

 
Water Quality Issues in the 113th Congress: 
An Overview 
Claudia Copeland 
Specialist in Resources and Environmental Policy 
April 30, 2014 
Congressional Research Service 
7-5700 
www.crs.gov 
R42883 
 
Water Quality Issues in the 113th Congress: An Overview 
 
Summary 
Much progress has been made in achieving the ambitious goals that Congress established 40 
years ago in the Clean Water Act (CWA) to restore and maintain the chemical, physical, and 
biological integrity of the nation’s waters. However, long-standing problems persist, and new 
problems have emerged. Water quality problems are diverse, ranging from pollution runoff from 
farms and ranches, city streets, and other diffuse or “nonpoint” sources, to toxic substances 
discharged from factories and sewage treatment plants. 
There is little agreement among stakeholders about what solutions are needed and whether new 
legislation is required to address the nation’s remaining water pollution problems. For some time, 
efforts to comprehensively amend the CWA have stalled as interests have debated whether and 
exactly how to change the law. Congress has instead focused legislative attention on enacting 
narrow bills to extend or modify selected CWA programs, but not any comprehensive proposals. 
For several years, the most prominent legislative water quality issue has concerned financial aid 
for municipal wastewater treatment projects. House and Senate committees have approved bills to 
reauthorize CWA assistance on several occasions since the 107th Congress, but, for various 
reasons, no legislation other than appropriations has been enacted. At issue has been the role of 
the federal government in assisting states and cities in meeting needs to rebuild, repair, and 
upgrade wastewater treatment plants, especially in light of capital costs that are projected to be 
nearly $300 billion over the next 20 years.  
Programs that regulate activities in wetlands also have been of interest, especially CWA Section 
404, which has been criticized by landowners for intruding on private land-use decisions and 
imposing excessive economic burdens. Environmentalists view this regulatory program as 
essential for maintaining the health of wetland ecosystems, and they are concerned about court 
rulings that have narrowed regulatory protection of wetlands and about related administrative 
actions. Many stakeholders desire clarification of the act’s regulatory jurisdiction, but they differ 
on what solutions are appropriate. On March 25, 2014, a proposed rule intended to clarify 
jurisdictional issues was proposed by the Environmental Protection Agency (EPA) and the Army 
Corps of Engineers, but interpretive questions about the proposal remain controversial. 
A number of other CWA issues have been the subject of congressional oversight and legislation, 
with some legislators highly critical of recent regulatory initiatives and others more supportive of 
EPA’s actions. Some issues have drawn policy makers’ attention following court rulings that 
addressed and in several cases expanded the regulatory scope of water quality protection efforts 
under the law. Among the topics of interest are environmental and economic impacts of 
Chesapeake Bay restoration efforts, federal promulgation of water quality standards in Florida, 
regulation of surface coal mining activities in Appalachia, and other CWA regulatory actions. 
Congressional interest in several of these issues has been reflected in specific legislative 
proposals and debate over policy provisions of legislation to provide appropriations for EPA. In 
the 112th Congress, Members from both parties raised questions about the cost-effectiveness of 
some of EPA’s actions and/or whether the agency has exceeded its authority. Attention to these 
issues continues in the 113th Congress. 
 
Congressional Research Service 
Water Quality Issues in the 113th Congress: An Overview 
 
Contents 
Introduction ...................................................................................................................................... 1 
Legislative and Oversight Issues ..................................................................................................... 2 
Authorization of Clean Water Infrastructure Funding ............................................................... 3 
Legislative Responses ......................................................................................................... 7 
Regulatory Protection of Wetlands ............................................................................................ 8 
Judicial Proceedings Involving Section 404 ....................................................................... 8 
Proposed Rule to Define “Waters of the United States” ................................................... 10 
Other Clean Water Act Issues .................................................................................................. 12 
Chesapeake Bay Restoration ............................................................................................. 13 
Florida Nutrient Water Quality Standards ......................................................................... 14 
Mountaintop Mining in Appalachia .................................................................................. 16 
The Relationship Between the CWA and FIFRA .............................................................. 18 
CWA Permits for Logging Road Discharges ..................................................................... 19 
Continuing Issue: Appropriations .................................................................................................. 20 
FY2014 Appropriations ........................................................................................................... 20 
FY2015 Appropriations ........................................................................................................... 21 
 
Tables 
Table 1. CWA Wastewater Treatment Funding ................................................................................ 5 
 
Contacts 
Author Contact Information........................................................................................................... 21 
 
Congressional Research Service 
Water Quality Issues in the 113th Congress: An Overview 
 
Introduction 
Much progress has been made in achieving the ambitious goals that Congress established 40 
years ago to restore and maintain the chemical, physical, and biological integrity of the nation’s 
waters. However, long-standing problems persist, and new problems have emerged. Water quality 
problems are diverse, ranging from pollution runoff from farms and ranches, city streets, and 
other diffuse or “nonpoint” sources, to “point” source discharges of metals and organic and 
inorganic toxic substances from factories and sewage treatment plants. 
The principal law that deals with polluting activity in the nation’s streams, lakes, estuaries, and 
coastal waters is the Federal Water Pollution Control Act (P.L. 92-500, enacted in 1972), 
commonly known as the Clean Water Act, or CWA. It consists of two major parts: regulatory 
provisions that impose progressively more stringent requirements on industries and cities to abate 
pollution and meet the statutory goal of zero discharge of pollutants; and provisions that authorize 
federal financial assistance for municipal wastewater treatment plant construction. Both parts are 
supported by research activities, plus permit and enforcement provisions. Programs at the federal 
level are administered by the Environmental Protection Agency (EPA); state and local 
governments have primary day-to-day responsibilities to implement CWA programs through 
standard-setting, permitting, enforcement, and administering financial assistance programs.1 
The water quality restoration objective declared in the 1972 act was accompanied by statutory 
goals to eliminate the discharge of pollutants into navigable waters by 1985 and to attain, 
wherever possible, waters deemed “fishable and swimmable” by 1983. Although those goals have 
not been fully achieved, considerable progress has been made, especially in controlling 
conventional pollutants (suspended solids, bacteria, and oxygen-consuming materials) discharged 
by industries and sewage treatment plants. 
Progress has been mixed in controlling discharges of toxic pollutants (heavy metals, inorganic 
and organic chemicals), which are more numerous and can harm human health and the 
environment even when present in very small amounts—at the parts-per-billion level. Moreover, 
efforts to control pollution from diffuse sources, termed nonpoint source pollution (rainfall runoff 
from urban, suburban, and agricultural areas, for example), are more recent, given the earlier 
emphasis on “point source” pollution (discharges from industrial facilities and municipal 
wastewater treatment plants). Overall, data reported by EPA and states indicate that 44% of river 
and stream miles assessed by states and 64% of assessed lake acres do not meet applicable water 
quality standards and are impaired for one or more desired uses.2 In 2006 EPA issued an 
assessment of streams and small rivers and reported that 67% of U.S. stream miles are in poor or 
fair condition and that nutrients and streambed sediments have the largest adverse impact on the 
aquatic species in these waters.3 Approximately 95,000 lakes and 544,000 river miles in the 
United States are under fish-consumption advisories (including 100% of the Great Lakes and 
their connecting waters), due to chemical contaminants in lakes, rivers, and coastal waters, and 
one-third of shellfishing beds are closed or restricted, due to toxic pollutant contamination. 
                                                 
1 For further information, see CRS Report RL30030, Clean Water Act: A Summary of the Law, by Claudia Copeland. 
2  U.S. Environmental Protection Agency, National Water Quality Inventory: Report to Congress, 2004 Reporting 
Cycle, EPA 841-R-08-001, January 2009, http://water.epa.gov/lawsregs/guidance/cwa/305b/2004report_index.cfm. 
3  U.S. Environmental Protection Agency, Wadeable Streams Assessment: A Collaborative Survey of the Nation’s 
Streams, EPA 841-B-06-002, December 2006, http://www.epa.gov/owow/streamsurvey/. 
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Water Quality Issues in the 113th Congress: An Overview 
 
