Section 404 requires a permit before discharging dredged or fill material into waters of the United States, including many wetlands, and the threshold jurisdictional determination — whether the specific area even qualifies as a covered water — is typically the most litigated question in a 404 dispute. The Supreme Court's decision in Sackett v. EPA narrowed federal wetlands jurisdiction to areas with a relatively permanent, continuous surface water connection to a traditional navigable water, sharply reducing the category of wetlands subject to federal permitting compared to prior agency practice.

Once jurisdiction is established, applicants proceed either through an individual permit, which involves a project-specific public interest review, or a faster nationwide or general permit for activities the Corps has pre-determined to have minimal impact, and disputes frequently arise over which pathway applies and whether an activity truly fits within a general permit's conditions. Compensatory mitigation — commonly through purchasing credits from an approved wetland mitigation bank — is a routine permit condition and its required ratio relative to filled acreage is a frequent point of negotiation and dispute.

Because the jurisdictional threshold question can eliminate the need for a permit entirely, its resolution often drives the practical value of the entire dispute more than the downstream mitigation terms. A Juricratic simulation can model jurisdictional-determination confidence separately from mitigation-cost exposure, letting a developer or challenger rehearse how each stage of the analysis shapes overall project risk.

Section 404 disputes typically arise when a developer seeks a jurisdictional determination or permit for a fill activity and either the Corps denies the permit, an advocacy group challenges an issued permit as inadequately protective, or a landowner contests the threshold finding that its property contains a federally jurisdictional wetland at all.