California Department of Transportation

Last Updated: Thursday, June 23, 2016 10:25 AM

Chapter 4 - Endangered Species Act Procedures


All projects must be evaluated to determine if any endangered or threatened species may be affected. The Federal Endangered Species Act (FESA) and the California Endangered Species Act (CESA) are the Federal and State laws to enforce protection of threatened and endangered species. This chapter is a summation of the laws, documentation, and processing requirements of those laws.

The purpose of the procedure is to determine whether a project will actually involve proposed or listed species or critical habitat at the earliest possible time in the project development process. If proposed or listed species or critical habitat are present, there will be time to modify the project to avoid or minimize impacts. If proposed or listed species or critical habitat are not present, then no further formal involvement with the Endangered Species Act procedure is required. Further discussions may be held for other special status species impacted by the project.

4-1.1 Federal Endangered Species Act of 1973

The purpose of this law is to provide a means whereby the ecosystems upon which endangered and threatened species depend may be conserved and to provide a program for the conservation of such endangered and threatened species. Section 7 of this Act outlines the responsibilities of Federal agencies in protecting endangered and threatened species. It states: "...each Federal agency shall, in consultation with, and with the assistance of the Secretary, insure that any action authorized, funded, or carried out by such agency... is not likely to jeopardize the continued existence of any endangered species or threatened species or result in the destruction or adverse modification of habitat of such species which is determined by the Secretary, after consultation as appropriate with the affected States, to be critical...".

Section 7 has been amended several times since being signed into law in 1973. The latest requirements for consultation can be found at 50 CFR Part 402. This establishes the procedural regulations governing interagency cooperation.

4-1.2 California Endangered Species Act

The CESA became effective on January 1, 1985 to provide a means to conserve, protect, restore, and enhance any endangered or threatened species and its habitat. Unlike FESA, there are no state agency consultation procedures under CESA. For projects that affect both a state and federal listed species, compliance with the Federal Endangered Species Act (FESA) will satisfy CESA if the Department of Fish and Game (DFG) determines that the federal incidental take authorization is "consistent" with CESA under F&G Code Section 2080.1. For projects that will result in a take of a state only listed species, Caltrans must apply for a take permit under Section 2081(b).


4-2.1 Determining the Need for a Biological Assessment

The evaluation procedure for endangered and threatened species parallels the project development process. This procedure is designed to develop the listed species information required for the preparation of the environmental document.

If listed species may be involved a Biological Assessment must be prepared. The U.S. Fish and Wildlife Service (FWS) defines Biological Assessment as "...the information prepared by or under the direction of the Federal agency concerning listed and proposed species and designated and proposed critical habitat that may be present in the action area and the evaluation of the potential effects of the action on such species and habitat". Caltrans has expanded this definition to also include those species listed by the California Department of Fish and Game (DFG).

The following sections are presented as a guide. The circumstances of each project will determine if, and when, a given task will actually be performed.

Evaluate Project Proposal

The preliminary evaluation should be performed early in the project development process so it can be used in the selection of alternatives to be studied in the environmental document.

Once the list of potential alternatives is established, a library search and check of the California Natural Diversity Data Base (CNDDB) can be completed. When a list of resources that have the potential of occurring in the project vicinity is established, a windshield survey or walk through of the project can be completed. During the site visit the existing habitats should be roughly drawn on a base map. With a list of species potentially in the project area and a map of the existing habitats, a comparative estimate of endangered species involvement can be made for each alternative.

Determine If Species List Request Is Required

The purpose of requesting a list from FWS is to assure that the Biological Assessment addresses all listed, proposed, and candidate species that FWS believes may be in the project area. The District Biologist determines whether a list request is required from FWS. The list request should normally be initiated no later that the Notice of Intent/Notice of Preparation stage of the environmental document procedure. Circumstances under which a request is made depends upon the type of environmental document and potential for impacts. If preparation of biological assessment does not begin within 90 days of receipt of (or concurrence with) the species list, project biologist must verify (formally or informally) with the Service(s) the current accuracy of the species list at the time the preparation of the assessment is begun (50 CFR 402.12 (e)).

Environmental Impact Statement (EIS). Caltrans is required to request a list when an EIS will be prepared. The list should be requested at the earliest time the District believes an EIS will be prepared for a project and the resources are available to perform the necessary surveys (appropriate time of year, surveyors available, project defined, etc.) and updated with 180 days of the DED or FED milestones.

