On February 15, 2024, a federal court in the District of Columbia issued a ruling formally vacating the Environmental Protection Agency’s (“EPA”) December 2020 decision to allow the state of Florida to assume permitting authority for section 404 of the Clean Water Act (“CWA”). Section 404 of the CWA is traditionally implemented by the U.S. Army Corps of Engineers (“the Corps”). While states can assume section 404 permitting authority, prior to Florida, only two other states had done so – Michigan and New Jersey. In Ctr. for Biological Diversity v. Regan, No. 21-119 (D. D.C. Feb. 15, 2024), the court determined that EPA’s decision to allow Florida to assume section 404 permitting authority should be overturned because EPA failed to comply with the Endangered Species Act (“ESA”). Following the court’s decision, anyone seeking a section 404 permit in the state of Florida will need to work with the Corps instead of the Florida Department of Environmental Protection (“FDEP”) which could increase the amount of time and resources spent on acquiring a permit.

Statutory Background

The process for allowing a state to assume CWA Section 404 permitting authority is complex. It involves coordination between states and the federal government, and centers on the intersection between the CWA and the ESA. Understanding both statues is crucial to understanding the application process.

The Endangered Species Act

The ESA was adopted by Congress in 1973 for the primary purpose of conserving endangered and threatened species and the ecosystems on which those species depend. 16 U.S.C. § 1531(b). The statute is administered jointly by the U.S. Fish and Wildlife Service (“FWS”) and the National Marine Fisheries Service (“NMFS”) (collectively “the Services”), which are both responsible for identifying species to be listed under the ESA as either threatened or endangered. Once a species is listed under the ESA, it receives a variety of ESA protections. One of the most important protections granted to listed species is the ESA’s prohibition on “take.” “Take” is defined very broadly under the ESA as “to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect” any listed species. 16 U.S.C. § 1532(19). This prohibition applies to all persons, including private parties, states, and the federal government. There are only two ways to take a species without violating the ESA. A federal agency may be authorized to take species incidental to an otherwise lawful activity through an Incidental Take Statement issued under Section 7 of the ESA, or a state or private party may be authorized to take species after receiving an incidental take permit issued under Section 10 of the ESA.

Under Section 7 of the ESA, all federal agencies are required to consult with the Services to ensure that any action the agency authorizes, funds, or carries out will not result in jeopardy of a species. 16 U.S.C. § 1536(a)(2). Here, jeopardy of a species refers to any action that would “reduce appreciably the likelihood of both the survival and recovery of a listed species.” 50 C.F.R. § 402.02. The first step of the consultation process requires the agency taking action, typically referred to as the action agency, to determine whether its proposed action “may affect” a listed species. 50 C.F.R. § 402.14. If the action agency reaches a “may affect” finding, its next step is to determine whether the action is “likely to adversely affect” a listed species. If the action agency concludes that its proposed action is likely to adversely affect a listed species, then it must proceed with formal Section 7 consultation. 50 C.F.R. § 402.14.

The end result of formal Section 7 consultation is a document called a Biological Opinion, or “BiOp.” The BiOp is a thorough document, and is required to include a a detailed discussion of the “environmental baseline” of the listed species impacted by the action describing the condition of the species prior to the proposed action occurring; a detailed discussion of the effects the proposed action is expected to have on listed species; and the consulting Service’s opinion on whether the proposed action is likely to result in jeopardy of a species. 50 C.F.R. § 402.14(h)(1). If the BiOp results in a jeopardy finding, then the consulting Service shall include a discussion of any “reasonable and prudent alternatives” that the action agency can take which will still accomplish the goals of the proposed action without resulting in jeopardy of a species. 16 U.S.C. § 1356(b)(3)(A); 50 C.F.R. §§ 402.14(h)(3), (g)(5).