Mercury is a contaminant of growing concern—as of 2003, 45 states had issued partial or 
statewide fish or shellfish consumption advisories because of elevated mercury levels. 
The last major amendments to the CWA were the Water Quality Act of 1987 (P.L. 100-4). That 
legislation culminated six years of congressional efforts to extend and revise the act and were the 
most comprehensive amendments since 1972. Authorizations of appropriations for some 
programs provided in P.L. 100-4, such as general grant assistance to states, research, and general 
EPA support, expired in FY1990 and FY1991. Authorizations for wastewater treatment funding 
expired in FY1994. None of these programs has lapsed, however, as Congress has continued to 
appropriate funds to implement them. EPA, states, industry, and other citizens continue to 
implement the 1987 legislation, including meeting the numerous requirements and deadlines in it. 
The Clean Water Act has been viewed as one of the most successful environmental laws in terms 
of achieving its statutory goals, which have been widely supported by the public. Lately, 
however, some have questioned whether additional actions to achieve further benefits are worth 
the costs, especially in view of the continuing problems of the U.S. economy. Criticism has come 
from industry, which has been the long-standing focus of the act’s regulatory programs and often 
opposes imposition of new stringent and costly requirements. Criticism also has come from 
developers and property rights groups who contend that federal regulations (particularly the act’s 
wetlands permit program) are a costly intrusion on private land-use decisions. States and cities 
have traditionally supported water quality programs and federal funding to assist them in carrying 
out the law, but many have opposed CWA measures that they fear might impose new unfunded 
mandates. Many environmental groups believe that further fine-tuning and strengthening of the 
law is needed to maintain progress achieved to date and to address remaining water quality 
problems. 
Legislative and Oversight Issues 
October 2012 marked the 40th anniversary of passage of the Clean Water Act and 25 years since 
the last major amendments to the law were enacted. While, as noted, there has been measurable 
clean water progress as a result of the act, observers and analysts agree that significant water 
pollution problems remain. However, there is less agreement about what solutions are needed and 
whether new legislation is required. Several key water quality issues exist: what additional 
actions should be taken to implement existing provisions of the law, whether additional steps are 
necessary to achieve overall goals of the act that have not yet been attained, how to ensure that 
progress made to date is not lost through diminished attention to water quality needs, and what is 
the appropriate federal role in guiding and paying for clean water infrastructure and other 
activities. For some time, efforts to comprehensively amend the act have stalled as interests have 
debated whether and exactly how to change the law. Many issues that might be addressed involve 
making difficult tradeoffs between impacts on different sectors of the economy; taking action 
when there is technical or scientific uncertainty; and allocating governmental responsibilities 
among federal, state, local, and tribal entities for implementing the law. 
These factors partly explain why Congress has recently focused legislative attention on narrow 
bills to extend or modify selected CWA programs, rather than taking up comprehensive proposals. 
Other factors also have been at work. These include a general reluctance by some Members of 
Congress to address controversial environmental issues in view of the relatively slim majorities 
held by political parties in the House and the Senate; a lack of legislative initiatives by the 
Administration on clean water issues (neither the Clinton nor the Bush Administration proposed 
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Water Quality Issues in the 113th Congress: An Overview 
 
CWA legislation, nor has the Obama Administration); and the high economic cost of addressing 
water infrastructure issues. 
Two CWA issues that have been the focus of much of legislators’ interest in recent Congresses 
received some attention again in the 112th Congress—water infrastructure financing, and 
regulatory protection of wetlands—but with different focus than in the recent past. After the 2010 
election, congressional leadership and priorities shifted—particularly in the House, which used 
both oversight and legislation to focus criticism on EPA regulatory activities. The 112th Congress 
enacted two bills that amend the CWA. One extended the moratorium for CWA permitting of 
certain vessels for an additional year, until December 18, 2014 (P.L. 112-213), and the other 
extends authorization of funds for the Lake Pontchartrain Basin program in Section 121 of the act 
through FY2017 (P.L. 112-237). With the 113th Congress divided like the 112th into a Republican-
controlled House and a Democratic-controlled Senate, and President Obama having been re-
elected, consideration of environmental issues generally, including water quality, may reflect 
those of the previous two years. 
Authorization of Clean Water Infrastructure Funding 
Meeting the nation’s needs to build, upgrade, rebuild, and repair wastewater infrastructure is a 
significant element in achieving the CWA’s water quality objectives. The act’s program of 
financial aid for municipal wastewater treatment plant construction is a key contributor to that 
effort. Since 1972 Congress has provided nearly $90 billion to assist cities in constructing 
projects to achieve the act’s requirements for secondary treatment of municipal sewage 
(equivalent to 85% reduction of wastes), or more stringent treatment where required by local 
water quality conditions. State and local governments have spent more than $25 billion of their 
own funds for construction, as well. Federal funds can only be used for construction purposes 
(i.e., new plants or upgrades), but not for operation and maintenance of facilities, which are 
funded from local sources. 
Still, funding needs remain very high: an additional $298 billion, according to the most recent 
Needs Survey estimate by EPA and the states, released in June 2010, a 17% increase above the 
estimate reported four years earlier.4 This current estimate includes $187.9 billion for wastewater 
treatment and collection systems ($26.7 billion more than the previous report), which represent 
more than 60% of all needs; $63.6 billion for combined sewer overflow corrections ($1.4 billion 
less than the previous estimate); $42.3 billion for stormwater management ($17 billion more than 
the previous estimate); and $4.4 billion to build systems to distribute recycled water ($700 
million less than the previous estimate).  
EPA reported several reasons for increased total needs for wastewater treatment, which were $23 
billion higher than in the previous report: improvements needed to meet more protective water 
quality standards, rehabilitation of aging infrastructure, and expanding capacity to meet 
population growth. Needs for stormwater management increased by $17 billion and were mostly 
due to emerging needs to provide “green” infrastructure (e.g., use of wetland and other natural 
systems to capture stormwater) as a supplement to traditional stormwater treatment structures, 
                                                 
4  U.S. Environmental Protection Agency, Clean Watersheds Needs Survey 2008, Report to Congress, Washington, 
June 2010, http://water.epa.gov/scitech/datait/databases/cwns/upload/cwns2008rtc.pdf. 
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Water Quality Issues in the 113th Congress: An Overview 
 
according to EPA. The estimates do not explicitly include funding needed to address security 
issues, or funding possibly needed for treatment works to adapt to climate change impacts. 
Debate over the nation’s efforts regarding wastewater infrastructure was a central and 
controversial part of the 1987 amendments to the act. The 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), which are 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 a state fund established pursuant to Title VI. Under the revolving fund 
concept, monies used for wastewater treatment construction are 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, continuing large funding needs 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.5 
SRF monies may be used for specified activities, including making 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 national estuary programs and nonpoint pollution 
management. Since the SRF program began, states have used $4.0 billion to assist more than 
14,500 nonpoint management projects. 
All states have established the mechanisms to administer the new loan programs and have been 
receiving SRF capitalization funds under Title VI. Congressional oversight has examined the 
progress toward reducing the backlog of wastewater treatment facilities needed to achieve the 
act’s water quality objectives, while newer estimates of future funding needs have drawn 
increased attention to the role of the SRF program in meeting such needs. Although there has 
been some criticism of the SRF program, and debate continues over specific concerns, the basic 
approach is well supported. Congress used the clean water SRF as the model when it established 
a drinking water SRF in 1996 (P.L. 104-182).6 
Although the initial intent was to phase out federal support for this program, Congress has 
continued to appropriate SRF capitalization grants to the states, providing an average of $1.35 
billion annually in recent years. Table 1 summarizes wastewater treatment funding under Title II 
(the traditional grants program) and Title VI (capitalization grants for revolving loan programs) 
since the 1987 amendments. This table does not include appropriations for congressionally 
                                                 
5 For further information on the clean water SRF program, see CRS Report 98-323, Wastewater Treatment: Overview 
and Background, by Claudia Copeland. 
6 For additional information, see CRS Report RS22037, Drinking Water State Revolving Fund (DWSRF): Program 
Overview and Issues, by Mary Tiemann. 
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Water Quality Issues in the 113th Congress: An Overview 
 
directed special project grants in individual cities (that is, congressional earmarks), which for 
several years represented about 15% of water infrastructure funds.7 
Table 1. CWA Wastewater Treatment Funding 
(billions of dollars) 
Authorizations 
Appropriations 
Fiscal Year 
Title II 
Title VI 
Title II 
Title VI 
1986 2.400 
— 
1.800 
— 
1987 2.400 
— 
2.360 
— 
1988 2.400 
— 
2.300 
— 
1989 
1.200 1.200 0.941 0.941 
1990 
1.200 1.200 0.960 0.967 
1991  — 2.400 
— 2.048 
1992  — 1.800 
— 1.950 
1993  — 1.200 
— 1.928 
1994  — 0.600 
— 1.218 
1995 — 
— 
— 1.235 
1996 — 
— 
— 2.074 
1997 — 
— 
— 0.625 
1998 — 
— 
— 1.350 
1999 — 
— 
— 1.350 
2000 — 
— 
— 1.345 
2001 — 
— 
— 1.350 
2002 — 
— 
— 1.350 
2003 — 
— 
— 1.341 
2004 — 
— 
— 1.342 
2005 — 
— 
— 1.091 
2006 — 
— 
— 0.887 
2007 — 
— 
— 1.084 
2008 — 
— 
— 0.689 
2009 — 
— 
— 0.689 
2009 ARRAa — 
— 
— 
4.000 
2010 — 
— 
— 2.100 
2011 — 
— 
— 1.522  
2012 — 
— 
— 1.466 
                                                 
