Compliance with the Federal Endangered Species Act

Section 7 of the Endangered Species Act

The Endangered Species Act (ESA) was passed by congress in 1973 with the purpose to protect and recover imperiled species and the ecosystems upon which they depend. The Endangered Species Act is administered by two agencies, the United States Fish and Wildlife Service (USFWS) and the National Marine Fisheries Service (NMFS). The USFWS has primary responsibility for terrestrial and freshwater species, while the NMFS has responsibility over marine wildlife and anadromous fish. Under the ESA, species may be listed as either endangered or threatened. If a species is listed as endangered, it is in danger of extinction throughout all or a significant portion of its range. If a species is listed as threatened, it is likely to become endangered within the foreseeable future. All plants and animals, except for pest insects, are eligible for listing as endangered or threatened for the purposes of ESA.

Section 7(a)(2) of the ESA requires that for actions authorized, funded, or carried out by a Federal agency, that the agency shall, in consultation with USFWS and/or NMFS, ensure that the action is not likely to jeopardize the continued existence of any endangered or threatened species or result in the destruction or adverse modification of the critical habitat of the endangered or threatened species. Therefore, before any activity can be authorized by the Corps under Section 404 of the Clean Water Act or Section 10 of the Rivers and Harbors Act of 1899, we must ensure that the project is in compliance with ESA.

Expand to learn about the Section 7 Consultation Overview

For any activity that requires authorization under Section 404 of the Clean Water Act or Section 10 of the Rivers and Harbors Act, the Corps will need to make a determination on whether the activity would affect a Federally listed endangered or threatened species. This requirement stands whether the activity would qualify for authorization under a Nationwide Permit or Regional or Programmatic General Permit or whether the activity would require processing under a Letter of Permission or Standard Permit. The consultation requirements for compliance with Section 7 of the ESA outlined below apply in cases where the applicant is not a Federal agency or in cases where the Corps is the lead Federal agency. Activities in which another Federal agency is the lead Federal agency for compliance with Section 7 of the ESA have an alternate process, which is described below.

No Effect

If the Corps determines that the activity requiring authorization would not affect a listed species, no consultation is required with the USFWS and/or NMFS. A determination that the activity would not affect a listed species is made by the Corps and cannot be made by the applicant, and must be made by the Corps. Generally, a determination of no effect would only be made if listed species do not occur and do not have the potential to occur on a site. If the Corps determines that the activity requiring authorization would affect a listed species, the Corps must initiate either informal or formal consultation with the USFWS and/or NMFS.

Informal Consultation

Informal consultation is defined within the ESA regulations (50 CFR 402.02) as a “process that includes all discussions, correspondence, etc., between the Service and the Federal agency or the designated non-Federal representative prior to formal consultation, if required.” Informal consultation with the USFWS and/or NMFS is initiated by a letter only when the Corps determines that a project may affect, but is not likely to adversely affect a Federally listed endangered and/or threatened species. This not likely to adversely affect (NLAA) determination is generally made by the Corps if it is determined that a species or habitat may exist on site, but either will not be affected by the project, or certain avoidance and minimization measures would be adopted by the applicant that would minimize the effects to the extent that the species or habitat would not be adversely affected. If the USFWS and/or NMFS agree with the Corps’ NLAA determination, they will respond via a letter of concurrence. In many cases a letter of concurrence for Section 7 of the ESA is based on mitigation measures (e.g. timing restrictions, best management practices, etc.) that are proposed by the applicant.

Formal Consultation

Formal consultation is defined within the ESA regulations (50 CFR 402.02) as a “process between the Service and the Federal agency that commences with the Federal agency’s written request for consultation under section 7(a)(2) of the Act and concludes with the Service’s Issuance of the biological opinion under section 7(b)(3) of the Act.” Formal consultation with the USFWS and/or NMFS is initiated by a letter only when the Corps determines that a project may affect and is likely to adversely affect a Federally listed endangered and/or threatened species. This determination of adverse affect is made by the Corps if it is determined that a species or habitat is present on the site and would be adversely affected by the project. The biological opinion will state the opinion of the USFWS and/or NMFS as to whether or not the Federal action is likely to jeopardize the continued existence of listed species or result in the destruction or adverse modification of critical habitat.