Categorical Exclusion (CE) and Finding of No Significant Impact (FONSI). A list is requested when it is suspected that the project will affect a Federally listed or proposed species. In this way, the required study to determine a project's impact on Federally listed and proposed species will cover all the species monitored by FWS. Therefore, if a consultation/conference is required, the District will not have to retrace the process to perform a study on a species they may have overlooked.

FWS List Request

Request the list at the proper time of year to complete field studies for suspected special status species. FWS has 30 days to respond to list requests. Studies not started within 90 days of list receipt should have a new list request or verification that the original list is still valid. Surveys for many species can only be done during very specific periods of the year so the timing of list requests is very important.

The district initiates the list request with a written request to the Field Office of FWS that has responsibility for the county in which the project is located. A list request from the National Marine Fisheries Service (NMFS) will only include species under their jurisdiction.

If the response from FWS is that no special status species are present, there will be no further involvement with Section 7. However, if the response from FWS is that special status species are or may be present, proceed to Complete Field Studies.

Complete Field Studies

Once aware that special status species are or may be present in the project area, the District must initiate a biological study to determine any effects that the proposed project may have on the species. The initial effort is determining the actual presence or absence of a species in the area of impact. If identified as being present in the area, the project's effect on the species must be determined. The level of study must be sufficient to determine the type and extent of the effects a project will have on a special status species.

4-2.2 Preparation of the Biological Assessment

Once the field study is complete, a Biological Assessment must be prepared which clearly states what the probable impact will be from constructing the project as proposed. If the conclusion is that the project may affect special status species or critical habitat, the Biological Assessment should be prepared as a working draft. If there are no impacts to special status species or critical habitat, the document should be in a final form for later processing.

A Biological Assessment is required when an EIS is being prepared and FWS has included a listed or proposed species in the list request. As a matter of practice, a report should also be prepared whenever the District Biologist determines that the project may affect a listed or proposed species or listed or proposed critical habitat, regardless of document type.

While the Biological Assessment is in draft form, the Project Manager and District Biologist should meet with representatives of the Federal Highway Administration (FHWA), FWS/NMFS, and DFG to explore methods of reducing project impacts. This includes evaluating methods of avoiding the impact, minimizing the impact or developing appropriate mitigation to off-set project impacts, in that order. After all participants are satisfied, a final Biological Assessment is prepared.

Regardless of whether or not a list is requested, if studies show a project will affect a special status species (other than listed or proposed) discussions with FWS/NMFS or DFG should occur as appropriate. The goal is to eliminate impacts or minimize them as much as possible. Species may be listed before the project is actually constructed. If this is a distinct possibility, then the additional work may avert problems during project construction. This decision is a judgment call. Committing the same resources for special status species that would be committed for listed species is not always possible.

4-2.3 Biological Assessment Report Format

he approved template for the Biological Assessment is found on the Forms & Templates page of the SER.

4-2.4 Processing of the Biological Assessment

Processing the Biological Assessment depends on the environmental document type and the species status.

If the determination is: Then:
Listed species, may affect; Consultation.
Listed species, not likely to adversely affect or no effect; Concurrence in finding.
Proposed species, may jeopardize; Conference.
Proposed species, not likely to adversely affect or no effect; Concurrence after listed.
Candidate/species of concern, may affect; Technical Assistance.
Candidate/species of concern, no effect; Summarize in document, backup in file.
Listed or proposed species, no effect. * Summarize in document, backup in file.
If list was requested from FWS, no effect. Notify FWS of no effect to close file.
All others. Same as EIS.

* It is the Caltrans biologist's responsibility, with FHWA concurrence, to make the determination of "may affect" for a project which would trigger the requirement to consult with FWS/NMFS. Caltrans/FHWA also assumes the risk of making an erroneous decision.

Multiple requests from the same agency on a single project will be handled under a single letter of request. Consultation, conference, and concurrence are the only formal processes that require a written request. All others are informal and may be handled by phone, mail, or electronically.

Formal Consultation, 50 CFR Part 402.14

As with all formal FESA processes, the Caltrans District Biologist prepares the package that FHWA will use to make the request to FWS/NMFS. It is transmitted by letter to FHWA with a request that they initiate consultation. As the Federal agency, FHWA is required to initiate consultation when a project with Federal participation has the potential to affect a Federally listed species and/or destroy or adversely modify designated critical habitat. Formal consultation is held between a Federal agency and FWS/NMFS. Consultation is initiated through a written request from FHWA to FWS/NMFS and includes the Biological Assessment for the project and any other relevant reports or studies with information on the action, the affected listed species, or critical habitat.

