Order Code RL33466
CRS Report for Congress
Received through the CRS Web
Water Quality: Implementing the Clean Water Act
June 12, 2006
Claudia Copeland
Specialist in Resources and Environmental Policy
Resources, Science, and Industry Division
Congressional Research Service ˜ The Library of Congress

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Water Quality: Implementing the Clean Water Act
Summary
Congress enacted the last major amendments to the Clean Water Act in 1987
(P.L. 100-4). Since then, the Environmental Protection Agency (EPA), states, and
others have been working to implement the many program changes and additions
mandated in the law. At issue today — more than 30 years after enactment of the
core law — is what progress is being made to achieve its goals. In general, states and
environmental groups fault EPA for delays in issuing guidance and providing
assistance to carry out the law. EPA and others are critical of states, in turn, for not
reaching beyond conventional knowledge and approaches to address their water
quality problems. Environmental advocates have been criticized for insufficient
recognition of EPA’s and states’ need for flexibility to implement the Act. Finally,
Congress has been criticized for not providing adequate resources to meet EPA and
state needs. Appropriations for clean water programs, especially water infrastructure,
are a continuing issue.
Three issues have predominated recently in connection with implementation of
the law. The first involves funding to construct municipal wastewater treatment
plants under the state revolving fund (SRF) provisions of the 1987 amendments.
Budgetary constraints on federal aid for wastewater treatment and large remaining
funding needs are a long-standing concern. For FY2006, Congress enacted
legislation (P.L. 109-54) providing $887 million for clean water SRF grants ($204
million less than in FY2005). The President’s FY2007 budget requests $688 million
for these SRF grants, 22% less than FY2006 funding, and in May the House passed
legislation providing the level requested by the President (H.R. 5386).
Appropriations for water infrastructure assistance programs remain a controversial
issue for Congress, and between Congress and the Administration.
The second issue involves progress in implementing the nonpoint pollution
management provisions added in 1987. States are developing management programs
describing methods that will be used to reduce nonpoint pollution, which may be
responsible for as much as 50% of the nation’s remaining water quality problems.
Most observers agree that implementation of nonpoint source control measures is
significantly hindered by limited resources. EPA has adopted program guidance
intended to give states more flexibility and to speed up progress in nonpoint source
control. The third issue is impacts and implementation of requirements under current
law for states to develop total maximum daily loads (TMDLs) to restore
pollution-impaired waters.
Reauthorization of the Act has been on Congress’ agenda for several years, but
no comprehensive amendments have been enacted. In the 108th Congress, legislation
focused on water infrastructure funding legislation, but no bill was enacted.
This report replaces CRS Issue Brief IB89102, Water Quality: Implementing the
Clean Water Act, by Claudia Copeland. It will be updated as warranted by
developments.

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Contents
Most Recent Developments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
The Act and Most Recent Amendments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Legislative Activity after P.L. 100-4 . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
State Revolving Fund Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Nonpoint Pollution Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Adequacy of Plans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Funding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Program Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Significance for TMDLs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Total Maximum Daily Load (TMDL) Requirements . . . . . . . . . . . . . . . . . . . . . . 8
Other Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Stormwater Discharges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Combined and Separate Sewer Overflows . . . . . . . . . . . . . . . . . . . . . . 11
Wetlands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Strategy Concerning Animal Feeding Operations . . . . . . . . . . . . . . . . 14
Continuing Issue: Appropriations and the Federal Budget . . . . . . . . . . . . . . . . . 15
FY2007 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
FY2006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
For Additional Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
List of Tables
Table 1. Wastewater Treatment Funding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

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Water Quality:
Implementing the Clean Water Act
Most Recent Developments
Congress has begun consideration of legislation to fund EPA’s clean water and
other programs for FY2007. The President’s budget, released in February, requested
$687.6 million for grants to capitalize clean water state revolving funds (SRFs), 22%
less than FY2006 funding. On May 18 the House passed H.R. 5386, providing EPA
appropriations, and agreed to the clean water funding level requested by the
President.
In July 2005, Congress passed the conference report on energy policy
legislation, H.R. 6 (P.L. 109-58); one provision (Section 323) provides a permanent
exemption from stormwater runoff rules for the construction of exploration and
production facilities by oil and gas companies or the roads that service those sites.
In January, EPA proposed a rule to implement this provision of P.L. 109-58.
The Act and Most Recent Amendments
The Federal Water Pollution Control Act, or Clean Water Act, is the principal
law concerned with polluting activity in the nation’s streams, lakes, and estuaries.
Originally enacted in 1948, it was totally revised by amendments in 1972 (P.L. 92-
500) that gave the Act its current form and spelled out ambitious programs for water
quality improvements that are now being put in place by industries and cities.
Congress made certain fine-tuning amendments in 1977 (P.L. 95-217) and 1981 (P.L.
97-117) and enacted comprehensive amendments in 1987 (P.L. 100-4).
The Act consists of two major parts: regulatory provisions that impose
progressively more stringent requirements on industries and cities in order to meet
the statutory goal of zero discharge of pollutants, and provisions that authorize
federal financial assistance for municipal wastewater treatment construction.
Industries were to meet pollution control limits first by use of Best Practicable
Technology and later by improved Best Available Technology. Cities were to
achieve secondary treatment of municipal wastewater (roughly 85% removal of
conventional wastes), or better if needed to meet water quality standards. Both major
parts are supported by research activities authorized in the law, plus permit and
penalty provisions for enforcement. Programs are administered by the
Environmental Protection Agency (EPA), while state and local governments have the
principal day-to-day responsibility for implementing the law.1
1 For additional information, see CRS Report RL30030, Clean Water Act: A Summary of
(continued...)