In cases where the USFWS and/or NMFS determines that the action will not violate Section 7(a)(2) of the ESA, the biological opinion will contain a statement concerning incidental take that: (1) specifies the impacts (amount of take) on the species; (2) specifies reasonable and prudent measures that are necessary or appropriate to minimize impacts; (3) in the case of marine mammals, specifies measures necessary to comply with Section 101(a)(5) of the Marine Mammal Protection Act of 1972 and applicable regulations with regard to the taking; (4) set forth terms and conditions (including, but not limited to reporting requirements) that must be complied with to implement the reasonable and prudent measures; and (5) specifies the procedures to be used to handle or dispose of any individuals of a species actually taken.

Formal consultation with the USFWS and/or NMFS is concluded with the issuance of the biological opinion.

Expand for Consultation Procedures, Information Requirements & Compliance
Information Required to Initiate Consultation

In order to facilitate consultation with the USFWS and/or NMFS, applicants need to submit the following information to the Corps:

  1. A description of the action to be considered.
  2. A description of the specific area that may be affected by the action.
  3. A description of any listed species or critical habitat that may be affected by the action.
  4. A description of the manner in which the action may affect any listed species or critical habitat and an analysis of any cumulative impacts.
  5. Relevant reports including any environmental impact statement, environmental assessment, or biological assessment prepared.
  6. Any other relevant available information on the action, the listed species, or critical habitat.

Electronic submissions should be sent to SPKRegulatoryMailbox@usace.army.mil.

This information is required and should be provided with all permit requests. Failure to do so may result in a delay in the Section 7 Consultation process. In addition, we recommend that you complete the ESA Information Guidelines, to assist in ensuring all of the required information is submitted. You should also provide us with an extra copy of the information so that it can be forwarded to the appropriate agency with our request for consultation. If consultation is required with both USFWS and NMFS, please send two additional sets of this information along with your application. If available, please provide an electronic version of the information on a compact disc.

How to Obtain Information on Listed Species

In many cases, applicants will utilize a consultant to prepare the information required to be submitted to the Corps for compliance with Section 7 of the ESA.

Federally listed species that may be affected by an activity will depend on the location of the activity. The Sacramento District boundaries include Nevada and Utah and portions of California and Colorado.

Within California, Federally listed endangered and/or threatened species include those under the jurisdiction of both the USFWS and the NMFS. Because Nevada and Utah do not have marine mammals or anadromous fish, Federally listed endangered and/or threatened species are under the jurisdiction of just the USFWS. Information on species that may occur within specific geographic areas in the Sacramento District boundaries may be obtained by visiting the IPaC website.

Federal Agency Procedures

In accordance with ESA regulations at 50 CFR 402.07, when an action involves more than one Federal agency, compliance with Section 7 of the ESA may be fulfilled through a lead agency. Factors used to determine the lead Federal agency include: the time sequence in which the agencies would become involved, the magnitude of their respective involvement, and their relative expertise with respect to the environmental effects of the action. For an activity that requires authorization from the Corps, the Federal applicant (or lead Federal agency) should conduct early coordination with the Corps on the determination of the permit area. Prior to initiating consultation with the USFWS and/or NMFS, the Federal applicant should request that the Corps designate them to act on the Corps’ behalf for compliance with Section 7 of the ESA. Following completion of ESA consultation, the lead Federal agency should provide all relevant documentation to the Corps demonstrating any previous consultation efforts as it pertains to the Corps’ permit area. If the Corps does not designate another Federal agency as the lead for ESA, or if the documentation submitted does not demonstrate compliance with Section 7 of the ESA, the Corps will initiate consultation for compliance, as appropriate.