7 Issues associated with special project grants are discussed in CRS Report RL32201, Water Infrastructure Projects 
Designated in EPA Appropriations: Trends and Policy Implications, by Claudia Copeland. Since FY2011, Congress 
has placed a moratorium on earmarks, but the practice could resume in the future. 
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Authorizations 
Appropriations 
Fiscal Year 
Title II 
Title VI 
Title II 
Title VI 
2013 — 
— 
— 1.376b 
2014 — 
— 
— 1.449 
TOTAL 7.2 
8.4 
8.4 
37.77 
Source: Compiled by CRS. 
a.  The American Recovery and Reinvestment Act of 2009 (P.L. 111-5) provided $4.0 billion in supplemental 
FY2009 appropriations.  
b.  FY2013 appropriations reflect post-sequester/post-rescission amount.  
One issue of continuing interest is impacts of paying for water infrastructure projects on small 
communities, many of which have found it difficult to participate in the SRF loan program. This 
is due to a number of factors: many are characterized by narrow or weak tax bases, limited or no 
access to capital markets, lower relative household incomes, higher per capita needs, and limited 
ability to demonstrate economies of scale. 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. 
Because remaining clean water funding needs are still so large nationally, at issue is whether and 
how to extend SRF assistance to address those needs, how to allocate SRF funds among the 
states, and how to prioritize projects and funding. Additionally, there is concern about the 
adequacy of SRF or other funding specifically for high-cost projects dealing with problems of 
overflows from municipal combined and separate sewers which can release partially treated or 
untreated wastewaters that harm public health and the environment. EPA estimates that the cost of 
projects to control sewer overflows and manage stormwater runoff is nearly $64 billion 
nationwide—nearly twice the total of SRF capitalization grants appropriated since 1987. And 
more recently, wastewater utilities have sought assistance to assess operational vulnerabilities and 
upgrade physical protection of their facilities against possible terrorist attacks that could threaten 
the water infrastructure system.8 
In 2010 EPA issued a “Clean Water and Drinking Water Infrastructure Sustainability Policy” 
addressing management and pricing of infrastructure funded through SRFs to encourage 
conservation and provide adequate long-term funding for future capital needs. EPA is working 
with water utilities to promote planning processes that reflect not only public health and water 
quality, but also conservation of natural resources and innovative treatment. Further, EPA is 
working with states to target SRF assistance to projects that focus on system upgrade and 
replacement in existing communities, reflect full life cycle costs of infrastructure assets, and 
conserve natural resources or use alternative approaches. 
                                                 
8 For additional information on many of these topics, see CRS Report RL31116, Water Infrastructure Needs and 
Investment: Review and Analysis of Key Issues, by Claudia Copeland and Mary Tiemann. 
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Legislative Responses 
Congress has considered water infrastructure funding issues several times since the 107th 
Congress, but no legislation other than appropriations has been enacted. Throughout this period, 
several factors have contributed to difficulties in moving bills through the legislative process. 
They include Bush Administration opposition to higher authorization levels, controversies over 
application of prevailing wage requirements of the Davis-Bacon Act to water infrastructure 
projects, and disputes over the formula for allocating clean water SRF grants among the states. 
The issue of the applicability of the Davis-Bacon Act to SRF-funded projects has been especially 
controversial, because that act has both strong supporters and critics in Congress and elsewhere. It 
requires, among other things, that not less than the locally prevailing wage be paid to workers 
employed, under contract, on federal construction work “to which the United States or the District 
of Columbia is a party.” Critics of Davis-Bacon say that it unnecessarily increases public 
construction costs and hampers competition, while supporters say that it helps stabilize the local 
construction industry by preventing competition that would undercut local wages and working 
conditions. Under the original SRF program authorization enacted in 1987, the Davis-Bacon Act 
applied to so-called “first use” monies provided by a state from its SRF (that is, loans made from 
initial federal capitalization grants, but not to subsequent monies provided from repayments to the 
SRF). When that authorization expired at the end of FY1994, Davis-Bacon requirements also 
expired. Thus, the recent issue has been whether to restore the applicability of those 
requirements.9 
A second issue that has complicated enactment of legislation is the method of allocating SRF 
capitalization grants among the states. CWA Section 205(c)(3) contains a table that identifies each 
state’s percentage share of appropriated funds. Changing the formulation of how funds are 
distributed matters to every state, because inevitably it results in “winners” and “losers.” But 
because the existing statutory allotment has not been revised since 1987, while needs have 
changed considerably, the issue is important to considering clean water infrastructure 
legislation.10  
Despite these specific issues that have stalled legislation, the act’s water infrastructure program is 
widely supported both inside and outside Congress. However, because the House and Senate have 
focused extensively on reducing federal spending and deficit reduction recently, proposals 
concerning new or expanded federal spending for water infrastructure investments have not 
advanced. In the 113th Congress, reauthorization legislation has been introduced in the House 
(H.R. 1877). 
Most policy makers acknowledge that communities face formidable challenges in providing 
adequate and reliable water infrastructure services to their citizens, and Congress is considering 
ways to help meet those challenges. Several policy options have recently been discussed at 
hearings held by House and Senate committees. Some of the options exist and are well 
established—such as the SRF program—while some are newer—such as creating a national 
infrastructure bank. Some are intended to provide long-term revenue to support infrastructure 
                                                 
9 For information, see CRS Report R41469, Davis-Bacon Prevailing Wages and State Revolving Loan Programs Under 
the Clean Water Act and the Safe Drinking Water Act, by Gerald Mayer and Jon O. Shimabukuro. 
10 For additional information on the current statutory formula, see CRS Report RL31073, Allocation of Wastewater 
Treatment Assistance: Formula and Other Changes, by Claudia Copeland. 
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financing programs, and some are intended to encourage private participation in providing 
wastewater services. At this point, there is no consensus favoring a preferred policy, and many 
advocate a combination of options to expand the financing “toolbox.”11 
Regulatory Protection of Wetlands 
How best to protect the nation’s remaining wetlands and regulate activities taking place in 
wetlands has become one of the most contentious environmental policy issues. Much of the 
debate has focused on the CWA, which contains a key wetlands regulatory tool. The permit 
program in CWA Section 404 requires landowners or developers to obtain permits for disposal of 
dredged or fill material that is generated by construction or similar activity into navigable waters 
of the United States, including wetlands. Section 404 has evolved through judicial interpretation 
and regulatory change to become one of the principal federal tools used to protect wetlands, 
although that term appears only once in Section 404 itself and is not defined there. At the same 
time, its implementation has come to be seen as intrusive and burdensome to those whose 
activities it regulates. At issue today is how to address criticism of the Section 404 regulatory 
program while achieving desired goals of wetlands protection in the context of meeting the goals 
and objectives of the CWA.12 
Unlike the rest of the act, the permit aspects of Section 404 are administered by the U.S. Army 
Corps of Engineers, rather than EPA, although the Corps uses environmental guidance jointly 
developed with EPA to evaluate permit applications. Other federal agencies including the Fish 
and Wildlife Service (FWS) and Natural Resource Conservation Service (NRCS) have more 
limited roles in the Corps’ permitting decisions. Tension has existed for many years between the 
regulation of activities in wetlands under Section 404 and related laws, on the one hand, and the 
desire of landowners to develop property that may include wetlands, on the other hand. The 
conflicts over wetlands regulation have for the most part occurred in administrative and judicial 
proceedings, as Congress has not amended Section 404 since 1977, when it provided exemptions 
for categories of routine activities, such as normal farming and forestry. Controversy has grown 
over the extent of federal jurisdiction and impacts on private property, burdens and delay of 
permit procedures, and roles of federal agencies and states in issuing permits. 
Judicial Proceedings Involving Section 404 
One issue involving long-standing controversy and litigation is whether isolated waters are 
properly within the jurisdiction of Section 404. Isolated waters—wetlands which are not 
physically adjacent to navigable surface waters and may be wet only for portions of the year—
often appear to provide only some of the values for which wetlands are protected, such as flood 
control or water purification, even if they meet the technical definition of a wetland. 
SWANCC and Rapanos 
In 2001, the Supreme Court ruled on the question of whether the CWA provides the Corps and 
EPA with authority over isolated waters. The Court’s 5-4 ruling in Solid Waste Agency of 
                                                 