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The last major amendments to the law are the Water Quality Act of 1987 (P.L.
100-4). These amendments culminated six years of congressional efforts to extend
and revise the Act and were the most comprehensive amendments to it since 1972.
They recognize that, despite much progress to date, significant water quality
problems persist. Among its many provisions, the 1987 legislation: (1) established
a comprehensive program for controlling toxic pollutant discharges, beyond that
already provided in the Act, to respond to so-called “toxic hot spots;” (2) added a
program requiring states to develop and implement programs to control nonpoint
sources of pollution, or rainfall runoff from farm and urban areas, plus construction,
forestry, and mining sites; (3) authorized a total of $18 billion for wastewater
treatment assistance under a combination of the Act’s traditional construction grants
program and a new program of grants to capitalize State Revolving Funds; (4)
authorized or modified a number of programs to address water pollution problems
in diverse geographic areas such as coastal estuaries, the Great Lakes, and the
Chesapeake Bay; and (5) revised many of the Act’s regulatory, permit, and
enforcement programs.
Legislative Activity after P.L. 100-4. Congressional oversight of water
quality issues was limited immediately after enactment of P.L. 100-4.
Subcommittees held general oversight hearings, as well as several hearings on
individual issues (wetlands protection, Chesapeake Bay programs, and toxics
contamination of Great Lakes waters), but reserved extensive review and oversight
until implementation had been underway for some time.
EPA, states, industry, and other citizens continue to implement the 1987
legislation, including meeting the numerous requirements and deadlines in it. Three
sets of issues have been the focus of attention regarding the pace and effectiveness
of implementation: the toxic pollutant control provisions, nonpoint pollution
management provisions, and the State Revolving Fund provisions to transfer
wastewater treatment funding responsibility to the states after 1994. Attention has
also focused on the cost-effectiveness of clean water requirements and flexibility of
implementation.
Implementation issues discussed below were the basis for legislation to
reauthorize the Clean Water Act during the 103rd Congress. Committees held
hearings in 1993, and the Senate Environment and Public Works Committee reported
a comprehensive reauthorization bill, S. 2093, in May 1994. Legislation also was
introduced in the House, but no further action occurred because of controversies
specific to the Act and the pending bills, as well as controversies over regulatory
relief issues that became barriers to a number of bills in 1994.
In the 104th Congress, the House moved quickly on Clean Water Act
legislation, approving a comprehensive reauthorization bill in May 1995. H.R. 961
would have amended many of the regulatory and standards provisions of the law,
required EPA to use extensive new risk assessment and cost-benefit analysis
procedures, and increased flexibility with regulatory relief from current clean water
1 (...continued)
the Law, by Claudia Copeland.

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CRS-3
programs. However, the Senate did not take up the Clean Water Act during the 104th
Congress; thus, no legislation was enacted.
1997 marked the 25-year anniversary of the 1972 Clean Water Act amendments,
which established the goals, objectives, and structure that continue to guide the law
today. In the 105th Congress, no major committee activity over the Act occurred
either in the House or the Senate. Since the 104th Congress, attention has focused on
individual program areas of the law; no comprehensive reauthorization legislation
has been introduced. However, activity on bills dealing with specific water quality
issues has occurred. Congress passed a bill to strengthen protection of coastal
recreation waters through upgraded water quality standards and coastal waters
monitoring programs (P.L. 106-284) and also passed a bill reauthorizing several
existing CWA programs (i.e., Chesapeake Bay, clean lakes, and the National Estuary
Program; P.L. 106-457). Further, Congress passed a bill to authorize CWA grant
funding for wet weather sewerage projects (included as a provision of P.L. 106-554,
FY2001 Consolidated Appropriations). The 107th Congress approved the Great
Lakes Legacy Act (P.L. 107-303), which authorized $200 million for EPA to carry
out projects to remediate sediment contamination in the Great Lakes. The 108th
Congress enacted legislation amending the Act to extend the National Estuary
Program through FY2010 (P.L. 108-399).
More generally, following the September 11, 2001 terrorist attacks on the World
Trade Center and the Pentagon, congressional attention has focused on security,
preparedness, and emergency response issues. Among the many topics of interest is
protection of the nation’s water infrastructure facilities (both wastewater and drinking
water) from possible physical damage, biological/chemical attacks, and cyber
disruption.2 Policymakers are considering a number of legislative options in this
area, including enhanced physical security, communication and coordination, and
research. Physical security of wastewater treatment plant operations is one issue
under consideration. In the 108th Congress, the House passed legislation to provide
$200 million in grants for security activities at wastewater treatment plants (H.R.
866). A similar Senate bill was approved by the Senate Environment and Public
Works Committee (S. 1039). No further action occurred, due in part to concerns
expressed by some that the legislation would not require that vulnerability
assessments be mandatory and be submitted to EPA, as is the case with assessments
of drinking water utilities required by the 2002 Bioterrorism Preparedness Act (P.L.
107-288). The issue is again receiving attention in the 109th Congress.3
Although much progress has been made in achieving the ambitious goals
established in the law 30-plus years ago to restore the maintain the chemical,
physical, and biological integrity of rivers, lakes, and coastal waters, problems
persist. Based on the limited water quality monitoring that is done by states, EPA
reported in the 2000 National Water Quality Inventory Report that 39% of assessed
river and stream miles and 45% of assessed lake acres do not meet applicable water
2 For information, see CRS Report RL32189, Terrorism and Security Issues Facing the
Water Infrastructure Sector, by Claudia Copeland and Betsy Cody.
3 See CRS Issue Brief IB10142, Clean Water Act Issues in the 109th Congress, by Claudia
Copeland.