The consultation is initiated when the project has been defined and the Biological Assessment completed. Consultation concludes within 90 days, at which time FWS/NMFS has 45 days to complete the Biological Opinion. If there is any potential that a listed species could be taken as the result of the project, a statement authorizing this take is included in the Biological Opinion. There are basically three potential outcomes from consultation:

  1. Action will promote the conservation of listed species.
  2. Action is not likely to jeopardize the continued existence of a listed species and is not likely to destroy or modify designated critical habitat.
  3. Action is likely to jeopardize the continued existence of a listed species and/or is likely to destroy or modify designated critical habitat.

Conference, 50 CFR Part 402.10

FHWA is required to initiate a conference when a project with Federal participation has the potential to jeopardize a Federally proposed species and/or destroy or modify proposed critical habitat. A conference is held between a Federal agency and FWS/NMFS. A conference is initiated through a written request from FHWA to FWS/NMFS and includes the Biological Assessment for the project and any other relevant reports or studies with information on the action, the affected proposed species or proposed critical habitat.

The written request should include a request that the conference be conducted in accordance with the procedures for formal consultation. This way, if the species becomes listed, FWS/NMFS could accept the conference opinion as the Biological Opinion without interrupting the project. This is not automatic. The FWS/NMFS will have to be contacted with a request that they accept their conference opinion as their Biological Opinion. The potential outcomes from a conference are the same as those from a consultation but are only advisory until the species is actually listed.

Informal Consultation, 50 CFR Part 402.13

All correspondence between the FWS/NMFS and FHWA or their delegate, including a request for a list of species, is considered informal consultation. All formal negotiations should be preceded by informal consultation. Resolution of conflicts between a project and special status species during this process could eliminate the need to enter a formal process. If complete agreement can be reached during this process and a formal process is still required, it can be accomplished in a minimum of time.

During informal consultation, if any impacts to listed species can be reduced to the point of "not likely to adversely affect," the District should seek the written concurrence of FWS/NMFS. The Biological Assessment is submitted to FWS/NMFS by FHWA with the request for concurrence in the findings. This is done in accordance with 50 CFR Part 402.12 (j) and (k). The FWS/NMFS should respond in 30 days from the date that they receive the request. In those instances where the list provided by FWS/NMFS includes several listed species each will require closure. For those species that a "not likely to adversely affect" conclusion can be reached, a request for concurrence in that finding will be required. For those species where a "may affect" still exists, a request for consultation will be required. Both requests should be handled in a single letter. Don't assume that FWS/NMFS will automatically include their concurrence for other species when they write their Biological Opinion for the species on which consultation was required.

Technical Assistance

Technical assistance refers to informal discussions between Caltrans and resource agencies for the purpose of removing or reducing impacts to special status species that are neither listed nor proposed for listing. There are several classifications of species that are considered special status (candidates and species of concern at the Federal level and species of special concern at the State level) and should be considered during the Biological Assessment. While these species do not receive protection under either of the endangered species laws, they could be listed at any time. If any of these species are listed before construction is completed and there is a potential for impact, work would have to be suspended while consultation is completed. The closer the agreement concerning impacts and mitigation during the early stages of project development, the shorter the work stoppage for consultation. Technical assistance is informal; however, it should be taken as seriously as if the species were listed. FWS/NMFS technical assistance also includes recommendations for studies, persons to contact, etc. for listed species.

4-2.5 Programmatic Biological Assessments

Similar projects with recurring minor impacts to the same species are candidates for a programmatic consultation with FWS/NMFS. FWS/NMFS and Caltrans/FHWA agree to the type and magnitude of project impacts that will be allowed under the programmatic. A Programmatic Biological Assessment is completed that outlines what types of impacts would occur and what would be required to offset those impacts. Once the Programmatic Biological Opinion is issued and a project meeting the conditions of the programmatic is proposed, the District completes a project specific Biological Assessment. If FWS/NMFS concurs with the conditions in the Biological Assessment the project is appended to the programmatic Biological Opinion. The time savings in the process occurs through prior agreement to conditions (negotiation time) and the difference between the time it takes to append the project to the programmatic opinion (30 days) and the time it takes to complete a new consultation (135 days).

4-2.6 Incidental Take Permits

Caltrans is required to obtain an Incidental Take Permit when a project without Federal participation has the potential to take a Federally listed species. This permit is often referred to as a 10(a)(1)(B) permit, which is the section in the law which states "...if such taking is incidental to, and not the purpose of, the carrying out of an otherwise lawful activity." Permit application procedures can be found at 50 CFR Part 13 - General Permit Procedures, and Part 17 - Endangered and Threatened Wildlife and Plants for species under the jurisdiction of FWS. Procedures for species under the jurisdiction of NMFS can be found at 50 CFR Part 217 - General Provisions, Part 220 - General Permit Procedures, and Part 222 - Endangered Fish or Wildlife.

