Federal court strikes down Florida’s CWA section 404 permit program

The U.S. District Court for the District of Columbia has vacated the Environmental Protection Agency’s (EPA) approval of Florida’s application to assume permitting under section 404 of the Clean Water Act (section 404). While not setting aside issued permits, the ruling applies to all pending and future permit applications for activities in Waters of the United States (WOTUS) that had been assumed by the state. Thus, the U.S. Army Corps of Engineers (ACOE) has resumed control of the section 404 permits throughout the state, leaving only New Jersey and Michigan with state-run section 404 programs.

Section 404 regulates dredge and fill activities in WOTUS, and permitting of such activities is typically handled by the ACOE; however, section 404(g) creates a mechanism for states to assume this permitting with EPA approval over a subset of WOTUS in the state; “retained” waters remain under ACOE jurisdiction. In December 2020, EPA approved Florida’s section 404 program, one of only three such programs in the country. Various environmental organizations quickly sued on procedural and substantive grounds in January 2021. Over the last three years, several rulings have been issued in the case narrowing its scope, but the February ruling was the first with substantive effects on the state program.

On February 15, 2024, Judge Moss vacated Florida’s section 404 program as violative of the Endangered Species Act (ESA). Section 7 of the ESA requires all federal agencies to consult with the U.S. Fish & Wildlife Service (FWS) and/or the National Marine Fisheries Service (NMFS) on federal actions that may affect a listed species or its designated critical habitat to confirm that the action will not jeopardize the continued existence of the species. As part of that consultation process, the wildlife agencies must issue a biological opinion (BO) meeting certain criteria; the incidental take (harm, harassment, or death) of a listed species can be authorized in an incidental take statement (ITS) appended to the BO if reasonable and prudent measures are incorporated. The only other mechanism to authorize the “take” of a species is through the ESA’s section 10 permitting process.

The FWS issued a BO covering EPA’s action in approving Florida’s section 404 program and determined in the BO that the technical assistance process established between the Florida Department of Environmental Protection, FWS, and the Florida Fish & Wildlife Conservation Commission prevented “jeopardy” to listed species. The BO included an ITS for the program as a whole, authorizing take if permits were issued pursuant to the technical assistance process and included FWS-recommended conditions to avoid and minimize species impacts. This method of complying with the ESA was unique; Michigan and New Jersey, the only other states that have assumed the section 404 program, did not include a programmatic biological opinion or blanket incidental take authorizations.

Judge Moss held that both the BO and ITS violated the ESA because of their lack of specificity; the documents failed to identify the species at issue or the amount or extent of the take, and failed to set standards for determining when the authorized level of take was exceeded. Due to the scope of Florida’s section 404 program, the judge found that the BO and ITS did not meet the demanding standards of the ESA with regard to species-specific analysis, effects analysis, or quantification of take. He vacated both the BO and ITS.

Judge Moss recognized that the majority of section 404 permits issued by the state likely have no listed species implications and was cognizant that vacating the entire program would have serious disruptive consequences. He therefore vacated EPA’s approval of Florida’s section 404 program prospectively and allowed any party to seek a limited stay. “Any such request should exempt all pending and future permit applications that ‘may affect’ any listed species under the jurisdiction of the FWS or the NMFS and should propose a mechanism for determining which permit applications ‘may affect’ listed species.” In other words, he would only entertain a stay as to applications that will not affect listed species.

The Florida Intervenors sought a limited stay as to pending and future permit applications not affecting listed species. In the alternative, they asked the court to modify the state’s section 404 program to match New Jersey’s approach to listed species, which was never challenged. Florida suggested a procedure for wildlife agencies to review applications and make determinations as to whether the project will affect listed species and steps to be taken if a “may affect” determination is reached. However, both the federal defendants and plaintiffs opposed the stay, arguing that a bifurcated program that federalized permit applications that “may affect” listed species would be impractical and inconsistent with the CWA, given EPA rules that disallow partial assumption. The Florida Intervenors also sought entry of a final judgment on all counts, arguing any remaining counts were mooted by vacatur, to enable the state to appeal. On April 12, the Court denied Florida’s motion for stay, but granted the request for entry of final judgment on all but one count of the complaint (against the ACOE as to which waters it must retain). The Court also made minor revisions to its February 15 Memorandum Opinion, correcting some erroneous references to New Jersey’s section 404 program.

ACOE’s Jacksonville District has begun accepting section 404 applications and committed in court filings to accepting pending applications “as is,” i.e., not requiring the applicant to start anew. Florida filed a notice of appeal on April 15.