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The Army Lawyer


Creek on a Leash


A Primer on the Clean Water Act’s Section 404

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(Credit: istockphoto.com/batuhan toker)

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You are the Chief of Administrative Law at Fort Blackacre, an expansive installation located thirty miles from the Mississippi River. In recent years Fort Blackacre has undergone a series of major construction projects in an effort to modernize the installation and restore it as one of the preeminent military training sites in the United States. Although you are new to the installation, you are aware of the modernization initiatives and look forward to making your own contributions to its success.

One morning you are summoned to the garrison commander’s office. She excitedly informs you that funding has finally been approved for the construction of a large artillery range on the outer limits of the base. “This project is the final piece we need to accomplish our modernization mission,” she explains as she unfolds a large map of the installation on a table and shows you the proposed site. It appears to consist mostly of undeveloped wetlands that directly abut a large creek, which flows continuously off the installation and eventually empties into the Mississippi River. When you ask whether the wetlands will present an obstacle to the development and use of the range, the commander assures you that plans are already in place to make it a viable training environment. “We will obviously have to fill in areas of the site that are extremely saturated, but there shouldn’t be any major barriers we cannot overcome. So, Judge, any initial legal issues I should be considering?”

Actions arising under Section 404 of the Clean Water Act are likely unfamiliar to many judge advocates. However, as many installation projects may implicate Section 404, and violations can carry severe civil and criminal penalties, it is important that judge advocates have at least a working knowledge of the program in order to proactively identify and mitigate potential issues. This article is intended to facilitate that level of understanding. As such, it does not discuss every aspect of the Section 404 program, but rather provides a primer that will help judge advocates properly spot Section 404 issues, render appropriate counsel to commanders, and understand which personnel from other agencies can be contacted for assistance. The remainder of this article provides an overview of the statutory and regulatory framework associated with the Section 404 program, with a particular emphasis on the long-disputed issue of which waters constitute “waters of the United States”; discusses Section 404 permits and the permitting process; and illustrates the issues the Administrative Law Chief should be considering in the Fort Blackacre scenario.1

Legal Framework


The Federal Water Pollution Control Act (FWPCA), more commonly known as the Clean Water Act2 (CWA or Act) after the 1972 amendments, is a landmark piece of environmental legislation, the objective of which is to “restore and maintain the chemical, physical, and biological integrity of the Nation’s waters.”3 The CWA seeks to accomplish this by generally prohibiting “the discharge of any pollutant by any person”4 unless the discharger “obtain[s] a permit and compl[ies] with its terms.”5 A “discharge of a pollutant” occurs when a person adds “any pollutant to navigable waters from any point source.”6 “Navigable waters” are defined simply as “waters of the United States.”7 Thus, there are four criteria required to invoke CWA jurisdiction—(i) a discharge; (ii) of a pollutant; (iii) from a point source; (iv) into waters of the United States—and each will be examined as they relate to Section 404.

The Act established two permitting regimes to effectuate its objective—Section 402, which created the National Discharge Pollutant Elimination System (NPDES) for the regulation of most pollutants, and Section 404 for the regulation of dredged and fill material. The former is administered by the Environmental Protection Agency (EPA), the latter generally by the Secretary of the Army acting through U.S. Army Corps of Engineers (Corps) (together, Agencies) with oversight by the EPA. The Army’s mandate to administer the Section 404 program stems from the Corps’ longstanding mission to protect and maintain the navigability of the Nation’s waterways beginning, in large part, with the Rivers and Harbors Act of 1899 (RHA). Although most of the RHA focused on restricting obstructions to navigation, Section 13 makes it unlawful to discharge any refuse into any navigable water of the United States, or tributary thereof, without a permit from the Secretary of the Army.8 Thus, by authorizing the Corps to administer Section 404, Congress was able to leverage the Corps’ experience with a similar permitting regime while also ensuring that the Corps’ RHA authority would not be usurped by the expansive NPDES program.9

A “discharge of a pollutant” is defined to include “any addition of any pollutant to navigable waters from any point source.”10 The term pollutant is broadly construed under the CWA; however, most relevant to Section 404 is the CWA’s coverage of dredged and fill materials. Dredged material under Section 404 is material that is dredged or excavated from waters of the United States and then reintroduced to a jurisdictional water.11 Fill material is material introduced to a jurisdictional water that has the effect of replacing any portion of the water with dry land or changing the bottom elevation of the water.12 The term “point source” is also broadly construed and encompasses nearly any medium through which pollutants are or may be discharged.13 Simply put, anytime one takes any action that would add any dredged or foreign material to a body of water, they should consider whether they are conducting a jurisdictional act under Section 404.