Compliance with Section 7

Provided there are no other outstanding information needs (e.g. alternatives information) and the project is in compliance with all other Federal laws (e.g. Section 106 of the National Historic Preservation Act, Section 401 of the Clean Water Act), following completion of Section 7 consultation (through either the receipt of a letter of concurrence for NLAA determinations or through the receipt of a biological opinion) the Corps will make a decision on whether to verify the project under a Nationwide Permit or Regional/Programmatic General Permit, or whether to issue or deny a Letter of Permission or Standard Permit. If the Corps determines that it is appropriate to authorize the project, a special condition will be placed on the verification or permit requiring that the applicant comply with all of the terms and conditions of the biological opinion and/or follow all of the mitigation measures proposed as part of the project, which were relied on for the letter of concurrence. Failure to comply with the terms and conditions of the letter of concurrence and/or biological opinion may result in an enforcement action by the Corps and/or USFWS and/or NMFS.

Expand to view Programmatic Biological Opinions
Expand to learn about Habitat Conservation Plans (HCPs)
What is a Habitat Conservation Plan (HCP)?

Section 10(a)(1)(B) of the federal Endangered Species Act (ESA) authorizes the United States Fish and Wildlife Service (USFWS) and/or National Marine Fisheries Service (NMFS) to issue permits to non-federal entities for the incidental take of a federally-listed threatened and/or endangered species. In order to obtain authorization under Section 10(a)(1)(B) of the ESA, non-federal entities must develop a conservation plan that meets specific requirements as identified in the ESA, apply for an incidental take permit, and once issued, implement the project as specified in their permit.

A Habitat Conservation Plan (HCP) is a planning document designed to accommodate economic development to the greatest extent possible by authorizing the limited and unintentional take of listed species when that take occurs incidental to otherwise lawful activities. The plan is designed not only to help landowners and communities but also to provide long-term benefits to species and their habitats.

HCPs describe the anticipated effects of the proposed taking from an impact to waters of the US, how those impacts will be minimized or mitigated, and how the conservation measures included in the plan will be funded.

If the USFWS or NMFS finds that an HCP meets the specified criteria, it issues an incidental take permit. This allows the permit holder to proceed with an activity that could otherwise result in the unlawful take of a listed species. (see https://www.fws.gov/service/habitat-conservation-plans and/or https://www.fisheries.noaa.gov/permit/permits-incidental-taking-endangered-and-threatened-species for more information on Section 10(a)(1)(B) of the ESA and habitat conservation plans).

What is the U.S. Army Corps of Engineers, Sacramento District (Corps’) role in HCPs?

The Corps does not have a direct role in compliance with Section 10(a)(1)(B) of the ESA, nor in the development of HCPs, as these are for activities conducted by non-federal entities. However, in cases where activities conducted by non-federal entities would require authorization by the Corps under Section 10 of the Rivers and Harbors Act (RHA) for work or structures in navigable waters of the U.S., and/or Section 404 of the Clean Water Act (CWA) for the discharge of dredged and/or fill material into waters of the U.S., the Corps must ensure compliance with Section 7 of the ESA. Section 7 of the ESA requires the Corps to consult with USFWS and/or NMFS for proposed activities that may affect a federally-listed threatened and/or endangered species, or their designated critical habitat.

Because many of the activities covered under two regional HCPs, in Sacramento and Placer counties, also require authorization by the Corps under Section 404 of the CWA, the Corps agreed to be a cooperating agency on the U.S. Fish and Wildlife Service’s (USFWS) Environmental Impact Statements prepared in accordance with the National Environmental Policy Act (NEPA) for two habitat conservation plans in the Sacramento region: the South Sacramento Habitat Conservation Plan (SSHCP) and the Placer County Conservation Program (PCCP). Because many of the listed species to be covered by the SSHCP and PCCP spend some or all of their lifecycles in aquatic environments, the Sacramento District has worked with the Plan Partners and other agencies since the plans’ formative stages. In 2019, the Corps finalized a permit strategy for the SSHCP and in 2021 finalized a permit strategy for the PCCP.