If the consulting Service finds that either the proposed action or one of the reasonable and prudent alternatives will not result in jeopardy, then the BiOp must also include an incidental take statement. 50 C.F.R. § 402.14(i)(1). “Incidental take” refers to “takings that result from, but are not the purpose of, carrying out an otherwise lawful activity[.]” 50 C.F.R. § 402.02. An incidental take statement, or “ITS,” that is issued as part of a BiOp must specify the extent of incidental take that is expected to occur as part of the agency action; clarify the reasonable and prudent measures identified by the Services as necessary to minimize incidental take; and set forth the term and conditions, including reporting requirements, that the action agency must comply with in order to appropriately carry out the ITS. 50 C.F.R. § 402.14(i). Crucially, if the action agency exceeds the amount of incidental take authorized by the ITS, then the agency must reinitiate consultation with the Services immediately. 50 C.F.R. § 402.14(i)(4). However, any take of a listed species that is “in compliance” with the terms and conditions laid out in an ITS is not considered a violation of the ESA’s take prohibition. 16 U.S.C. § 1563(o)(2).

Once a BiOp is issued the Section 7 consultation process is over and the action agency may proceed with its proposed action. If an ITS was issued as part of the BiOp, then the action agency is authorized to engage in a certain amount of incidental take as part of the agency action. There is only one other way that incidental take may be authorized under the ESA. While an ITS issued as part of a BiOp is only available to federal agencies, private parties may apply to the Services for an incidental take permit under Section 10 of the ESA. Under this portion of the statute, the Services may authorize “any taking otherwise prohibited [under the ESA] if such taking is incidental to, and not the purpose of, the carrying out of an otherwise lawful activity.” 16 U.S.C. § 1539 (a)(1)(B). To obtain a Section 10 incidental take permit, an applicant must submit a conservation plan, known as a Habitat Conservation Plan or “HCP” to the Services. Such a plan must include descriptions of the impacts that are likely to result from the proposed taking; what steps the applicant will take to minimize and mitigate impacts to listed species; what alternative actions to the proposed taking the applicant considered and reasons why such actions were not utilized and any other measures the [Services] may required as necessary for the HCP. 16 U.S.C. § 1539(a)(2)(A). Prior to issuing a Section 10 incidental take permit, the issuing Service must determine that the taking “will not appreciably reduce the likelihood of the survival and recovery of the species[.]” 16 U.S.C. § 1539(a)(2)(B)(iv). Finally, should the permittee fail to comply with the terms of the Section 10 permit, the ESA instructs the issuing Service to revoke the permit. 16 U.S.C. § 1539(a)(2)(C).

The Clean Water Act

The CWA was passed by Congress for the primary purpose of “restor[ing] and maintain[ing] the chemical, physical, and biological integrity of the Nation’s waters.” 33 U.S.C. § 1251(a). To achieve these goals, the CWA implements various pollution control programs, including the Section 404 permitting program. Under Section 404 of the CWA, the U.S. Army Corps of Engineers (“the Corps”) is authorized to issue permits “for the discharge of dredged or fill material” into waters protected by the CWA. 33 U.S.C. § 1344(a). The discharge of dredged material is defined as “discharges of pollutants into [protected waters] resulting from the onshore subsequent processing of dredged material that is extracted for any commercial use[.]” 40 C.F.R. § 232.2. In other words, the discharge of dredged material refers to earth or other material that is extracted onshore as the result of construction or similar commercial activities that falls back into a protected water. The discharge of fill material is more broadly defined and includes fill material added to a protected water as part of the construction of any building or other infrastructure, dams and levees, artificial islands, and placement of slurry, tailings, or similar mining-related materials. 40 C.F.R. § 232.2.

While the Corps is traditionally responsible for administering the Section 404 permitting program, the CWA allows states to assume Section 404 permitting authority. 33 U.S.C. § 1251(b). In order for a state to take over implementation of the Section 404 program, it must first submit an application to EPA including “a full and complete description of the program it proposes to establish and administer under State law” along with a statement from the state’s attorney general affirming that “the laws of such State […] provide adequate authority to carry out the described program.” 33 U.S.C. § 1344(g)(1). Once a state has submitted a complete application, EPA has 120 days to either approve or disapprove the program. 40 C.F.R. § 233.15(a). EPA will base its decision on whether the state’s program would fulfill the requirements of the CWA and its implementing regulations. 40 C.F.R. § 233.15(g). Importantly, authorizing a state to assume 404 permitting responsibilities is an agency action that requires ESA Section 7 consultation. Consultation will likely occur during this four-month period.