4-2.7 Exemption Process

When FWS/NMFS issues a Jeopardy Opinion for a project and there is no alternative to the project, there is a process in place that would allow an exemption to the ESA. However, proof must be demonstrated that not building the project would be of national concern. It is highly unlikely that Caltrans will ever seek an exemption. Instructions for application of an exemption can be found at 50 CFR Part 450 - General Provisions, Part 451 - Application Procedure, Part 452 - Consideration of Application by the Secretary, and Part 453 - Endangered Species Committee.


4-3.1 Consistency Determination, Section 2080.1 Fish and Game Code

For projects that impact species that are listed both under the state and federal acts, Section 7 consultation has been completed and a Biological Opinion and Incidental Take Statement have been obtained, the requirements of CESA can be met if DFG determines that the Incidental Take Statement is consistent with CESA. Therefore, when conducting consultations under Section 7 of FESA you should include DFG in the consultation process.

Upon receipt of an Incidental Take Statement, the district notifies the director of DFG, in writing, that an Incidental Take Statement has been issued pursuant to the Federal Endangered Species Act of 1973 (16 U.S.C.A. Sec. 1536) and requests DFG to make a determination as to whether the Incidential Take Statement is consistent with CESA. Submit 2 copies of the Biological Opinion and Incidental Take Statement with the request and send a copy, with attachment, to the appropriate DFG Regional Manager, since they will be conducting the actual review.

DGF will publish, in the General Public Interest section of the California Regulatory Notice Register, the receipt of that notice. Within 30 days DFG will determine whether the incidental take statement is consistent with CESA. The determination will be published in the General Public Interest section of the California Regulatory Notice Register.

4-3.2 Incidental Take Permit, Section 2081(b) Fish and Game Code

For projects that involve the take of a state listed only species, a permit must be obtained from DFG. Regulations for issuing take permits are found in Sections 783.1 through 783.8 of Title 14 of the California Code of Regulations. Normal processing of a permit application should take about four months, but can take up to seven months to complete. Fortunately, there are only 26 animal species that are state listed only. Thus, most CESA compliance should be accomplished through a determination, by DFG, that the federal incidental take authorization is "consistent" with CESA.

During the preparation of a permit application, you should consult with DFG in order to ensure that the application will meet the requirements of the regulations when submitted to the DFG. Applications for permits are submitted to the appropriate DFG Regional Manager. Each application must include all of the following:

(1) Applicant's full name, mailing address, and telephone number(s). Include the name and address of the person responsible for the project or activity requiring the permit.

(2) The common and scientific names of the species to be covered by the permit and the species' status under CESA.

(3) A complete description of the project or activity for which the permit is sought.

(4) The location where the project or activity is to occur or to be conducted.

(5) An analysis of whether and to what extent the project or activity for which the permit is sought could result in the taking of species to be covered by the permit.

(6) An analysis of the impacts of the proposed taking on the species.

(7) An analysis of whether issuance of the Incidental Take Permit would jeopardize the continued existence of a species. This analysis shall include consideration of the species' capability to survive and reproduce, and any adverse impacts of the taking on those abilities in light of (A) known population trends; (B) known threats to the species; and (C) reasonably foreseeable impacts on the species from other related projects and activities.

(8) Proposed measures to minimize and fully mitigate the impacts of the proposed taking.

(9) A proposed plan to monitor compliance with the minimization and mitigation measures and the effectiveness of the measures.

(10) A description of the funding source and the level of funding available for implementation of the minimization and mitigation measures.

(11) Certification in the following language:

I certify that the information submitted in this application is complete and accurate to the best of my knowledge and belief. I understand that any false statement herein may subject me to suspension or revocation of this permit and to civil and criminal penalties under the laws of the State of California.

In addition, since DFG will be a responsible agency for purposes of issuing an Incidental Take Permit where Caltrans is the lead agency for purposes of CEQA compliance, the following must be included in the permit application:

(1) The name, address, telephone number and contact person of the lead agency.

(2) A statement as to whether an environmental impact report, negative declaration, mitigated negative declaration, initial study or other document has been prepared or is being considered.

(3) At the option of the applicant, a notice of preparation, notice of determination, or draft or final environmental document may be attached.