Chapter 14 - Biological Resources

What does this topic include?

This chapter discusses the framework within which biological resources are considered during project planning, development and implementation. The laws, regulations and policies that apply to biological resources are discussed within the context of project delivery timelines. Biological resources discussed include:

  • Habitats and Vegetative Communities
  • Migratory Corridors
  • Plants
  • Wildlife
  • Fisheries
  • Special Status Species (regulated by a law, regulation or policy, such as threatened and endangered species)
  • Avoidance, Minimization and/or Mitigation

Biological Processes Flowchart

This flowchart provides information on how to prepare and review Biology projects.
This flowchart provides information on how to prepare and review Biology projects.
This flowchart provides information on how to prepare and review Biology projects.

Laws, Regulations, and Guidance

Chapter 1 of the SER provides links and information for general Federal Laws, Regulations and Guidance.

Federal Laws

Federal Regulations

Federal Executive Orders

Federal Guidance and Policy

State Laws


Policy Memos

Identification of Regulatory/Management Agencies

Federal Agencies

Agency Resource Regulated
U.S. Fish and Wildlife Service (USFWS) Threatened and endangered species
National Marine Fisheries Service (NOAA Fisheries) Threatened and endangered species, anadromous fisheries, marine mammals
U.S. Army Corps of Engineers (USACE) Waters of the U.S., including wetlands
Environmental Protection Agency (U.S. EPA) Waters of the U.S., including wetlands
National Park Service (NPS) Wild and Scenic Rivers
U.S. Forest Service (USFS) Survey and Managed Species
Bureau of Land Management (BLM) Survey and Managed Species

State Agencies

Agency Resource Regulated
California Department of Fish and Wildlife (CDFW) Natural resources including fish, wildlife, and plants
California Coastal Commission (CCC) Natural resources within the Coastal Zone
Regional Water Quality Control Board (RWQCB) Waters of the State
California Department of Parks and Recreation State parkland, natural, cultural and recreational resources

Inter-agency Coordination

Interagency coordination is required by several laws, including NEPA and CEQA. Coordination allows participation in the preparation of the documents in an effort to meet the requirements of all parties.

When the Department or a local agency is the CEQA lead agency, they must coordinate with any responsible and trustee agencies as defined by CEQA.  A responsible agency is an agency other than the lead agency that has a legal responsibility for also carrying out or approving a project. A responsible agency must actively participate in the lead agency's CEQA process. A trustee agency has jurisdiction over certain resources held in trust for the people of California, but do not have a legal authority over approving or carrying out the project. The state agencies most involved in the biological reviews and approvals are identified above.

On August 10, 2005, President George W. Bush signed into law the Safe, Accountable, Flexible, Efficient Transportation Equity Act: A Legacy for Users (SAFETEA-LU). SAFETEA-LU established a project delivery pilot program for 5 states (specified as Alaska, Ohio, Oklahoma, Texas, and California), allowing them to apply to FHWA to assume all FHWA environmental responsibilities under NEPA and other environmental laws (excluding the Clean Air Act and transportation planning requirements). California participated in the "Surface Transportation Project Delivery Pilot Program" (Pilot Program) pursuant to 23 USC 327, for more than five years, beginning July 1, 2007 and ending on September 30, 2012. When Title 23 USC 327 was amended by MAP-21 on July 6, 2012, to establish a revised and permanent Surface Transportation Project Delivery Program, the Department submitted a MOU pursuant to 23 USC 327, as amended, which FHWA approved and became effective October 1, 2012. The Department will continue to assume FHWA responsibilities under NEPA and other federal environmental laws in the same manner as was assigned under the Pilot Program, with minor changes. Refer to the SER Chapter 38 on NEPA Assignment for specific information.

Chapter 1 of the SER provides an overview of the Federal Endangered Species Act (FESA). This act and subsequent amendments provide for the conservation of endangered and threatened species and the ecosystems upon which they depend. The Department, acting as the federal lead agency will coordinate with USFWS or NOAA Fisheries, under FESA and request and receive species lists, prepare the biological assessment, and conduct the formal consultation.

For Department projects and when the Department is overseeing local agency prepared documents for federal funding, the Department's responsibilities are to review all environmental documents and studies for completeness and make the determination under NEPA that the documents are sufficient. This includes biological studies such as the Natural Environment Study (NES), the Biological Assessment (BA).

