Mississippi River Water Quality and the Clean Water Act: Progress, Challenges, and Opportunities (2008)

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3 The Clean Water Act C ongress first enacted the Federal Water Pollution Control Act (FWPCA) in 1948. Substantial amendments to that act—first in 1972 and again in 1977—created the statute now known as the Clean Water Act. Congress amended the FWPCA repeatedly from 1956 on; however, substantial amendments in 1972 created the contemporary structure of the act, which acquired the name “Clean Water Act” in 1977. The 1972 amendments represented a significant change in approach in that they shifted the emphasis in water quality regulation from an earlier focus on state-level water quality standards, to a federal permitting scheme setting technology-based and water quality-based effluent limits for individual dis- chargers. Moreover, Congress designed the 1972 act “to restore and main- tain the chemical, physical, and biological integrity of the Nation’s waters” (Section 101(a)). The Clean Water Act authorizes water quality programs, requires state water quality standards, requires permits for discharges of pollutants into navigable waters, and authorizes funding for wastewater treatment works, construction grants, and state revolving loan programs. The act underwent subsequent amendments in 1981, 1987, and 1990. The U.S. Environmental Protection Agency (EPA), the U.S. Army Corps of Engineers, and the states are jointly responsible for implementing the Clean Water Act and for achieving the goals of attaining water quality that is, according to the act, at least “fishable and swimmable.” In general, the Clean Water Act requires states to establish water quality standards for waters within their borders by designating specific uses for their waters (so-called designated uses) and establishing criteria by which to protect those uses, control pollutant sources, and monitor and assess water quality. 65 

66 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT States are responsible for submitting periodic water quality assessment re- ports—Section 305(b) reports—and lists—Section 303(d) lists—of impaired waters to the EPA. They then are supposed to restore impaired waters by developing Total Maximum Daily Loads (TMDLs), which are limits that in theory, if fully implemented, should ensure that the state’s waters achieve the relevant quality standards. The EPA establishes federal guidance water quality criteria and oversees the establishment of state water quality stan- dards to ensure that they are consistent with the requirements of the Clean Water Act, including ensuring that state-adopted water quality criteria are sufficient to attain the designated uses assigned by the state.The EPA also oversees state National Pollutant Discharge Elimination System (NPDES) permitting, issuing NPDES permits to dischargers in states that have not assumed this permitting authority and helping to resolve interstate water pollution issues. Finally, the U.S. Army Corps of Engineers implements the “dredge-and-fill” (wetlands) permit program in almost all states, subject to EPA oversight. The Clean Water Act (CWA) is a lengthy and complex body of legisla- tion, and this chapter does not attempt to examine all of its provisions. Instead, for purposes of this report and its emphasis on the Mississippi River, the chapter focuses on the CWA sections and the federal and state authorities and responsibilities that are important in understanding Clean Water Act applications and challenges along the Mississippi River. This report focuses on point and nonpoint source pollution of the mainstem Mis- sissippi River, not ancillary issues that may arise with regard to the dredging and filling of wetlands. As a result, at the federal level, this report focuses on EPA’s regulatory authority, not that of the Corps of Engineers. The EPA’s jurisdiction to regulate discharges of pollutants into the Mississippi River and its major tributaries is clear, despite recent U.S. Supreme Court decisions and agency guidance regarding the extent of federal jurisdiction over wetlands and isolated waters. This chapter also discusses interstate and federal-state water quality interactions and the relevance of the CWA to these interactions. The chapter is divided into four sections: origins of the Clean Water Act; Federal Water Pollution Control Act amendments of 1972; state-level authority in protecting water quality; and interstate water quality protection. ORIGINS OF THE CLEAN WATER ACT The Refuse Act Congress enacted the Rivers and Harbors Act of 1899 to preserve and enhance navigation in the nation’s waters. Section 13, the Refuse Act, pro- hibits pollution of the nation’s “navigable waters.” The language of Section 

THE CLEAN WATER ACT 67 13 is broad, and throughout the 1960s the federal government increasingly used it to prosecute water pollution cases. In an attempt to formalize the federal government’s use of the Refuse Act to address water pollution, President Richard Nixon in 1970 ordered the Corps of Engineers and the administrator of the newly formed Environmental Protection Agency “to implement a permit program . . . to regulate the discharge of pollutants and other refuse matter into the navigable waters of the United States or their tributaries” (Nixon, 1970). These agencies promulgated their regulations within a year, creating the first federal water pollution permit program in the United States. Nevertheless, despite the breadth of the Refuse Act’s language and Supreme Court rulings upholding the use of that act to punish polluters, the Rivers and Harbors Act’s focus on navigation limited its usefulness for water quality regulation. In particular, the only waters subject to the Refuse Act are waters that are or can be made navigable-in-fact, including waters subject to the ebb and flow of the tide (33 C.F.R. Section 329.4). Thus, the Refuse Act could not address water quality problems comprehensively, even with the new permit program. This prompted Congress to expand the defi- nition of regulated “navigable waters” in the Clean Water Act to encompass “the waters of the United States, including the territorial seas” and at least some non-navigable-in-fact waters, as discussed more fully below. The Federal Water Pollution Control Act of 1948 Congress addressed more general water quality concerns through the Federal Water Pollution Control Act of 1948. The FWPCA was not a regu- latory program, however; instead, its primary purpose was to encourage states to improve water quality, largely through federal grants and loans for the construction of publicly owned treatment works (POTWs, or sewage treatment plants; FWPCA, 1948). Under this act, the federal Surgeon Gen- eral (the EPA did not exist until 1970) could institute abatement actions, but only to protect interstate waters and only to abate pollution “which endangers the health or welfare of persons in a state other than that in which the discharge originates” (FWPCA, 1948, Section 2(d)). Congress amended the FWPCA in 1952, 1956, 1961, 1965, 1966, and 1970, slowly expanding the federal government’s abatement authority. In 1961, for example, Congress allowed the Secretary of Health, Education, and Welfare to bring abatement actions when pollution of any navigable- in-fact water (as opposed to interstate waters) affected the health or welfare of any person (FWPCA Amendments, 1961). In 1966, federal enforcement authority expanded again; this time Congress gave the Secretary of the Interior authority to take abatement actions to control pollution of inter- 

68 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT national waters, through the Clean Water Restoration Act of 1966 (CWRA, 1966). However, until 1972 Congress had never created a general federal permit program to control water pollution. Instead, in 1965 Congress amended the FWPCA to create a state-focused, water quality standards approach to water quality regulation (WQA, 1965). Under these amend- ments, states could continue to receive federal grants and loans to aid in water quality improvements, but now only if they established water qual- ity standards. However, the federal government could eventually set water quality standards for any states that refused to do so. Slow progress by the states in establishing water quality criteria and related programs raised interest in a technology-based regulatory approach and prompted the pas- sage of amendments in 1972. Another significant problem with the 1965 water quality standards program was the difficulty of enforcing an ambient standard regime without source-specific limitations. FEDERAL WATER POLLUTION CONTROL ACT AMENDMENTS OF 1972 Congress enacted the contemporary version of the Clean Water Act through the Federal Water Pollution Control Act Amendments of 1972 (FWPCA, 1972), which set out “to restore and maintain the chemical, physical, and biological integrity of the Nation’s waters” (Section 101(a)). More specifically, the act established “national goal[s] that the discharge of pollutants into the navigable waters be eliminated by 1985” and “that wherever attainable, an interim goal of water quality which provides for the protection and propagation of fish, shellfish, and wildlife and provides for recreation in and on the water be achieved by July 1, 1983”—the act’s so-called (and still unattained) fishable and swimmable goal (Section 101(a)(1), (2)). The 1972 amendments pursued these goals by transforming the FWPCA’s previously state-focused water quality standards approach into a federal permitting scheme based primarily on end-of-the-pipe effluent limitations for individual dischargers (Craig, 2004). Table 3-1 lists the major sections of the Clean Water Act. This table illustrates clearly the act’s broad scope. It encompasses sewage and indus- trial waste treatment (Title II), point source discharge permitting (Section 402), ambient water quality objectives (Section 303), state water quality standards, TMDLs and reporting requirements (Sections 303 and 305), nonpoint source management (Section 319), water quality in estuaries (Sec- tion 320), ocean discharges (Section 403), wetland protection (Section 404), and other aspects of protection and restoration of surface water quality in the United States. 