Once EPA has transferred Section 404 permitting authority to a state, the agency will continue to oversee the state’s implementation of the program. The CWA requires states to send copies of each 404 permit application it receives to EPA. 33 U.S.C. § 1344(j). In turn, EPA sends a copy of each permit application to the Services, and may also provide written comments to the state within 90 days of receiving a copy of the permit application. To facilitate EPA’s continued oversight, the agency and the state must enter into a Memorandum of Agreement that lays out “the State and Federal responsibilities for program administration and enforcement[.]” 40 C.F.R. § 233.13(b). Typically, it is in the Memorandum of Agreement where the state and EPA will outline how ESA responsibilities will be handled. In general, there are two options that states will consider. Either the state will agree to “federalize” any section 404 permit application that may impact listed species and will pass the permit on to the Services for independent Section 7 review, or the state may require anyone receiving a 404 permit that may impact listed species to obtain a Section 10 incidental take permit.

While there are many reasons why a state may choose to take over Section 404 permitting authority, including the state having better knowledge of the waters located within its boundaries than the federal government, only two other states besides Florida have been approved to administer the 404 program – Michigan which was approved in 1984, and New Jersey which was approved in 1994. Both New Jersey and Michigan adopted the first approach and agreed to federalize any 404 permit that may impact listed species. Florida, on the other hand, chose to pursue a completely novel approach and requested that EPA and FWS develop a programmatic BiOp.

Florida’s Assumption of 404 Permitting Authority & the Court’s Decision

In August 2020, Florida submitted to EPA an application to assume Section 404 permitting authority within its borders. Nearly four months later, in December 2020, EPA approved the request, making Florida the third state to ever administer the 404 program. While Florida was the third state to assume 404 permitting authority, it was the first state to seek protection for itself and future 404 permittees through a programmatic BiOp and ITS issued via ESA Section 7 consultation. Ultimately, this novel approach prompted environmental plaintiffs to file suit.

In a Consultation Handbook issued jointly by FWS and NMFS in 1998, the Services describe programmatic consultation as a “consultation addressing an agency’s multiple actions on a program, regional, or other basis.” The ESA’s implementing regulations define a “framework programmatic action” as “a Federal action that approves a framework for the development of future action(s) that are authorized, funded, or carried out at a later time, and any take of a listed species would not occur unless and until those future action(s) are authorized, funded, or carried out and subject to further section 7 consultation.” 50 C.F.R. § 402.02. In other words, a programmatic section 7 consultation is appropriate when an agency is proposing to authorize an entire program or other framework from which other future actions will flow and no take of listed species is expected to occur until those future actions are carried out. Typically, an ITS is not required at a programmatic level because any incidental take that occurs as a result of future agency actions carried out under the program or framework must themselves be addressed in future Section 7 consultations. 50 C.F.R. § 402.14(i)(6).

In assuming Section 404 permitting authority, Florida sought a programmatic BiOp and a novel programmatic ITS to cover all future 404 permittees.  While Florida considered both federalizing 404 permit applications that could impact listed species or requiring 404 permittees to apply for Section 10 incidental take permits, the state ultimately rejected both options, concluding that either one would place unreasonable burdens on 404 permittees. Instead, Florida and EPA agreed to pursue a programmatic BiOp and ITS that would cover all incidental take that occurred as a result of Florida assuming Section 404 permitting authority. Additionally, Florida agreed to send a copy of every permit application that could result in take of listed species to FWS for review and “technical assistance.” Specifically, the Florida Department of Environmental Protection (“FDEP”) would send FWS a copy of all 404 permit applications that could impact listed species so that FWS could make comments and recommend protection measures to minimize or mitigate impacts. Then, those recommendations would be included as conditions in the resulting 404 permit.

The programmatic BiOp and ITS were finalized in November 2020. The BiOp did not contain any species-specific analyses of the baseline status of listed species in Florida. Similarly, the did not ITS specify the level of take allowed or clarify when reinitiation of consultation would be required. In the BiOp, FWS explained that exact impacts to protected species could not be accurately determined because it was impossible to identify the exact number or locations of future 404 permits that would be issued by Florida. Instead, the BiOp considered whether the Florida program was “structured” to ensure that no future 404 permit would be likely to jeopardize any listed species. Because Florida had agreed to pass some permits onto FWS for technical assistance, the BiOp concluded that jeopardy of species was not likely to occur.