Waters of the United States

The current definition of “waters of the United States” (i.e., which waters are subject to CWA jurisdiction) is the product of decades of evolution and influence from all three branches of the federal government. In order to understand where we are now, it is important to understand how and why we got here. Congress’ authority to regulate navigable waters stems from its authority to regulate interstate commerce pursuant to the Commerce Clause.14 Early statutes regulating waterways, such as the RHA, used this hook by limiting the extent of its jurisdiction to “navigable water[s] of the United States.”15 The Supreme Court initially construed this term as being limited to waters that are “navigable in fact” meaning that “they are used, or are susceptible of being used, in their ordinary condition, as highways of commerce, over which trade and travel are or may be conducted in the customary modes of trade and travel on water.”16

In 1972, with passage of the CWA amendments, Congress instituted a new definition of “navigable waters”—“waters of the United States.” The first Corps regulations defining this term sought to equate “waters of the United States” with prior interpretations of navigable waters under preexisting statutes such as the RHA.17 However, in Natural Resources Defense Council v. Callaway, the U.S. District Court for the District of Columbia struck down the Corps’ definition, holding that “navigable waters,” as used in the CWA, is not limited to the traditional tests of navigability.18 In 1986, after a number of legislative and rulemaking efforts, the Corps and EPA ultimately settled on a common definition of “waters of the United States” which, in addition to traditionally navigable waters and the territorial seas, included: interstate waters, intrastate waters that do or could affect interstate commerce, impoundments of jurisdictional waters, tributaries of jurisdictional waters, and wetlands adjacent to jurisdictional waters (that are not themselves wetlands).19

Three key Supreme Court decisions also informed the Agencies’ interpretation of “waters of the United States.” In United States v. Riverside Bayview Homes, the Court deferred to the Corps’ assertion of jurisdiction over wetlands adjacent to “waters of the United States” because such wetlands are “inseparably bound up” with the adjacent waters and may have “significant effects on water quality and the aquatic ecosystem.”20 In Solid Waste Agency of Northern Cook County v. U.S. Army Corps of Engineers, the Corps was challenged on its claim of jurisdiction over any water that was used or may be used by migratory birds crossing state lines.21 The Court held that federal jurisdiction could not be extended to nonnavigable, isolated waters that lack a sufficient connection to a jurisdictional water on the basis of the Corps’ Migratory Bird Rule.22 Finally, in Rapanos v. United States, the Court further considered the degree to which a wetland may be attenuated from a navigable water while remaining jurisdictional under the CWA.23 The case failed to produce a majority decision and yielded two competing approaches set out in Justice Scalia’s plurality opinion and Justice Kennedy’s concurrence. Under Justice Scalia’s test, jurisdictional wetlands require a “continuous surface connection” to a jurisdictional water so that there is “no clear demarcation between waters and wetlands.”24 Justice Kennedy, however, indicated the critical factor in determining jurisdiction is whether a water has a “significant nexus” to traditionally navigable waters such that it significantly affects the chemical, physical, and biological integrity of the downstream navigable water.25

In 2015, the Agencies promulgated a final rule, setting forth a revised definition of “waters of the United States” (2015 Rule).26 Utilizing Justice Kennedy’s significant nexus standard as informed by the Rapanos plurality and previous Supreme Court precedent, the 2015 Rule grouped waters into three categories: (i) waters that are jurisdictional per se, (ii) waters that are excluded from jurisdiction, and (iii) waters subject to case-specific analysis to determine whether they are jurisdictional.27 The 2015 Rule has been mired in litigation since its promulgation and, due to various injunctions, has never been implemented in all fifty states. As of this article’s publication, the 2015 Rule is in effect in twenty-two states, the District of Columbia, and the territories of the United States. Therefore, one must determine whether the 2015 Rule or pre-2015 regulatory regime applies based on the jurisdiction in which the proposed activity will take place.