THE CLEAN WATER ACT 69 TABLE 3-1  Major Clean Water Act Provisions Section 101, 33 U.S.C. § 1251 Congressional goals and policies Section 103, 33 U.S.C. § 1253 Interstate cooperation Section 106, 33 U.S.C. § 1256 Grants for pollution control programs Title II, §§ 201-221, 33 U.S.C. Grants for the construction of POTWs §§ 1281-1301 Section 208, 33 U.S.C. § 1288 Areawide waste treatment management programs Section 301, 33 U.S.C. § 1311 Act’s basic prohibition; technology-based effluent limitations Section 302, 33 U.S.C. § 1312 Water quality-based effluent limitations Section 303, 33 U.S.C. § 1313 Water quality standards; TMDLs Section 305, 33 U.S.C. § 1315 State water quality reporting Section 309, 33 U.S.C. § 1319 Enforcement Section 319, 33 U.S.C. § 1329 Nonpoint source management programs Section 320, 33 U.S.C. § 1330 National estuary program Section 401, 33 U.S.C. § 1341 State certification of federally authorized activities Section 402, 33 U.S.C. § 1342 NPDES permit program Section 403, 33 U.S.C. § 1343 Ocean discharge criteria Section 404, 33 U.S.C. § 1344 Dredge-and-fill permit program Section 502, 33 U.S.C. § 1362 Definitions Section 505, 33 U.S.C. § 1365 Citizen suits Section 510, 33 U.S.C. § 1370 State authority Three aspects of the current Clean Water Act are particularly relevant to Mississippi River water quality and are discussed in the following sec- tions: (1) the sewage treatment works or POTW construction grant and loan programs (which carried over from the pre-1972 versions of the FWPCA); (2) the two federal permit programs incorporated in the Clean Water Act, especially the NPDES permit program, but also the Section 404 dredge-and-fill permit program; and (3) a continuing water quality stan- dards program, with new provisions to ensure linkage between permitting and overall water quality protection. Federal Funding for Sewage Treatment Plants The National and Interstate Problem of Sewage Pollution The direct discharge of untreated sewage into the nation’s waterways was a well-recognized public health problem that stimulated water qual- ity protection legislation long before Congress enacted even the original FWPCA in 1948. Indeed, uncontrolled and lightly controlled discharges of sewage into interstate waterways—especially the Mississippi River and its tributaries—inspired much of the nation’s pre-1972 interstate pollution 

70 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT law, based on the federal common law of nuisance. Progress in addressing the problem of untreated sewage discharges was steady but slow prior to the Clean Water Act of 1972. Fittingly, it was an interstate sewage pollution case that established the Clean Water Act’s supremacy regarding the regulation of water pollution. In 1972, Illinois sued four Wisconsin cities and two Wisconsin sewage com- missions regarding their sewage pollution of Lake Michigan. By the time the case made its way to the Supreme Court for a final resolution almost a decade later, the Clean Water Act was firmly established as Congress’s comprehensive regulatory regime for protecting and restoring water quality. Thus, while interstate water pollution lawsuits involving sewage pollution remain an important aspect of interstate water quality interactions, the Clean Water Act’s requirements for sewage treatment and for interstate negotiations now control such conflicts (Craig, 2004). The Clean Water Act and Sewage Treatment Congress’s approach to addressing sewage pollution through the Clean Water Act has been twofold. First, because collection and treatment of sewage generally is considered a government responsibility, Congress has provided funding to state and local governments to improve their sewage treatment capacity through the construction and improvement of POTWs. Second, Congress subjected these POTWs to a number of regulatory require- ments to reduce the impact of their discharges on the nation’s waterways. With respect to sewage treatment capacity, the federal government be- gan funding the construction of POTWs as early as the 1956 amendments to the FWPCA (WPCAA, 1956). However, Congress greatly expanded this grant program (known as the “construction grants program”) in Title II of the Clean Water Act of 1972. Although grants initially were available for any POTW-related project, from October 1984 on, grants “shall be made only for projects for secondary treatment or more stringent treatment, or any cost effective alternative thereto, new interceptors and appurtenances, and infiltration-in-flow correction” (Section 201(g)). Title II authorized grant funds through FY 1990, ranging from $1 billion to $7 billion per year, which could pay up to 55 percent of each project’s total costs (Section 207). By 1999, Congress had authorized $65 billion and had appropriated $73 billion for the grant program, resulting in the construction of thou- sands of new POTWs. However, by 1989, the Title VI Clean Water State Revolving Fund (CWSRF) program had replaced the Title II grants program. Under this program, the EPA administrator “make[s] capitalization grants to each State” (Section 601(a)), which the states can then use to make loans to municipalities for three purposes: (1) to construct or improve POTWs; (2) 

THE CLEAN WATER ACT 71 to implement states’ nonpoint source management program; and (3) to de- velop management plans under the National Estuary Program. To receive the initial grant, each state had to agree to a number of conditions, includ- ing matching at least 20 percent of the grant with state funds. Congress initially authorized a total of $8.4 billion for CWSRF capi- talization grants for FY 1989 through FY 1994 (Section 607), but it ap- propriated far more. “Since 1987, states have used 96 percent (about $50 billion) of their CWSRF dollars to build, upgrade, or enlarge conventional wastewater treatment facilities and conveyances. Projects to build or im- prove wastewater treatment plants alone account for over 60 percent of this amount, with the remainder supporting the construction or rehabilitation of sewer and storm water collection systems” (GAO, 2006a). States use the remaining 4 percent for nonpoint source control in Section 319 pro- grams. The Title II grant program and the Title VI CWSRF program have financed the construction and improvement of thousands of POTWs. For example, in 1972, only 32 percent of the nation’s population was served by sewage treatment plants; by 1998, 74 percent of the population had such service (USEPA, 2003a). This program thus produced measurable improve- ments in the quality of the nation’s waters, including the Mississippi River (Meade, 1995). The program—specifically, the construction and improve- ment of sewage treatment works—also resulted in some improvements to fish populations in the Mississippi River basin (see, for example, Lerczak and Sparks, 1995). Beyond the construction of sewage treatment infrastructure is the issue of adequate sewage treatment within existing POTWs. Such treatment can be complicated by combined sewer overflow (CSO) events, which occur be- cause many older sewer systems carry both sewage and stormwater runoff to the POTW. Although these systems normally are designed to handle small storm events, large storms often result in untreated discharges to surface waters. Moreover, in addition to the domestic sewage, POTWs receive in- dustrial wastes, including some toxic pollutants that are discharged directly to waterways during CSO events. POTWs also can channel toxic pollutants into waterways from indirect dischargers. The Clean Water Act addresses these POTW-related water quality problems in three main ways. First, POTWs that discharge into the nation’s waters are subject to the act’s National Pollutant Discharge Elimination System permit program, de- scribed below. Moreover, NPDES permits for POTWs must contain effluent limitations at least as stringent as secondary treatment (Section 301(b)(1)), requiring POTWs to engage in biological treatment of the sewage in addi- tion to settling of particles in primary treatment. Second, Congress amended the Clean Water Act specifically to address CSO problems. The act now requires that “each permit, order, or decree issued pursuant to [the Clean Water Act] . . . for a discharge from a munici- 

72 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT pal combined storm and sanitary sewer shall conform to the [EPA’s 1994] Combined Sewer Overflow Control Policy” (Section 402(q)). The EPA’s policy required that POTWs establish nine minimum controls on combined sewer systems by January 1, 1997 (USEPA, 1994). In addition to the nine minimum controls, communities with combined sewer systems are required to develop long-term plans to control combined sewer overflow events as necessary to meet water quality standards (USEPA, 1994). The control of combined sewer overflows, however, remains a significant national water quality issue (USEPA, 2003a). Third, indirect dischargers—industrial dischargers that discharge into sewers leading to POTWs rather than into waterways—have been recog- nized as a threat to water quality almost as long as the 1972 Clean Water Act has been in existence. Indirect dischargers must pretreat effluent before sending it to the POTW in order to eliminate or reduce pollutants—gener- ally toxic pollutants—“which are determined not to be susceptible to treat- ment by such treatment works or which would interfere with the operation of such treatment works” (Section 307(b)). As such, the pretreatment pro- gram seeks to eliminate “pass-through” pollution problems that otherwise occur when industrial dischargers, often seeking to avoid having to obtain their own NPDES permit, interfere with or pass through the POTWs. Federal Permit Programs for Point Sources The Clean Water Act’s most basic prohibition for individual dischargers states that “except as in compliance with [the Act], the discharge of any pol- lutant by any person shall be unlawful” (Section 301(a)). Behind this seem- ingly simple prohibition, however, are several definitional complexities. The Clean Water Act defines a “person” to be “an individual, corpo- ration, partnership, association, state, municipality, commission, political subdivision of a State, or any interstate body” (Section 502(5)). Notably absent from this list is the federal government, but the Clean Water Act does require federal facilities to comply with the act’s requirements “in the same manner, and to the same extent as any nongovernmental entity” (Section 313). Thus, persons covered by the Clean Water Act are broadly defined. More importantly, the Clean Water Act (Section 502(12)) defines the phrase “discharge of a pollutant” to mean: (A) any addition of any pollutant to navigable waters from any point source, (B) any addition of any pollutant to the waters of the contigu- ous zone or the ocean from any point source other than a vessel or other floating craft. The Clean Water Act further defines most of the terms in this definition. First, “point source” is defined broadly to include “any discernible, 

