Chapter 14 - Biological Resources

• National Environmental Policy Act (NEPA) (42 USC 4321 et seq.)
• Federal Endangered Species Act of 1973 (16 USC 1531-1543)
• National Wild and Scenic Rivers Act (16 USC 1271-1287)
• 16 USC 661-666: Fish and Wildlife Coordination Act
• 16 USC 703-711: Migratory Bird Treaty Act
• 16 USC 460: Land and Water Conservation Fund Act (Section 6(f))
• Marine Mammal Protection Act
• Clean Water Act (33 USC 1251-1376)
• Coastal Zone Management Act
• Rivers and Harbors Act (Section 10) (33 USC 401 et seq.)
• Magnuson-Stevens Fishery Conservation and Management Reauthorization Act (50 CFR Part 600)

• Inter-agency Cooperation - Endangered Species Act of 1973, as amended (50 CFR Part 402)
• Regulatory Programs of the Corps of Engineers (33 CFR 320 through 330)

• Executive Order 13112: Invasive Species
• Executive Order 11990: Protection of Wetlands
• Executive Order 12962: Recreational Fisheries
• Executive Order 11988: Floodplain Management

• NEPA/404 MOU
• FHWA Guidance on Invasive Species
• U.S. Fish and Wildlife Service Mitigation Policy
• The Final ESA Section 7 Consultation Handbook

Chapter 2 of the SER provides links and information for general State Laws, Regulations and Guidance.

• CEQA
• Sections 1601-1603 of the California Fish and Game Code
• California Endangered Species Act
• Fish and Game Code 1900-1913: Native Plant Protection Act
• Food and Agriculture Code 80001-80006: California Desert Native Plants Act
• Senate Concurrent Resolution No. 17: Oak Woodlands
• Sudden Oak Death Management Act of 2002

• Standard Environmental Reference Volume 3 - Biological Resources

• Delegation of Biology-Related Non-Standard Special Provisions (NSSPs), Jay Norvell (June 30, 2006)
• Clarification Regarding Federal Endangered Species List Validity, Phil Stolarski (January 9, 2017). This policy memo was released to clarify that federal endangered species lists should not be older than 180 days.
• Tracking Federal Endangered Species Act Consultations and Automatic Elevation Procedures, Jay Norvell (March 18, 2011)
• Review Procedures for Environmental Mitigation Cooperative Agreements, Kelly C. Dunlap (February 3, 2011)
• Remediation and Enhancement of Fish Passage Locations, Rick D. Land (December 16, 2010)
• Guidance for District submittals for Alternative Natural Environment Study (Minimal Impact) (NES MI) - No Effect, Gregg Erickson (July 22, 2010)
• Standard Biological Technical Document Quality Control Process, Jay Norvell (August 26, 2009)
• Administrative agreement on fish barrier remediation requirements presented in Assembly Bill (AB) 1189, Will Kempton (May 26. 2009)
• Guidance for the Joint Issue Memo for the Dispute Resolution Process for Section 7 Endangered Species Act Consultation, Jay Norvell (April 8, 2009)
• Interim Policy for Establishing Funding Assurance for Mitigation Requirements, Jay Norvell (November 14, 2008)
• Advanced Mitigation Planning Project - The Next Step of Gathering, Sharing, and Disseminating District Information and Ideas, Jay Norvell (January 20, 2006)
• Requirements for assessing and remediating barriers to fish passage at stream crossings, Jay Norvell (January 1, 2006)
• Environmental Commitments Record, Rick Land (June 10, 2005)
• HQ-DEA Reviews of Biological and Cultural Mitigation Costs Greater than $500,000 (follow-up), Gary R. Winters (January 28, 2005)
• HQ-DEA Reviews of Biological and Cultural Mitigation Costs Greater than $500,000, Gary R. Winters (November 10, 2004)
• Guidance for Combined Essential Fish Habitat and Endangered Species Act Consultation Process, Gary R. Winters (September 20, 2004)
• Essential Fish Habitat Delegation Authority, Gary R. Winters (June 7, 2004)
• Guidelines for Funding Pre-Project Capital Costs, Including Mitigation, Brice D. Paris and Gary R. Winters (June 30, 2003)
• Conducting Endangered Species Act Consultations with Services, Michael G. Ritchie (FHWA) (April 24, 2002)
• FHWA Implementing Guidance on Invasive Species for Executive Order 13112, Brian Smith (October 22, 1999)

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

• 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

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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

State Permits