Dredged Material Laws: Permits, Testing, and Disposal Sites

Dredging in U.S. waters requires a federal permit from the U.S. Army Corps of Engineers, and in most cases a state water quality certification as well. The specific dredging permit requirements depend on where the work happens, what’s in the sediment, and where the material will go. Civil penalties for unauthorized dredging currently run up to $68,446 per day, so getting the authorizations right before any equipment enters the water is not optional.

Which Federal Permits You Need

Three federal statutes control dredging, and a single project can trigger more than one of them.

Section 404 of the Clean Water Act is the one most applicants deal with. It requires an Army Corps permit before anyone discharges dredged or fill material into waters of the United States, including wetlands. The Corps issues the permit after public notice and can attach conditions to protect water quality and aquatic ecosystems.¹

Section 103 of the Marine Protection, Research, and Sanctuaries Act applies when dredged material will be transported for disposal in ocean waters. The Corps still issues the permit, but only after finding that the dumping will not unreasonably harm human health, marine ecosystems, or economic resources. The EPA has 45 days after receiving complete information to concur, add conditions, or block the permit. If the EPA declines to concur, no permit issues.²

Section 10 of the Rivers and Harbors Act covers work performed in, over, or under navigable waters that could affect the waterway’s course, condition, or capacity. Dredging is specifically listed.³ Many projects need both Section 10 and Section 404 authorization; the Corps typically processes them together on a single application.

State and Interagency Reviews You Also Need

Federal permits are not the only step. Several parallel reviews can add conditions to your permit or stop it entirely.

Section 401 Water Quality Certification

Before the Corps can issue a permit involving any discharge into U.S. waters, you must obtain a Section 401 certification from the state (or authorized tribe) where the discharge originates. This confirms the project won’t violate state water quality standards. States have up to one year to act; failure to act within that window is treated as a waiver. If the state denies certification, the federal permit cannot issue.⁴ Fees vary significantly by state.

Endangered Species Act Consultation

The Corps must evaluate whether a project could affect federally listed threatened or endangered species. Projects that may affect a species but are unlikely to cause harm trigger informal consultation with the U.S. Fish and Wildlife Service or the National Marine Fisheries Service. Where harm is likely, formal consultation produces a Biological Opinion specifying allowable impact and required mitigation, and those measures become enforceable permit terms.⁵

Historic Preservation Review

Dredging can disturb shipwrecks, submerged structures, and archaeological sites. Section 106 of the National Historic Preservation Act requires the Corps to assess whether a permitted activity could affect properties listed in or eligible for the National Register of Historic Places. No activity that may affect historic properties can be authorized until the review is complete.⁶

General Permits vs. Individual Permits

The Corps uses two broad permit tracks, and which one applies drives your timeline and paperwork.

General permits cover categories of activities the Corps has already determined will cause only minimal environmental impact. They come as nationwide permits, regional general permits, and programmatic general permits. For dredging, Nationwide Permit 35 is often the relevant one; it covers maintenance dredging of existing basins. Qualifying projects can often be verified in weeks.⁷

Projects that exceed any general permit’s thresholds, or that have more than minimal individual or cumulative impact, require an individual permit. That means case-by-case evaluation, a full public interest review, and interagency consultation. A letter of permission is a streamlined subtype used for minor projects where the Corps decides public notice isn’t required.⁷

Sediment Testing Before You Apply

The Corps will not evaluate a permit application without knowing what’s in the sediment. Testing determines where the material can go and how it must be handled.

Grain size analysis classifies sediment as silt, sand, clay, or a mixture. Chemical analysis identifies contaminants such as heavy metals, pesticides, and petroleum compounds. Material headed for ocean placement is evaluated under the Ocean Testing Manual (the Green Book); river and lake projects follow the Inland Testing Manual. Both manuals set standardized sampling methods and toxicity thresholds that determine whether material is suitable for open-water placement or must go to a contained facility.

Testing is a significant expense. Basic chemical screening runs from a few hundred to several thousand dollars per sample. Specialized biological tests, such as whole-sediment toxicity testing for marine invertebrates or long-term bioaccumulation studies, can cost tens of thousands of dollars per test. Budget for testing early, because the results dictate every downstream decision.

What Goes Into the Application

The application form is ENG Form 4345, available on local Corps district office websites. The form itself is a cover sheet asking for the proposed activity, project purpose, and location.⁸ The substance is in the attachments.

At minimum, plan to submit:

A project footprint map with bathymetric data and marked sample collection points
Complete laboratory sediment analysis under the applicable testing manual
Volume calculations covering proposed acreage, depths, and cubic yards of material
A disposal plan describing where the material will go and how it will be managed on site

Fees are modest compared with the rest of the project. Non-commercial projects that provide only personal benefits carry a $10 processing fee.⁹ Commercial applications carry a separate, higher fee. Neither fee covers sediment testing, environmental surveys, or consultant work.

How Long Review Takes

Once the Corps has a complete application, it issues a public notice within 15 days inviting comments from agencies, adjacent property owners, and the public.¹⁰ The EPA reviews Clean Water Act compliance and the acceptability of the disposal method and location. The state runs its Section 401 review at the same time. Endangered species consultations proceed in parallel where applicable.

