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Control of Nonpoint Source Pollution under the Clean Water Act: A Matter of Political Will

Robin Rotman and Ashley Hollis


  • Examines legal and political issues surrounding nonpoint source pollution.
  • Discusses the Clean Water Act as it relates to nonpoint source pollution.
  • Offers recommendations for policy makers and practitioners who want to drive reductions in nonpoint source pollution.
Control of Nonpoint Source Pollution under the Clean Water Act: A Matter of Political Will
Aldo Pavan via Getty Images

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Fifty years after the passage of the Clean Water Act, 33 U.S.C. §§ 1251–1387, the majority of U.S. waterbodies fail to meet water quality standards. Certainly, there are notable Clean Water Act success stories, such as Lake Erie and the Cuyahoga River. More waterbodies are safe for swimming and fishing than ever before, and the Act is often regarded as one of the most effective federal environmental laws.

The Clean Water Act has proven effective at controlling point source pollution, including effluent from industrial sources and wastewater treatment plants. But the Act has always been hamstrung in addressing nonpoint source pollution such as agricultural stormwater discharges and return flows from irrigated agriculture. States are largely left to regulate, or not regulate, nonpoint pollution as they see fit, and only a few states have chosen to implement and enforce robust controls over nonpoint sources. As a result, nonpoint source pollution is the leading cause of water quality problems in the United States today.

This article examines legal and political issues surrounding nonpoint source pollution, and concludes that political will is key to controlling nonpoint source pollution under the Clean Water Act. It begins with a short summary of the history of water quality regulation in the United States. It then discusses recent rulemaking and litigation, the County of Maui case. County of Maui v. Hawaii Wildlife Fund, 140 S. Ct. 1462 (2020). The article then offers recommendations for policy makers and practitioners who want to drive reductions in nonpoint source pollution, in order to improve the water quality of our nation’s lakes, rivers, wetlands, and coastal areas, to the benefit of human and environmental health.

A Brief History of Water Quality Regulation in the United States

The Clean Water Act regulates discharges of pollution into “navigable waters,” which it also refers to as “waters of the United States.” 33 U.S.C. § 1362(7) (2018). This regulatory scope is derived from the federal government’s authority to oversee interstate commerce pursuant to the Commerce Clause of the U.S. Constitution.

The first statutes and public law cases dealing with water quality pertained to dumping of debris that could impair navigability. Those legal origins continue to have a profound effect on the nature of water quality regulation in the United States today. Gibbons v. Ogden, 22 U.S. (9 Wheat.) 1 (1824), involving passenger steamship routes between New York and New Jersey, established that the federal government’s exclusive power to regulate interstate commerce pursuant to the Commerce Clause includes oversight over waterbodies where goods and services may travel by vessel. In Gilman v. City of Philadelphia, 70 U.S. 713 (1865), involving a proposed bridge over the Schuylkill River in Pennsylvania, the U.S. Supreme Court held that “[c]ommerce includes navigation” and that Congress has the “power to keep [navigable waters] open and free from any obstruction to their navigation, interposed by the States or otherwise.” Id. at 725.

Although Gibbons and Gilman both emphasized federal jurisdiction over navigable waters, neither actually defined the term “navigable waters.” The first case that specified criteria for navigability was The Daniel Ball, involving licensing requirements for vessels traveling on the Grand River in Michigan. 77 U.S. (10 Wall.) 557 (1871). The Supreme Court adopted a test based on navigability-in-fact, and explained that rivers are navigable-in-fact if “they are used, or are susceptible of being used, in their ordinary condition, as highways for commerce, over which trade and travel are or may be conducted in the customary modes of trade and travel on water.” Id. at 564.

The nation’s first federal environmental law, The Rivers and Harbors Act of 1899, made it illegal to deposit refuse into navigable waters without a permit. 33 U.S.C. § 407. Although the Act’s primary goal was to ensure that navigation was not impeded, it laid the statutory foundation for future regulation of water pollution by introducing permitting requirements for refuse discharges into waterbodies. Over the past 120 years, as public concerns have grown to include not only navigability, but also the quality and integrity of the nation’s waters and ecosystems, legislation and regulation have at times struggled to address these issues through their rooting in the Commerce Clause.

Not until the mid-twentieth century did Congress enact legislation to address water pollution explicitly. The Federal Water Pollution Control Act of 1948, 62 Stat. 1155, empowered the U.S. Surgeon General to investigate reports of interstate water pollution and to take legal action to enjoin discharges that were endangering public health—but only with the consent of the state where the pollution originated. While groundbreaking in concept, the Act was highly deferential to the states; there was no requirement for states to set water quality standards, no minimum criteria for water quality standards that were adopted by states, no required limits on pollution discharges, and no real enforcement mechanisms.