Chapter 1 of the SER also provides an overview of the Essential Fish Habitat (EFH) requirements under the Magnuson-Stevens Fishery Conservation and Management Reauthorization Act. This act governs marine fisheries management in United States federal waters. When required, EFH consultation will be initiated by the Department as assigned. Chapter 2 provides an overview of the California Endangered Species Act (CESA). The CESA (Fish and Game Code 2050 et seq.) establishes the policy of the state to conserve, protect, restore, and enhance threatened or endangered species and their habitats. Interagency coordination with the CDFW is recommended to assure that development of the project and any required mitigation is in accordance with the Fish and Game Code.

The District Biologist participates in the Clean Water Act Section 404 permitting process and NEPA/404 MOU by providing information relative to Waters of the U.S./wetland impacts from the project.

Early Coordination

Because of the complexity of biological issues and range of regulatory requirements, early coordination is often beneficial.  Early coordination may occur at various phases, including, but not limited to, the Regional Transportation Plan phase, the Project Initiation phase, and/or Draft Project Report phase. Under 23 USC 134-135, Metropolitan Planning Organizations (MPOs) and Regional Transportation Planning Agencies (RTPAs) are encouraged to consult or coordinate with planning officials responsible for other types of planning activities affected by transportation, including planned growth, economic development, environmental protection, airport operations and freight movement. Examples of early coordination could include:

  • Requests for Technical Assistance from USFWS/NOAA Fisheries
  • Information gathering
  • Informal consultation
  • Alternative Development Process

Discussion Points

  • Timing - construction, surveys, scheduling, project cost
  • Cumulative Effects
  • Overlapping regulatory jurisdictions
  • Regional variations in regulatory requirements
  • NEPA/404 MOU
  • Avoidance, minimization and compensation measures
  • Other project specific discussion points, as needed


Determining the Need for a Separate Technical Report

At the early scoping phase of a project, a preliminary environmental analysis report is completed to determine the level and type of technical studies and documentation needed to address the various effects to the environmental resources. The Biologist prepares the biological resource portion of the Preliminary Environmental Analysis Report (PEAR).

Typically a NES or NES (MI) summarizes technical documents related to effects on biological resources for use in the environmental document. If the scoping indicates potential affects to listed species, a Biological Assessment (BA) will be prepared. If waters of the U.S. may be affected, a Wetland Delineation/Assessment will be prepared. If mitigation will be required, a Habitat Mitigation and Monitoring Plan will be developed.

Examples of Biological Documents

Summary Reports:

  • Biological Section for the PEAR
  • Natural Environment Study (NES) or NES (MI)
  • Essential Fish Habitat Report (EFH)
  • Habitat Mitigation and Monitoring Plan (HMMP)

Technical Reports:

  • Biological Assessment (BA)
  • Supplemental BA
  • Wetland Delineation/ Assessment
  • Wetland ET II, Hydrogeomorphic Method (HGM), Rapid Assessment, etc.
  • Protocol Survey Reports

Information Packages:

  • Transmittal Memo(s) with Recommendations for Environmental Document
  • Permit Information
  • Commitment Summary
  • Notes to Resident Engineer Pending File
  • Water Quality Information

The Biological Section for the PEAR provides information relative to preliminary scoping for biological resources.

The Natural Environment Study (NES) summarizes technical documents related to effects on biological resources such as focused species studies, wetland assessments, biological assessments or other reports. A NES (MI) is an abbreviated version that is prepared for projects with minimal impacts to the biological resources and proportionally less need for documentation.

A NES or NES (MI) is prepared for all projects and serves as the technical basis for statements made in the environmental document, concerning plants, animals, and natural communities occurring in the biological study area. For additional guidance see the NES or NES (MI) format and SER, Volume 3. The author and the supervisor sign the NES and NES (MI).

Where the technical studies have determined that there could be an impact (positive or negative) to listed or proposed species or critical habitat, a species-focused biological assessment and/or biological evaluation provide supporting documentation during consultation with resource agencies.