Benefits of CWA 404 alignment with the HCPs?

The Sacramento District views the HCPs as a chance to improve both species and aquatic resource protection in a coordinated way on a regional scale, while taking into account planned development and providing greater certainty for the regulated public. With this in mind, the Sacramento District has coordinated with the USFWS, NMFS and Plan Participants to develop and implement a “streamlined” approach to permitting under CWA 404 that encompasses a number of different permit types and processes.

The Sacramento District requested and received programmatic consultations under Section 7 of the ESA with the USFWS and NMFS for all covered activities that require CWA permits to further streamline the CWA 404 regulatory review process. The Corps also received general 401 Water Quality Certifications from the Central Valley Regional Water Quality Control board for each of the programmatic general permits (PGPs) issued under the permit strategy.

Current HCPs in the Sacramento District

Placer County Conservation Program HCP/NCCP
What is the Placer County Conservation Program (PCCP)?

The PCCP applies to western Placer County and specific conservation activity areas in neighboring Sutter County. The PCCP includes the Western Placer Habitat Conservation Plan and Natural Community Conservation Plan (HCP/NCCP), the proposed Western Placer County Aquatic Resources Program (CARP), and the Western Placer In-Lieu Fee (ILF) Program.

The HCP/NCCP covers fourteen species of wildlife, including nine state and/or federally-listed as threatened or endangered. The CARP is the County’s program to provide a structure for protecting aquatic resources in western Placer County while streamlining the environmental permitting process for impacts to aquatic resources. The HCP/NCCP uses a regional approach to address issues related to planned development and species habitat conservation and restoration.

Where is the PCCP applicable?

The boundaries of the approximately 270,000-acre PCCP are generally Nevada and Yuba Counties on the north, the City of Auburn and California State Highway 49 on the east, Sacramento County on the South, and Sutter County on the west. The PCCP Plan Area also includes specific areas in western Placer County and a small area in adjacent Sutter County where specific covered activities may be conducted by the Plan Participants. The Plan Area excludes the Cities of Auburn, Roseville and Rocklin and the Town of Loomis, with the exception of specific activities within these cities that would be conducted by the Plan Participants.

Who are the PCCP Plan Participants?

The four PCCP Plan Participants are the County of Placer, City of Lincoln, South Placer Regional Transportation Authority (SPRTA), and Placer County Water Agency (PCWA). The Plan Participants have formed the Placer Conservation Authority (PCA), a joint exercise of powers agency, to implement the HCP/NCCP and the CARP commitments and requirements. Based on the HCP/NCCP, the U.S. Fish and Wildlife Service (USFWS) and National Marine Fisheries Service (NMFS) issued species incidental take permits to the Plan Participants and the PCA under Section 10 of the Endangered Species Act (ESA 10). The USFWS and NMFS have conducted internal consultations under Section 7 of the ESA (ESA 7) and complied with the National Environmental Policy Act (NEPA) and other related laws.

PCCP Permit Strategy (Grouped by impact on the human environment, including aquatic resources)
Minimal Impact Activities
Programmatic General Permit (PGP) 18 - Minimal Impact Activities under the Placer County Conservation Program

For certain covered activities identified in the Western Placer County Habitat Conservation Plan/Natural Community Conservation Plan (HCP/NCCP), under the Placer County Conservation Program (PCCP), that result in the discharge of dredged and/or fill material into waters of the United States (U.S.) resulting in no more than minimal individual and cumulative impacts. An activity is verified under the PGP when Placer County or the City of Lincoln issues an authorization in compliance with the February 2020, County Aquatic Resources Program (CARP), implementing ordinances, and all applicable terms and conditions of the HCP/NCCP.

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Regional General Permit (RGP) 19 - Minimal Impact Activities By PCWA under the PCCP

For covered activities conducted by the Placer County Water Agency (PCWA) under the Western Placer County Habitat Conservation Plan/Natural Community Conservation Plan (HCP/NCCP), that result in the discharge of dredged and/or fill material into waters of the United States (U.S.) resulting in no more than minimal individual or cumulative impacts.

