Adapting to Change: Navigating New Endangered Species Act Listings and Their Impact on Bay Area Projects

The U.S. Fish and Wildlife Service has proposed listing three species under the Endangered Species Act, impacting public and private project proponents across all nine Bay Area counties.  

Introduction 

Three species in the San Francisco Bay Area are proposed for listing under the federal Endangered Species Act (ESA) by the U.S. Fish and Wildlife Service (USFWS):  

• Northwestern pond turtle (Actinemys marmorata)—88 Federal Register (FR) 68370, October 3, 2023 
• Northern distinct population segment (DPS) of western spadefoot (Spea hammondii)—88 FR 84252, December 5, 2023 
• San Francisco Bay-Delta DPS of longfin smelt (Spirinchus thaleichthys)—87 FR 60957, October 7, 2022.  

Designated critical habitat for these species is not yet proposed, so critical habitat is not discussed herein. 

One or more of these species potentially occur in every Bay Area county.  

• The northwestern pond turtle range includes all nine Bay Area counties.  
• The western spadefoot range includes every Bay Area county other than San Francisco and San Mateo counties. 
• The longfin smelt range includes the entire San Francisco Bay Estuary and areas of the Pacific Ocean out to the Farallon Islands. 

All project sites in the Bay Area that overlap undeveloped lands or aquatic features may support populations of the western pond turtle, western spadefoot, and longfin smelt.  

Formal ESA listing is anticipated in the coming months. During a court hearing in April 2024, USFWS stated its intent to publish the listing of longfin smelt by July 2024.  

Implications  

Bay Area projects that occur in potential habitats for the newly listed species may require project design changes or additional regulatory review for potential effects to these species given the updated listing status. A proactive approach is recommended to avoid delays in project authorizations and to identify whether these listings could jeopardize a project or create other constraints or burdens. Anticipated projects threats include:  

• Delayed project timelines  
• New permitting requirements  
• Additional regulatory review  
• Increased project costs 
• Required changes to project design to avoid and minimize impacts to the species. 

Regulatory Background 

Section 9 of the ESA prohibits take of listed species except where incidental take coverage has been provided by the USFWS or the National Oceanic Atmospheric Administration National Marine Fisheries Service (NOAA Fisheries, collectively referred to as the Services). Under the ESA, take means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to engage in any such conduct (16 U.S.C. 1542(b)). There are two mechanisms to obtain incidental take coverage under the ESA, including one that applies to nonfederal entities and one that applies to federal agencies.  

• Nonfederal entities can receive take authorization from the Services through the development of a Habitat Conservation Plan (HCP) which includes an Incidental Take Permit (ITP) (Section 10 of the ESA).  
• Federal entities can receive take coverage from the Services for federal actions through the issuance of a Biological Opinion which includes an Incidental Take Statement (Section 7 of the ESA). Federal actions may include federal projects or nonfederal projects that require funding or a license or permit from a federal agency. Many nonfederal entities obtain incidental take coverage for their projects through the federal Section 7 consultation process. 

Federal agencies have additional obligations under Section 7 of the ESA that are triggered even when a federal action is not anticipated to result in take of a listed species. The Section 7 consultation process is triggered when a federal action may affect a listed species. Upon making a may affect determination, the federal action agency provides the Service with a biological assessment and request for consultation. Formal consultation, which results in a Biological Opinion and Incidental Take Statement, is conducted with the Services when the federal action may affect and is likely to adversely affect listed species. Informal consultation, which results in a Letter of Concurrence (LOC) and no incidental take coverage, is conducted with the Services when the federal action may affect and is not likely to adversely affect (NLAA) listed species. An NLAA determination is appropriate when the effects of the federal action on listed species are anticipated to be discountable (extremely unlikely to occur), insignificant (so small that take would not occur), or wholly beneficial. The informal consultation requirement for federal action agencies does not have an analog for nonfederal actions. 

Federal action agencies can preemptively fulfill Section 7 consultation obligations for species proposed for listing by requesting conference with the Services. Conference is required only when the proposed action is likely to jeopardize the continued existence of a proposed species, but federal action agencies may request conference on any proposed action that may affect proposed species to avoid having to reinitiate consultation if the species is listed. The conference process is analogous to the consultation process outlined above. Conference may be formal or informal and results in a conference opinion with an Incidental Take Statement or a conference report with an NLAA concurrence, respectively. The Incidental Take Statement does not become effective until the Services adopt the conference opinion as a Biological Opinion once the species is listed. 