On 28 February 2017, the President of the United States issued an Executive Order directing the Agencies to review the 2015 Rule and issue for notice and comment a proposed rule rescinding or revising the 2015 Rule.28 Consistent with the Executive Order, in July 2017, the Agencies issued a proposed rule, which, if finalized, would repeal the 2015 Rule.29 In July 2018, the Agencies issued a Supplemental Notice of Proposed Rulemaking to clarify that, in addition to proposing the permanent repeal of the 2015 Rule, the proposed rule would also recodify the pre-2015 regulations.30 As of this article’s publication, this proposed rule has not been finalized. On 14 February 2019, the Agencies issued a separate proposed rule that would revise the definition of “waters of the United States.”31 The public comment period for this rule closed on 15 April 2019.

Section 404 Permitting

Activities that result in the addition of dredged or fill material to a jurisdictional water generally require a Section 404 permit. Section 404 and its corresponding regulations provide for multiple permit types as well as certain limited instances in which a permit is not required. This section discusses the mechanics of determining whether a water is jurisdictional and, if so, the types of permit that may be required as well as the criteria for issuing such permits.

Having determined which waters are subject to Section 404, the question remains, “what steps should be taken if one believes a water is jurisdictional?” Whether a piece of property contains “waters of the United States” is often not a simple inquiry. Although certain waters may clearly be jurisdictional (e.g., the Mississippi River), other waters due to their attenuation from a traditionally navigable water (such as the wetlands at Fort Blackacre) may be less obvious. To aid in this inquiry the Corps offers “jurisdictional determinations” (JDs) which are written documents that indicate the presence or absence of “waters of the United States” on a given piece of property.32 Jurisdictional determinations may be either “preliminary” (PJD) or “approved” (AJD). Preliminary jurisdictional determinations are non-binding and merely advise “that there may be ‘waters of the United States’ on a parcel” whereas AJDs “definitively state the presence or absence of such waters” and constitute final agency action appealable under the Administrative Procedure Act.33 Upon confirming the existence of “waters of the United States” on a parcel, the applicant needs to consider, in collaboration with the Corps, which type of permit is required.

Section 404 provides for the issuance of two categories of permits—individual and general. Individual permits are issued on a case-by-case basis and all authorizations and conditions are tailored to the specific project for which the permit is granted. As such, individual permits require a comprehensive application process which includes, among other requirements, detailed project plans and drawings, a public interest review, consideration of the 404(b)(1) guidelines,34 and compliance with numerous other federal and state requirements including, the National Environmental Policy Act, Endangered Species Act, and National Historic Preservation Act. General permits are intended to reduce the administrative burdens on the Corps and regulated public for projects with minimal environmental impacts and thus offer applicants a more expedient and cost-effective alternative to individual permits.35 These permits are issued on a nationwide, regional, or state basis for certain categories of activities that have been determined to be similar in nature and will cause only minimal adverse environmental effects.36 In other words, the Corps effectively satisfies the requirements of an individual permit for an entire category of projects when it issues a nationwide permit, thereby eliminating such requirements for individual applicants.37 The effect of this is that parties are permitted to conduct the sort of activity described by the permit without needing to seek project-specific authorization (provided they comply with the conditions of the general permit).38 General permits are statutorily limited to a duration of five years.39

Notwithstanding the foregoing, the CWA provides for limited circumstances in which a permit is not required for the discharge of dredged or fill material. Section 404(f) carves out certain activities, such as normal farming, silviculture, and ranching activities, which are exempt from Section 404’s permit requirements.40 Additionally, Section 404(r) exempts certain federal projects from regulation. To qualify under Section 404(r) a project must (i) be specifically authorized by Congress, and (ii) a proper environmental impact statement is submitted to Congress prior to the actual discharge of dredged or fill material and prior to any authorizations or appropriations for such project.41