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CRS-4
quality standards and were found to be impaired for one or more desired uses.4 The
types of remaining water quality problems are diverse, ranging from runoff from
farms and ranches, city streets, and other diffuse sources, to metals (especially
mercury), organic and inorganic toxic substances discharged from factories, sewage
treatment plants, and nonpoint sources.
The Bush Administration has been reviewing a number of current clean water
programs and rules but has proposed few new initiatives. However, in January 2003,
the agency announced a Water Quality Trading Policy intended as an innovative
approach to assist industry and municipalities in meeting Clean Water Act
obligations. Trading allows one source to meet regulatory requirements by using
pollutant reductions created by another source that has lower pollution control costs.
The policy revised a May 2002 proposal which reflected lessons learned from a
similar policy issued by the Clinton Administration in 1996. Water quality or
effluent trading projects have occurred in the United States since the early 1980s.5
State Revolving Fund Program
The Act’s program of financial aid for municipal wastewater treatment plant
construction was a central and controversial aspect of debate on the 1987
amendments. Since 1972 Congress has provided more than $75 billion to assist
wastewater treatment construction, but funding needs remain very high: an additional
$181 billion nationwide for all types of projects eligible for funding under the act,
according to the most recent Needs Survey estimate by EPA and the states, published
in August 2003.6 In September 2002, EPA released a study called the Gap Analysis
that assesses the difference between current spending for wastewater infrastructure
and total funding needs (both capital and operation and maintenance).7 In that report,
EPA estimated that, over the next two decades, the United States needs to spend
nearly $390 billion to replace existing wastewater infrastructure systems and to build
new ones. Funding needs for operation and maintenance (not eligible for Clean
Water Act funding) are an additional $148 billion, the agency estimated. According
to the Gap Analysis, if there is no increase in investment, there will be about a $6
billion gap between current annual capital expenditures for wastewater treatment
($13 billion annually) and projected spending needs. The study also estimated that,
if wastewater spending increases by 3% annually, the gap would shrink by nearly
90% (to about $1 billion annually). At issue has been what should be the federal role
in assisting states and cities, especially in view of such high projected funding needs.
4 U.S. Environmental Protection Agency. The National Water Quality Inventory: 2000
Report. Washington, September 2002. EPA-841-R-2-001. 207 p.
5 For information, see CRS Report RS21403, EPA’s Water Quality Trading Policy, by
Claudia Copeland.
6 U.S. Environmental Protection Agency. Clean Watersheds Needs Survey 2000, Report to
Congress. Washington. August 2003. EPA 832-03-001. 1 vol.
7 U.S. Environmental Protection Agency. The Clean Water and Drinking Water
Infrastructure Gap Analysis. September 2002. EPA 816-R-02-020. 50 p.

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The 1987 amendments extended through FY1990 the traditional Title II
program of grants for sewage treatment project construction, under which the federal
share was 55% of project costs. The 1987 law initiated a program of grants to
capitalize State Water Pollution Control Revolving Funds (SRFs), or loan programs,
in a new Title VI. States are required to deposit an amount equal to at least 20% of
the federal capitalization grant in the Fund established under Title VI. Under the
revolving fund concept, monies used for wastewater treatment construction would
be repaid by loan recipients to the states (repayment was not required for grants under
the Title II program), to be recycled for future construction in other communities,
thus providing an ongoing source of financing. The expectation in 1987 was that the
federal contributions to SRFs would assist in making a transition to full state and
local financing by FY1995. Although most states believe that the SRF is working
well, early funding and administrative problems have delayed the anticipated shift to
full state responsibility. Thus, SRF issues have been prominent on the Clean Water
Act reauthorization agenda in recent Congresses.8
SRF monies may be used for certain types of financial activity, including loans
for as much as 100% of project costs (at or below market interest rates, including
interest-free loans), to buy or refinance cities’ debt obligation, or as a source of
revenue or security for payment of principal and interest on a state-issued bond. SRF
monies also may be used to provide loan guarantees or credit enhancement for
localities. Loans made by a state from its SRF are to be used first to assure progress
towards the goals of the Act and, in particular, on projects to meet the standards and
enforceable requirements of the Act. After states achieve those requirements of the
Act, SRF monies also may be used to implement nonpoint pollution management and
national estuary programs.
Table 1 summarizes wastewater treatment funding under Title II (traditional
grants program) and Title VI (capitalization grants for revolving loan programs).9

One issue of continuing interest is impacts on small communities. These
entities in particular have found it difficult to participate in the SRF loan program,
since many are characterized by narrow or weak tax bases, limited or no access to
capital markets, lower relative household incomes, and higher per capita needs. They
often find it harder to borrow to meet their capital needs and pay relatively high
premiums to do so. Meeting the special needs of small towns, through a
reestablished grant program, other funding source, or loan program with special rules,
has been an issue of interest to Congress.
Congressional oversight of wastewater/SRF issues has focused on several
points, including the fact that many small communities have found it difficult to
participate in the SRF loan program, and the lack of funds for high-cost categories
8 For further information, see CRS Report 98-323, Wastewater Treatment: Overview and
Background, by Claudia Copeland.
9 Note: Table 1 does not include appropriations for special project grants in individual cities.
Issues associated with special project grants are discussed in CRS Report RL32201, Water
Infrastructure Project Earmarks in EPA Appropriations: Trends and Policy Implications,
by Claudia Copeland.

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CRS-6
of projects such as correcting combined sewer overflows. Although there has been
some criticism of the SRF program, and debate continues over specific concerns
(such as small community impacts), the basic approach is well supported in Congress
and elsewhere. Congress used the clean water SRF as the model when it established
a drinking water SRF in the Safe Drinking Water Act in 1996 (P.L. 104-182).10
Table 1. Wastewater Treatment Funding
(billions of dollars)
Authorizations
Appropriations
Fiscal Year
Title II
Title VI
Title II
Title VI
1986
$2.4
—
$1.8
—
1987
2.4
—
2.36
—
1988
2.4
—
2.3
—
1989
1.2
1.2
0.941
0.941
1990
1.2
1.2
0.967
0.967
1991
—
2.4
—
2.1
1992
—
1.8
—
1.95
1993
—
1.2
—
1.93
1994
—
0.6
—
1.22
1995
—
—
—
1.24
1996
—
—
—
2.07
1997
—
—
—
0.625
1998
—
—
—
1.35
1999
—
—
—
1.35
2000
—
—
—
1.345
2001
—
—
—
1.35
2002
—
—
—
1.35
2003
—
—
—
1.34
2004
—
—
—
1.34
2005
—
—
—
1.09
2006
—
—
—
0.887
Nonpoint Pollution Management
The 1987 amendments added a new Section 319 to the Act, under which states
were required to develop and implement programs to control nonpoint sources of
pollution, or rainfall runoff from farm and urban areas, as well as construction,
forestry, and mining sites. Previously, the Act had largely focused on controlling
point sources, while helping states and localities to plan for management of diverse
nonpoint sources. Yet, as industrial and municipal sources have abated pollution,
10 For further information, see CRS Report RS22037, Drinking Water State Revolving Fund:
Program Overview and Issues, by Mary Tiemann.