A flowchart displaying the process for ESA compliance is provided in Figure 1.  

Figure 1. ESA compliance flowchart to help project proponents determine consultation and permitting requirements.

Federal actions that may affect listed species cannot occur until the lead federal agency has fulfilled Section 7 consultation requirements. However, even after completing any required Section 7 consultation, additional Section 7 consultation may still be required. Reinitiation of consultation is required under four circumstances:  

• The amount or extent of taking specified in the incidental take statement is exceeded  
• New information reveals effects of the action that may affect listed species in a manner or to an extent not previously considered  
• The identified action is subsequently modified in a manner that causes an effect to the listed species that was not considered in the Biological Opinion or LOC 
• A new species is listed that may be affected by the identified action.  

If any of the reinitiation triggers occur, the federal action agency is required to reinitiate consultation with the Services so long as the action is incomplete and federal agency still has regulatory authority over the action. 

Once consultation is initiated or reinitiated, Section 7(d) of the ESA prohibits the irreversible or irretrievable commitment of resources with respect to the agency action which has the effect of foreclosing the formulation or implementation of any reasonable and prudent alternative measures. Reasonable and prudent alternatives are formulated when the action is likely to jeopardize the continued existence of a listed species. Therefore, starting or continuing to implement a federal action during the consultation process may be in violation of the ESA. If initiation or reinitiation of consultation is required to obtain take coverage, any take that occurs during consultation would be in violation of Section 9 of the ESA regardless of whether a Section 7(d) violation occurs. 

Discussion 

Any nonfederal or federal action within potential habitat for northwestern pond turtle, western spadefoot, or longfin smelt may be delayed or fail to obtain ESA take authorizations in a reasonable time if these species are listed under the ESA, which appears likely. The effects of the listing on any action depend upon whether the action is federal or nonfederal, whether take coverage is required, whether conference with the USFWS has occurred, and whether the project is in the planning, agency engagement, or implementation phase. The following scenarios are sorted from least to most at-risk for project delay or failure. See Figure 2 for flowchart of likelihood range for project delay or failure.  

The following scenarios have a low likelihood of project delay or failure due to listing of a new species: 

• The project does not occur in potential habitat for the newly listed species. 
• The action is nonfederal and does not have the potential for incidental take of the newly listed species. 
• The action is federal, and a conference opinion or conference report was obtained by the federal action agency for the newly listed species. 
• The action is federal, may affect the newly listed species, and is in the planning phase. In this case, agency engagement has not yet begun, so the permitting process should not be significantly delayed. A biological assessment should be submitted to the lead federal action agency analyzing project effects to the newly listed species. 

The following scenarios have a moderate likelihood of project delay or failure due to listing of a new species: 

• The action is federal, may affect the newly listed species, and is in the agency engagement phase. In this case, if effects to the species were not previously analyzed, a biological assessment will need to be prepared, and the lead federal action agency will need to initiate consultation with the USFWS. The further that the project is into the agency engagement phase, the longer the permitting delay. 
• The action is federal, may affect but is not likely to adversely affect the newly listed species, and is in the implementation phase. In this case, the lead federal action agency would be required to initiate or reinitiate consultation with the USFWS if they still maintain regulatory authority over the action, but the legal risk associated with continuing construction during consultation would be relatively low. Whether construction can proceed during consultation would be at the discretion of the federal action agency and any nonfederal project proponent. 

The following scenarios have a high likelihood of project delay or failure due to listing of a new species: 

• The action is nonfederal and is anticipated to result in take of the newly listed species. In this case, the nonfederal entity would need to obtain incidental take coverage through the development of an HCP. 
• The action is federal, may result in take, and is in the implementation phase. In this case, the legal risk associated with continuing construction during consultation would be relatively high, and construction should likely cease while the lead federal action agency consults with the USFWS.  

Figure 2. Scenarios for project delay or failure due to listing of a new species.

Conclusions 

Listing of northwestern pond turtle, western spadefoot, and longfin smelt under the federal ESA have consequences for development projects across the Bay Area. Projects in all stages of execution should be assessed for effects to these species to avoid and minimize delays.  

Integral Consulting Inc. can assist with evaluating project effects on these species, developing strategies or project design changes to avoid delays, outlining the most expedient path through the regulatory process, and obtaining any necessary ESA permits or documentation from the USFWS.