Pulling It All Together

Let’s return now to Fort Blackacre and our Chief of Administrative Law. Upon being presented with the commander’s plan for construction of the range, two primary questions need to be analyzed to determine whether a Section 404 permit is required—(i) is there a jurisdictional act (i.e., will there be a discharge of dredged or fill material) and, if so, (ii) is the discharge into a jurisdictional area (i.e., a water of the United States). The answer to the former is almost certainly yes as the commander explicitly stated that they would need to fill areas of the wetlands, which would inevitably require the addition of dredged or fill material to the site. The latter requires application of the waters of the United States criteria to determine whether the wetlands on the proposed site are jurisdictional under the CWA. Regardless of which definition of “waters of the United States” is being implemented in Fort Blackacre’s jurisdiction, the wetlands here would likely be jurisdictional. Since the Mississippi River is jurisdictional by virtue of it being a traditionally navigable water, all of the tributaries that flow into it (with sufficiently regular flow) are also jurisdictional. Assuming the creek flows with sufficient regularity, it would constitute a jurisdictional tributary because it contributes flow directly into a traditionally navigable water. This, in turn, makes Fort Blackacre’s wetlands jurisdictional because they directly abut the jurisdictional tributary.

At this point, there are enough red flags that the Chief should advise the commander that they likely have obligations pursuant to Section 404 that need to be resolved before construction can begin. She should make contact with her local Corps district office, which will be able to further assist her in assessing whether a jurisdictional determination should be obtained, and whether any additional wetland delineation is required. The Corps will also assist in determining whether the project qualifies for a general permit, or if the project will have impacts sufficient to require an individual permit application. The project likely does not qualify for any of Section 404’s permit exemptions. It does not meet the standard for any of the Section 404(f) carve outs, nor would it satisfy Section 404(r) unless the project was specifically authorized by Congress and an environmental impact statement was submitted to Congress prior to any authorization or appropriation.


Although complex in practice, Section 404 offers military practitioners the opportunity to add substantial value to their command with even a basic understanding of its structure and application. TAL


CPT Menard is currently assigned as assistant to the general counsel, Headquarters, Department of the Army. The views expressed in this article are his own and do not necessarily reflect those of any other individual, organization, or the United States government.


1. To be sure, much of the process and analysis required by Section 404 is highly technically and will be conducted with substantial assistance from legal and regulatory experts from the U.S. Army Corps of Engineers, U.S. Environmental Protection Agency (EPA), and other organizations. That said, it is important that judge advocates are able to issue spot at a basic level so as to be able to raise issues as they arise and remain engaged throughout the process.

2. 33 U.S.C. § 1251 et seq. (1972).

3. Id. § 1251(a).

4. Id. § 1311(a).

5. Middlesex Cty. Sewerage Auth. v. Nat’l Sea Clammers Ass’n, 453 U.S. 1, 11 (1981) (citation omitted).

6. 33 U.S.C. § 1362(12).

7. Id. § 1362(7).

8. 33 U.S.C. § 407.

9. Section 402 authorizes the Administrator of the EPA to issue permits for the discharge of “any pollutant, or combination of pollutants” subject to two exceptions, one of which is Section 404. See 33 U.S.C. § 1342(a). For additional discussion on this topic see Michael C. Blumm, The Clean Water Act’s Section 404 Permit Program Enters Its Adolescence: An Institutional and Programmatic Perspective, 8 Ecology L. Q. 409, 414-16 (1980).

10. 33 U.S.C. § 1362(12), (14).

11. See 33 C.F.R. § 323.2(c).

12. See 33 C.F.R. § 323.2(e) (noting examples such as rock, sand, soil, clay, plastics, construction debris, wood chips, overburden from mining or other excavation activities, and materials used to create any structure or infrastructure in the waters of the United States but not including trash or garbage).

13. See 33 U.S.C. § 1362(14) (“The term ‘point source’ means any discernible, confined and discrete conveyance, including but not limited to any pipe, ditch, channel, tunnel, conduit, well, discrete fissure, container, rolling stock, concentrated animal feeding operation, or vessel or other floating craft, from which pollutants are or may be discharged. This term does not include agricultural stormwater discharges and return flows from irrigated agriculture.”).

14. See, e.g., Gibbons v. Ogden, 22 U.S. (9 Wheat.) 1 (1824); see also The Daniel Ball, 77 U.S. 557, 563 (1870) (construing the term “navigable waters,” as employed in federal statutes at issue, as covering those waters that 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”).

15. See 33 U.S.C. § 401 (“It shall not be lawful to construct or commence the construction of any bridge, causeway, dam, or dike over or in any . . . navigable water of the United States until the consent of Congress shall have been obtained . . . .”).