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uncontrolled nonpoint sources have become a relatively larger portion of remaining
water quality problems — perhaps contributing as much as 50% of the nation’s water
pollution. At issue today is what progress is being made to manage nonpoint source
pollution and what additional efforts may be needed involving Section 319 or other
public and private activities. Some observers are critical of the largely voluntary
nature of the Section 319 program, consisting of “all carrot but no stick,” while other
argue that the types of individual land management decisions that are needed to
manage nonpoint source pollution cannot be regulated in the same ways that
industrial sources are controlled.
States were required to identify waters not expected to meet water quality
standards because of nonpoint source pollution and to implement plans for managing
pollution from runoff. Federal grants totaling $400 million were authorized to cover
as much as 60% of the costs of implementing a state’s management plan.
The funding issue has become more urgent as states have moved from
assessment and plan development to management, since Congress intended that
Section 319 funds be used primarily to implement nonpoint pollution controls on the
ground. EPA has urged states to use a portion of monies that they receive under
Section 106 of the Act, water quality program assistance grants, for nonpoint source
activities. But, doing so utilizes money otherwise needed for core state efforts, such
as permit issuance, monitoring, enforcement, etc. Several concerns have been raised
about the Section 319 program.
Adequacy of Plans. Whether state plans have comprehensively addressed
nonpoint pollution problems is a lingering question. Some environmental groups
criticize EPA for providing inadequate guidance on methods, or management
practices, to advance control of nonpoint sources beyond known problems and
existing implementation steps, such as voluntary compliance and public education.
Moreover, some believe that states should be required to repeat the nonpoint source
assessments, which were one-time-only activities under the 1987 law, in order to
reflect improvements in technical and scientific information.
Funding. Precise estimates of the cost to manage nonpoint source pollution
are not available, because so much depends on the site-specific nature of problems
and solutions. However, in 1994 EPA estimated that current and planned spending
by private sources, states, and cities under provisions of current law is between $750
million and $1.1 billion per year. Without adequate funding to implement state
management plans, it is doubtful that much will be achieved under Section 319 to
control nonpoint source pollution.
Questions have been raised about the state grant program’s efficacy and overlap
with farm bill conservation funding, leading to proposed reductions in FY2004 and
FY2005 appropriations for Section 319 funds. In particular, the White House Office
of Management and Budget (OMB) found that EPA had not demonstrated results
under the program and urged the agency to shift its focus away from implementing
projects in agricultural areas and toward implementing plans in impaired waters.
State officials have been concerned that OMB is not fully aware of the extent to
which Section 319 funds address a range of nonpoint pollution control needs beyond
the agricultural sector.

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Program Changes. EPA and states negotiated changes intended to give the
319 program a new framework by giving states more flexibility. As a result, in 1996,
EPA issued revised guidance concerning state management of nonpoint source
programs that is intended to recognize that federal and state processes need to be
streamlined to increase program effectiveness and to speed progress towards solving
nonpoint pollution problems. The revised guidance outlines nine key elements to be
reflected in state programs (e.g., strong partnerships with stakeholders, explicit short-
and long-term goals for protecting surface and ground waters). States that meet the
nine criteria can be designated as leadership states, making them eligible for
incentives such as multi-year grants, reduced amount and frequency of reporting, and
self-assessment by states themselves. These incentives contrast with the previous
program approach, in which states competed for grants and those that did not meet
particular requirements received less grant money.
Significance for TMDLs. Attention has focused on nonpoint source
management efforts as a result of recent emphasis by EPA and states on meeting
TMDL requirements (see “TMDL Requirements,” next). Scrutiny of nonpoint
pollution problems and how they are being addressed has intensified as policymakers
and program officials assess additional steps to continue progress towards the Act’s
water quality goals. For several years, EPA has been explicitly linking
implementation of Section 319 with TMDL activities. For example, in 2001, EPA
published guidance saying that grants awarded under Section 319 should have a
concentrated focus on the development and implementation of TMDLs for nonpoint
sources of pollution, although funds will still be awarded to activities other than
TMDLs. However, states and agricultural interests criticized the guidance as being
too restrictive, and in August 2002, EPA modified the guidance which continues to
encourage development of nonpoint source TMDLs but gives states more flexibility
to do so, especially in areas that lack formally established TMDLs. Since FY2001,
$100 million of Section 319 grant funds (which totaled $204 million in FY2006, for
example) is being devoted annually to developing and implementing nonpoint source
TMDLs.
Total Maximum Daily Load (TMDL) Requirements
Section 303(d) of the Clean Water Act requires states to identify
pollutant-impaired water segments and develop “total maximum daily loads”
(TMDLs) that set the maximum amount of pollution that a water body can receive
without violating water quality standards. If a state fails to do so, EPA is required
to develop a priority list for the state and make its own TMDL determination. Most
states have lacked the resources to do TMDL analyses, which involve complex
assessment of point and nonpoint sources and mathematical modeling, and EPA has
both been reluctant to override states and has also lacked resources to do the
analyses. Thus, for many years there was little implementation of the provision that
Congress enacted in 1972. At issue today is continuing controversy over
implementation of this program which is intended to address uncontrolled sources
of water quality impairment and efforts to revise the rules and requirements for it.

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CRS-9
In recent years, national and local environmental groups have filed more than
40 lawsuits in 38 states against EPA and states for failure to fulfill requirements of
the Act. Of the suits tried or settled to date, 22 have resulted in court orders requiring
EPA to develop TMDLs expeditiously. EPA and state officials have been concerned
about diverting resources from other high-priority water quality activities in order to
meet the courts’ orders. In 1996, EPA created an advisory committee to solicit
advice on the TMDL problem. Recommendations from the advisory committee
formed the basis of program changes that EPA proposed in August 1999. The 1999
proposal set forth criteria for states, territories, and authorized Indian tribes to
identify impaired waters and establish all TMDLs within 15 years. It would require
more comprehensive assessments of waterways, detailed cleanup plans, and
timetables for implementation.11