Pursuant to 23 USC 326 and 23 USC 327, a Biological Assessment (BA) is prepared under the supervision and guidance of the Department when a project is likely to adversely affect a listed species or critical habitat or major actions and may require formal consultation. Where an existing programmatic biological opinion is applicable, a supplemental BA may be required.

Preparer Qualifications

Persons preparing biological technical reports should have education and experience equivalent to a State of California civil service classification of Environmental Planner (Natural Science). Where specialized studies are required, the preparer must have the additional qualifications necessary to perform the required studies. Specialized surveys required for biological technical reports may require special training, or permits or approval from the USFWS/NOAA Fisheries, and/or the California Department of Fish and Wildlife.

Recommended Methodologies

Protocols for conducting biological surveys must be chosen carefully to ensure the results are appropriate for the circumstances. The District Biologist should consult with regulatory and resource agencies to ensure that the protocol will be accepted. The District Biologist continues coordination with regulatory and resource agencies to ensure the studies are of a quality and nature to support the transportation decisions.

Surveys must be conducted by personnel familiar with the intricacies and details of the protocol to avoid misunderstandings.

Permits required for protocol surveys are rapidly changing and are best handled on a case-by-case basis in consultation with the resource and regulatory agencies having jurisdiction over the species.

Content and Recommended Format

The Department has developed forms, templates and guidance in partnership with FHWA to facilitate and streamline both the consistent development and the internal/external reviews of the biological technical studies. For projects on the State Highway System, all new biological technical documents will use the standard formats linked below. With NEPA Assignment, the use of these formats is required for the biological technical reports prepared for federal aid projects on local streets and roads.

Processing and Approval of Technical Reports

Each technical report has requirements for processing and approval.

For projects on the State Highway System, a Natural Environment Study (NES or NES [MI]) describes the existing biological environment, summarizes technical documents, and describes how the project alternatives affect the environment. The NES is the technical basis for statements made in the environmental document concerning plants, animals, and natural communities occurring in the project study area. The NES guidance requires a quality control process of peer review, technical writing review, specialty review, and supervisor approval. When an NES contains proposed mitigation or primary technical data and is the primary technical report for a study, approvals are required, as appropriate.

The Biological Assessment (BA) requires final approval from the Federal Highway Administration (FHWA) as the document represents their determination regarding effects. The BA is submitted to the USFWS/NOAA Fisheries.

Under 23 USC 326 and 23 USC 327, the BA does not require final approval from FHWA. The Department is the final signatory approval and submits the BA to the USFWS/NOAA Fisheries.

For projects off the State Highway System, processing of technical reports is covered in the Local Assistance Procedures Manual (LAPM), Chapter 6, Section 6.2. Categorical Exclusions are covered in LAPM, Chapter 6, Section 6.5 and 6.6.

When technical studies indicate that the project does not meet the criteria of a CE, the local agency should refer to SER Chapter 37 for detailed instructions on preparing and processing an EA or an EIS.

Consistent with the assignment of responsibility under 23 USC 326 and 23 USC 327, BA, NES, NES (MI), EFH and HMMP documents must include the signature of a biologist with professional standing as an Associate Environmental Planner (NS) or by a Senior Environmental Planner with experience as an Associate Environmental Planner (NS). The signature of the professional biologist on a document attests to: preparation according to generally accepted professional standards; data and professional conclusions; consistency with state policy and directives; accordance with state and federal regulatory law and regulation; that quality control processes have been followed including appropriate peer or specialist reviews with documented resolution of issues; and that the file documentation is complete. All consultant prepared documents will have a separate signature page for a biological professional signature as described above prior to submission to the Department for review.

At management discretion, Environmental Planner (NS) staff documented to have sufficient knowledge, skills and experience to independently conduct work of average difficulty, may be the professional biologist signer for non-complex NES (MI) reports with minimal impacts and/or mitigation commitments.

Information for Environmental Documentation

Categorical Exemption/Exclusion

The Natural Environment Study (NES) shall be placed in the project file to substantiate the CE determination. For minor projects, an abbreviated format (NES-MI) may be used to document consideration of biological impacts where impacts are de minimis.

Draft Environmental Documents

The District Biologist should provide the information required by the annotated outlines for environmental documents.