16. The Daniel Ball, 77 U.S. 557, 563 (1870). The Court subsequently expanded this definition to include waters that had been used in the past for interstate commerce, see Economy Light & Power Co. v. United States, 256 U.S. 113, 123 (1921), and waters that are susceptible for use with reasonable improvement, see United States v. Appalachian Elec. Power Co., 311 U.S. 377, 407-10 (1940).

17. 33 C.F.R §209.12(d)(1) (1974) (“The term “navigable waters of the United States” and “navigable waters,” as used herein mean those waters of the United States which are subject to the ebb and flow of the tide, and/or are presently, or have been in the past, or may be in the future susceptible for use for purposes of interstate or foreign commerce . . . .”). The Corps explained that it believed this interpretation was “limited to that which is Constitutionally permissible” and “soundly based on . . . the judicial precedents which have reinforced it.” Permits for Activities in Navigable Waters or Ocean Waters, 39 Fed. Reg. 12,115 (Apr. 3, 1974).

18. National Resources Defense Council, Inc. v. Callaway, 392 F. Supp. 685, 686 (D.D.C. 1975).

19. See 51 Fed. Reg. 41,206 (Nov. 13, 1986).

20. United States v. Riverside Bayview Homes, 474 U.S. 121, 131-35, n.9 (1985).

21. 531 U.S. 159 (2001). The Court of Appeals for the Seventh Circuit found that migratory birds provided a sufficient jurisdictional hook under the cumulative impact doctrine of the Commerce Clause because “each year millions of Americans cross state lines and spend over a billion dollars to hunt and observe migratory birds.” Solid Waste Agency of Northern Cook County v. U.S. Army Corps of Engineers, 191 F.3d 845, 580 (7th Cir. 1999).

22. 531 U.S. at 174. For the Migratory Bird Rule see 51 Fed. Reg. 41,217 (1986).

23. 547 U.S. 715 (2006).

24. Id. at 742 (internal quotations omitted).

25. Id. at 759, 780.

26. See 80 Fed. Reg. 37,054 (Jun. 29, 2015).

27. See id. at 37,057. For a complete list of waters that are jurisdictional under the 2015 Rule see 33 C.F.R. § 328.3.

28. Exec. Order No. 13,778, 82 Fed. Reg. 12,497 (Feb. 28, 2017).

29. Definition of Waters of the United States−Recodification of Pre-Existing Rules. 82 Fed. Reg. 34,899 (July 27, 2017).

30. 83 Fed. Reg. 32,227 (July 12, 2018).

31. Revised Definition of Waters of the United States. 84 Fed. Reg. 4,154 (Feb. 14, 2019).

32. 33 C.F.R. § 331.2 (2018).

33. Id.; see also United States Army Corps of Engineers v. Hawkes Co., Inc., 136 S.Ct. 1807, 1812 (2016).

34. The 404(b)(1) guidelines provide the standards by which Section 404 permit applications are evaluated. At bottom, “no discharge of dredged or fill material shall be permitted if there is a practicable alternative to the proposed discharge which would have less adverse impact on the aquatic ecosystem, so long as the alternative does not have other significant adverse environmental consequences.” 40 C.F.R. § 230.10(a).

35. See 33 U.S.C. § 1344(e). “The average applicant for an individual permit spends 788 days and $271,596 in completing the process, and the average applicant for a nationwide permit spends 313 days and $28,915—not counting costs of mitigation or design changes.” Rapanos, 547 U.S. at 720.

36. 33 U.S.C. § 1344(e). See also Issuance and Reissuance of Nationwide Permits, 82 Reg. 1,860 (Jan. 6, 2017) (Issuing 52 Corps-approved nationwide permits and conditions on such permits. For example, Nationwide Permit 12 authorizes discharges associated with the construction, maintenance, repair, and removal of utility lines provided certain conditions are met.).

37. See 82 Fed. Reg. 1,860.

38. See Keating v. Federal Energy Regulatory Commission, 927, F.2d 616, 619 (D.C. Cir. 1991).

39. 33 U.S.C. § 1344(e).

40. 33 U.S.C. § 1344(f).

41. 33 U.S.C. § 1344(r); see also Delaware Dept. of Natural Resources and Environmental Control v. U.S. Army Corps of Engineers, 685 F.3d 259, 280-81 (3rd Cir. 2012).