The 1999 proposal was highly controversial because of issues such as burdens
on states to implement a revised TMDL program and potential impacts on some
agriculture and forestry sources which are not now subject to CWA regulations. The
controversies also have drawn congressional attention, and 13 congressional hearings
were held during the 106th Congress by four separate House and Senate committees.
Public and congressional pressure on EPA to revise or withdraw the TMDL proposal
entirely was great. Several bills to modify EPA’s TMDL proposals or delay
implementation of final rules were introduced.
TMDL issues also were addressed in FY2001 appropriations bills. In July 2000,
the House and Senate approved an FY2001 Military Construction and emergency
supplemental appropriations bill that included a provision to prevent EPA from
spending any funds in FY2000 or FY2001 to finalize or implement new TMDL rules.
President Clinton signed the bill, in spite of the TMDL restriction, which the
Administration opposed (P.L. 106-246). However, the EPA Administrator signed
the new rules two days before the President signed the bill but delayed the effective
date until October 2001, when the limitation in P.L. 106-246 would expire. EPA’s
signing of the rule before the rider took effect led to more criticism.
The FY2001 appropriations act providing funds for EPA, P.L. 106-377,
included report language mandating studies by the National Academy of Sciences
(NAS) and EPA on the scientific basis of the TMDL program and on the potential
costs to states and businesses of implementing the revised TMDL rules. The NAS
report, examining the role of science in the TMDL program, was issued in June
2001.12 It did not specifically analyze the July 2000 revised regulations. The NAS
panel concluded that scientific knowledge exists to move forward with the TMDL
program and recommended that EPA and states use adaptive implementation for
TMDL development. In many cases, the report said, water quality problems and
solutions are obvious and should proceed without complex analysis. In other cases,
solutions are more complex and require a different level of understanding and
11 For additional information, see CRS Report 97-831, Clean Water Act and Total Maximum
Daily Loads (TMDLs) of Pollutants, by Claudia Copeland.
12 National Research Council, National Academy of Sciences. Assessing the TMDL
Approach to Water Quality Management. National Academy Press, Washington, D.C. June
2001. 82 p.

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something like phased implementation. A House Transportation subcommittee held
a hearing on the NAS report in June 2001. In August 2001, EPA issued a draft report
on costs of the 2000 TMDL program. It estimated that average annual costs to states
and EPA of developing TMDLs could be $63-$69 million, while implementation
costs for pollutant sources could be between $900 million and $4.3 billion per year,
depending on states’ actions.13 The General Accounting Office (now the Government
Accountability Office) reported in 2002 that inconsistent monitoring, data collection,
and listing procedures used by states to identify impaired waters have hindered
efforts to develop effective TMDL programs.14
The Bush Administration announced in October 2001 that it would delay the
effective date of the 2000 rule until April 30, 2003, to allow for further review. That
announcement came after a federal court granted the Administration’s request for a
similar 18-month suspension of litigation which is challenging the regulation (nearly
a dozen interest groups sued EPA over various parts of the TMDL rule). A House
Transportation and Infrastructure subcommittee held an oversight hearing in
November 2001 concerning EPA’s plans to revise the rule. Most recently, on March
19, 2003, EPA withdrew the July 2000 TMDL rule (68 Federal Register 13607).
EPA officials said that additional time beyond May 2003 was needed to decide
whether and how to revise the current program and that allowing the rule to take
effect would have disrupted ongoing review efforts. In the interim and continuing
for the present time, current program requirements under existing regulations issued
in 1992 and court-sanctioned TMDL schedules remain in place.
Having withdrawn the 2000 rule, EPA is reportedly considering other options,
including initiating an entirely new rule, but no specific plans or timeframe have been
announced. In mid-2002, EPA developed a draft revised rule that it informally
circulated among interest groups and federal agencies for many months, but no
formal proposal has occurred. One EPA view, widely reported, is that a new rule is
not essential, because EPA believes that states are and will continue to improve the
pace at which TMDLs are established, even under existing rules. Most
environmentalists say that, short of retaining the 2000 rule, the best action would be
to leave the 1992 rules in place, because, despite flaws, those rules are preferable to
a new rule that might significantly weaken the program. States, cities, and industry
groups have urged EPA to develop a new rule with more flexibility than either the
1992 regulations or the 2000 revisions.
Other Issues
A number of other Clean Water Act issues continue to receive attention, as well.
Like those discussed previously, many of these topics have recently been part of
Congress’ agenda in connection with reauthorization.
13 U.S. Environmental Protection Agency. The National Costs of the Total maximum Daily
Load Program (Draft Report). EPA 841-D-01-003. Aug. 1, 2001. 1 vol.
14 U.S. Government Accountability Office. Water Quality: Inconsistent State Approaches
Complicate Nation’s Efforts to Identify Its Most Polluted Waters, GAO-02-186, June 2001.
41 p.

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Stormwater Discharges. EPA has struggled since the 1970s to regulate
industrial and municipal stormwater discharges in a workable yet comprehensive
manner. In P.L. 100-4, Congress established firm deadlines and priorities for EPA
to require permits for discharges of stormwater that are not mixed or contaminated
with household or industrial waste. EPA issued rules in November 1990 (21 months
after the statutory deadline) that addressed Phase I of the program, detailing the
process of applying for stormwater permits for industries, medium and large
municipalities, and construction sites larger than 5 acres. The agency worked with
an advisory committee of stakeholders beginning in 1994 to develop rules for
regulating smaller stormwater dischargers, which were not covered by the 1990 rules.
Rules for smaller dischargers (unregulated industries, small construction sites, and
small cities), Phase II of the program, were issued in October 1999. The burden of
complying with the rules continues to be an issue with many affected industries and
municipalities, especially small cities, which faced compliance deadlines beginning
in March 2003.15
Stormwater issues were addressed in one provision of omnibus energy
legislation in the 108th Congress and now again in the 109th Congress. (For
information, see CRS Issue Brief IB10143.) Section 323 of H.R. 6 provides a
permanent exemption from stormwater runoff rules for the construction of
exploration and production facilities by oil and gas companies or the roads that
service those sites. As the March 2003 compliance deadline for small construction
sites to comply with stormwater permit rules approached, EPA proposed a two-year
extension of those rules for small oil and gas construction sites to allow the agency
to assess the economic impact on that industry. In March 2005, EPA again extended
the deadline, until June 2006.
Industry officials said that EPA’s original stormwater rule created costly
permitting requirements, even though the short construction period for drilling sites
carries little potential for stormwater runoff pollution. The provision in H.R. 6
makes EPA’s temporary delay permanent and makes it applicable to construction
activities at all oil and gas development and production sites, regardless of size,
including those covered by an earlier Phase I of the stormwater program. Opponents
argued that the provision did not belong in the energy legislation and that there was
no evidence that construction at oil and gas sites causes less pollution than other
construction activities. The conference report on H.R. 6, with the oil and gas
stormwater provision, passed the House and Senate on July 28 and 29, respectively.
President Bush signed it into law on August 8 (P.L. 109-58). On January 6, EPA
proposed a rule to conform the CWA to these provisions of P.L. 109-58.16
Combined and Separate Sewer Overflows. A total of 772 municipalities
have combined sewers where domestic sanitary sewage, industrial wastes, infiltration
15 For further information, see CRS Report 97-290, Stormwater Permits: Status of EPA’s
Regulatory Program, by Claudia Copeland.
16 U.S. Environmental Protection Agency. “Amendments to the National Pollutant
Discharge Elimination System (NPDES) Regulations for Storm Water Discharges
Associated with Oil and Gas Exploration, Production, Processing, or Treatment Operations,
or Transmission Facilities.” 71 Federal Register 894, Jan. 6, 2006.