THE CLEAN WATER ACT 73 confined, and discrete conveyance” (Section 502(14)) such as pipes and ditches. Although this definition is broad, it does not cover all sources of water pollutants. By negative implication, any source of water pollutants that is not a point source is a nonpoint source, and the Clean Water Act’s focus on “discernible, confined, and discrete conveyances” generally means that diffuse sources of water pollutants, such as agricultural or urban run- off or atmospheric deposition, do not qualify as point sources. The Clean Water Act assigns regulation of nonpoint source pollution to the states (Section 319). Second, like point source, the Clean Water Act defines “pollutant” broadly, to include “dredged spoil, solid waste, incinerator residue, sewage, garbage, sewage sludge, munitions, chemical wastes, biological materials, radioactive materials, heat, wrecked or discarded equipment, rock, sand, cellar dirt and industrial, municipal, and agricultural waste discharged into water” (Section 502(6)). Given the breadth of the definitions of person, point source, and pollutant, the Clean Water Act’s basic prohibition ef- fectively prohibits all human-controlled additions of almost any material into the navigable waters, the contiguous zone, and the ocean, with limited exceptions. Third, Congress purposely expanded the Clean Water Act’s jurisdic- tional waters beyond those included in the Rivers and Harbors Act of 1899. Specifically, “navigable waters” for the Clean Water Act are “the waters of the United States, including the territorial seas” (Section 502(7)). In turn, the “territorial seas” are the first 3 miles of ocean extending from shore (Section 502(8)). As a practical matter, the Clean Water Act’s navi- gable waters designate all of the waters that generally are subject to state jurisdiction, including both the inland waters (lakes, rivers, streams, and some wetlands) and, at least roughly, the offshore coastal waters whose submerged lands were given to states by Congress in the Submerged Lands Act (SLA, 2006). The definition of navigable waters has become controversial as it ap- plies to intrastate and apparently isolated wetlands or other waterbodies from both a statutory and a constitutional point of view. Since the 1985 de- cision in United States v. Riverside Bayview Homes (474 U.S. 121), the U.S. Supreme Court has struggled with the issue of how far CWA jurisdiction extends over wetlands and waterbodies that are obviously not navigable- in-fact. In that unanimous decision, the court held that the Clean Water Act extends to wetlands adjacent to navigable waters. In contrast, in Solid Waste Agency of Northern Cook County v. U.S. Army Corps of Engineers (531 U.S. 159 (2001)), a bare majority of justices decided that the Clean Water Act does not extend to isolated waters—specifically, to ponds that were not hydrologically connected to navigable waters. Most recently, in Rapanos v. United States (04-1034 U.S. 04-1384, 126 S. Ct. 2208 (2006)), 

74 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT the justices split 4-1-4 regarding the Clean Water Act’s applicability to wetlands adjacent to nonnavigable tributaries of traditionally navigable waters, leaving lower courts and regulators with no clear test for the act’s statutory and constitutional limitations. The proper constitutional balance between the states and the federal government—federalism—clearly was of concern. With respect to navigable, interstate rivers such as the Mississippi, how- ever, Congress’s constitutional authority to regulate to protect water quality is uncontested. Moreover, the connection of upstream waters to the Missis- sippi River has been used to justify CWA jurisdiction over many tributaries and, more controversially, upstream wetlands. Indeed, in the 2006 Rapanos Supreme Court decision, concurring Justice Kennedy argued for precisely this approach, noting in particular the importance of wetlands to Missis- sippi River and Gulf of Mexico water quality issues. “Important public in- terests are served by the Clean Water Act in general and by the protection of wetlands in particular. To give just one example, “. . . nutrient-rich runoff from the Mississippi River has created a hypoxic, or oxygen-depleted, ‘dead zone’ in the Gulf of Mexico that at times approaches the size of Massachu- setts and New Jersey. . . . Scientific evidence indicates that wetlands play a critical role in controlling and filtering runoff” (126 S. Ct. at 2246-47 [citations omitted]). The other two types of waters that the Clean Water Act covers are the “contiguous zone” and the “ocean.” Congress defined contiguous zone through a reference to the 1958 United Nations Convention on the Law of the Sea (Section 502(9)), and this zone refers to the area of ocean beyond the territorial sea, out to 12 miles. The ocean, in turn, is “any portion of the high seas beyond the contiguous zone” (Section 502(10)). In concert with what it claims to be customary international law, the United States asserts jurisdiction over a 200-nautical-mile-wide exclusive economic zone (EEZ) (Reagan, 1983) and has claimed a 200-nautical-mile-wide exclusive fish- ing zone since at least 1976 (see MSA, 1976). Thus, the Clean Water Act’s regulatory program extends 200 nautical miles out to sea (Craig, 2004). With respect to the Mississippi River, and in the context of this report, the Clean Water Act’s marine coverage is most relevant to the Mississippi River’s effects on the Gulf of Mexico. The act’s extension to the oceans gives the federal government legal authority to regulate water quality in the Gulf of Mexico out to 200 nautical miles. Moreover, state regulatory au- thority under the Clean Water Act extends only through the territorial sea, or 3 nautical miles offshore, although Florida and Texas do have more far- reaching state jurisdiction over the waters of the Gulf of Mexico, extending to 3 marine leagues or about 12 nautical miles. Thus, consideration of Gulf of Mexico water quality generally necessitates state and federal coopera- tion, although Gulf of Mexico hypoxia occurs primarily in federal waters. 

THE CLEAN WATER ACT 75 Section 404 Dredge-and-Fill Permit Program The Clean Water Act’s more limited permit program is the Section 404 permit program, more colloquially referred to as the dredge-and-fill or wetlands permit program. Under this program, the Secretary of the Army, acting through the U.S. Army Corps of Engineers, has the authority to “issue permits . . . for the discharge of dredged or fill material into the navigable waters at specified disposal sites” (Sections 404(a), 404(d)). States may acquire limited dredge-and-fill permitting authority (Section 404(g)), but to date only two states—Michigan and New Jersey—have done so (USEPA, 2007a). As a result, Section 404 permits remain almost entirely federal permits. The U.S. EPA oversees the Section 404 permitting program in two ways. First, it issued guidelines that govern all Section 404 permitting (Sec- tion 404(b)(1)), and these guidelines require dischargers of dredged and fill material to minimize their adverse impacts on aquatic ecosystems (40 C.F.R. Section 230.1(c)). Second, the EPA has the authority to veto any particular Section 404 permit for a proposed discharge (Section 404(c)), although it has exercised this authority only rarely. Given the CWA definition of “navigable waters,” the Section 404 per- mit program does not apply more than 3 nautical miles out to sea (Section 502(7); 33 C.F.R. Section 328.4(a)). In addition, the Clean Water Act also limits this permit program to discharges of dredged or fill material, elimi- nating discharges of all other Clean Water Act pollutants from its scope (Section 404(a)). For the Mississippi River, the Section 404 permit program most promi- nently applies to wetland filling activities along the river and its tributaries. For example, Section 404 permits have been required to build a marine ter- minal in coastal wetlands and to construct a sewer in wetlands along an Illi- nois River tributary (City of Shoreacres v. Waterworth, 332 F. Supp.2d 992, 1016-17 (S.D. Tex. 2004); United States v. Hummel, 2003 WL 1845365, at *4-*5 (N.D. Ill. 2003)). Wetland loss through dredging, draining, and filling has important implications for water quality in the Mississippi River. However, it is impor- tant to remember that most wetland loss in the Mississippi River Basin oc- curred before Congress enacted the 1972 amendments to the Federal Water Pollution Control Act, and Section 404 of the Clean Water Act has almost nothing to say about the restoration of these past wetland losses. Moreover, given the Mississippi River’s role in navigation and commerce, the Corps of Engineers has additional authority under other federal statutes, most no- tably the Rivers and Harbors Act of 1899, to engage in navigation-related dredging and construction activities that can continue to deplete Mississippi River wetlands. Therefore, although an environmentally conscious appli- 