11 For additional information, see CRS Report R42467, Legislative Options for Financing Water Infrastructure, by 
Claudia Copeland, Steven Maguire, and William J. Mallett. 
12 For additional information, see CRS Report RL33483, Wetlands: An Overview of Issues, by Claudia Copeland. 
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Northern Cook County (SWANCC) v. U.S. Army Corps of Engineers (531 U.S. 159 (2001)) held 
that the Corps’ denial of a 404 permit for a disposal site on isolated wetlands solely on the basis 
that migratory birds use the site exceeded the authority provided in the act. 
In 2006, the Supreme Court revisited issues related to the extent of CWA jurisdiction in two 
consolidated cases brought by landowners (Rapanos v. United States; and Carabell v. U.S. Army 
Corps of Engineers) seeking to narrow the scope of the 404 permit program as it applies to 
development of wetlands. The issue in both cases had to do with the reach of the CWA to cover 
“waters” that were not navigable waters in the traditional sense, but were connected somehow to 
navigable waters or “adjacent” to those waters. (The act requires a federal permit to discharge 
dredged or fill materials into “navigable waters.”) Many legal and other observers hoped that the 
Court’s ruling in these cases would bring greater clarity about the scope of federal jurisdiction. 
The Court’s ruling on the two cases was issued on June 19, 2006 (Rapanos, v. United States, 547 
U.S. 715 (2006)). In a 5-4 decision, a plurality of the Court, led by Justice Scalia, held that the 
lower court had applied an incorrect standard to determine whether the wetlands at issue are 
covered by the CWA. Justice Kennedy joined this plurality to vacate the lower court decisions 
and remand the cases for further consideration, but he took different positions on most of the 
substantive issues raised by the cases, as did four other dissenting Justices.13 Because the several 
opinions written by the Justices did not draw a clear line regarding which wetlands and other 
waters are subject to federal jurisdiction, one result has been more case-by-case determinations 
and continuing litigation. There also has been pressure on the Corps and EPA to clarify the issues 
through an administrative rulemaking. 
The full extent of impacts on the regulatory program resulting from these decisions still remains 
unclear, in part because of different interpretations of both rulings reflected in subsequent federal 
court cases. While it continues to be difficult to fully assess how regulatory protection of 
wetlands will be affected as a result of the decisions and other possible changes, the remaining 
responsibility to protect affected wetlands falls on states and localities. Environmentalists believe 
that the Court has misinterpreted congressional intent on the matter, while industry and 
landowner groups welcomed the rulings. Policy implications of how much the decisions restrict 
federal regulation depend on how broadly or narrowly the opinions are applied. Some federal 
courts have interpreted SWANCC and Rapanos narrowly, thus limiting effects on existing permit 
rules, while a few have read the decisions more broadly, resulting in a more restrictive 
interpretation of regulatory jurisdiction. 
Corps/EPA Guidance 
Following both the SWANCC and Rapanos rulings, EPA and the Corps issued guidance 
documents in 2003, 2007, and 2008 to enable their field staffs to make CWA jurisdictional 
determinations in light of the decisions. Some environmental groups have criticized the guidance, 
saying that the agencies are substantially limiting the scope of waters that are protected by the 
CWA. Industry groups such as developers remain frustrated by what they see as inconsistencies 
and delays in obtaining needed permits. 
                                                 
13 For additional information, see CRS Report RL33263, The Wetlands Coverage of the Clean Water Act (CWA): 
Rapanos and Beyond, by Robert Meltz and Claudia Copeland. 
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The Obama Administration entered this debate in April 2011, when EPA and the Corps proposed 
new guidance to replace the agencies’ 2003 and 2008 guidance (these earlier documents remain in 
effect until new guidance is finalized). The new guidance was intended to clarify regulatory 
jurisdiction over U.S. waters and wetlands, consistent with the Supreme Court decisions and 
agency regulations. Like previous guidance documents, the Obama draft examined current 
regulatory definitions of waters that are subject to CWA jurisdiction, such as interstate waters, and 
tributaries (at 33 CFR §328.3 and 40 CFR §230.3) in light of the Supreme Court’s rulings to 
determine which waters are clearly subject to the CWA, which waters are not, and which waters 
require a case-specific analysis in order to determine jurisdiction. The document stated that “after 
careful review of these opinions, the agencies concluded that previous guidance did not make full 
use of the authority provided by the CWA to include waters within the scope of the Act, as 
interpreted by the Court.” Based on current interpretations, the agencies expected that  
the extent of waters over which the agencies assert jurisdiction under the CWA will increase 
compared to the extent of waters over which jurisdiction has been asserted under existing 
guidance, though certainly not to the full extent that it was typically asserted prior to the 
Supreme Court decisions in SWANCC and Rapanos.14 
This conclusion was based on the agencies’ view that the draft guidance would clarify jurisdiction 
over some waters that previously were uncertain. EPA and the Corps believed that the resulting 
expanded jurisdiction would not be great, in terms of acreage or stream miles. 
The guidance proposed by EPA and the Corps quickly generated more controversy. Some critics 
argued that the guidance represented over-reaching by the agencies, beyond authority provided by 
Congress. Others faulted the continued reliance on federal guidance, which is not binding and 
lacks the force of law, yet can have significant impact on regulated entities.  
Proposed Rule to Define “Waters of the United States” 
For various reasons, the 2011 draft guidance was not finalized, and in September 2013, EPA and 
the Corps announced that the document had been withdrawn from interagency review and 
announced that revised regulations to define “waters of the United States” were being developed. 
On March 25, 2014, the agencies released a proposed rule.15 The agencies are accepting public 
comment on the proposal until July 21, 2014.16 
According to the agencies, the proposed rule would revise the existing administrative definition 
of “waters of the United States” consistent with legal rulings and science concerning the 
interconnectedness of tributaries, wetlands, and other waters and effects of these connections on 
the chemical, physical, and biological integrity of downstream waters. It is particularly focused 
on clarifying the regulatory status of waters located in isolated places in a landscape, the types of 
waters with ambiguous jurisdictional status following the Supreme Court’s 2001 ruling in 
                                                 