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Regional General Permit (RGP) 20 - Minimal Impact Activities Under the Western Placer County ILF Program

For activities conducted under the Western Placer County In-lieu Fee (WPILF) Program and covered by the Western Placer County Habitat Conservation Plan/Natural Community Conservation Plan (HCP/NCCP), that result in the discharge of dredged and/or fill material into waters of the United States (U.S.) resulting in no more than minimal individual and cumulative impacts.

The activities authorized would be conducted to meet the Conservation Strategy as identified in the HCP/NCCP. An activity is authorized under this RGP after this office approves the individual In-lieu fee project under the WPILF Program.

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Activities with more than minimal but less than significant impact
A Letter of Permission (LOP) procedure

Letter of Permission Procedure for Covered Activities Under the Western Placer County Habitat Conservation Plan/Natural Community Conservation Plan With Less Than Significant Impact

To efficiently authorize activities covered by the HCP/NCCP which involve discharges of dredged or fill material into waters of the United States (U.S.) under Section 404 of the Clean Water Act (CWA 404) with more than minimal, but less than significant, impacts on the aquatic environment. This HCP/NCCP LOP Procedure is an optional abbreviated permit process available to all applicants seeking Department of the Army (DA) authorization for activities meeting the criteria and conditions described in this notice. If the proposed activity does not meet the terms and conditions of this LOP or the applicant chooses not to use this process, the activity may be authorized under a different permit type or procedure.

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Per the procedures, a pre-application meeting is required for the LOP:

  • Email: SPKRegulatoryMailbox@usace.army.mil
  • It is suggested to state the following in the subject of email: HCP Pre-application meeting request for ‘NAME PROJECT’ and include the relevant SPK-YEAR-### if there is one.
  • Additionally, to facilitate an effective pre-application meeting among the agencies, please submit the following prior to the meeting:
    • The applicant’s name and company/agency/organization;
    • Telephone number, mailing address, and email;
    • A delineation of wetlands and other waters of the U.S. for the proposed activity site;
    • A location map and appropriate aerial and other imagery of the activity site and a vicinity map showing the proposed site and its geographical, physical and environmental context;
    • A complete description of the proposed activity, including as much of the information identified under 33 CFR 325.1 (d) “Content of application” as is available, including plan and profile views of the proposed work relative to potential waters of the U.S., showing areas, types and acreages of aquatic resources proposed to be impacted;
    • Draft information, in report form, concerning on-site practicable alternatives and the relative environmental impacts of those alternatives as compared to the environmental impacts of the proposed activity, in accordance with 33 CFR 325.1 (e) and 323.6 (a). The information must address compliance with the Environmental Protection Agency’s 404(b)(1) Guidelines at 40 CFR part 230, and;
    • An explanation of how impacts associated with the proposed activity are to be avoided, minimized, and compensated for, and a draft compensatory mitigation plan for the impacts and losses of waters of the U.S., in accordance with 33 CFR part 332.
Other activities consistent with the PCCP that may have a significant impact and require the preparation of an EIS
Abbreviated Standard Permit (SP) process

Abbreviated Standard Permit Process for Covered Activities Under the Placer County Conservation Program With Significant Impacts on the Human Environment

For the small number of HCP/NCCP covered activities requiring authorization under Section 404 of the Clean Water Act (CWA 404) that may significantly affect the quality of the human environment under the National Environmental Policy Act (NEPA), requiring the preparation of an Environmental Impact Statement (EIS). As a result of coordination and alignment with the HCP/NCCP and the CARP, the Corps' evaluation process for SP applications under this process will be streamlined or “abbreviated” to produce higher quality and faster decisions.