On December 22, 2020, EPA formally approved Florida to take over administration of the CWA Section 404 permitting program within its state boundaries. The decision was made effective immediately. On January 14, 2021, multiple environmental groups filed suit against EPA, FWS, and the state of Florida to challenge this decision, claiming that the defendants had failed to fully comply with the ESA. Specifically, the plaintiffs challenged the programmatic BiOp and ITS for failing to provide species-specific analysis or include a take limit. Plaintiffs asked for EPA’s decision to be overturned, and for Florida’s section 404 permitting authority to be revoked.

Ultimately, after several years of litigation, the judge ruled in favor of the plaintiffs, finding that the Section 7 consultation between EPA and FWS violated key aspects of the ESA. In Ctr. for Biological Diversity v. Regan, No. 21-119 (D. D.C. Feb. 15, 2024), the court focused on both the lack of species-specific analysis in the BiOp, and the lack of take limits in the ITS statement to reach its decision. According to the court, under the “plain language” of the ESA, FWs as required to prepare a BiOp “detailing how the agency action affects the species or its critical habitat,” which FWS failed to do. The court highlighted regulatory language that requires every BiOp to contain “a detailed discussion of the environmental baseline of the listed species” and a “detailed discussion of the effects of the action on listed species[.]” 50 C.F.R. § 402.14(h). Because the BiOp failed to include any species-specific analysis, the court found that it failed to meet minimum necessary requirements. While FWS argued that it was unable to conduct species-specific analysis because it lacked enough information to determine the impacts that future 404 permits would have to listed species, the court was unconvinced. Specifically, the court noted that FWS had conducted numerous Section 7 analyses of listed species located in Florida before, but FWS failed to consider any information generated from those past analyses. Accordingly, the court vacated the BiOp.

Next, the court turned to the programmatic ITS. The court began its analysis by noting that according to the text of the ESA, the purpose of an ITS is two-fold. First, an ITS serves to define the extent of allowable take of listed species as the result of an agency action, and second, an ITS ensures that incidental take will not jeopardize any listed species. 16 U.S.C. § 1536(b)(4). The court stressed the requirement that each ITS include a specified level of authorized take, and a trigger for when consultation between the Services and the action agency must be reinitiated. Because the programmatic ITS issued to Florida contained neither a specified level of incidental take or a trigger for when consultation must be reinitiated, the court found that the programmatic ITS violated the ESA and should be set aside.

Having vacated both the programmatic BiOp and the programmatic ITS, the court concluded that the only appropriate course of action was to also vacate EPA’s approval of Florida’s assumption of CWA Section 404 permitting responsibility.


There are many benefits that come when states assume Section 404 permitting authority, including improved resource protection as state and federal agencies coordinate their efforts, increased program efficiency as states are often able to act more quickly than EPA and have a better understanding of the waters located within their borders, and better allocation of state and federal resources. Similarly, for permittees it is often easier to seek state approval rather than federal approval. However, the process for allowing a state to take over 404 permitting authority is complex. It requires coordination between the state, EPA, and the Services. Both the CWA and the ESA come into play. It is rare for states to assume Section 404 permitting authority, in part because of the complexity required to successfully take over administration of the program.

While the court’s ruling in Ctr. for Biological Diversity v. Regan would not prevent other states from seeking to assume Section 404 permitting authority, the decision casts doubt on whether a state could successfully pursue a programmatic BiOp or ITS in the future. States looking to take over Section 404 responsibilities may need to adopt the same court of action as New Jersey and Michigan, or engage in a more thorough Section 7 consultation before receiving program approval.

It is currently unclear how the Section 404 program will be administered in Florida going forward. Currently, the federal government and Florida have filed separate briefs with the court presenting different options for how the 404 program could be administered. The federal government argues that it should immediately resume all 404 permitting authority, while Florida claims that it should maintain control over the program while it seeks a stay of the court’s vacatur decision.


To read the court’s decision in Ctr. for Biological Diversity v. Regan, click here.

To read the text of the ESA, click here.

To read the text of the CWA, click here.

For more National Agricultural Law Center resources on the ESA, click here.

For more National Agricultural Law Center resources on the CWA, click here.