The regulatory target for individual permits is 120 days, but that is aspirational. Most individual permits take six to twelve months, and complex projects run longer. The most common causes of delay are incomplete applications, project modifications, endangered species consultations, cultural resource surveys, and substantial public opposition. Submitting a genuinely complete package, with all testing results, is the single most effective way to shorten the wait.

How Long the Permit Lasts

Dredging permits expire, and the rules depend on the work authorized. Construction-type dredging permits specify a completion deadline and may require work to begin within one year of issuance. Ocean disposal permits are capped at three years. Maintenance dredging permits can be authorized for up to ten years, though the holder must notify the Corps before each episode of work.¹¹

Extensions are available but must be requested before the permit expires. Let it lapse and you’ll apply for a new permit from scratch. The district engineer grants extensions unless doing so would be contrary to the public interest. For maintenance permits nearing the ten-year cap, the Corps recommends applying for a new permit at least six months before expiration.¹¹

Where the Dredged Material Can Go

Clean sediment is a resource. When testing confirms the material is free of harmful contamination, it can be used for beach nourishment, shoreline rebuilding, wetland restoration, upland habitat development, levee construction, or fill for development sites.¹² Both the Corps and the EPA favor beneficial reuse when material quality supports it, so including a reuse plan can strengthen an application.

Material headed for open water qualifies only if sediment toxicity and bioaccumulation testing show it won’t harm aquatic organisms at the disposal site. Fail those tests and open-water placement is off the table.

Contaminated material that can’t go to open water is placed in a Confined Disposal Facility, an engineered structure (often a diked enclosure) designed to isolate sediment from the surrounding environment. Water quality monitoring at the discharge point runs during dredging, and disposal stops if effluent quality approaches regulatory limits.¹³

After the Work Is Done

The permit’s obligations don’t end when the equipment leaves. Permit holders submit a Self-Certification Statement of Compliance to the issuing district office, listing the permit number, start and completion dates, work performed, acreage impacted, any mitigation completed, and any deviations from the authorized plan. Deviations require drawings showing what changed. The permit holder signs certifying that all work and mitigation complied with the permit.¹⁴

Penalties for Dredging Without a Permit

Dredging without authorization or violating permit conditions carries steep consequences. The Section 404 statutory civil penalty is up to $25,000 per day for each violation.¹ After inflation adjustments, that figure now stands at up to $68,446 per day. Administrative penalties (assessed by the EPA without going to court) can reach $27,379 per violation, capped at $68,446 per enforcement action.¹⁵

Criminal penalties are heavier. Negligent violations start at $2,500 per day and one year of imprisonment; knowing violations can reach $50,000 per day and three years, doubling to $100,000 per day and six years for repeat offenders.¹⁶ Beyond fines, the EPA can order a violator to stop unauthorized activity and restore the site to its prior condition.¹⁷

If Your Permit Is Denied

A denial can be appealed to the division engineer above the district office that issued the decision. You have 60 days from the date of the Notice of Appealable Action to file a Request for Appeal, and the request must give specific reasons; generic disagreement won’t be accepted. Once the division office accepts the request, an appeal conference is scheduled within 60 days (unless both sides waive it), and the division engineer normally issues a final decision within 90 days of receiving the appeal.¹⁸

One boundary matters: no work can begin in waters of the United States while an appeal is pending. If you’ve already started work or altered the hydrology of the waterway, you lose the right to appeal.¹⁸

1
Office of the Law Revision Counsel. 33 USC 1344 – Permits for Dredged or Fill Material
2
Office of the Law Revision Counsel. 33 USC 1413 – Dumping Permit Program for Dredged Material
3
U.S. Army Corps of Engineers. What Is the Regulatory Program
4
U.S. Environmental Protection Agency. Overview of CWA Section 401 Certification
5
U.S. Army Corps of Engineers Sacramento District. Endangered Species Agency Consultations
6
Federal Register. Processing of Department of the Army Permits – Procedures for the Protection of Historic Properties
7
U.S. Army Corps of Engineers Mobile District. Permit Types
8
U.S. Army Corps of Engineers. ENG Form 4345 – Application for Department of the Army Permit
9
eCFR. 33 CFR 325.1 – Applications for Permits
10
U.S. Army Corps of Engineers. Permitting Process Information
11
eCFR. 33 CFR 325.6 – Duration of Permits
12
U.S. Environmental Protection Agency. Beneficial Uses of Dredged Materials Fact Sheet – Project Partners and Decision Makers
13
U.S. Army Corps of Engineers. Great Lakes Confined Disposal Facilities
14
U.S. Army Corps of Engineers, Jacksonville District. Self-Certification Statement of Compliance
15
Federal Register. Civil Monetary Penalty Inflation Adjustment Rule
16
Office of the Law Revision Counsel. 33 USC 1319 – Enforcement
17
U.S. Environmental Protection Agency. Enforcement Under CWA Section 404
18
eCFR. 33 CFR Part 331 – Administrative Appeal Process