14 U.S. Environmental Protection Agency and Department of the Army, Corps of Engineers, “Draft Guidance on 
Identifying Waters Protected by the Clean Water Act,” April 27, 2011, p. 3, on file with author. 
15 For information on the proposal, see CRS Report R43455, EPA and the Army Corps’ Proposed Rule to Define 
“Waters of the United States”, by Claudia Copeland. 
16 Department of Defense, Department of the Army, Corps of Engineers, and Environmental Protection Agency, 
“Definition of ‘Waters of the United States’ Under the Clean Water Act, Proposed Rule,” 79 Federal Register 22188-
22274, April 21, 2014. 
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SWANCC, and small streams, rivers that flow for part of the year, and nearby wetlands, the types 
of waters affected by the Court’s 2006 ruling in Rapanos.  
The proposed rule would not modify some categories of waters that currently are jurisdictional by 
rule (traditional navigable waters, interstate waters and wetlands, the territorial seas, and 
impoundments). But, proposed changes would increase the asserted scope of CWA jurisdiction, in 
part as a result of expressly declaring some types of waters categorically jurisdictional (such as all 
waters adjacent to a jurisdictional water), and also by application of new definitions, which give 
larger regulatory context to some types of waters, such as tributaries. The proposal also would 
identify waters that are categorically not jurisdictional, such as ditches in uplands that have less 
than perennial flow. EPA and the Corps believe that the proposed rule will provide greater clarity 
and certainty to the regulated community regarding waters that are and are not jurisdictional 
under the CWA, but some waters will continue to require case-specific evaluation to determine if 
there is a “significant nexus” to a jurisdictional water. 
The agencies believe that the proposal does not exceed the CWA’s coverage or protect new types 
of waters that have not been protected historically. While it would enlarge jurisdiction beyond 
that under the existing (2008) EPA-Corps guidance, they believe that it would not enlarge 
jurisdiction beyond what is consistent with the Supreme Court’s narrow reading of jurisdiction. 
Others disagree: agriculture and other stakeholder groups assert that the agencies are proposing to 
expand the jurisdiction of the CWA beyond what the law and the courts allow. 
Also in September 2013, EPA released a draft report that reviews and synthesizes the peer-
reviewed scientific literature on the connectivity or isolation of streams and wetlands relative to 
large water bodies such as rivers, lakes, estuaries, and oceans.17 The purpose of the review, which 
summarizes more than 1,000 published and peer-reviewed scientific reports, is to summarize 
current understanding about these connections, the factors that influence them, and mechanisms 
by which connected waters affect the function or condition of downstream waters. EPA and the 
Corps used the draft report during development of the proposed rule. 
EPA has asked its Science Advisory Board (SAB) to review the draft report and to comment on 
whether its conclusions and findings are supported by the available science. The draft report is 
not intended as a policy document—it does not reference either the Scalia plurality or Kennedy 
tests in Rapanos, nor does it address legal standards for CWA jurisdiction. Nevertheless, EPA and 
the Corps say that the proposed rule takes into consideration the latest peer-reviewed science 
reflected in the draft science report. The report, when finalized, will provide a scientific basis 
needed to clarify CWA jurisdiction, but the rule will not be finalized until the SAB’s review and a 
final science report are complete, according to EPA.18 Some stakeholders have expressed concern 
that the scientific study could allow the agencies to assert jurisdiction in a blanket fashion over 
ephemeral and intermittent streams, rather than subjecting them to case-by-case determination of 
a “significant nexus” to downstream navigable waters. 
                                                 
17 U.S. Environmental Protection Agency, Office of Research and Development, Connectivity of Streams and Wetlands 
to Downstream Waters: A Review and Synthesis of the Scientific Evidence, External Review Draft, EPA/600/R-11-
098B, September 2013, http://yosemite.epa.gov/sab/sabproduct.nsf/0/7724357376745F48852579E60043E88C/$File/
WOUS_ERD2_Sep2013.pdf. 
18 See U.S. Environmental Protection Agency, “Clean Water Act Definition of ‘Waters of the United States,’” 
http://water.epa.gov/lawsregs/guidance/wetlands/CWAwaters.cfm. 
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Legislative Responses 
Congressional committees have held oversight hearings on both the SWANCC and Rapanos 
decisions, seeking clarification of interpretations and impacts of the rulings. But the uncertainties 
about federal jurisdiction over wetlands and other waters raised by the rulings remain highly 
controversial. In response, legislation to overturn the decisions by providing a broad definition of 
“waters of the United States” has been introduced regularly since the 107th Congress, and such a 
bill was reported by a Senate committee in the 111th Congress (for information, see CRS Report 
RL33263, The Wetlands Coverage of the Clean Water Act (CWA): Rapanos and Beyond). 
Legislation that instead would narrow the definition of “waters of the United States” also has 
been introduced, as described below.  
Environmental advocates and others contend that Congress must clarify the important issues left 
unsettled by the Supreme Court’s 2001 and 2006 rulings and by the Corps/EPA guidance. They 
also argue that legislation is needed to “reaffirm” what Congress intended when the CWA was 
enacted in 1972 and what EPA and the Corps have subsequently been practicing until the two 
Supreme Court rulings, in terms of CWA jurisdiction. But critics have questioned the 
constitutionality of legislation that has been proposed, and have asserted that it would expand 
federal authority, thus likely increasing confusion, rather than settling it. 
Obama Administration officials have addressed concerns about the continuing uncertainties 
regarding the proper scope of CWA regulatory jurisdiction. In 2009, the heads of EPA, the Corps, 
the Department of Agriculture, the Department of the Interior, and the Council on Environmental 
Quality jointly wrote to congressional leaders to support the need for legislative clarification of 
the issues.19 However, the Administration did not develop or support particular legislation. 
While interest in these issues has remained high, future prospects for legislation are highly 
uncertain because of the widely differing views of proponents and opponents. However, EPA’s 
and the Corps’ efforts to develop revised Rapanos guidance and revised regulations have been 
controversial and have received congressional attention. Legislative provisions to prohibit the 
agencies from funding activities related to revising the guidance were included in several 
appropriations bills since the 112th Congress, but none of these provisions has been enacted. 
Interest in similar legislation concerning the guidance has continued with bills in the 113th 
Congress, such as S. 1006 and H.R. 1829, to prevent the agencies from finalizing the 2011 draft 
guidance, which has now been withdrawn; and S. 890/H.R. 3377, which would amend the CWA 
with a narrow definition of waters that are subject to the act’s jurisdiction.  
Other Clean Water Act Issues 
A number of other issues affecting efforts to achieve the goals and objectives of the CWA have 
drawn interest recently and been the subject of congressional oversight and legislation. Some 
legislators have been highly critical of recent regulatory initiatives, while others have been more 
supportive of EPA’s implementation efforts. 
Over the past four years, EPA has proposed and promulgated numerous regulations implementing 
the CWA and other pollution control statutes that it administers. Critics of the Administration, 
                                                 
19 See http://epw.senate.gov/public/index.cfm?FuseAction=Majority.PressReleases&ContentRecord_id=64739ae3-
802a-23ad-4c30-36fc58cc1014&Region_id=&Issue_id=. 
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both within Congress and outside of it, have accused the agency of reaching beyond the authority 
given it by Congress and ignoring or underestimating the costs and economic impacts of these 
rules. Republican leaders in the House conducted vigorous oversight of the agency in the 112th 
Congress. Bills seeking to overturn specific regulations or to limit the agency’s authority also 
were introduced, along with proposals to bar EPA funding for specific activities (see “Continuing 
Issue: Appropriations” below). Environmental groups disagree that the agency has overreached, 
and EPA itself contends that critics’ focus on the cost of controls obscures the benefits of new 
regulations, which, EPA estimates, far exceed the costs, while investing in pollution control is an 
important source of economic activity, exports, and American jobs. While particular attention is 
being paid to the Clean Air Act, a number of EPA’s initiatives concerning the CWA also have 
received legislators’ scrutiny.20 Similar scrutiny of EPA’s activities continues in the 113th 
Congress. 
Chesapeake Bay Restoration 
Despite several decades of activity by governments, the private sector, and the general public, 
efforts to improve and protect the Chesapeake Bay have been insufficient to meet restoration 
goals. Although some specific indicators of Bay health have improved slightly or remained steady 
(such as blue crabs and underwater bay grasses), others remain at low levels of improvement, 
especially water quality. Overall, the Bay and its tributaries remain in poor health, with polluted 
water, reduced populations of fish and shellfish, and degraded habitat and resources. The primary 
pollutants causing impairments are nutrients (nitrogen and phosphorus) and sediment discharged 
from multiple urban, suburban, and rural sources around the Bay.  
In May 2009, President Obama issued an executive order that declared the Bay a “national 
treasure” and charged the federal government with assuming a strong leadership role in restoring 
the Bay.21 The executive order established a Federal Leadership Committee for the Chesapeake 
Bay to develop and implement a new strategy for protecting and restoring the Chesapeake region. 
The resulting strategy, released in May 2010, launched major specific environmental initiatives to 
establish new clean water regulations on stormwater discharges and pollution discharges from 
animal feedlots in the Bay watershed, put new agricultural conservation practices on farms in the 
region, and restore land and water habitat.22 
A central feature of the overall strategy is EPA’s establishment of a Total Maximum Daily Load 
(TMDL) for Chesapeake Bay. Section 303 of the CWA requires states to identify waters that are 
impaired by pollution, even after application of pollution controls. For those waters, states must 
establish a TMDL to ensure that water quality standards can be attained. A TMDL is essentially a 
pollution budget, a quantitative estimate of what it takes to achieve standards, setting the 
maximum amount of pollution that a waterbody can receive without violating standards. If a state 
fails to do this, EPA is required by the CWA to make its own TMDL determination for the state. 
Throughout the United States—including the Chesapeake Bay watershed—more than 20,000 
waterways are known to be violating applicable water quality standards and to require a TMDL.23 
                                                 
