 

water quality permit officials in the Environmental Protection Agency’s 

(EPA) Region 5, and state environmental agency officials in each of the 

Great Lakes states—Illinois, Indiana, Ohio, Michigan, Minnesota, New 

York, Pennsylvania, and Wisconsin. Specifically, for each state agency, we 

obtained information from state National Pollution Discharge Elimination 

System (NPDES) permit databases regarding the location and number of 

NPDES permits covered under GLI in each state, including those permits 

that included BCCs. We questioned officials knowledgeable about the data 

and systems that produced them and determined the data were sufficiently 

reliable for the purposes of this report. In two instances where we noticed 

inconsistencies in the data, we verified with state officials the correction of 

the data. 

To determine the status of GLI’s adoption by the states, we analyzed the 

Clean Water Act, as amended by the Great Lakes Critical Programs Act of 

1990, and its requirements for the Great Lake states to adopt standards, 

policies, and procedures consistent with GLI. We also gathered and 

analyzed documentation from EPA on its approval process for states’ 

submissions of their standards, policies, and procedures and whether they 

reflected GLI requirements; and we interviewed EPA Region 5 and Great 

Lakes states’ officials on any unresolved matters regarding EPA’s rulings on 

state submissions. To identify any challenges that might exist to achieving 

GLI’s intended goals, we reviewed the water quality criteria established for 

pollutants in the GLI, particularly BCCs, and interviewed EPA Region 5 and 

state officials to determine how many pollutants covered by GLI did not 

have methods and water quality criteria yet developed. We also collected 

and analyzed data from officials of EPA’s Office of Science Technology to 

determine EPA’s current efforts in developing new methods for BCCs.

To identify the steps EPA has taken for ensuring the full and consistent 

implementation of GLI, we reviewed the GLI to see what actions EPA had 
Appendix I

Scope and Methodology

Page 41 GAO-05-829 Great Lakes Initiative

committed itself to taking. We obtained information from EPA Region 5 and 

EPA Headquarters on the status of these activities, such as the 

establishment of a database clearinghouse and mercury permitting 

strategy. We collected and analyzed opinions from several of the eight 

Great Lakes states on the need for these GLI requirements and any 

consequences resulting from delays in their implementation. To determine 

the steps EPA has taken for assessing progress toward achieving GLI’s 

goals, we interviewed EPA Region 5 officials on its processes for 

determining progress made under GLI in improvements to water quality, 

including the agency’s use of available databases in this exercise, and its 

monitoring of the states’ implementation of GLI. 

We performed our work from October 2004 to June 2005 in accordance 

with generally accepted government auditing standards. 
Page 42 GAO-05-829 Great Lakes Initiative

Appendix II

Purpose and Status of Bioaccumulative 

Chemicals of Concern (BCC) Identified in GLIApendxiI

Chemical Purpose Status

Chlordane Pesticide Uses banned

4,4'-DDD; p,p'-DDD; 4,4'-TDE Pesticide Uses banned

4,4'-DDE; p,p'-DDE No commercial use Chemical by-product—not deliberately 

manufactured

4,4'-DDT; p,p'-DDT Pesticide Uses banned

Dieldrin Pesticide for crops like cotton and corn Uses banned

Hexachlorobenzene Pesticide, fireworks, synthetic rubber No longer used commercially

Hexachlorobutadiene; hexachloro-1, 3-

butadiene

To make rubber compounds and lubricants; used 

as a solvent

Still in use

Hexachlorocyclohexanes (HCH); 

benzene hexachlorides or BHCs

Insecticide No longer produced or used in the United 

States 

alpha-Hexachlorocyclohexane; alphaBHCOne of eight chemical forms that comprise 

technical grade HCH 

No longer produced in the United States

beta-Hexachlorocyclohexane; betaBHCOne of eight chemical forms that comprise 

technical grade HCH 

No longer produced in the United States

delta-Hexachlorocyclohexane; deltaBHCOne of eight chemical forms that comprise 

technical grade HCH 

No longer produced in the United States

gamma-Hexachlorocyclohexane; 

gamma BHC or Lindane

Insecticide on fruit and vegetable crops. Still used 

as a treatment for lice

Not produced in the United States since 

1977, but is still imported to the United 

States

Mercury Metallic mercury to produce chlorine gas and 

caustic soda and used in thermometers, dental 

fillings, and batteries

Still in use

Mirex Control of fire ants; flame retardant in plastics, 

rubber, paint, paper and electrical goods

No longer manufactured or used

Octachlorostyrene Not available Chemical by-product—not deliberately 

manufactured

PCBs; polychlorinated biphenyls Products made before 1977 that may still contain 

PCBs include electrical equipment, such as 

transformers and capacitors

Manufacture and certain uses banned 

Pentachlorobenzene Used to make pentachloronitrobenzene, a 

fungicide and used as a 

fire retardant

Still in use

Photomirex Created from the decomposition of mirex when 

exposed to sunlight

Chemical by-product—not deliberately 

manufactured

2,3,7,8-TCDD; dioxin Formed during chlorine bleaching process at pulp 

and paper mills, during chlorination by water 

treatment plants, and are released in emissions 

from municipal and industrial incinerators

Chemical by-product—not deliberately 

manufactured

1,2,3,4-Tetrachlorobenzene Used as a dielectric fluid and as an organic 

intermediate

Still in use
Appendix II

Purpose and Status of Bioaccumulative 

Chemicals of Concern (BCC) Identified in 

GLI

Page 43 GAO-05-829 Great Lakes Initiative

Sources: GAO, EPA, and the Agency for Toxic Substances and Disease Registry, Center for Disease Control.

1,2,4,5-Tetrachlorobenzene Used as an intermediate or building block to make 

herbicides, insecticides, defoliants, and other 

chemicals

Still in use

Toxaphene Insecticide primarily used on agricultural crops 

and livestock and to kill unwanted fish in lakes

Banned

(Continued From Previous Page)

Chemical Purpose Status
Page 44 GAO-05-829 Great Lakes Initiative

Appendix III

Comments from the Environmental 

Protection Agency ApendxiI
Appendix III

Comments from the Environmental 

Protection Agency

Page 45 GAO-05-829 Great Lakes Initiative
Appendix III

Comments from the Environmental 

Protection Agency

Page 46 GAO-05-829 Great Lakes Initiative
Page 47 GAO-05-829 Great Lakes Initiative

Appendix IV

GAO Contact and Staff Acknowledgments ApendxiIV

GAO Contact John Stephenson (202) 512-3841 (stephensonj@gao.gov)

Staff 

Acknowledgments 

In addition to the individual named above, Kevin Averyt, Greg Carroll, 

John Delicath, John Wanska, and Amy Webbink made key contributions to 

this report.

(360515)
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