  • Natural Communities
  • Wetland and Other Waters
  • Plant Species
  • Animal Species
  • Threatened and Endangered Species
  • Invasive Species

The District Biologist should provide a transmittal memo that briefly summarizes the results of the biological studies for inclusion in the environmental document and proposed mitigation measures, if appropriate. (Note: Considerations to potential impacts to vegetative communities are required under both CEQA and NEPA and do not necessarily have to be tied to the plants' status as threatened or endangered or to its value as habitat for protected animals.)

Transmittal memo should include the following:

  • Impacts
  • Recommended significance findings
  • Needed actions such as permits and consultations
  • Avoidance, Minimization and/or Mitigation options and recommendations
  • Relevant text for the environmental document as appropriate.

Final Environmental Documents

The District Biologist should provide the information required by the annotated outlines for environmental documents.

The District Biologist should prepare a summary of any revisions, additional studies, species updates, approvals and opinions, as appropriate, to submit for inclusion in the environmental document.

Cumulative Impacts


It is recommended to use the Guidance for Preparers of Cumulative Impact Analyses and the Guidance for Preparers of Growth-related, Indirect Impact Analyses and for preparation of analysis under NEPA and CEQA. The document provides direction on the establishment of resource study areas, actions to be included, and documentation of standards and criteria for the cumulative analysis.

A cumulative impact is defined in the NEPA Regulations as "the impact on the environment which results from the incremental impact of the action when added to other past, present, and reasonably foreseeable future actions regardless of what agency (federal or non-federal) or person undertakes such other actions. Cumulative impacts can result from individually minor, yet collectively significant, actions taking place over a period of time." CEQ regulations at 40 CFR Section 1508.7 


An environmental document must discuss the cumulative impacts of a project when the project's incremental effect is cumulatively considerable. "Cumulatively considerable" means that the incremental effects of an individual project are considerable when viewed in connection with the effects of past projects, the effects of other current projects, and the effects of probable future projects. When examining a project with an incremental effect that is not "cumulatively considerable," it is not necessary to consider that effect significant, but the document must briefly describe its basis for concluding that the incremental effect is not cumulatively considerable.


When considering cumulative effects to federally listed species, Section 7 of the Federal Endangered Species Act considers cumulative effects to include the effects of future state, tribal, local or private actions that are reasonably certain to occur in the action area. Future federal actions that are unrelated to the proposed action are not considered because they require separate consultation.

Section 7 regulations require the federal action agency to provide an analysis of cumulative effects, along with other information, when requesting initiation of formal consultation. Cumulative effects are defined differently under Section 7 than NEPA. The Final ESA Section 7 Consultation Handbook provides the following definition "cumulative effects include the effects of future state, tribal, local or private actions that are reasonably certain to occur in the action area considered in this biological opinion. Future federal actions that are unrelated to the proposed action are not considered in this section because they require separate consultation pursuant to section 7 of the Act. The concept of cumulative effects is frequently misunderstood as it relates to determining likely jeopardy or adverse modification." If the difference between the FESA cumulative impact analysis and the NEPA/CEQA cumulative analysis is substantial, this should be noted in the transmittal memo to the Environmental Generalist discussed in the section - "Information for the Environmental Document".

Because cumulative impact assessment is an area of complexity and limited guidance, this should be refined in consultation with the federal lead and resource agency. Guidance regarding cumulative impacts should come from the Functional Manager and Project Manager/Project Development Team.

Timing of Studies with the Environmental Process

There are three main types of biological resource studies conducted at various phases of a project:

  1. PID Phase - Preliminary project review to develop the scope of biological resource studies.
  2. PA&ED Phase - Focused studies to determine project impacts to species, support the BA, or to develop mitigation plans.
  3. PS&E and Construction - Supplemental studies to confirm results or to address additional issues that arise during design, coordination and/or consultation.

Information Needed for Project Delivery

Regional Transportation Plan

A Regional Transportation Plan (RTP) requires the preparation of a CEQA environmental document, normally a program or master Environmental Impact Report. Under 23 USC 134-135, MPOs and RTPAs are encouraged to consult or coordinate with planning officials responsible for other types of planning activities affected by transportation and to include the following information, as appropriate, in the environmental document for the plan:

  • List of vegetation, wetland, and aquatic communities that may occur
  • Endangered and threatened species known or suspected to be present
  • List of known or possible wildlife corridors
  • Designated and proposed critical habitat
  • Other special status wildlife or plants known or that may occur

Project Initiation Document

For projects that require a Project Study Report - Project Development Support (PSR-PDS), a Preliminary Environmental Analysis Report (PEAR) is prepared as part of the Project Initiation Document (PID). The PSR identifies the purpose and need, scope, schedule and estimated cost of a project, including the capital outlay components, such as right-of-way acquisition and construction costs. The PEAR provides information about potential environmental issues and potential costs of the environmental work related to the project.