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South Sacramento HCP

The SSHCP covers 28 species of plants and wildlife, including ten that are state and/or federally-listed as threatened or endangered. The SSHCP is a regional approach to address issues related to planned development and species habitat conservation, following a comprehensive conservation strategy, over a 50-year period. The SSHCP is implemented locally concurrently with a local Aquatic Resource Protection Program (ARP). The ARP is enacted by local ordinances to authorize local Aquatic Resource Impact Permits. Compensatory mitigation requirements are fulfilled by payment into the Corps-authorized South Sacramento In-Lieu Fee (ILF) Program.

The boundaries of the 317,655-acre SSHCP Plan Area are generally U.S. Highway 50 to the north, the Sacramento River levee and County Road J11 to the west, the county line with El Dorado and Amador Counties to the east, and the county line with San Joaquin County to the south. The seven SSHCP Plan Permittees are the County of Sacramento, City of Galt, City of Rancho Cordova, Sacramento County Water Agency, Sacramento Regional County Sanitation District the Southeast Connector Joint Powers Authority, and the South Sacramento Conservation Agency Joint Powers Authority (SSCA).

SSHCP Permit Strategy:

  • Programmatic General Permit (PGP) 17, founded on a local aquatic resources protection program and implemented by local ordinances, and designed to reduce duplication with that program, for activities with minimal individual and cumulative effects on the aquatic environment.
  • Regional General Permit (RGP) 15 for minimal impact activities to implement the HCP/NCCP conservation strategy under the South Sacramento ILF program.
  • A Letter of Permission (LOP) procedure for activities with more than minimal but less than significant effects on the human environment, including aquatic resources; and
  • An abbreviated standard permit (SP) procedure for other activities consistent with the SSHCP that may have a significant impact on the human environment and require the preparation of an EIS.
  1. Permit Strategies for the South Sacramento HCP:
    • PGP 17: 2024.07.24-PGP17-w-attachments-SPK-1995-00386.pdf
    • RGP 15: 07.24.2024-RGP15-with-attachments-SPK-1995-00386.pdf
    • LOP Procedure: SSHCP LOP_Procedure-199500386-July2019-w-Attach-1.pdf
      1. Per the procedures, a pre-application meeting is required for the LOP:
      • Email: SPKRegulatoryMailbox@usace.army.mil
      • It is suggested to state the following in the subject of email: HCP Pre-application meeting request for ‘NAME PROJECT’ and include the relevant SPK-YEAR-### if there is one.
      • Additionally, to facilitate an effective pre-application meeting among the agencies, please submit the following prior to the meeting:
        • The applicant’s name and company/agency/organization;
        • Telephone number, mailing address, and email;
        • A delineation of wetlands and other waters of the U.S. for the proposed activity site;
        • A location map and appropriate aerial and other imagery of the activity site and a vicinity map showing the proposed site and its geographical, physical and environmental context;
        • A complete description of the proposed activity, including as much of the information identified under 33 CFR 325.1 (d) “Content of application” as is available, including plan and profile views of the proposed work relative to potential waters of the U.S., showing areas, types and acreages of aquatic resources proposed to be impacted;
        • Draft information, in report form, concerning on-site practicable alternatives and the relative environmental impacts of those alternatives as compared to the environmental impacts of the proposed activity, in accordance with 33 CFR 325.1 (e) and 323.6 (a). The information must address compliance with the Environmental Protection Agency’s 404(b)(1) Guidelines at 40 CFR part 230, and;
        • An explanation of how impacts associated with the proposed activity are to be avoided, minimized, and compensated for, and a draft compensatory mitigation plan for the impacts and losses of waters of the U.S., in accordance with 33 CFR part 332.
    • Abbreviated SP process: SSHCP SP Abbreviated_USACE-July-2019.pdf
  2. Link to South Sacramento ILF in RIBITS:
  3. USFWS Biological Opinion for SSHCP (includes programmatic coverage of Section 404 Permit Strategy):
    2019.04.30-SSHCP-BO-81420-2008-F-1526-10 South Sacramento HCP.pdf
  4. Partner webpages/links: