Wetlands Permitting Under the Clean Water Act

Section 404 of the Clean Water Act, codified at 33 U.S.C. 1344, requires a federal permit before discharging dredged or fill material into waters of the United States. The Army Corps of Engineers issues the permits; the Environmental Protection Agency writes the substantive environmental guidelines the Corps must apply and retains authority to prohibit or restrict a disposal site. The threshold question in nearly every case is jurisdictional — whether the feature on the property is a covered water at all — and the answer to that question changed significantly in 2023.

1.The jurisdictional question

Coverage extends to navigable waters, defined in the statute as waters of the United States. That phrase has been litigated for decades. In Sackett v. Environmental Protection Agency in 2023, the Supreme Court held that the Act extends to wetlands only where the wetland has a continuous surface connection to a relatively permanent body of water connected to traditional interstate navigable waters, such that it is difficult to determine where the water ends and the wetland begins.

That decision displaced the broader significant nexus approach that had governed many determinations. Agencies revised the regulatory definition to conform, and as of mid-2026 implementation continues to generate guidance and litigation over how the standard applies to ditches, ephemeral features, and wetlands separated by berms or roads.

Caution: A feature that falls outside federal jurisdiction is not necessarily unregulated. Many states regulate wetlands and waters under their own statutes, and several apply standards broader than the federal one. A negative federal jurisdictional determination answers one question, not all of them.

Landowners can obtain a jurisdictional determination from the Corps. An approved determination states definitively whether covered waters are present and is generally valid for a stated period; a preliminary determination assumes jurisdiction without deciding, which is faster but concedes the point. The Corps regulatory program publishes the procedures and district contacts.

2.Permit types

Not every authorization is a full individual permit, and identifying the right track early saves months.

General permits carry conditions that are easy to breach inadvertently — acreage and linear-foot limits, restrictions on work in certain aquatic resource types, and requirements to avoid particular species and historic properties. Exceeding a condition converts the project into one needing an individual permit, usually discovered mid-construction.

3.How an application proceeds

1. Delineate. A qualified consultant maps aquatic resources using the applicable federal manual and regional supplement; the Corps verifies.
2. Determine jurisdiction. Request an approved or preliminary determination, or proceed on the consultant's delineation at the applicant's risk.
3. Apply the sequence. Avoid impacts where practicable, minimize what cannot be avoided, and compensate for the remainder.
4. Choose the track. Preconstruction notification under a general permit, or a full individual permit application.
5. Coordinate parallel reviews. Endangered species consultation, historic preservation review, and state water quality certification run alongside and can control the schedule.
6. Public notice and decision. For individual permits, a public notice period, comment review, and a written decision with conditions.
7. Implement and monitor. Compliance with permit conditions, mitigation construction, and monitoring reports for a defined period.

For an individual permit the applicant must show that there is no practicable alternative with less adverse aquatic effect. For projects not water-dependent, alternatives are presumed to exist, and rebutting that presumption is a substantive burden that shapes site selection from the beginning.

Two parallel reviews deserve particular attention. State water quality certification under section 401 gives the state authority to certify, condition, or deny, and a denial blocks the federal permit. And where listed species may be affected, consultation applies — the mechanics are set out in endangered species restrictions on land use.

4.Mitigation and enforcement

Compensatory mitigation offsets unavoidable impacts, and federal rules establish a preference order: credits from an approved mitigation bank, then in-lieu fee program credits, then permittee-responsible mitigation. Banks and in-lieu programs transfer long-term responsibility to the sponsor, which is why they are preferred over a permittee's obligation to build and maintain a site itself.

Mitigation plans must address site selection, work plan, performance standards, monitoring, long-term protection through an easement or comparable instrument, adaptive management, and financial assurances. A plan without funded long-term stewardship is the most common deficiency.

• Enforcement can be pursued by the Corps or by the Environmental Protection Agency, and both civil and criminal penalties are available.
• Restoration orders requiring removal of fill and re-establishment of the resource are a routine remedy.
• The Act contains a citizen suit provision, so private parties can bring enforcement actions after notice.
• Separate consequences attach under farm program rules, where converting a wetland can affect eligibility for federal benefits.

That last point matters for agricultural landowners. Wetland conservation provisions administered with technical determinations by the Natural Resources Conservation Service operate independently of section 404: an activity may need no Corps permit and still cost a producer program eligibility. The two systems use different definitions and different maps.

Program guidance sits at the EPA section 404 pages and in the broader material at EPA, with district-level procedures published by the Corps. Where a project also involves a pipeline or transmission crossing, the acquisition questions in pipeline and utility easements and condemnation run in parallel with permitting.

5.Questions this raises

Is a permit needed to clean out an existing ditch?

Maintenance of currently serviceable drainage ditches is among the exempted activities, but the exemption is limited to restoring original dimensions and does not authorize deepening, widening, or extending. Sidecasting excavated material can itself be a discharge in some circumstances. Districts differ in how they view marginal maintenance work, so a written confirmation before starting is worth the delay.

How long is a jurisdictional determination good for?

An approved determination is generally valid for a defined period stated in the document, subject to revision if conditions or the governing legal standard change. Given how much the definition of covered waters has moved, older determinations should be treated cautiously. A preliminary determination has no such effect because it decides nothing; it simply assumes jurisdiction for processing purposes.

Can a permit decision be challenged?

Yes. Approved jurisdictional determinations are final agency actions subject to judicial review, and permit decisions can be challenged under administrative law standards by applicants and by opponents. Administrative appeal within the Corps is available first for certain decisions. Citizen suits address violations rather than permit terms, and each route has its own notice and timing requirements that are easy to miss.

Who is liable for an unpermitted discharge by a contractor?

Liability can reach the landowner, the project sponsor, and the contractor who performed the work, because the Act reaches any person who discharges. Contracts allocating responsibility do not bind the agencies. Owners should require permit compliance obligations in construction contracts, name the authorization by number, and should not assume a contractor verified anything before moving material onto the site.

6.Working order

Delineate before designing. Knowing where the aquatic resources are, and whether they are federally jurisdictional, is what allows a layout to avoid impacts — and avoidance is both the cheapest mitigation and the strongest position in an alternatives analysis.

Then check the other systems at the same time: state wetland regulation, state water quality certification, farm program wetland rules, listed species, and historic properties. These reviews run concurrently and any one of them can control the critical path.

Finally, treat conditions as permanent obligations. Track acreage and linear-foot limits against as-built quantities during construction, keep the mitigation monitoring schedule, and confirm long-term protection instruments were actually recorded. Most enforcement in this area follows drift from permitted quantities, not deliberate unpermitted work.