Biological scoping is conducted at the PID phase to inventory potential resources affected by the project, associated timing constraints, permit requirements, environmental commitments and costs.

The Biology Section of the PEAR Handbook directs the District Biologist to:

  • Conduct a literature search
  • Perform appropriate level of survey
  • Prepare report
    • Setting and sensitive biological resources
    • Specific surveys needed-schedule, protocols, and approvals
    • Agency contacts, sources consulted, and coordination
    • Potential effects and mitigation-costs and preliminary schedules
    • Permits required
    • Summary and delineation (map or diagram) of potential resources
    • Resource estimate by WBS activity code
    • Time estimate and seasonal constraints for delivery of studies

Note: The Biologist should document situations or assumptions that might affect the alternatives, cost, timing, scheduling, or viability of the project.

The PEAR is an important part of the Project Study Report. The PEAR provides the initial environmental evaluation of a project and all feasible alternatives before it is programmed. Because the environmental process can have a substantial impact on the project alternatives, design, costs, schedule, and delivery, the PEAR must clearly present and discuss the results of preliminary environmental studies in order to identify environmental constraints that may affect design. The PEAR also estimates the scope, schedule, and costs associated with gaining environmental approval. The information contained in the PEAR provides foundational information to the environmental team as they begin studies in the Project Report phase, facilitating early consultation with state and federal resource agencies. The Biologist should identify the anticipated biological documents that are necessary support for the environmental document.

For projects on the State Highway System that do not require a PSR-PDS, "it is highly recommended" that a PEAR be prepared per the policy memo.

For projects off the State Highway System, complete the Preliminary Environmental Studies (PES) form. The information required for the PES satisfies the environmental requirements for the PSR equivalent.

Draft Project Report

The Draft Environmental Document (DED) is prepared simultaneously with the Draft Project Report. Typically a NES or NES (Minimal Impacts) summarizes technical documents related to effects on biological resources for use in the environmental document such as,

  • The methods and results of studies completed and/or in progress
  • Identification of effects, quantified as appropriate, for each biological resource and alternative
  • Identification of proposed mitigation, avoidance, minimization, and conservation measures
  • A listing of permits and agreements needed, and other agency coordination

Note: Once a project is funded and enters the project delivery phase, it is important to revisit the cost, schedule, scope, and assumptions made in the project initiation document. This is especially important where new species have been listed, regulations have changed, or seasonal constraints may apply. A biology specific work plan can be a useful tool to assist with the scoping effort.

Project Report

The Final Environmental Document includes the following information:

Verification of all information from RTP stage, PID stage and Draft Project Report stage, and:

  • Identification of impacts to biological resources and proposed mitigation measures
  • Cost estimates for selected environmental commitments
  • Biological Opinion(s)
  • Fish and Game Code 2080.1 Consistency Determination

Permit Requirements

The following is a list of commonly required permits and does not represent a complete list of all federal or state requirement or agreements for biological resources. For additional information related to biological resource permits and requirements see SER, Volume 3.

Federal Permits

Agency Law or Code Type of Permit or Agreement

U.S. Fish and Wildlife Service

Endangered Species Act Section 7

Incidental Take Statement (Biological Opinion)

U.S. Fish and Wildlife Service

Endangered Species Act—Section 10(A)(1)b

Incidental Take Statement (Biological Opinion)

U.S. Fish and Wildlife Service

Migratory Bird Act

Migratory Bird Special Purpose Permits

NOAA Fisheries

Endangered Species Act—Section 7 and 10

Incidental Take Statement (Biological Opinion) or (Habitat Conservation Plan)

NOAA Fisheries

Marine Mammal Protection Act

Incidental Harassment Authorization

NOAA Fisheries

Magnuson Stevens Act

Essential Fish Habitat (EFH)