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from groundwater, and stormwater runoff are collected. These systems serve
approximately 40 million persons, mainly in older urban and coastal cities. Normally
(under dry-weather conditions), the combined wastes are conveyed to a municipal
sewage treatment plant.
Properly designed, sized, and maintained combined sewers can be an acceptable
part of a city’s water pollution control infrastructure. However, combined sewer
overflow (CSO) occurs when the capacity of the collection and treatment system is
exceeded due to high volumes of rainwater or snowmelt, and the excess volume is
diverted and discharged directly into receiving waters, bypassing the sewage
treatment plants. Often the excess flow that contains raw sewage, industrial wastes,
and stormwater is discharged untreated. Many combined sewer systems are found
in coastal areas where recreational areas, fish habitat and shellfish beds may be
contaminated by the discharges.
In 1994, following negotiations with key stakeholder groups, EPA issued a CSO
permitting strategy. Cities were to implement nine minimum controls by January 1,
1997 (e.g., proper operation and maintenance programs for sewer systems and
pollution prevention programs). The EPA strategy did not contain a deadline for
issuance of permits or for controlling CSOs. Deadlines will be contained in plans
developed by permitting authorities, which primarily are states. Controls are available
and generally are based on combinations of management techniques (such as
temporary retention of excess flow during storm events) and structural measures
(ranging from screens that capture solids to construction of separate sewer systems).
EPA officials stated in 1998 that only about one-half of the cities with combined
sewers implemented the minimum measures called for in the 1994 strategy. EPA is
now working with states to remind cities of their obligations to address CSO
problems. However, a formal enforcement strategy is not contemplated.
A more recent issue concerning some cities is the problem of overflows from
municipal separate sanitary sewers (SSOs) that are not CSOs because they transport
only sanitary wastes. Discharges of untreated sewage from these sewers occur from
manholes, broken pipes and deteriorated infrastructure, and undersized pipes, and can
occur in wet or dry weather. EPA estimates that there are about 18,000
municipalities with separate sanitary sewers, all of which can, under certain
circumstances, experience overflows. No explicit EPA or statutory control policy
currently exists. In 1995, EPA convened a stakeholders’ group to discuss how to
address those overflows that pose the highest environmental and public health risk
first. On January 5, 2001, the Clinton Administration finalized regulations to
improve the operation of municipal sanitary sewer collection systems, reduce the
frequency and occurrence of overflows, clarify the existing CWA prohibition on SSO
discharges, and clarify circumstances appropriate for enforcement action. The
Clinton proposal was not finalized and remains under review by the Bush
Administration.
Funding for CSO and SSO projects is a major concern of states and cities. The
most recent clean water needs survey estimating the cost of projects to meet
objectives of the CWA found that the largest needs category, totaling $51 billion, is
to address CSOs. EPA estimates that costs to restrict SSOs are $88.5 billion. In
December 2000, Congress passed legislation, the Wet Weather Water Quality Act,

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authorizing a two-year $1.5 billion grants program to reduce wet weather flows from
municipal sewer systems. This bill was included in the FY2001 Consolidated
Appropriations bill (Section 112 of Division B, P.L. 106-554), which codified EPA’s
CSO policy on sewer overflows (discussed above). Congress provided no
appropriations for these wet weather grants during the two years of authorization
(FY2002-FY2003).
Wetlands. Public debate over the nation’s wetlands has come to focus on
questions of the effectiveness and costs of wetland resource protection efforts, rather
than on whether such resources should be preserved. The permit program authorized
by Section 404 of the Clean Water Act is one of the major federal programs that
protects wetlands. However, environmentalists and others have criticized Section
404 as being inadequate to prevent the continuing loss of wetlands, due to statutory
exemption of certain types of actions on farmlands and weak enforcement. Those
wishing to develop wetlands maintain that existing laws are already an intrusion on
private land-use decisions and that further federal involvement is unwarranted. How
best to protect remaining wetlands and regulate activities taking place in wetlands has
become one of the most contentious environmental policy issues facing Congress and
was a prominent element of clean water debate during the 103rd and 104th
Congresses. Although there has been no recent legislative activity on Section 404,
committee hearings were held on several issues arising from judicial decisions,
administrative actions of interest, and implementation of current law. Particular
attention has focused on issues related to a 2001 Supreme Court case which
narrowed the government’s regulatory jurisdiction over isolated waters, Solid Waste
Agency of Northern Cook County (SWANCC) v. U.S. Army Corps of Engineers (531
U.S. 159 (2001)). Since that ruling, some federal courts have interpreted SWANCC
narrowly, thus limiting its effect on current permit rules, while a few have read the
decision more broadly. On February 21, the Supreme Court heard arguments in two
more cases brought by landowners (Rapanos v. United States; Carabell v. U.S. Army
Corps of Engineers) seeking to narrow the scope of the Section 404 permit program.
Decisions in these cases are expected by the end of June.17
On January 15, 2003, EPA and the Corps issued guidance to their staffs in the
field for regulating in light of SWANCC and related cases. At the same time, the
agencies issued an advanced notice of proposed rulemaking (ANPRM), seeking
public comment on possible rule changes not yet proposed but which may be needed
in response to the legal decisions. The agencies received more than 130,000 public
comments on the ANPRM, most of them negative, according to EPA and the Corps.
Since the 2001 ruling, House and Senate committees have held several hearings to
examine issues and frustrations arising from government and judicial interpretations
of the decision. On December 16, 2003, EPA and the Corps announced that the
Administration will not pursue development of rule changes concerning federal
regulatory jurisdiction over isolated wetlands. The EPA Administrator said that the
Administration wanted to avoid a contentious and lengthy rulemaking debate over
the issue. Environmentalists and state representatives expressed relief at the
17 For additional information, see CRS Report RL33263, The Wetlands Coverage of the
Clean Water Act is Revisited by the Supreme Court: Rapanos and Carabell, by Robert Meltz
and Claudia Copeland.