20 For information, see CRS Report R41561, EPA Regulations: Too Much, Too Little, or On Track?, by James E. 
McCarthy and Claudia Copeland. 
21  Executive Order 13508, “Chesapeake Bay Protection and Restoration,” 74 Federal Register 23099-23104, May 15, 
2009. 
22 For information, see http://www.chesapeakebay.net/news_federalstrategy.aspx?menuitem=51207. 
23 For background information, see CRS Report R42752, Clean Water Act and Pollutant Total Maximum Daily Loads 
(continued...) 
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Lawsuits have been brought with the intention of pressuring EPA and states to develop TMDLs; 
under a consent decree in one such lawsuit, EPA was required to establish a Chesapeake Bay 
TMDL, which the agency did on December 29, 2010. The Chesapeake Bay TMDL is the largest 
single TMDL developed to date. It addresses all segments of the Bay and its tidal tributaries that 
are impaired from discharges of nitrogen, phosphorus, and sediment, with a goal of having 
TMDL implementation measures in place by 2025. The TMDL allocates needed reductions of 
these pollutants to all jurisdictions in the 64,000 square mile watershed. Detailed plans 
identifying specific reductions are to be developed by the six states located in the Chesapeake 
Bay watershed in Watershed Implementation Plans (WIPs).24 
As part of the TMDL development process, Chesapeake Bay jurisdictions are to prepare WIPs 
identifying specific control measures to achieve needed pollutant reductions from point sources 
(i.e., industrial and municipal facilities) and nonpoint sources (i.e., farms and forests), as well as 
two-year milestones to implement the plans. The first phase of WIPs, providing a general outline 
of steps that states will take to implement the TMDL, were developed in December 2010. States 
now have developed Phase II WIPs to provide more localized identification of controls and best 
management practices needed to meet the goals of the TMDL. 
EPA’s TMDL plans and the overall federal Bay restoration strategy under the executive order are 
controversial with a number of groups that are concerned about the likely mandatory nature of 
many of EPA’s and states’ upcoming actions. Legal challenges to the TMDL were brought by 
agricultural and home builder groups, who argue that EPA has exceeded its CWA authority. In 
September 2013, a federal court upheld the TMDL, in a lawsuit that had challenged EPA’s 
authority to set pollution limits in the multistate plan. That ruling has been appealed. On the other 
hand, environmental activists in particular are pleased that the federal government is now 
asserting a leadership role to restore the Bay and have supported legislation that would codify 
requirements for the Bay TMDL in the CWA, while authorizing grants and other assistance for 
implementing required measures.  
The 112th Congress expressed interest in early implementation of the Chesapeake Bay TMDL, 
with particular focus on impacts of the plan on agricultural sources in the Bay watershed. A 
House Agriculture subcommittee held oversight hearings in 2011. In addition, legislation was 
introduced (H.R. 4153) that would give states, not EPA, authority to set nutrient and sediment 
limits for the Bay and would increase USDA’s role in Bay restoration. 
Florida Nutrient Water Quality Standards 
The CWA directs states to adopt water quality standards for their waters and authorizes EPA to 
promulgate new or revised standards if a state’s actions fail to meet CWA requirements. Water 
quality standards consist of designated uses, criteria to protect the designated uses, and an 
antidegradation statement. They serve as the framework for pollution control measures specified 
by states for individual sources. 
Florida waters are severely impaired by nutrients (nitrogen and phosphorus) from diverse sources 
including agriculture and livestock, municipal and industrial wastewater discharges, and urban 
                                                                  
(...continued) 
(TMDLs), by Claudia Copeland. 
24 For information on the TMDL, see http://www.epa.gov/chesapeakebaytmdl/. 
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stormwater runoff. EPA determined in 2009 that Florida’s existing narrative water quality 
standards for nutrients must be revised in the form of numeric criteria that will enable Florida to 
better control nutrient pollution. In 2009 EPA entered into a consent decree with environmental 
litigants requiring the agency to promulgate numeric nutrient water quality standards for Florida. 
To meet the legal deadline, EPA issued the first phase of these standards on November 15, 2010, 
establishing standards for lakes and flowing waters in the state. The EPA rule does not establish 
any requirements directly applicable to regulated entities or other sources of nutrient pollution. 
Water quality standards do not have the force of law until the state translates them into permit 
limits or otherwise imposes pollution control requirements on dischargers in the state.  
The rule did not yet go into effect, as EPA delayed the effective date to prepare for 
implementation and state efforts to develop a rule that EPA could approve. In response to 
criticism of the proposed standards, EPA delayed the effective date of the 2010 rule to allow local 
governments, businesses, and the state of Florida time to review the standards and develop 
implementation strategies. While few dispute the need to reduce nutrients in Florida’s waters, 
EPA’s actions have been controversial, involving disputes about the data underlying the proposal, 
potential costs of complying with numeric standards when they are incorporated into discharge 
permit limitations, and disputes over administrative flexibility. 
EPA said all along that it prefers that Florida implement its own numeric nutrient water quality 
criteria, and in June 2012 the state submitted revised standards with numeric nutrient criteria. In 
response, EPA indicated to the state that the agency likely would approve the standards, at which 
time the agency would initiate administrative action to repeal the 2010 federal rule. Consequently, 
EPA delayed the effective date of the 2010 rule several times to allow the state to complete its 
process and to avoid confusion that could occur if federal criteria became effective while state 
criteria are being reviewed.  
At the same time, separate legal challenges to the 2010 rule were filed in federal court by 
environmental advocates, several industry groups, and Florida’s agriculture commissioner. In 
February 2012, a federal court ruling largely upheld EPA’s authority and methodology in setting 
numeric criteria for nutrient pollution in Florida waters, but it remanded a portion of the rule 
concerning numeric criteria for streams, saying they were arbitrary and capricious.  
Further, EPA’s deadline for issuing the second phase of standards, for estuaries, coastal waters, 
and flowing waters in the South Florida Region, also was extended several times to allow the 
state to develop its own standards. 
In March 2013, EPA and the state reached agreement on steps to put the state in charge of 
determining numeric limits on nutrient pollution in Florida waterways. Groundwork for the 
agreement was laid in November 2012 when EPA approved the state’s June 2012 submission for 
lakes, rivers, streams, and some estuaries. Under the March agreement, Florida pledged to move 
forward with rulemaking and legislation to complete the job of setting numeric nutrient criteria 
for Florida waterways. The proposed state legislation would require completion of nutrient 
criteria rulemaking for remaining coastal and estuarine waters by December 1, 2014, and 
establishment of interim nutrient standards until then. In response to the state’s actions, EPA 
approved the state’s implementation plan for controlling nutrient pollution in Florida waters and 
petitioned the federal court in Florida to allow it to approve the state’s water quality standards, 
although they lack numeric criteria for all waters. In January 2014, the court agreed to amend the 
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2009 consent decree in light of the adoption of new nutrient criteria, thus lifting the requirement 
for EPA to issue numeric nutrient standards under the second phase of rulemaking.25 
Industry groups endorsed the agreement and the court’s modification of the consent decree. 
However, it was criticized by environmental advocacy groups, who said that the plan lacks many 
elements that EPA previously said were essential and fails to cover large portions of the state’s 
waters by, for example, exempting tidal waters, marine lakes, and flowing waters in the southern 
portion of the state, unless they are being used for “frequent recreation.” Environmental groups’ 
legal challenge to the plan was rejected by the court’s January 2014 ruling, but the groups have 
appealed the ruling. 
Some industry groups fear that EPA’s actions in Florida—even if now resolved—will be a 
precedent for similar regulatory action elsewhere. For example, although EPA officials have said 
they have no specific plans to do so, environmental advocacy groups have petitioned or filed 
lawsuits seeking to require EPA to establish numeric nutrient water quality standards in Kansas 
and for the Upper Mississippi River Basin (in July 2012, EPA denied the petition seeking similar 
federal water quality standards for the Upper Mississippi River Basin). 
Nonetheless, EPA’s actions have drawn congressional attention. A bill in the 113th Congress (H.R. 
1948) would restrict EPA’s oversight of state water quality standards by allowing the agency to 
promulgate a water quality standard for a state only if EPA has previously approved the state’s 
standard and the state concurs that a new or revised standard is necessary. Similar legislation 
passed the House in the 112th Congress. Even with EPA’s approval of Florida’s rules, 
controversies persist, and attention to these issues is likely to continue in the 113th Congress. 
Mountaintop Mining in Appalachia 
Mountaintop removal coal mining involves removing the top of a mountain in order to recover 
the coal seams contained there. This practice occurs in six Appalachian states (Kentucky, West 
Virginia, Virginia, Tennessee, Pennsylvania, and Ohio). It creates an immense quantity of excess 
spoil, which is typically placed in nearby valleys, burying streams that flow through the valleys. 
Critics say that, as a result of valley fills, stream water quality and the aquatic and wildlife habitat 
that streams support are destroyed. The mining industry argues that mountaintop mining is 
essential to conducting surface coal mining in the Appalachian region and that surface coal 
mining would not be economically feasible there if producers were restricted from using valleys 
for the disposal of mining overburden.26 
Mountaintop mining is regulated under several laws, including the CWA Section 404 permit 
program (discussed above) and the Surface Mining Control and Reclamation Act. In June 2009, 
officials of EPA, the Corps of Engineers, and the Department of the Interior’s Office of Surface 
Mining and Reclamation (OSM) signed a Memorandum of Understanding outlining a series of 
administrative actions under these laws to reduce the harmful environmental impacts of 
mountaintop mining and surface coal mining in Appalachia. The plan includes a series of near-
term and longer-term actions that emphasize specific steps, improved coordination, and greater 
transparency of decisions. The actions are being implemented through regulatory proposals, 
                                                 