76 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT cation of Section 404 and the EPA guidelines can help to prevent further wetlands loss and require compensatory mitigation and restoration for any new filling and destruction of wetlands, Section 404 of the Clean Water Act is an insufficient legal vehicle to address the full scope of potential wetland restoration in the Mississippi River Basin. Section 402 National Pollutant Discharge Elimination System Permit Program The NPDES permit program governs most point source discharges of pollutants into the nation’s waters. Moreover, the Clean Water Act allows states to assume NPDES permitting authority (Section 402(b)), and most states have done so (USEPA, 2006a), subject to EPA oversight (Section 402(b), (c)). Thus, in all but a few states, NPDES permits are for all practi- cal matters state permits. NPDES permit conditions usually depend on technology-based effluent limitations, which the EPA generally establishes (Sections 301, 304), or wa- ter quality-based requirements, whichever are more restrictive. Technology- based effluent limitations establish quantitative restrictions on pollutant discharges depending on the kind of pollution-reduction technology avail- able to the discharger’s industry for the particular industrial processes the discharger is using (Section 301(b)). Specifically, an “effluent limitation” is essentially a numeric limitation on the amount of a given pollutant that can be discharged at the end of the pipe, measured by quantity, rate, or concentration (Section 502(11)). Most effluent limitations for discharges from POTWs are based on the reductions of pollutants achievable through secondary treatment, or settling and biological treatment, of the sewage (Section 301(b)(1)). For industrial dischargers, effluent limitations have become progressively more stringent since 1972, and the Clean Water Act now requires that effluent limitations for most pollutants, including toxic pollutants, be based on “the best avail- able technology economically achievable,” or BAT (Section 301(b)(2)). Several other requirements also dictate the terms of NPDES permits. For example, many new point source dischargers must comply with the relevant new source performance standards (NSPS) (Section 306). NSPS are technol- ogy-based standards that “reflect the greatest degree of effluent reduction which the Administrator determines to be achievable through application of the best available demonstrated technology” (BADT)—“including, where practicable, a standard permitting no discharge of pollutants” (Section 306). As such, NSPS often are more stringent than BAT-based effluent limitations. Similarly, the EPA administrator may set effluent standards for toxic pollutants that are more stringent than the BAT-based effluent limita- tions, up to and including a complete prohibition on discharges of certain toxic pollutants from specific industrial processes (Section 307(a)). Finally, 

THE CLEAN WATER ACT 77 all dischargers are also subject to inspection, monitoring, recordkeeping, and reporting requirements (Section 308). In a typical NPDES permit, technology-based effluent limitations dic- tate the majority of the discharge requirements for the point source. How- ever, if the discharge “would interfere with the attainment or maintenance of that water quality in a specific portion of the navigable waters which shall assure protection of public health, public water supplies, agricultural and industrial uses, and the protection and propagation of a balanced population of shellfish, fish, and wildlife, and allow recreational activities in and on the water,” the NPDES permit must include more stringent water quality-related effluent limitations to ensure that these uses are protected (Section 302(a)). These water quality-based effluent limitations help ensure that the Clean Water Act achieves its overall water quality goals by estab- lishing effluent limitations that meet the water quality standards established by the states for particular waterbodies. Agricultural Exemptions Importantly for Mississippi River water quality, the CWA’s exempts many agricultural sources of water pollutants from its regulatory scope (Ruhl, 2000). For example, beyond implicitly eliminating nonpoint source pollution from the CWA’s regulatory scheme, the act’s definition of “point source” explicitly excludes “agricultural stormwater discharges and re- turn flows from irrigated agriculture” (Section 502(14)). The Clean Water Act reinforces this exemption by prohibiting the EPA administrator from requiring an NPDES permit “for discharges comprised entirely of return flows from irrigated agriculture, nor shall the Administrator directly or indirectly, require any State to require such a permit” (Section 402(l)). Finally, the act explicitly excludes from the dredge-and-fill permit require- ment any discharges of dredged or fill material: (1) “from normal farming, silviculture, and ranching activities such as plowing, seeding, cultivating, minor drainage, harvesting for the production of food, fiber, and forest products, or upland soil and water conservation practices”; (2) “for the purpose of construction or maintenance of farm or stock ponds or irriga- tion ditches, or the maintenance of drainage ditches”; and (3) “for the purpose of construction or maintenance of farm roads . . . , where such roads are constructed and maintained in accordance with best management practices” (Section 404(f)). However, the Clean Water Act’s definition of point source does explicitly include “concentrated animal feeding opera- tions,” or CAFOs, as sources whose discharges of pollutants are subject to the act (Section 503(14)). Thus, discharges from these large-scale “factory farms” are regulated under the Clean Water Act, generally through NPDES permits (Ruhl, 2000). 

78 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT STATE-LEVEL AUTHORITY IN PROTECTING WATER QUALITY Water Quality Standards As discussed above, beginning in 1965, the FWPCA took a state- focused, water quality standards approach to improving the nation’s wa- ter quality. The virtues of this approach are local control and flexibility, which the states fought to retain in the 1972 amendments that created the contemporary Clean Water Act, despite considerable evidence that a pure water quality standards approach was not improving water quality (Houck, 1999). These state demands, coupled with environmentalists’ demands for a regulatory backstop and congressional need to reconcile the Senate and the House approaches to regulatory reform, led to Section 303 of the trans- formed Clean Water Act (Houck, 1999). Section 303 remains a significant element of contemporary water quality regulation, primarily because of the TMDL provisions added to the pre-1972 water quality standards approach (Houck, 1999). Box 3-1 contains further discussion of the TMDL program and process. BOX 3-1 The TMDL Program and Process The Total Maximum Daily Load program was created by the 1972 Federal Water Pollution Control Act Amendments (now the Clean Water Act ) and today is the foun- dation for the nation’s efforts to meet state water quality standards. TMDL represents the amount of a pollutant that can be discharged daily into a waterbody consistent with applicable water quality standards. The TMDL process refers to the process whereby the TMDL is developed and implemented. Failure to meet water quality standards is a major concern across the United States. Roughly 21,000 river segments, lakes, and estuaries have been identified by states as being in violation of one or more water quality standards. The TMDL program is mandated by Section 303(d) of the Clean Water Act. The TMDL process was little utilized during the 1970s and 1980s, as states focused on bringing point source polluters into compliance with permit limits issued as part of the National Pollutant Discharge Elimination System. Although the NPDES program has been successful on many counts, it has not achieved the CWA water quality goals of fishable and swimmable waters, largely because discharges from other unregulated nonpoint sources of pollution have not been reduced sufficiently. Today, nonpoint sources of pollution (e.g., those involving discharges of nutrients and sediments from agricultural operations) are jeopardizing water quality and shifting the focus of water quality management among the states from effluent-based to ambient water quality- based regulations and other controls. 

THE CLEAN WATER ACT 79 Under the 1972 amendments, the states retain their pre-1972 author- ity to set water quality standards for the waters within their borders. “A water quality standard shall consist of the designated uses of the navigable waters involved and water quality criteria for such waters based upon such uses. Such standards shall be such as to protect the public health or welfare, enhance the quality of water and serve the purposes of this chapter. Such standards shall be established taking into consideration their use and value for public water supplies, propagation of fish and wildlife, recreational purposes, and agricultural, industrial, and other purposes, and also taking into consideration their use and value for navigation” (Section 303(c)(2); emphasis added). Thus, state water quality standards (which consist of designated use and water quality criteria) establish ambient water quality goals that a given waterbody is required to achieve. The standards represent social and economic considerations, as well as physical, chemical, and biologi- cal considerations (NRC, 2001). Designated uses specify the uses that the state wants the body of water to be able to support. Water quality criteria Under TMDL regulations promulgated in 1992, EPA requires states to list waters that are not meeting water quality standards, which establish both criteria and designated uses for waterbodies. For each impaired waterbody, the state must identify the amount by which the point and nonpoint source discharges must be reduced for the waterbody to attain its stated water quality standards. A TMDL is developed for these listed wa- terbodies. The TMDL determines a numerical quantity that will not violate state water quality standards, allocating that load among point and nonpoint sources (the Waste Load Allocation [WLA] and the Load Allocation [LA], respectively). The final step in the process is implementation of the TMDL, with the objective of delisting the waterbody. Creating required TMDLs has become one of the pressing water quality challenges for states in the last two decades. Water quality monitoring and data play a key role in the TMDL process. They are important in the decision to add waters to the list of impaired waterbodies required by Section 303(d) and in developing TMDLs for listed waters. They are also important in allocating pollutant loads among point and nonpoint sources in a given watershed or river basin. The TMDL process is cyclical, as TMDLs are periodically assessed for their achievement of water quality standards including designated uses. If implementation of the TMDL is not achieving attainment of the designated uses, the use of scientific data and information is part of the process for revising the TMDL. SOURCE: NRC (2001). 

80 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT specify the characteristics of the water quality necessary to support those designated uses. The EPA establishes federal reference water quality criteria for states to use in setting their water quality standards (Section 304). These federal criteria usually do not legally bind the states to any particular water quality criteria, and the Clean Water Act leaves the states free to establish their own water quality criteria, as long as those state criteria are either (1) more strin- gent than the federal water quality criteria or (2) scientifically defensible as protecting the designated uses, even if the state criteria are less stringent than the federal. However, Congress occasionally creates exceptions to the “guidance” status of federal water quality criteria. For example, Congress specified that the EPA’s relatively recent bacteria water quality criteria would apply in any state with coastal recreation waters (fresh or salt) that did not adopt its own such criteria by 2004 (Section 303(i)). Box 3-2 dis- cusses these new bacteria water quality criteria and EPA’s accommodation of individual state needs and preferences at the federal level. Nevertheless, although most of the federal water quality criteria le- gally function merely as guidance for the states—not requirements—states often use them in setting their own water quality standards. These EPA-set criteria reflect the latest scientific knowledge regarding a variety of water quality impacts from many different pollutants, including impacts on hu- man health, various kinds of aquatic life, and aesthetics and recreation. For example, human health-related criteria would be appropriate water quality criteria for waters designated for drinking water use, while criteria based on aquatic toxicity would be appropriate for waters designated to support fish- ing and aquatic life. Thus, federal water quality criteria play an important role in the development of state water quality standards. Section 303 also requires each state to adopt an antidegradation policy as part of its water quality standards program. The federal antidegradation policy limits a state’s discretion to allow the existing condition of its waters to deteriorate and generally prohibits the loss of existing uses (Section 303(d)(4)). The EPA reviews state-submitted water quality standards for con- sistency with the Clean Water Act and must promulgate water quality standards for any state that will not either submit its own water quality standards or adequately respond to the EPA’s disapproval (Section 303(c)). However, given the Clean Water Act’s emphasis on the states’ roles in set- ting water quality standards, such EPA intervention is rare and most states have promulgated their own water quality standards. As noted above, how- ever, the reference water quality criteria that EPA establishes significantly influence state water quality standards. 