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announcement. Interest groups on all sides have been critical of confusion in
implementing the 2003 guidance, which constitutes the main tool for interpreting the
reach of the SWANCC decision. However, environmentalists remain concerned
about diminished protection resulting from the 2003 guidance, while developers said
that without a new rule, confusing and contradictory interpretations of wetland rules
likely will continue.18
Strategy Concerning Animal Feeding Operations. Public and policy
attention has been increasing on steps to minimize public health and environmental
impacts of runoff from animal feeding operations (AFOs). AFOs are agricultural
facilities that confine livestock feeding activities, thus concentrating animal
populations and waste. Animal waste is frequently applied to land for disposal and
to utilize the nutrient value of manure to benefit crops. If not managed properly,
however, it can pose risks to water quality and public health, contributing pollutants
such as nutrients, sediment, pathogens, and ammonia to the environment. In 1999,
EPA and the U.S. Department of Agriculture initiated a national AFO strategy to
improve compliance and strengthen regulations that are intended to control adverse
environmental impacts of these agricultural activities.
EPA regulations, issued in the 1970s, required CWA discharge permits for the
largest AFOs, termed confined animal feeding operations (CAFOs). However, EPA
acknowledged that compliance and enforcement of these permit rules was poor (less
than one-third of covered facilities actually have permits) and that the regulations
themselves were outdated. In December 2000, EPA proposed a rule to increase the
number of AFOs required to obtain CWA permits and to restrict land application of
animal wastes. In May 2001, a House Transportation and Infrastructure
subcommittee held an oversight hearing on the proposal. Issues that Congress has
addressed during this period include impacts and costs imposed on the agricultural
sector, especially small farmers, and how the proposed combination of regulatory and
incentive-based measures in the 1999 National AFO Strategy would achieve control
of agricultural runoff that adversely affects water quality.19
On December 15, 2002, the EPA Administrator signed a final revised rule to
regulate waste discharges from CAFOs. The final rule, which the agency was under
court order to issue by December 2002, modified the Clinton Administration’s 2000
proposal in a number of areas. The final rule retains much of the structure of the
existing rule, such as regulatory thresholds and definitions, but includes requirements
for development of nutrient management plans to better manage land application of
manure. EPA estimated that 15,500 CAFOs will be regulated by the rule (compared
with 26,000-39,000 under the proposal), at an annual compliance cost of $335
million (versus $850-$980 million under the proposal). Farm groups said that the
regulations are generally workable and consistent with environmental initiatives in
the 2002 farm bill (P.L. 107-171), but environmental groups criticized the rule for
18 For additional information, see CRS Issue Brief IB97014, Wetland Issues, by Jeffrey Zinn
and Claudia Copeland.
19 For additional information, see CRS Report RL30437, Water Quality Initiatives and
Agriculture, by Claudia Copeland.

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inadequately addressing animal waste runoff problems.20 A January 2003 GAO
report concluded that the rule will be ineffective unless EPA increases its oversight
of state regulatory programs, which have primary responsibility for ensuring
compliance by feedlot operators.21
In February 2005, a federal court issued a ruling in a set of challenges to the
CAFO rule (Waterkeeper Alliance, American Farm Bureau, et al. v. EPA, 399 F.3d
486 (2d Cir. 2005)). The litigation involved challenges to the permitting scheme of
the rule, the type of discharges subject to regulation, and the effluent limitations
established in the rules. The court upheld major parts of the EPA rule, held in favor
of some of industry’s challenges, held in favor of several of environmentalists’
challenges, and in some cases directed EPA to explain more fully why it did or did
not do certain things with regard to specific provisions of the rule. It remanded the
rule to EPA in light of the court’s ruling. The court overturned the “duty to apply”
part of the rule, which industry had challenged, that would require all CAFOs to
apply for a permit. It also rejected parts of the rule, challenged by environmentalists
as inadequate, regarding regulatory review of permits, inclusion of nutrient
management plans in CAFO permits, and public participation requirements. EPA
announced in November 2006 that it is extending the 2006 deadlines for livestock
operations to obtain clean water permits and develop nutrient management plans, at
least until the agency finishes revising the 2002 rule in compliance with the court’s
2005 ruling. EPA now expects to issue a final revised rule in March 2007.
Continuing Issue:
Appropriations and the Federal Budget
Although the 1987 Clean Water Act amendments dealt extensively with
financial aid issues, funding questions have continued to arise and be addressed in
the context of appropriations.22
FY2007. The President’s FY2007 budget requested $687.6 million for clean
water SRF capitalization grants, which is 22% less than was appropriated in FY2006
(see following section) and 37% below the FY2005 funding level. As in recent
budgets, the Administration proposed no funding for congressionally designated
water infrastructure grants, but it did seek a total of $40.6 million for Administration
priority projects in Puerto Rico, Alaska Native Villages, and at the U.S.-Mexico
border. Advocates of the SRF program (especially state and local government
officials) contend that the cuts will impair their ability to carry out needed municipal
20 For additional information, see CRS Report RL31851, Animal Waste and the
Environment: EPA Regulation of Concentrated Animal Feeding Operations, by Claudia
Copeland.
21 U.S. Government Accountability Office. Increased EPA Oversight Will Improve
Environmental Program for Concentrated Animal Feeding Operations, GAO-03-285.
January 2003. 42 p.
22 For additional information, see CRS Report 96-647, Water Infrastructure Financing:
History of EPA Appropriations, by Claudia Copeland.