The Water Quality Act of 1965, 79 Stat. 903, was the first federal legislation that required states to take action to attempt to limit pollution and improve water quality. It ordered states to identify the intended uses (which the Clean Water Act later termed “designated uses”) of all navigable waters within their borders and to develop water quality standards corresponding to each of the designated uses, for review and approval by the Federal Water Pollution Control Administration (FWPCA). States were given broad discretion to determine which sources of water pollution would be regulated and to what extent, and the Act did not differentiate between point and nonpoint sources. The Act also did not provide the FWPCA with an effective mechanism to compel states to comply with its requirements, and many did not.

By 1969, the year of the Cuyahoga River and Lake Erie fires and the Santa Barbara oil spill, the general public had turned its attention to the burgeoning problem of water pollution in the United States. With a groundswell of public support, Congress passed, by a sweeping majority, the Federal Water Pollution Control Act of 1972, which has come to be known as the Clean Water Act. The Clean Water Act is primarily implemented by the U.S. Environmental Protection Agency (EPA), with certain sections administered by the U.S. Army Corps of Engineers (ACE), as discussed below.

The Clean Water Act provides for the establishment and enforcement of water quality standards through the so-called triad of designated uses, water quality criteria, and anti-degradation provisions. It requires that designated use(s) be identified for all navigable waterbodies, water quality criteria be developed to correspond to these uses, and permits issued and enforced in a manner that will result in the standards being achieved. The Act directs the EPA to perform these functions, and also sets forth a relatively clear mechanism by which states can obtain delegated authority to perform these functions. The Clean Water Act is hailed as a classic example of cooperative federalism, and rightfully so. All states currently have some degree of delegated authority for water quality standard setting. State standards must be at least as strict as the federal minimum criteria promulgated by the EPA; states have the option of setting stricter standards in most cases, but rarely do so. The vast majority of states, as well as 80 federally recognized Indian tribes, currently have delegated authority to administer one or more Clean Water Act permitting programs. The EPA can take enforcement action against states that do not properly implement the Clean Water Act, as well as against individual polluters. It can refer civil enforcement cases to the U.S. Department of Justice (DOJ) for penalties and injunctive relief, and refer criminal cases to DOJ prosecution. The Act also empowers members of the public to file citizen suits against alleged violators to seek injunctive relief and recovery of attorney fees.

The Clean Water Act’s Approach to Point and Nonpoint Source Pollution

The Clean Water Act differentiates between point and nonpoint sources of water pollution. The point source definition encompasses most pollution that is discharged through a pipe, such as discharges from wastewater treatment plants and industrial facilities, and discharges of urban stormwater collected through municipal separate storm sewer systems. 33 U.S.C. § 1362(14). It expressly does not include “agricultural stormwater discharges and return flows from irrigated agriculture.” Pursuant to section 402 of the Act, point sources are subject to the National Pollution Discharge Elimination System (NPDES) program and must obtain an NPDES permit before discharging into a “navigable water.” 33 U.S.C. §§ 1342, 1362. The NPDES program has been generally effective in controlling point source pollution in the United States.

Nonpoint sources are simply defined as any source of water pollution that is not a point source. See Ecological Rts. Found. v. Pac. Gas & Elec. Co., 713 F.3d 502, 508 (9th Cir. 2013) (internal citations omitted) (nonpoint pollution “arises from many dispersed activities over large areas,” “is not traceable to any single discrete source,” and due to its “diffuse” nature, “is very difficult to regulate through individual permits”). The Clean Water Act contains provisions to address nonpoint source pollution, but these have proven less effective. Congress intended section 208 of the Act to be a counterpart to the NPDES program. It directs states to create Areawide Waste Treatment Management Plans for controlling nonpoint source pollution from agriculture, silviculture, mining, and construction. It does not actually require states to implement their plans, however; and congressional appropriations to support plan implementation were depleted by the 1980s. Although section 208 remains in effect today, it is of little relevance in most states.