THE CLEAN WATER ACT 81 BOX 3-2 EPA Oversight of Water Quality Standards: Bacteria Criteria for Coastal Recreation Waters On November 16, 2004, the EPA promulgated bacteria water quality criteria for states to incorporate into their coastal water quality standards (69 Fed. Reg. 67,218). In the Beaches Environmental Assessment and Coastal Health (BEACH) Act of 2000, Congress had required these criteria for any coastal state—includ- ing the Great Lakes states—that had designated areas of its coastal waters for recreation (the state-established designated use), setting a deadline of April 10, 2004, for state submissions of bacteria water quality standards. Although 14 coastal states and territories complied with this deadline, 21 others states did not and thus became subject to the EPA-set criteria (69 Fed. Reg. at 67,234). Several aspects of EPA’s bacteria water quality criteria could be relevant to EPA actions for the Mississippi River. First, even though defaulting states are bound by the EPA criteria, in response to requests from New York and Pennsyl- vania, the EPA promulgated two sets of criteria for different bacteria indicators for the Great Lakes and then allowed the states the flexibility to choose which set to use (69 Fed. Reg. at 67,223). The EPA provided “this flexibility to all Great Lakes States in the rule because the Great Lakes States have a history of cooperating to protect the Great Lakes resource, and may find a need to agree on a consistent pathogen indicator for the Great Lakes” (67 Fed. Reg. at 67,223). Thus, interstate cooperation became relevant to the implementation of federal criteria in interstate waters. Second, the EPA adopted “single sample maximum” criteria that required state action (notification of the public and potential beach closure) from a single unusually high sample of bacteria-contaminated waters. However, it left states “the discretion to use single sample maximum values as they deem appropriate in the context of Clean Water Act implementation programs [such as NPDES per- mitting and TMDLs] other than beach notification and closure” (69 Fed. Reg. at 67,225-67,226). Thus, the EPA envisioned a multi-federal-criteria system in which violation of criteria would trigger different state responsibilities. Third, the EPA included a five-year compliance schedule for existing point source dischargers that would be affected by the new criteria (69 Fed. Reg. at 67,229). Thus, the EPA recognized that immediate compliance with the federal water quality criteria might not be economically realistic and allowed for phased-in implementation. Fourth, the EPA allowed individual states to avoid the federal bacteria criteria, which were based on Escherichia coli and Enterococci, when the state already had some other regulatory mechanism that effectively ensured the attainment of the purpose of the federal bacteria criteria—to protect human health. Thus, when the State of Washington demonstrated that its own criterion for fecal coliform adequately ensured limits on other bacteria and protected human health, the EPA released the state from the federal requirement (69 Fed. Reg. at 67,231). Overall, the bacteria water quality criteria demonstrate that the EPA can im- pose a federal layer of water quality regulation while retaining state flexibility in implementation and sensitivity to concerns of consistency among states in inter- state waters. 

82 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT Nonpoint Source Pollution Programs As noted, the Clean Water Act does not define “nonpoint source”; instead, by implication, the term refers to any source of water pollutants that is not a point source. Examples of nonpoint source pollution are runoff from a mall parking lot or from agricultural land into a stream. As a result, nonpoint source pollution is not subject to either of the Clean Water Act’s two permitting programs and therefore remains a weakly regulated water quality issue: “The United States has made tremendous advances in the past 25 years to clean up the aquatic environment by controlling pollution from industries and sewage treatment plants. Unfortunately, we did not do enough to control pollution from diffuse, or nonpoint sources. Today, non- point source pollution remains the Nation’s largest source of water quality problems” (USEPA, 2004a). The Clean Water Act leaves regulation of nonpoint source pollution to the states. Prior to 1987, states addressed nonpoint source pollution, if at all, only through areawide waste treatment management plans (Section 208). Although designed primarily to encourage each state to plan for the construction of POTWs throughout the state, such plans also required states to “identify, if appropriate, agriculturally and silviculturally related nonpoint sources of pollution” and “set forth procedures and methods (including land use requirements) to the extent feasible for such sources” (Section 208(b)). Nevertheless, area-wide management plans were largely considered a failure with respect to effectively addressing nonpoint source pollution. In 1987 Congress amended the Clean Water Act to establish the non- point source management program (WQA, 1987). Under this program, each state had to identify those navigable waters within its boundaries that could not achieve the applicable water quality standards without non- point source pollution controls (Section 319(a)(1)). In addition, the state had to identify the significant nonpoint sources contributing pollutants to these waters, describe a process for identifying best management practices (BMPs) and measures to control those sources, and identify existing state and local controls on such sources. After the states filed their initial nonpoint source management reports with the EPA, the new program required them to develop a state nonpoint source management program (Section 319(b)). Each state program had to meet six requirements, including a schedule of annual milestones for imple- menting BMP requirements for nonpoint sources (Section 319(b)(2)). States submitting reports and programs that the EPA approved became eligible for federal grants (Section 319(h), (i)). Moreover, coastal states had to coordi- nate their Clean Water Act nonpoint source management plans with their Coastal Nonpoint Pollution Control Programs established pursuant to the 

THE CLEAN WATER ACT 83 federal Coastal Zone Management Act (16 U.S.C. Section 1455b). Finally, additional information about pollutant sources and their contributions, including nonpoint source airborne contributions to water impairment, can come from the Toxics Release Inventory (TRI) database established through the Emergency Planning and Community Right-to-Know Act (42 U.S.C. Sections 11001-11050). State Reports on Water Quality The Clean Water Act requires states, beginning in 1976, to prepare and submit to the EPA administrator biennial reports on the quality of navigable waters within their borders (Section 305). These Section 305(b) biennial reports must cover five topics: (1) “a description of the water qual- ity of all navigable waters in such State during the preceding year”; (2) an analysis of the extent to which the navigable waters in the state achieve the act’s fishable and swimmable goals; (3) an analysis of the extent to which the Clean Water Act’s mechanisms have allowed or will allow the state to achieve the fishable and swimmable goal in all its waters, “together with recommendations as to additional action necessary to achieve such objec- tives and for what waters such additional action is necessary”; (4) estimates of the environmental impact and the economic and social costs of achieving the Clean Water Act’s goals, the benefits such achievement would produce, and an estimated date of achievement; and (5) a description of the role of nonpoint source pollution within the state, with recommendations for con- trolling such pollution (Section 305(b)(1)). The states’ water quality reports are accessible through most state environmental agencies’ web sites, and summaries are available from the EPA (USEPA, 2007b). Federal Consistency with State Water Quality Requirements The Clean Water Act essentially allows states to veto or condition fed- erally authorized projects that may cause discharges into the state’s waters, including the waters of the territorial sea (Section 401). A federal agency cannot issue a permit if the state denies certification (Section 401(a)), and states can condition the certification on specific requirements designed to ensure compliance with the act (Section 401(d)). The U.S. Supreme Court has twice upheld broad state authority to condition federal licenses and permits in order to protect water quality and designated uses, including allowing states to force federally permitted or licensed projects to maintain instream flows for fish and reestablish recreational access to the waters (PUD No. 1 of Jefferson County v. Washington Department of Ecology, 511 U.S. 700 (1994); S.D. Warren Co. v. Maine Board of Environmental Protection U.S., 126 S. Ct. 1843 (2006)). 

84 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT Nationally, this state certification requirement can apply to a variety of federal permits and licenses, including hydroelectric dam licenses from the Federal Energy Regulatory Commission (FERC), which were at issue in both PUD No. 1 of Jefferson County and S.D. Warren Co.; NPDES permits from the EPA in states that still lack delegated permitting authority, which was the subject of the Supreme Court’s interstate water pollution decision in Arkansas v. Oklahoma (503 U.S. 91 (1992)); and Coast Guard licensing and permitting in coastal waters. However, by far the most common triggers for state certifications along the Mississippi River are applications for Clean Water Act Section 404 permits from the Corps of Engineers for activities occurring in wetlands, followed by Corps of Engineers permits under the Rivers and Harbors Act of 1899 for navigation-related projects (ADEQ, 2006; IADNR, 2006; ILDNR, 2006; KDOW, 2006; LDEQ, 2006; MDEQ, 2006a; MDNR, 2006; MPCA, 2006; TDEC, 2006; WDNR, 2006). The limited case law that exists indicates that the state certification requirement does not apply to federally permitted or licensed nonpoint sources of pollutants. However, the Clean Water Act’s nonpoint source management program contains its own consistency provision. This pro- vision requires each relevant federal department and agency to “accom- modate . . . the concerns of the State regarding the consistency of such applications or projects with the State nonpoint source pollution manage- ment program” (Section 319(k)). TMDLs and the Legal Intersection of Point and Nonpoint Source Pollution As discussed previously, states set water quality standards to help achieve ambient water quality goals for a given waterbody. Moreover, the NPDES permitting agency must ensure that the effluent limitations in a particular permit are stringent enough to ensure that the receiving water achieves its water quality standards. The Clean Water Act’s primary mechanism for connecting water quality standards, NPDES permit require- ments, and nonpoint source regulation is the TMDL analysis. This analysis involves determination of the pollutant loads (mass discharges to the water in a specified period) that a particular waterbody can accept and not exceed the applicable water quality criteria. At the start of the TMDL process, each state has to “identify those waters within its boundaries for which the [technology-based] effluent limitations . . . are not stringent enough to implement any water quality standard applicable to such waters” and then rank those water quality- limited waters in order of priority, “taking into account the severity of the pollution and the uses to be made of such waters” (Section 303(d)). After generating this Section 303(d) list, the state then sets TMDLs for the spe- 

THE CLEAN WATER ACT 85 cific pollutants that are causing the impairments for each listed waterbody “at a level necessary to implement the applicable water quality standards with seasonal variations and a margin of safety which takes into account any lack of knowledge concerning the relationship between effluent limita- tions and water quality” (Section 303(d)). The TMDL represents the total amount of a particular pollutant that can be added to the waterbody over a particular period of time without violating the applicable water quality standard. Permitting agencies then must modify the effluent limitations in NPDES permits to implement the established TMDL (Section 303(d)). Moreover, until the waterbody attains its water quality standards, effluent limitations based on the TMDL “may be revised only if (i) the cumulative effect of all such revised effluent limitations based on the total maximum daily load or waste load allocation will assure the attainment of such water quality standard, or (ii) the designated use which is not being attained is removed in accordance with regulations established under this section” (Section 303(d)). However, if a waterbody is impaired—that is, does not meet its water quality standards—as a result of nonpoint source pollution, TMDLs can also be a means for encouraging states to address both point and nonpoint sources affecting that waterbody. EPA regulations regarding TMDLs ex- pressly recognize that both point source loadings, termed the waste load allocation, and nonpoint source loadings, termed the load allocation, are components of the total TMDL (40 C.F.R. Section 130.2(i)). Moreover, the U.S. Court of Appeals for the Ninth Circuit has upheld the EPA’s authority to set TMDLs for waterbodies polluted only by nonpoint sources of pollut- ants (Pronsolino v. Nastri, 291 F.3d 1123 (9th Cir. 2002)). INTERSTATE WATER QUALITY PROTECTION State Authorities and Responsibilities with Respect to Interstate Water Pollution As noted above, since long before 1972, interstate water pollution problems have been deemed to be matters for federal law and federal agen- cies. Nevertheless, the Clean Water Act provides several interstate-related provisions authorizing state action. Interstate Compacts and Interstate Agencies Related to Water Quality Congress explicitly gave its consent to the creation of interstate com- pacts related to water pollution. Specifically, Congress encouraged states to 

86 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT use interstate compacts for “cooperative effort and mutual assistance for the prevention and control of pollution and the enforcement of their respec- tive laws relating thereto” and to establish interstate agencies to coordinate and enforce interstate regulation (Section 103(b)). However, unlike the states themselves, these interstate agencies no longer are entitled to federal funding. The Clean Water Act generally autho- rizes “grants to States and interstate agencies to assist them in administering programs for the prevention, reduction, and elimination of pollution” (Sec- tion 106). However, to be entitled to such grants, interstate agencies had to apply to the EPA by early 1973. Thus, interstate agencies created since then to address issues such as Mississippi River water quality are ineligible. Interstate Considerations in State NPDES Permitting The state delegation provisions impose interstate obligations on states that choose to issue NPDES permits. Specifically, in order to obtain NPDES permit program authority, each state had “to insure that . . . any other State the waters of which may be affected, receive[s] notice of each application for a permit and to provide an opportunity for public hearing before ruling on such an application” (Section 402(b)). In addition, each delegated state (Section 402(b)) must insure that any State . . . whose waters may be affected by the issuance of a permit may submit written recommendations to the permitting State (and the Administrator) with respect to any permit application and, if any part of such written recommendations are not accepted by the permitting State, that the permitting State will notify such affected State (and the Administrator) in writing of its failure to so accept such recommendations together with its reasons for so doing. Finally, the state issuing the permit must send copies of each permit applica- tion, permit action, and permit to the EPA administrator, who can object to the permit’s issuance. If the permit-issuing state does not adequately address EPA concerns regarding a downstream state’s water quality, the EPA can veto the state permit. Federal Interstate Authorities and Responsibilities EPA’s General Authority and Duty to Coordinate Transboundary Pollution Regulation The EPA has multiple sources of authority, and multiple duties, re- garding efforts to control transboundary, and especially interstate, water pollution. Most generally, the EPA administrator has three overarching 

THE CLEAN WATER ACT 87 mandatory duties regarding interstate water pollution issues. First, the EPA must “encourage cooperative activities by the States for the prevention, re- duction, and elimination of pollution” (Section 103). Second, the EPA must “encourage the enactment of improved and, so far as practicable, uniform State laws relating to the prevention, reduction, and elimination of pollu- tion” (Section 103). Finally, the EPA must “encourage compacts between States for the prevention and control of pollution” (Section 103). Various other Clean Water Act provisions reinforce these general federal coordination obligations regarding transboundary problems. For example, as noted, Congress gave the EPA responsibility for developing nonbinding guidance water quality criteria and information regarding the implementa- tion of those criteria for states to use in their Clean Water Act programs (Section 304), and the EPA’s transboundary responsibilities extend into the international arena (Section 310). Some of the most important of the EPA’s interstate authorities and duties are described below. EPA’s Role in Addressing Federally Licensed or Permitted Sources of Interstate Pollution As discussed above, the Clean Water Act’s state certification provisions give states authority to condition federal licenses and permits to ensure that federally licensed activities do not violate state water quality standards and other water quality requirements. However, the certification provision also requires that other states potentially affected by the discharge—generally referred to as downstream states, but for border rivers such as the Mis- sissippi, also including cross-stream states—be given the opportunity to ensure that their water quality requirements will be met, as well. Most importantly, “[i]f the imposition of conditions cannot ensure such compli- ance such agency shall not issue such license or permit” (Section 401(a)). Thus, downstream and cross-stream states are also given an opportunity to object to federal permits and licenses, as are the states in which the pro- posed discharge will originate. States have increasingly been exercising this authority to protect their water quality. It is, however, the EPA that represents and evaluates the interests of downstream and cross-stream states’ interstate water pollution concerns (see Arkansas v. Oklahoma, 503 U.S. 91 (1992)). Specifically, the federal licensing or permitting agency must notify the EPA administrator of the discharge, and “[w]henever such a discharge may affect, as determined by the Administrator, the quality of the waters of any other State, the Ad- ministrator within thirty days . . . shall so notify the other State” (Section 401(a)(2)). Affected (downstream or cross-stream) states then have 60 days to determine whether “such discharge will affect the quality of waters so as to violate any water quality requirement in such State”; if so, they can notify the EPA and the licensing agency of objections, and the EPA adminis- 

88 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT trator must then hold a public hearing on the objections (Section 401(a)(2)). The EPA administrator presents the licensing agency with recommendations regarding the affected state’s objections. Then, that agency, “based on the recommendations of such State, the Administrator, and upon any additional evidence, if any is presented to the agency at the hearing, shall condition such license or permit in such manner as may be necessary to insure compli- ance with applicable water quality requirements” (Section 401(a)(2)). EPA’s Interstate Oversight of State NPDES Permitting As noted above, states that assume NPDES permitting authority also acquire interstate obligations to potentially affected downstream and cross- stream states. However, the EPA is the final source of authority in address- ing these interstate permitting issues. Ultimately, interstate considerations depend on the EPA’s authority to veto state-issued permits that do not consider interstate effects and to take over the permitting process for that NPDES permit. In keeping with congressional intent, the EPA rarely invokes its veto authority. However, federal courts have upheld the agency’s authority to take over the NPDES permitting process to address the concerns of down- stream states. Thus, in Champion International Corp. v. EPA (850 F.2d 182 (4th Cir. 1988)), when Tennessee complained about an NPDES permit that upstream North Carolina was issuing and negotiations failed to resolve the issue, the U.S. Court of Appeals for the Fourth Circuit upheld the EPA’s issuance of an NPDES permit that included terms designed to address Tennessee’s concerns. EPA’s Authority to Convene Interstate Nonpoint Source Management Conferences When upstream nonpoint sources impair downstream water quality and interfere with the attainment of downstream water quality standards, the downstream state can petition the EPA to convene a management con- ference of all of the relevant states, with the goal of reaching an interstate agreement to regulate the upstream nonpoint sources sufficiently to achieve downstream water quality requirements (Section 319(g)). If the states reach such an agreement, moreover, they must incorporate that agreement into their respective nonpoint source management programs. These nonpoint source management conferences thus could result in the elimination of much state discretion in nonpoint source pollution management. Moreover, through EPA’s role and especially as a result of any interstate compact that might arise from the conference, which would have to be approved by Con- gress, interstate nonpoint source management conferences could effectively federalize this state-based area of water quality management. 

THE CLEAN WATER ACT 89 Perhaps for these reasons, formal nonpoint source management con- ferences are not used as often as they might be. Several states, including Alabama, Kentucky, and the Long Island Sound states of New York and New Jersey have made use of the nonpoint source management conference concept and have solicited grants from the EPA to do so. One of the few formal Section 319(g) petitions to the EPA, however, was Louisiana’s peti- tion regarding the Gulf of Mexico, which the EPA transformed into the Mississippi River-Gulf of Mexico Watershed Nutrient Task Force. As with the rest of the nation, interstate cooperation to address non- point source pollution in the Mississippi River tends to occur outside the CWA nonpoint source provisions. For example, the Mississippi River-Gulf of Mexico Watershed Nutrient Task Force is addressing nutrient pollution caused by both point and nonpoint sources along the entire river (USEPA, 2006a). In contrast, when states such as Louisiana work to address non- point source pollution of the Mississippi River through their own nonpoint source management programs, they do not appear to use the Clean Water Act’s conferencing mechanism (LDEQ, 1999). EPA-Led Interstate Management Conferences for the National Estuary Program In 1987, Congress established the Clean Water Act’s National Estuary Program (WQA, 1987). Once an estuary is selected for inclusion in the pro- gram because of its national significance, the CWA requires the EPA to hold a management conference in order to assess the overall water quality trends within the estuary, to “develop the relationship between the in place loads and point and nonpoint source loadings of pollutants in the estuarine zone and the potential uses of the zone, water quality, and natural resources,” and (Section 320(b)) to develop a comprehensive conservation and management plan that recom- mends priority corrective actions and compliance schedules addressing point and nonpoint sources of pollution to restore and maintain the chemi- cal, physical, and biological integrity of the estuary, including restoration and maintenance of water quality, a balanced indigenous population of shellfish, fish and wildlife, and recreational activities in the estuary, and assure that the designated uses of the estuary are protected. The National Estuary Program thus provides states and the EPA with a mechanism for comprehensively addressing estuarine water quality, includ- ing point, nonpoint, and interstate sources of pollutants. There are seven National Estuaries along the Gulf coast, including the Barataria-Terrebonne Estuary in Louisiana (USEPA, 2006b). 

90 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT Interstate Implications of EPA-Set TMDLs State-set TMDLs are predominantly intrastate in focus. For example, the Clean Water Act requires each state to identify water quality-limited waters for “those waters within its boundaries” and to establish TMDLs for those waters (Section 303(d)). Moreover, each state must then use the information generated as part of a continuing planning process within the state (Section 303(e)). Two kinds of interstate water quality authority issues are relevant to TMDLs. First, a downstream state with impaired waters might attempt to use the TMDL process to directly force particular point and nonpoint sources in upstream or cross-stream states to comply with more stringent discharge limitations and BMP requirements, respectively, in order to help achieve the downstream state’s water quality standards. Because sources within the upstream and cross-stream states are the regulatory province of those other states, the Clean Water Act’s TMDL provisions probably do not authorize downstream states to engage in this kind of direct cross-border regulation. For example, Florida, which is in the process of establishing a TMDL for mercury in the Everglades, recently implied that it lacked au- thority to reach out-of-state sources of mercury deposited via the air, even though such cross-boundary atmospheric deposition may be a significant nonpoint source of mercury pollution in the Everglades (FDEP, 2003). Second, TMDLs must deal with cross-border effects. As noted previ- ously, TMDLs technically have an intrastate focus—the upstream state establishes TMDLs to meet its own water quality standards for its waters. Nevertheless, given that the Clean Water Act, as interpreted by EPA, im- poses obligations on upstream states to protect downstream water quality through the adoption of their own water quality standards (40 C.F.R. Section 131.10), Section 303(d) effectively requires an upstream state to adopt a TMDL at a level such that it will prevent interference by its point and nonpoint sources with attainment of downstream state water quality standards. Otherwise stated, in achieving its own water quality standards through compliance with the TMDL, the upstream state will eliminate the downstream effects. Regardless of an upstream state’s interstate TMDL obligations, how- ever, the EPA has the authority to establish TMDLs with both downstream and upstream interstate effects. There are also regulatory requirements (at least for point sources), in the form of more stringent discharge limitations, which are based on water quality criteria developed by the EPA explicitly to address interstate water quality problems. For example, the Clean Wa- ter Act requires the EPA to set TMDLs when states fail to do so (Section 303(d)), and the federal courts have upheld the EPA’s authority to set fed- 

THE CLEAN WATER ACT 91 eral TMDLs even when only nonpoint source pollutants are contributing to the water quality impairment. The Clean Water Act also specifies that the EPA must “encourage the enactment of improved and, so far as practicable, uniform State laws relating to the prevention, reduction, and elimination of pollution” (Sec- tion 103). TMDLs certainly could be one mechanism for providing such encouragement, especially in combination with EPA-recommended water quality criteria for problematic pollutants. The EPA increasingly has been asserting its own interstate water quality authority. For example, the EPA has developed a watershed program to en- courage states to address water quality issues cooperatively and comprehen- sively on a watershed basis (USEPA, 2006c; Box 7-2 further discusses EPA’s watershed approach to water management). The most active component of the EPA’s watershed program thus far is the targeted watershed grant pro- gram. Since 2003, the EPA has been funding projects designed to improve the overall water quality, fish productivity, and other qualities of targeted watersheds. Indeed, three targeted watershed projects funded in 2004—the Upper Mississippi River project in Iowa, the Sangamon River project in Illinois, and the Fourche Creek project in Arkansas—were designed spe- cifically to address one of the largest interstate pollution problems: Gulf of Mexico hypoxia caused by Mississippi River pollution. There is also the potential of cross-border water quality trading to implement cross-border TMDLs (Chapter 6 contains further discussion of the water quality trading concept). As a practical matter, the EPA is already establishing TMDLs that must have interstate regulatory effects if they are to achieve water quality stan- dards. For example, in February 2002, EPA Region 4 set a total mercury TMDL for the Ochlockonee River in Georgia (near its southern border) to satisfy a legal agreement (USEPA Region 4, 2002). Atmospheric deposition of mercury accounts for 99 percent of the mercury loading to the Ochlock- onee watershed, and the sources of atmospheric mercury are both local and distant. Thus, achievement of the mercury water quality standard in the Ochlockonee River will require increased regulation of out-of-state sources, probably through the EPA’s interstate authority under the Clean Air Act. Addressing nutrient pollution in the mainstem Mississippi River to im- prove water quality in the Gulf of Mexico almost would certainly require TMDLs with interstate effects, as Gulf of Mexico TMDLs are already demonstrating. For example, as described in Box 3-3, interstate effects were inevitable when EPA Region 6 and Louisiana developed a mercury TMDL for the Louisiana coastal waters of the Gulf of Mexico. Finally, EPA’s reference water quality criteria must “accurately reflect the latest scientific knowledge . . . on the kind and extent of all identifiable effects on health and welfare . . . which may be expected from the presence 

92 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT BOX 3-3 The EPA-Set Louisiana Coast-Gulf of Mexico Mercury TMDL In June 2005, EPA Region 6 and the State of Louisiana established a fish tissue mercury TMDL for the coastal bays and Gulf of Mexico waters of Louisiana (USEPA Re- gion 6, 2005). This TMDL necessarily implicates the entire Mississippi River, because “the Mississippi River represents a significant source of [mercury] to the Coastal Bays and Gulf Waters of Louisiana because of the large drainage area and massive flow rate. . . . The total mercury load from the Mississippi River is estimated at 2,117,000 grams per year. Classification of [mercury] loading from the Mississippi River as a nonpoint source is necessary since it was beyond the scope of these TMDLs to differentiate point sources from nonpoint sources of mercury for a geographic area covering almost two-thirds of the continental United States.” The sources of mercury pollution on the Louisiana Gulf Coast, and the necessary reductions in mercury loadings from those sources, including the Mississippi River, are shown in the following table. Load Allocations for Coastal Basins Point Source NPS Total Hg Load NPS Load Coastal Hg Load Hg Load Hg Load Reduction Allocation Segment Segment Name (g/yr) (g/yr) (g/yr) (g/yr) (g/yr) 010901 Afchafalaya Bay and 174 55,629 56,803 32,924 22,705 Delta 021102 Barataria Basin 324 94,590 94,914 56,000 38,591 Coastal Bays 042209 Lake Pontchartrain 527 52,188 52,715 31,102 21,086 Basin Coastal Bays 070601 Mississippi River 0 2,127,578 2,127,578 1,255,271 872,307 Basin Coastal Bays 110701 Sabine River Basin 57 20,077 20,134 11,879 8,198 Coastal Bays 120806 Terrebonne River 985 115,321 116,306 68,620 46,700 Basin Coastal Bays NOTE: NPS = nonpoint source. of pollutants in any body of water” (Section 304(a)(1); emphasis added). This broad command certainly extends to interstate water quality effects and the cumulative impacts of pollutants along large rivers such as the Mississippi. Coupled with the EPA’s authority to approve and disapprove state water quality standards and to encourage cooperative interstate ef- forts, this broad grant of water quality criteria-setting authority could allow 

THE CLEAN WATER ACT 93 Given these contributions and necessary reductions, EPA Region 6 assigned the mercury waste load allocations (WLA; point sources), load allocations (LA; nonpoint sources), and margin of safety (MOS) as follows: TMDL Summary Coastal TMDL WLA LA MOS Segment Segment Name (g/yr) (g/yr) (g/yr) (g/yr) 010901 Afchafalaya Bay and Delta 22,879 174 22,705 0 021102 Barataria Basin Coastal Bays 38,915 324 38,591 0 042209 Lake Pontchartrain Basin Coastal Bays 21,613 527 21,086 0 070601 Mississippi River Basin Coastal Bays 872,307 0 872,307 0 110701 Sabine River Basin Coastal Bays 8,255 57 8,198 0 120806 Terrebonne River Basin Coastal Bays 47,685 985 46,700 0 Simultaneously, however, EPA Region 6 noted the load allocation for the Mississippi River basin accounts for the mercury load from upstream sources in the basin (including point and nonpoint sources). Because of the large geographic scope of the basin and the difficulty in identifying specific sources, EPA has not allocated spe- cific waste loads to point sources in the Mississippi River basin upstream of the TMDL area. Thus, EPA Region 6 assumed that it had authority to impose a load allocation on the entire upstream Mississippi River basin. Moreover, it assumed that it had further author- ity to assign specific waste load allocations to upstream point sources to achieve the Gulf of Mexico TMDL, even though, because of the complexity, EPA Region 6 actually chose not to do so. the EPA to guide multistate attention to interstate water quality issues on large rivers. Moreover, the Clean Water Act expressly directs the EPA to consider scientific information regarding “the concentration and dispersal of pollutants” and effects such as “rates of eutrophication and rates of organic and inorganic sedimentation for varying types of receiving waters” (Section 304(a)(1)), again indicating that Congress wanted the EPA to look 

94 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT broadly—including across state borders—when establishing its water qual- ity criteria. SUMMARY The Clean Water Act of 1972 represented a significant change in U.S. water quality regulation in that the emphasis shifted from a focus on state- level water quality standards to a federal permitting scheme according to technology-based or more stringent water quality-based limits for indi- vidual dischargers. The Clean Water Act authorizes water quality programs, requires state water quality standards, requires permits for discharges of pollutants into navigable waters, and authorizes funding for publicly owned wastewater treatment works. The Clean Water Act has been effective in addressing point sources of water pollutants. In particular, its NPDES permit program’s technology- based effluent limitations ensure that easily identifiable industrial point sources and POTWs employ effective pollution control technology. More- over, while states now issue most NPDES permits and engage in a signifi- cant portion of enforcement, the NPDES permit program has the additional advantages of being subject to federal and citizen enforcement (Sections 309 and 505). The Clean Water Act also addresses ambient water quality goals for the nation that its regulatory mechanisms are supposed to achieve. Specifically, the CWA requires states to develop water quality standards that consist of designated uses and water quality criteria that define acceptable pollutant levels for the waterbody given those designated uses. Notably, however, the Clean Water Act addresses nonpoint source pollution only in a limited, indirect manner. This is a crucial difference given the significance of nonpoint source water pollution throughout the nation and its special importance to Mississippi River and northern Gulf of Mexico water quality. The Clean Water Act’s nonpoint source provisions depend on the states’ political will to adopt and their economic capacity to enforce legally binding management measures to control runoff and other forms of nonpoint source pollution. State nonpoint source management programs, reinforced through the state water quality standard goals and specified TMDLs, could do much to address nonpoint source pollution. This would require states to have sufficient scientific and technological information to enact enforceable nonpoint source pollution control require- ments, along with sufficient financial strength and political will to enforce those requirements. The Clean Water Act provides a regulatory role for interstate agencies in appropriate circumstances (Sections 103 and 106). The Mississippi River presents an opportunity for states to share regulatory authority with one or more interstate water quality regulatory organizations (although the 

THE CLEAN WATER ACT 95 CWA does not provide for the financing for interstate bodies of this type formed after 1972). Even if the EPA and the states use these interstate water quality mechanisms to improve Mississippi River water quality, however, Mississippi River water quality will continue to suffer from several prob- lems that the Clean Water Act cannot address. Some of these problems derive from statutory choices that Congress potentially could change. For example, many agricultural sources of water pollution are exempt from the Clean Water Act’s provisions that regulate point sources. Furthermore, some impairments of Mississippi River water and environmental qual- ity stem from legacy problems that the Clean Water Act is not designed to address. For example, the Clean Water Act has nothing to say about endangered species, invasive species, habitat destruction, or other threats to biological diversity except to mandate the attainment and maintenance of water quality sufficient to support native fish, shellfish, and ecological communities. The statute can be used only indirectly to influence decisions made regarding navigation or flood control activities that can affect water quality, such as lock-and-dam construction or the dredging of navigation channels, in that it gives states the opportunity to condition federally is- sued permits and licenses. It does not mandate restoration of wetlands filled or otherwise altered long before the act took its current form. Moreover, some water quality issues—notably mercury contamination—derive from atmospheric deposition. Since the Clean Water Act does not authorize direct regulation of air pollution, it can only respond to these types of problems, but not really prevent them. As a result, the Clean Water Act cannot be used as the sole legal vehicle to achieve all water quality objectives along the Mississippi River and into the northern Gulf of Mexico. Nevertheless, the Clean Water Act provides a legal framework that, if comprehensively implemented and rigorously enforced, can effectively address many aspects of intrastate and interstate water pollution, although the emphasis to date has been predominantly on the former. Section 303 of the Clean Water Act requires states or the EPA to develop TMDLs for waters that do not meet water quality standards. TMDLs require regulators to look comprehensively at all sources of water pollution—point source, nonpoint source, and background. As a result, the TMDL provisions are becoming and are likely to remain key provisions of the Clean Water Act in finally achieving the goal of all of the nation’s wa- ters being at least fishable and swimmable. For TMDLs and water quality standards to be employed effectively to manage water quality in interstate rivers such as the Mississippi, it is essential that the effects of interstate pol- lutant loadings be considered fully in developing the TMDL. The Clean Water Act assigns most interstate water quality coordina- tion authority to the EPA. The EPA has mandatory duties to “encourage cooperative activities by the States for the prevention, reduction, and elimi- 

96 MISSISSIPPI RIVER WATER QUALITY AND THE CLEAN WATER ACT nation of pollution” and to “encourage the enactment of improved and . . . uniform State laws relating to the prevention, reduction, and elimination of pollution” (Section 103). Moreover, the EPA has clear statutory authority to (1) take over from states the setting of water quality standards and TMDLs when state efforts do not comply with the Clean Water Act’s requirements; (2) convene, at a state’s request, interstate nonpoint source management conferences; (3) convene multistate conferences to develop comprehensive water quality management plans to protect National Estuaries; (4) hold hearings to address interstate pollution caused by federally licensed or permitted activities, including water-based activities permitted by the U.S. Army Corps of Engineers; and (5) veto state NPDES permits and take over the permitting process to ensure that interstate pollution from upstream or cross-stream point sources is adequately addressed. As a result, the EPA has the authority to establish TMDLs with interstate effects and, at least for point sources, regulatory requirements designed to achieve those TMDLs, including water quality criteria set at levels designed to address interstate water quality problems. The Clean Water Act also encourages the EPA to stimulate and support interstate cooperation to address larger-scale water quality problems. The act provides the EPA with multiple authorities that would allow it to assume a stronger leadership role in addressing Missis- sippi River and northern Gulf of Mexico water quality.