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wastewater treatment plant improvement projects. Administration officials say that
cuts for the SRF in FY2007 are necessary because Congress boosted funds above the
requested level in FY2005 and 2006. A group of state environmental officials
contend that the budget unfairly targets state and local environmental grants.
On May 18 the House passed H.R. 5386 (H.Rept. 109-465), providing FY2007
funds for EPA and other agencies under the Interior and Environment Appropriations
account. The House bill endorses the President’s proposed cut to the clean water
SRF program by providing $687.6 million for this popular program. It also includes
$200 million for congressionally earmarked water infrastructure grants in 146
communities and $41 million for Administration-designated priority projects. The
House-passed bill also includes $29.6 million for cleanup of contaminated sediments
in the Great Lakes ($20 million less than requested), $204 million for Section 319
grants ($10 million more than requested), and $221.7 million for Section 106 state
program administration grants (as requested).
During debate on H.R. 5386, the House approved an amendment (by a 222-198
vote) to block EPA from spending funds to implement controversial 2003 policy
guidance that limited Clean Water Act jurisdiction over isolated streams, wetlands,
ponds, and other non-navigable intrastate waters. The guidance, issued jointly by
EPA and the Army Corps of Engineers, was intended to interpret the scope of the
Act’s jurisdiction following the 2001 Supreme Court SWANCC case (discussed
above, see “Wetlands”). Supporters of the amendment said that the guidance goes
beyond what the Supreme Court required in SWANCC, has allowed many streams
and wetlands to be unprotected from development, and has been more confusing than
helpful. Opponents predicted that the amendment would make EPA’s and the Corps’
job of regulating activities that affect wetlands more difficult than it already is.23
FY2006. In July 2005, the House and Senate approved legislation providing
FY2006 appropriations for EPA (H.R. 2361, H.Rept. 109-188). President Bush
signed the bill into law on August 2 (P.L. 109-54). One of the most controversial
issues in the bill concerned funding for clean water SRF grants. The final measure
includes $900 million for these grants — $170 million more than requested by the
President for 2006. In its budget submission for FY2006, the Administration had
requested $730 million for SRF grants, 17.5% less than the FY2005 appropriation
and 45.6% below the FY2004 funding level, and said that cuts for the SRF in
FY2006 were because Congress boosted funds above their requested level in FY2005
(see following discussion). The White House said that it plans to invest a total of
$6.8 billion in the clean water SRF program between FY2004 and FY2011, after
which federal funding would end and the state SRFs would have an annual revolving
level of $3.4 billion. If Congress were to appropriate more than EPA requests in any
given year, the Administration has said, that target will be met sooner, leading to
reduced requests for the SRF in subsequent years until a planned phaseout in
FY2011. State and local officials say that the SRF reductions will impede their
ability to meet clean water goals. The President’s budget also requested no funds for
congressionally earmarked water infrastructure projects, but did seek $70 million in
23 For information, see CRS Issue Brief IB97014, Wetland Issues.

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funding for Administration priorities — U.S.-Mexico border projects and Alaska
Native Villages projects.
The final measure passed by Congress exceeded the Administration’s request
by providing $900 million for clean water SRF grants and $285 million for a total of
259 earmarked special projects. However, these totals were reduced slightly as a
result of a provision in P.L. 109-54 requiring a 0.476% across-the-board rescission
for all accounts in that bill, and were reduced further by another across-the-board
rescission of 1.0% affecting all domestic programs except those for veterans that
Congress included in a subsequent appropriations bill, P.L. 109-148. As a result of
the two required rescissions, the final FY2006 appropriations for clean water SRF
grants is $886.8 million, and the total amount provided for earmarked water
infrastructure project grants is $280.8 million.

The President’s FY2006 budget included increases for some water quality
programs (in particular, requesting $50 million for cleanup of Great Lakes
contaminated sediment, up from $22 million in FY2005). The budget also included
increases for some categorical clean water grant programs (state grants for program
administration, $23.6 million more than in FY2005; and nonpoint source pollution
management grants, $1.8 million more than in FY2005) and decreases elsewhere in
order to fund other Administration priorities (such as elimination of Water Quality
Cooperative Agreement grants, which support a variety of innovative permitting,
management, and research projects and were funded at $17 million in FY2005). As
enacted, P.L. 109-54 provides $30 million for cleanup of Great Lakes contaminated
sediment. It includes nonpoint source pollution grants at the FY2005 level and state
program grants (CWA Section 106) slightly higher than in FY2005, but less than
requested. The bill endorses the Administration’s request for no funding of Water
Quality Cooperative Agreement grants. The final bill also includes a House-passed
provision to prohibit EPA from using funds to finalize or implement a draft policy
proposed in November 2003 concerning sewage blending by municipal wastewater
treatment plants.24
For Additional Reading
Goplerud, C. Peter. “Water Pollution Law: Milestones from the Past and
Anticipation of the Future.” Natural Resources & Environment. v. 10, no. 2,
fall 1995. pp. 7-12.
Loeb, Penny. “Very Troubled Waters.” U.S. News & World Report, v. 125, no. 12,
September 28, 1998: 39, 41-42.
U.S. Congressional Budget Office. Future Investment in Drinking Water and
Wastewater Infrastructure. Washington, November 2002. 58 p.
24 For information, see CRS Report RL32384, EPA’s Proposed Policy on Wastewater
Blending: Background and Issues, by Claudia Copeland.

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U.S. Environmental Protection Agency. The National Water Quality Inventory:
2000 Report. Washington, September 2002. “EPA-841-R-2-001.”
U.S. Government Accountability Office. Key EPA and State Decisions Limited by
Inconsistent and Incomplete Data. (GAO/RCED-00-54) March 2000. 73 p.
——Water Infrastructure: Information on Financing, Capital Planning, and
Privatization. (GAO-02-764) August 2002. 79 p.
——Improved EPA Guidance and Support Can Help States Develop Standards That
Better Target Cleanup Efforts. (GAO-03-308) January 2003. 74 p.

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