Section 303(d) of the Clean Water Act addresses all sources of pollution that affect water quality, including point and nonpoint sources. 33 U.S.C. § 1313(d). It requires states to identify waterbodies that repeatedly fail to meet their water quality standards (called “impaired waters”) and prescribe a total maximum daily load (TMDL) of pollutants that these waterbodies can receive while still meeting their water quality standards. If a waterbody is impaired primarily due to point source discharges, a TMDL plan typically calls for existing NPDES permits to be revised and new NPDES permits to be issued sparingly. For waters that are primarily impaired by nonpoint source pollution, TMDL plans often call for other measures, such as financial incentive programs to encourage farmers and ranchers to utilize riparian buffers that reduce sedimentation and fertilizer runoff.

For decades, EPA largely ignored its authority under the Act to require the development and implementation of TMDL plans. A wave of citizen suits in the late 1990s and early 2000s brought attention to this issue. In 2002, the U.S. Court of Appeals for the Ninth Circuit ruled in Pronsolino v. Nastri, 291 F.3d 1123, 1125–26 (9th Cir. 2002), that states are required to establish TMDLs for all impaired waterbodies, even those impaired solely due to nonpoint source pollution. Pronsolino further held that that if a state does not establish a TMDL for an impaired waterbody, EPA must do so. Yet, Pronsolino did not expressly require the implementation of TMDL plans—and neither does the text of section 303(d) itself. In the past two decades, a handful of states have adopted state laws requiring a state agency to ensure that TMDL plans are implemented; others simply encourage residents to voluntarily adopt practices that are consistent with the TMDL plans. Although section 303(d) has led to significant improvements in water quality in certain areas, in states without sufficient political will to implement TMDL plans, particularly plans involving controls on nonpoint source position, it has done little to remediate impaired waters.

In addition to Areawide Waste Treatment Management Plans under section 208 and TMDLs under section 303(d), the Clean Water Act provides a third mechanism for addressing nonpoint source pollution: section 319, which was introduced in the Clean Water Act Amendments of 1987. 33 U.S.C. § 1329. Section 319 requires states to develop Nonpoint Source Management Programs to address nonpoint source pollution. Focusing on the carrot and not the stick, Congress did not give EPA authority to compel states to implement Nonpoint Source Management Programs or to implement them directly. The main incentive for states to comply with section 319 is eligibility for an EPA grant program that offers financial assistance, technical assistance, training, and technology transfer to control nonpoint source pollution. To qualify for the grant program, states must make “satisfactory progress” in controlling nonpoint source pollution, as determined by EPA. It gives states broad discretion on the approach. Some states, such as California, have implemented a command-and-control approach to addressing nonpoint source pollution under section 319, and these have generally proven to be fairly effective. Other states have focused more on ever-popular voluntary measures, such as agricultural practices cost share, with varying results.

Because it has been politically impossible to amend the Clean Water Act to give it additional “teeth” to address nonpoint source pollution directly, EPA/ACE and advocacy groups have at times attempted to do so indirectly. For example, a broad definition of “navigable waters” has been used to capture some nonpoint source discharges. Courts have largely played along, perhaps recognizing the many environmental benefits that result from this imperfect, and arguably overreaching, approach. Most recently, the U.S. Supreme Court held in County of Maui that nonpoint sources can constitute the “functional equivalent” of a point source, and therefore be subject to NPDES permitting requirements.

A Political Question

The jurisdictional scope of the Clean Water Act has been a subject of uncertainty and debate since passage of the Act 50 years ago. While a detailed commentary on the “waters of the United States” definition is beyond the scope of this article, we briefly summarize the issue here as it relates to nonpoint source pollution.

Like the Rivers and Harbors Act of 1899 and its progeny, the Clean Water Act governs “navigable waters,” which, by spectacularly circular drafting, are defined as “waters of the United States.” In 1975, ACE issued interim final regulations defining “the waters of the United States” to include not only navigable-in-fact waters but also tributaries of such waters, all freshwater wetlands adjacent to navigable waters, all interstate waters and their tributaries regardless of navigability, and non-navigable intrastate waters if their use could affect interstate commerce. This definition was tested by a series of U.S. Supreme Court cases and refined through subsequent rulemakings. Notable developments include United States v. Riverside Bayview Homes, Inc., 474 U.S. 121 (1985) (upholding the 1975 ACE definition of “waters of the United States”); the Migratory Bird Rule promulgated by EPA and ACE in 1986, 51 Fed. Reg. 41,217 (Nov. 13, 1986) (defining “navigable waters” to also include isolated intrastate waters that provide habitat for migratory birds that travel across state or international borders); Solid Waste Agency of N. Cook Cnty. v. U.S. Army Corps of Engineers, 531 U.S. 159 (2001) (vacating the Migratory Bird Rule definition and holding that a wetland is a “water of the United States” only if there is a “significant nexus” between it and navigable-in-fact waters); Rapanos v. United States, 547 U.S. 715 (2006) (with a plurality decision that “navigable waters” include only “relatively permanent,” standing or flowing bodies of water, and not “intermittent” or “ephemeral” flows of water, and a concurring opinion that would have upheld that “significant nexus” test); and an EPA/ACE legal “guidance memorandum” to agency staff that attempted to marry aspects of the various U.S. Supreme Court opinions. EPA, Clean Water Act Jurisdiction Following the U.S. Supreme Court’s Decision in Rapanos v. United States & Carabell v. United States (2008).