U.S. Army Corps of Engineers

Section 404 of the Clean Water Act

Individual or General (Nationwide or Regional) Permit

U.S. Army Corps of Engineers

Section 10 of the Rivers and Harbors Act

Individual or General (Nationwide or Regional) Permit

State Permits

Agency Law or Code Type of Permit or Agreement

California Department of Fish and Game

Fish and Game Code 1600

Streambed Alteration Agreement

California Department of Fish and Game

Fish and Game Code 2081 or 2080.1

Incidental Take Permit
Consistency Determination

California Department of Fish and Game

Fish and Game Code 1002 and Title 14 Sections 650 and 670.1

Collection permits

Coastal Commission

California Coastal Act of 1976 Sections 30250–30255

Coastal Development Permit

Regional Water Quality Control Board

Section 401 of the Clean Water Act

Certificate of Waste Discharge Requirements

Activities That May Occur During the Project Design Phase

During the Project Design phase, coordination between Environmental and Design must continue to ensure that the conditions of the Environmental Document are met. The membership of the PDT may change as the design develops. Because changes in project design can arise during the Design phase, the Biologist must continue to review the changing project footprint and coordinate with the design changes with biological studies and proposed permits and mitigation. Even small changes in design features can result in changes to project impacts, mitigation and permits needed. The Biologist participates in the reevaluation process to ensure that any resulting changes to the biological environment are appropriately evaluated, (review of Draft PS&E package, participate in PDT meetings, work with resource agencies, renegotiate permits, etc.). Failure to address these changes in a timely fashion may result in project delivery delay.

The District Biologist coordinates with the Project Development Team to provide information regarding such items as compliance with approvals, opinions, permits, conditions, requirements and deadlines to include in the contract and the RE Pending File.

The bid package and contract informs the Contractor about the project and project related requirements necessary for the Contractor to develop appropriate bids for the work that must be undertaken to complete all aspects of the project. The District Biologist prepares the information to input into the Environmental Commitments Record (ECR).

The contract contains instructions to the Contractor regarding such items as compliance with approvals, opinions, permits, conditions, requirements and deadlines.

The RE Pending File contains instructions to the Resident Engineer regarding such items as compliance with approvals, opinions, permits, conditions, requirements and deadlines that come from the ECR.

The RE Pending File and contract should both contain permits, agreements or requirements related to biological resources.

Activities That May Occur During the Construction Phase

The District Biologist participates in the pre-construction meetings, pre-construction surveys, construction monitoring and coordination to ensure compliance with approvals, opinions, permits, conditions, requirements and deadlines.

The RE has the responsibility for the construction site and for ensuring the Contractor's compliance with applicable laws, permits, contract plans and specifications, and constraints identified in the Biological Technical Reports that are also identified in the ECR. All communication and site visits regarding activities or issues at the construction site must go through the RE. The RE communicates biological concerns to the Contractor or to the Biologist.

During construction, the District Biologist assists the RE to ensure that all biological requirements and considerations in the contract are understood by, and those necessary preparations are made by, the RE and the Contractor. The Biologist may conduct construction monitoring or oversee a consultant's biological construction monitoring.

Activities that May Occur During Maintenance

Maintenance and owner operator activities must adhere to biological or natural resource laws, regulations, policies, agreements, permit requirements, or contractual agreements regarding their activities within the operating Right of Way. The District Biologist coordinates with Maintenance to ensure compliance with various laws and regulations and with the Department's Stewardship responsibilities. For example, use of mitigation or Environmentally Sensitive Area (ESAs) placards may be used by Maintenance to identify sensitive areas. The District Biologist may coordinate with Maintenance and/or act as a liaison to update ESAs and ESA information on Maintenance Right of Way maps. The District Biologist works proactively to assist Maintenance in addressing biological issues.

For example, the District Biologist may coordinate with the Maintenance Supervisor regarding activities in or around mitigation areas or ESAs. Mitigation areas or ESAs may be found on Right of Way maps. Activities such as mowing, spraying, or culvert cleaning may impact natural resources and may require review of regulations, permits, or agreements. Advanced coordination and planning of maintenance activities may allow timing of work to avoid impacts to sensitive natural resources and delays to maintenance activities.


(Last content update: 8/12/14: JH)