25 For additional information, see http://www.epa.gov/lawsregs/rulesregs/florida_index.cfm. 
26 For additional information, see CRS Report RS21421, Mountaintop Mining: Background on Current Controversies, 
by Claudia Copeland. 
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guidance documents, and review of pending applications for permits to authorize mountaintop 
mining-valley fill operations. In July 2009, the Army Corps suspended the use of a particular 
CWA general permit for surface coal mining activities in Appalachia and proposed a rule to 
prohibit its use entirely and issued a final rule in February 2012 to apply more stringent CWA 
rules to these coal mining operations.27 
Also in 2009 EPA and the Corps began conducting detailed evaluations of 79 pending CWA 
permit applications for surface mining activities in order to limit environmental impacts of the 
proposed activities under a process called Enhanced Coordination Procedures (ECP). Coal 
industry groups and coal state officials contended that the ECP process resulted in costly delay in 
issuance of permits. They challenged the process in federal court, and in October 2011, the court 
struck down the ECP as an unlawful transfer of legal authority from the Corps to EPA.28 The 
agencies are continuing to review permit applications for surface coal mining projects in 
Appalachia under existing rules, but not the vacated ECP. 
In July 2011 EPA issued guidance on review of CWA Section 402 and 404 permit requests for 
surface coal mining in Appalachia. The guidance tightened oversight of permit reviews in several 
ways, most notably by establishing two benchmarks for stream conductivity, which is a measure 
of the level of salinity in water and is a proxy for dissolved solids in stream waters associated 
with mining activity that may contribute to toxicity. The guidance has been very controversial 
with industry. The House Transportation Subcommittee on Water Resources and Environment 
held hearings on these issues in May 2011. A hearing also was held by the House Government 
Reform and Oversight Committee in July 2011. In July 2012, the same federal court that struck 
down the ECP also invalidated the 2011 guidance document intended to help assess a mine’s 
water quality impacts, ruling that EPA had overstepped its statutory authority. The government 
has appealed both of these rulings. 
In the 113th Congress (as in several prior Congresses), legislation intended to sharply restrict the 
practice of mountaintop mining has been introduced (H.R. 1837, the Clean Water Protection Act). 
It would narrow the CWA definition of “fill material,” and thus narrow the types of materials that 
can be discharged into U.S. waters under a Section 404 permit. The significance of the bill is that 
discharges of materials that are not eligible for a Section 404 permit are regulated under CWA 
Section 402. Because Section 402 discharge requirements are more restrictive than those for 
Section 404, some discharges that could be permitted under Section 404 cannot be authorized 
under Section 402. Supporters favored making it more difficult to use Section 404 to authorize 
activities that they consider to be environmentally harmful. On the other hand, critics of the 
legislation say that, as a practical matter, economically important activities such as coal mining 
could not meet the more stringent limitations of a Section 402 permit and, thus, would be 
infeasible. Another 113th Congress bill, H.R. 526, would place a moratorium on permitting for 
mountain removal coal mining until certain health studies are conducted.29 
                                                 
27 For information, see CRS Report 97-223, The Army Corps of Engineers’ Nationwide Permits Program: Issues and 
Regulatory Developments, by Claudia Copeland. 
28 At the time of the court’s ruling, 8 of the 79 projects under ECP review had received permits; 50 permit applications 
had been withdrawn by the applicants; 3 project reviews were underway or nearly complete; and 18 reviews had not yet 
begun. 
29 For additional information, see CRS Report RL31411, Controversies over Redefining “Fill Material” Under the 
Clean Water Act, by Claudia Copeland. 
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Another aspect of the mountaintop mining issue that has drawn congressional attention is EPA’s 
2011 veto of a CWA Section 404 permit for a surface coal mining operation in West Virginia, the 
Spruce No. 1 mine. EPA’s action has been controversial, particularly because the veto occurred 
after the permit had been issued by the Army Corps. EPA’s veto of the permit was challenged, and 
in March 2012, a federal district court overturned the veto, ruling that EPA had exceeded its 
statutory authority in the Spruce No. 1 action. However, in April 2013, a federal appeals court 
reversed the lower court’s decision and upheld EPA’s authority to retroactively veto permits 
(Mingo Logan Coal Company v. U.S. Environmental Protection Agency, 714 F.3d 608 (D.C. Cir. 
2013)).30 In March 2014, the Supreme Court declined to review the decision that upheld the veto. 
The appeals court ruling was applauded by environmental groups and criticized by the mining 
industry. In response, bills have been introduced to limit or prohibit EPA’s ability to exercise this 
veto authority. Several proposals in the 113th Congress (H.R. 524/S. 830 and H.R. 1829/S. 861) 
would bar EPA from vetoing a 404 permit retroactively. Another bill, S. 2156, would prohibit 
retroactive vetoes and also would restrict prospective vetoes in advance of a 404 permit 
application being submitted. 
Congressional interest in the government’s multiple actions on mountaintop mining—which some 
critics consider part of a “War on Coal”—is continuing in 2013. 
The Relationship Between the CWA and FIFRA 
In recent years, federal courts have held that aerial application of a pesticide over and into U.S. 
waters requires authorization under the CWA’s National Pollutant Discharge Elimination System 
(NPDES) permit program, even when the pesticide use meets other requirements of federal law, 
including the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA). These decisions drew 
the attention of many pesticide applicators, including public health entities (such as mosquito 
control districts), concerned with how the rulings might affect their need to control pests 
associated with diseases such as the West Nile virus. In 2006, EPA finalized a rule seeking to 
resolve the conflict over the regulatory scope of the CWA and FIFRA related to pesticide use, in 
light of the recent litigation, by promulgating clarifying circumstances under which a CWA 
permit is or is not required for activities carried out pursuant to FIFRA. However, in 2009, a 
federal court rejected EPA’s argument that residual and excess pesticides do not require a CWA 
permit because they are adequately regulated by FIFRA, and the court vacated the rule.31 In 
response, EPA developed a general CWA permit for pesticide applications covered by the ruling.32 
General permits are intended to minimize regulatory burdens on pesticide applicators and state 
permitting officials, but there still has been significant concern about impacts of EPA’s actions.  
EPA issued the pesticide general permit on October 31, 2011, as required by the court.33 EPA 
estimated that the universe of affected activities subject to CWA permits is approximately 5.6 
million applications annually, which are performed by 365,000 applicators covering four use 
                                                 
30 For background on the veto, see CRS Report RS21421, Mountaintop Mining: Background on Current Controversies, 
by Claudia Copeland. 
31 National Cotton Council of America v. U.S. Environmental Protection Agency, 553 F.3d 927 (6th Cir. 2009). 
32 For additional information, see CRS Report RL32884, Pesticide Use and Water Quality: Are the Laws 
Complementary or in Conflict?, by Claudia Copeland. 
33  U.S. Environmental Protection Agency, “Final National Pollutant Discharge Elimination System (NPDES) Pesticide 
General Permit for Point Source Discharges From the Application of Pesticides; Notice of final permit,” 76 Federal 
Register 68750-68756, November 7, 2011. 
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Water Quality Issues in the 113th Congress: An Overview 
 
patterns: (1) mosquito and other flying insect pest control; (2) aquatic weed and algae control; (3) 
aquatic nuisance animal control; and (4) forest canopy pest control. EPA and states are now 
implementing the permit requirements.34 
In spite of EPA’s efforts to issue a general permit to respond to the 2009 court ruling, legislation 
to affirm that a CWA permit is not required for use of FIFRA-approved pesticides has received bi-
partisan support. In the 113th Congress, legislation has been introduced that would amend FIFRA 
and the CWA to provide that neither EPA nor a state may require a CWA permit for discharge of a 
pesticide whose use has been authorized pursuant to FIFRA (H.R. 935). Language identical to 
this bill was included in 2013 farm bill legislation approved by the House in July 2013 (H.R. 
2642; the provision was not included in the farm bill that Congress approved in February 2014, 
P.L. 113-79). Other legislation has been introduced, as well (S. 175 and S. 802). 
CWA Permits for Logging Road Discharges 
Another federal court ruling concerning the extent of CWA permit requirements has drawn public 
and congressional attention. In Northwest Environmental Defense Center v. Brown (640 F.3d 
1063 (9th Cir. 2011)), the Ninth Circuit held that stormwater runoff from certain logging roads 
that is collected by and discharged from a system of ditches, culverts, and channels is a point 
source for which a CWA NPDES permit is required. This ruling invalidated EPA’s position in 
regulations since 1976, that stormwater runoff from logging roads is nonpoint source pollution 
that does not require such a permit, even if the runoff is channeled and discharged through a 
discrete conveyance. Environmental groups contend that timber hauling on logging roads is a 
major source of sediment (rocks, dirt, gravel) that flows into streams and harms aquatic life. 
Critics of the court’s decision say that the existing process has worked well for 35 years, with 
states regulating runoff and EPA not requiring permits. In June 2012, the Supreme Court granted 
a petition by timber industry groups and others, including a number of states, to review the 
logging roads ruling. The U.S. solicitor general asked the Court to let the appeals court ruling 
stand and to not accept the petition for certiorari, because EPA stated that it would issue a rule to 
nullify the ruling and specify that logging roads do not need discharge permits for stormwater 
runoff. Given the September 30 end to the congressional ban, EPA moved quickly on the rule, 
which the EPA Administrator signed on November 30, three days before the Supreme Court heard 
arguments in the case.35  
On March 20, 2013, the Court issued its decision in the case, upholding EPA’s interpretation of its 
original stormwater rule as not requiring CWA permits for channeled stormwater runoff from 
logging roads.36 In a 7-1 ruling, the Court reversed and remanded the 2011 ruling by the Ninth 
Circuit. Justice Antonin Scalia dissented in part, saying he would have affirmed the appeals court 
decision because EPA had failed to follow its own regulations. The Court’s ruling did not 
specifically address EPA’s November 2012 rule. 
                                                 
34 The EPA pesticide general permit applies in six states where EPA is the permitting authority (Alaska, Idaho, 
Massachusetts, New Hampshire, New Mexico, and Oklahoma), the District of Columbia, most U.S. territories, and on 
Indian Tribal lands. Elsewhere, states have developed permits comparable to the federal permit. 
35  U.S. Environmental Protection Agency, “Revisions to Stormwater Regulations To Clarify That an NPDES Permit Is 
Not Required for Stormwater Discharges From Logging Roads,” 77 Federal Register 72970-72975, December 7, 2012. 
For additional information, see CRS Report R42587, Whether Logging Road Runoff Requires a Clean Water Act 
Permit: Decker v. Northwest Environmental Defense Center, by Robert Meltz and Claudia Copeland. 
36 Decker v. Northwest Environmental Defense Center, 133 S. Ct. 1326 (2013). 
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In response to the Ninth Circuit ruling and uncertainty about permit requirements, legislation in 
the 113th Congress would amend the CWA to exempt any silviculture activity from requiring an 
NPDES permit under CWA Section 402 (H.R. 2026/S. 971). A provision similar to this legislation 
was included in H.R. 2642, the farm bill that Congress approved in February 2014 (P.L. 113-79). 
The final bill states that no NPDES permit shall be required for a discharge of runoff from 
specified silviculture activities (such as nursery operations, thinning, prescribed burning, or pest 
and fire control) that are conducted in accordance with standard industry practice. It also states 
that discharges from silvicultural activities are not exempted from permitting requirements under 
CWA Section 404 (the act’s dredge and fill permit program), existing permitting requirements 
under Section 402, or from any other federal law.  
Continuing Issue: Appropriations 
Clean water policy and program issues also have been addressed regularly by Congress in the 
context of annual appropriations acts. EPA’s appropriations are included in the Interior, 
Environment, and Related Agencies appropriations acts.37 
FY2014 Appropriations 
The Administration presented the FY2014 budget request in April 2013. It sought $8.15 billion 
overall for EPA, including $1.095 billion for clean water SRF capitalization grants (25% less than 
the FY2013 enacted level), $165 million for Section 319 grants, $259 million for Section 106 
grants, and $300 million for the Great Lakes Restoration Initiative. 
In mid-2013, the House Appropriations Subcommittee on Interior, Environment, and Related 
Agencies drafted a bill (unnumbered) that would reduce overall funding for EPA by 34% from the 
FY2013 enacted level, including an 83% reduction for clean water SRF capitalization grants (the 
bill would provide $250 million). According to subcommittee documents, the reduction is 
appropriate because, despite recent federal support, little progress has been made to reduce the 
known water infrastructure gap.38 The draft bill would provide $60 million for the Great Lakes 
Restoration Initiative. The full committee did not complete markup of this bill. 
The Senate Appropriations Subcommittee on Interior, Environment, and Related Agencies drafted 
an alternative bill that would maintain funding for the clean water SRF program at $1.45 billion 
and would provide small funding increases for several EPA programs above FY2013 enacted 
levels, including the Great Lakes Restoration Initiative ($300 million).39 There was no further 
action on this bill. 
Congress did not reach final agreement on FY2014 appropriations before the start of the fiscal 
year on October 1, but did agree to a short-term continuing appropriations measure (P.L. 113-46), 
which provided funding through January 15, 2014. Final action on appropriations for EPA and all 
                                                 
37 For additional information, see CRS Report 96-647, Water Infrastructure Financing: History of EPA Appropriations, 
by Claudia Copeland. 
38 See http://appropriations.house.gov/uploadedfiles/hrpt-113-hr-fy2014-interior.pdf, p. 62. 
39 See http://www.appropriations.senate.gov/news.cfm?method=news.view&id=b3e22f9d-a060-45eb-90ef-
1225244125a7. 
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Water Quality Issues in the 113th Congress: An Overview 
 
other federal agencies and departments occurred as part of the Consolidated Appropriations Act, 
2014 (H.R. 3547, P.L. 113-76), signed by the President on January 17. This bill provides $1.45 
billion for clean water SRF capitalization grants (5% more than FY2013 funds and 32% higher 
than the President’s FY2014 budget request) and $300 million for the Great Lakes Restoration 
Initiative. For water quality grants provided to states, the bill includes $159.3 million for Section 
319 nonpoint pollution management ($3.4 million more than in 2013), $230.8 million for Section 
106 state management ($3.8 million more than in 2013), and $9.5 million for beaches grants 
($200,000 more than in 2013; the Administration had requested zero funding for this grant 
program). 
FY2015 Appropriations 
The Administration’s FY2015 budget was presented on March 4, 2014. It seeks $7.89 billion 
overall for EPA (3.6% below the FY2014 enacted level), including $1.018 billion for clean water 
SRF capitalization grants, $15 million for Alaska Native Village and U.S.-Mexico Border 
projects, and $1.13 billion for state categorical grants. The total amount requested for clean water 
SRF capitalization grants is 26% below the FY2014 enacted level. Among the state categorical 
grants, the budget seeks 8% more for clean water pollution control grants (CWA Section 106) and 
3.6% more for nonpoint pollution management grants (CWA Section 319). As in FY2014, the 
budget seeks no funds for the beaches grant program. The request also includes $275 million for 
the Great Lakes Restoration Initiative ($25 million less than in FY2014) and a total of $119 
million for other geographic programs, such as Chesapeake Bay (3% more than these programs 
received in FY2014). 
 
Author Contact Information 
 
Claudia Copeland 
   
Specialist in Resources and Environmental Policy 
ccopeland@crs.loc.gov, 7-7227 
 
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