The definition of “waters of the United States” is now squarely a political question. The Obama administration’s EPA advanced a broad definition in the Clean Water Rule, 80 Fed. Reg. 37,054 (June 29, 2015), with ensuing litigation brought by mostly states and the agricultural lobby. The Trump administration’s EPA significantly narrowed the definition through the Navigable Waters Protection Rule, 85 Fed. Reg. 22,250 (Apr. 21, 2020), with ensuing litigation brought mostly by environmental groups, as well as some farming and ranching groups, which argued that, while narrower, the definition was still overbroad. Most recently, the Biden administration’s EPA issued a proposed rule to re-broaden “waters of the United States,” reinstating the Obama-era definition. 86 Fed. Reg. 69,377 (Dec. 7, 2021). Over 100,000 public comments were filed, and no doubt, the next wave of litigation will soon be underway.

We trace this chronology to make a broader point: If the Clean Water Act contained an effective mechanism for controlling the nonpoint solution, the definition of “waters of the United States” would not matter so much. Over the past 50 years, research has shown that, like surface and groundwater, interstate and intrastate waters are hydrologically connected. This is not to say that all waterbodies should be held to the same water quality standards, or that all sources of pollution should be regulated in the same way. But the outdated notion that some waterbodies are relevant to interstate commerce and some are not has been disproven by science. It is a matter of degree.

Today, the debate over the definition of “waters of the United States” is in some ways a proxy fight for the more politically sensitive question of what, if anything, to do about agricultural runoff, irrigation return flows, and other nonpoint sources of water pollution. Congress has mostly sidestepped this issue, leaving executive branch agencies in the difficult position of trying to craft and defend definitions that inevitably are not durable, and leaving the courts to evaluate geohydrological data and reverse-engineer legal opinions in order to make policy.

The County of Maui is a prime example of judicial policy making in the face of congressional abdication. The case centered on injection of treated wastewater into underground wells at the Lahaina Wastewater Reclamation Facility. The effluent traveled one-half of a mile through groundwater before discharging to the Pacific Ocean. The majority opinion, authored by Justice Breyer, centered on the meaning of the word “from” in the Clean Water Act’s provision requiring an NPDES permit for “any addition of any pollutant to navigable waters from any point source.” The Court found that the pollutants in the effluent came “from” the Lahaina facility even though they traveled through groundwater before reaching the ocean, and as such, were the “functional equivalent” of a point source, and therefore must be regulated by EPA under the NPDES program. While a major win for environmental quality, County of Maui’s vague “functional equivalent” standard, to be implemented on a case-by-case basis, offers little clarity to regulators or the public.

Where There’s a Will, There’s a Way

A real conversation is needed about what to do about nonpoint source pollution: What to do about rising drinking water treatment costs in states such as Iowa, where surface waters are so heavily contaminated with nitrites and nitrates from fertilizer runoff that advanced drinking water treatment technologies are needed. See Bd. of Water Works Trs. of City of Des Moines v. Sac Cnty. Bd. of Supervisors, No. C15-4020-LTS, 2017 WL 1042072 (N.D. Iowa Mar. 17, 2017). What to do about the quality of water in private wells in rural America, which are not subject to federal oversight and in many counties are not tested at all. What to do about Gulf of Mexico hypoxia. Let’s celebrate all that the Clean Water Act has accomplished and turn our attention to the next 50 years and all the work that remains to be done to address nonpoint source pollution in the United States. See, e.g., Robin Rotman et al., Realigning the Clean Water Act: Comprehensive Treatment of Nonpoint Source Pollution, 48 Ecology L.Q. 101 (2021).

The appropriate place for this conversation is Congress, not the executive agencies and not the courts. It may well be that Congress keeps doing exactly what it has been doing on nonpoint source pollution, continuing to eschew binding regulations, instead focusing on financial incentives for voluntary programs. We hope not. But at least the issue will be addressed head on and the American public will be able to hold the decision-makers accountable through the political process.