Regulatory Update: Navigating the Shifting Waters - The Clean Water Act and Florida’s 404 Program Challenges

Posted on March 25, 2025

The Clean Water Act (CWA), enacted in 1972, has long been a cornerstone of environmental protection in the United States, safeguarding the nation’s waterways from pollution and degradation. However, the past four years have seen seismic shifts in its interpretation and implementation, driven by Supreme Court rulings and federal regulatory changes. These developments have not only redefined the scope of federal jurisdiction but also complicated state-level efforts, such as Florida’s assumption of the Section 404 permitting program.

Supreme Court Rulings: A Four-Year Recap

The past four years have delivered a trio of pivotal Supreme Court decisions that have reshaped CWA’s reach, each with ripple effects for federal and state regulators alike.

1. Sackett v. EPA (May 25, 2023)
   The Sackett decision was a game-changer. In a 5-4 ruling, the Court narrowed the definition of “waters of the United States” (WOTUS) to include only wetlands with a continuous surface connection to traditionally navigable waters. This overturned decades of broader interpretations that protected isolated wetlands based on ecological significance or subsurface connections. The ruling forced the Environmental Protection Agency (EPA) and Army Corps of Engineers to scramble, pausing jurisdictional reviews and prompting a regulatory rethink.

2. County of Maui v. Hawaii Wildlife Fund (April 23, 2020)
   Though just outside the four-year window, this 2020 decision set the stage for later debates. In a 6-3 ruling, the Court held that the CWA applies to pollution discharges that reach navigable waters through groundwater if the discharge is the “functional equivalent” of a direct release. This expanded the Act’s scope beyond surface-level pipes, challenging regulators to address indirect pollution pathways. While not directly tied to wetlands, it underscored the Court’s willingness to grapple with the CWA’s ambiguities—foreshadowing tighter scrutiny in Sackett.

3. San Francisco v. EPA (Certiorari Granted, May 28, 2024)
   The Supreme Court’s latest CWA chapter is still unfolding. San Francisco challenged EPA permit conditions under Section 402, arguing they were vague and unenforceable. With certiorari granted in mid-2024, a ruling expected in 2025 could further refine the EPA’s regulatory authority—potentially impacting how states like Florida implement delegated programs. This case signals ongoing judicial skepticism toward broad agency discretion, a theme resonating with Sackett and Florida’s 404 struggles.

Federal Regulation Changes: A Reactive Dance

Post-Sackett, the EPA and Corps revised their WOTUS definition in late 2023, aligning it with the Court’s narrow view. Gone were the “significant nexus” test and protections for ephemeral streams or isolated wetlands lacking surface connections. This rollback, while clarifying federal jurisdiction, shifted burdens to states to fill gaps. Meanwhile, the earlier 2022 WOTUS rule, which sought to restore broader protection and leaving regulators in limbo.

On the Section 404 front, the EPA finalized sweeping revisions to tribal and state assumption regulations in December 2024. Aimed at streamlining processes, these updates clarified minimum program requirements while preserving flexibility—a response to long-standing calls from states like Florida. 

Florida’s 404 Assumption: A Bold Move Meets Rough Waters

In December 2020, Florida became the third state (after Michigan and New Jersey) to assume Section 404 permitting authority under the CWA, aiming to streamline dredge-and-fill permits for state-assumed waters. Championed as a win for efficiency—cutting overlap with federal processes—the program promised faster approvals for projects from housing developments to ecological restoration. The Florida Department of Environmental Protection (FDEP) touted its local expertise as a better fit for managing the state’s unique wetlands and waterways.

But the honeymoon was short-lived. In February 2024, a U.S. District Court in Washington, D.C., vacated the EPA’s approval of Florida’s program, citing flaws in Endangered Species Act (ESA) compliance. Environmental groups argued that the EPA’s programmatic consultation with the U.S. Fish and Wildlife Service (FWS) lacked species-specific analysis, risking harm to endangered species like the Florida panther. The court agreed, sending the permitting authority back to the Corps and sparking chaos for pending applications.

Florida and the EPA appealed to the D.C. Circuit in September 2024, defending the program’s legality. The state insists the lower court misinterpreted ESA requirements, while the EPA admitted a minor oversight in not consulting the National Marine Fisheries Service—though it claims this affects only three species in non-tidal waters outside Florida’s purview. As of March 2025, the appeal remains unresolved, leaving the program in limbo.

Challenges in the Shadow of Supreme Court Rulings

Florida’s 404 saga doesn’t exist in a vacuum—it’s entangled with the Supreme Court’s recent CWA overhaul:

• Sackett’s Narrow Scope: The Sackett ruling shrunk federal jurisdiction, potentially easing Florida’s burden to regulate only “connected” waters. Yet, the state’s broader Environmental Resource Permitting (ERP) program already covers many non-WOTUS wetlands, creating a dual system. If Florida regains 404 authorities, aligning state and federal definitions post-Sackett could streamline efforts. 

• Maui’s Indirect Reach: While Maui focused on Section 402 discharges, its “functional equivalent” test could indirectly pressure Florida’s 404 program to address groundwater-linked impacts in permitting.

• San Francisco’s Looming Impact: A 2025 ruling limiting EPA discretion could further constrain Florida’s delegated authority, especially if it tightens permit specificity or oversight. The state’s novel ESA consultation process might face additional scrutiny, delaying its revival.

What’s at Stake?

Florida’s 404 program is a microcosm of broader tensions: state autonomy versus federal oversight, development versus conservation. The Supreme Court’s conservative bent—evident in Sackett and hinted at in San Francisco—leans toward curbing federal overreach, aligning with Florida’s push for control. Yet, the ESA challenge highlights a countercurrent: environmental protections can’t be sidestepped, even under state management.

For developers, the uncertainty means delays—some projects now restart with the Corps, while others await appellate clarity. For ecosystems, the stakes are higher. Wetlands, dubbed nature’s “kidneys,” filter pollutants and store floodwaters—roles Florida can’t afford to lose amid rising seas and sprawl.

Looking Ahead

Florida’s appeal could restore its 404 program, bolstered by new EPA rules, but Supreme Court trends suggest ongoing limits on federal power. States may increasingly shoulder water protection. For now, Florida and the nation watch the courts, hoping for clarity in these shifting waters.