Chapter 1 - General Information

This volume provides guidance to identify and evaluate biological resources, process biological resource documents, and implement all biologically related construction, maintenance, and encroachment activities.

Situations in biological resource management that are not covered in Volume 3 should be handled on a case-by-case basis. Districts are encouraged to consult with Headquarters staff members at any time, especially when unusual situations occur. Communication between Districts is also highly recommended for the purpose of sharing similar experiences.

Volume 3 of the Environmental Handbook should be used with other project planning and development guides and references including Volume 1 of the Environmental Handbook and the Project Development Procedures Manual.

This handbook:

• presents Caltrans policies and procedures regarding biological resources;
• details procedures and activities required by law, regulation, and Executive Order pertaining to biological resources;
• sets forth biological resource management roles and responsibilities; and
• sets forth guidelines to promote consistency, uniformity, and effective handling of biological resources in the conduct of Caltrans' activities.

Caltrans is required to comply with Federal and State biological resource laws and regulations. The following is a summary of the evolution of these laws and Caltrans' involvement in managing biological resources under its jurisdiction.

In the mid-1960s, increased public concern and support for protection of the natural environment resulted in stronger and more comprehensive Federal and State laws. The National Environmental Policy Act of 1969 (NEPA) and the California Environmental Quality Act of 1970 (CEQA) established environmental policy specifically addressing the impacts of human activities on the natural and human environment. These laws require public agencies to be responsive to the effects of their actions on the environment, including biological resources.

In 1973, Congress passed the Federal Endangered Species Act (FESA). A similar California Endangered Species Act (CESA) was passed in 1985.

In response to public concern over the loss of wetlands, in the mid-1970s the Army Corps of Engineers (ACOE) expanded its jurisdiction over fill materials in traditional navigable waters to cover essentially all water bodies, including wetlands. In 1977, a Federal Executive Order was issued which directed Federal agencies to avoid impacts to wetlands whenever there was a practicable alternative.

The 1973 legislation that created Caltrans from the Program of Highways emphasized consideration of the environment and required that "environmental impacts of transportation should be taken into consideration." The Director's Environmental Policy (1992) states that "Caltrans protects and enhances the environment..." and "evaluates the environmental benefits and consequences of its activities and implements practices that minimize environmental impacts."

- See also Environmental Handbook, Volume 1, Chapter 1

National Environmental Policy Act (42 U.S.C. 4321 et seq.). NEPA declares a continuing Federal policy "to use all practicable means and measures...to create and maintain conditions under which man and nature can exist in productive harmony, and fulfill the social, economic, and other requirements of present and future generations." NEPA directs "a systematic, interdisciplinary approach" to planning and decision making and requires environmental statements for "major Federal actions significantly affecting the quality of the human environment." Implementing regulations by the Council on Environmental Quality (CEQ) (40 CFR Parts 1500-1508) requires Federal agencies to identify and assess reasonable alternatives to proposed actions that will restore and enhance the quality of the human environment and avoid or minimize adverse environmental impacts. Federal agencies are further directed to emphasize significant environmental issues in project planning and to integrate impact studies required by other environmental laws and Executive Orders into the NEPA process. The NEPA process should therefore be seen as an overall framework for the environmental evaluation of Federal actions.

Endangered Species Act of 1973 (16 U.S.C. 1531-1543). This act and subsequent amendments provide guidance for the conservation of endangered and threatened species and the ecosystems upon which they depend.

• Section 7 requires Federal agencies, in consultation with, and with the assistance of the Secretary of the Interior or the Secretary of Commerce, as appropriate, to insure that actions they authorize, fund, or carry out are not likely to jeopardize the continued existence of threatened or endangered species or result in the destruction or adverse modification of critical habitat for these species. The U. S. Fish and Wildlife Service (FWS) and National Marine Fisheries Service (NMFS) share responsibilities for administering the Act. Regulations governing interagency cooperation under Section 7 are found at 50 CFR Part 402. The opinion issued at the conclusion of consultation will include a statement authorizing take that may occur incidental to an otherwise legal activity.
• Section 9 lists those actions that are prohibited under the Act. Take of a species listed in accordance with the Act is prohibited. There are two processes whereby take is allowed when it is incidental to an otherwise legal activity.
• Section 10 provides a means whereby a non-Federal action with a potential to result in the take of a listed species could be allowed under an incidental take permit. Application procedures are found at 50 CFR Parts 13 and 17 for species under the jurisdiction of FWS and 50 CFR Parts 217, 220 and 222 for species under the jurisdiction of NMFS.

Migratory Bird Treaty Act (16 U.S.C. 703-711). This treaty with Canada, Mexico and Japan makes it unlawful at any time, by any means or in any manner, to pursue, hunt, take, capture, or kill migratory birds. The law applies to the removal of nests (such as swallow nests on bridges) occupied by migratory birds during the breeding season.

Clean Water Act (33 U.S.C. 1251-1376). The Clean Water Act (CWA) provides guidance for the restoration and maintenance of the chemical, physical, and biological integrity of the nation's waters.

• Section 401 requires that an applicant for a Federal license or permit that allows activities resulting in a discharge to waters of the United States, must obtain a state certification that the discharge complies with other provisions of CWA. The Regional Water Quality Boards administer the certification program in California.
• Section 402 establishes a permitting system for the discharge of any pollutant (except dredge or fill material) into waters of the United States.
• Section 404 establishes a permit program administered by ACOE regulating the discharge of dredged or fill material into waters of the United States (including wetlands). Implementing regulations by ACOE are found at 33 CFR Parts 320-330. Guidelines for implementation are referred to as the Section 404 (b)(1) Guidelines and were developed by the Environmental Protection Agency (EPA) in conjunction with ACOE (40 CFR Parts 230). The Guidelines allow the discharge of dredged or fill material into the aquatic system only if there is no practicable alternative that would have less adverse impacts.

Section 10 of the Rivers and Harbors Act (33 U.S.C. 401 et seq.). Section 10 of the Rivers and Harbors Act is administered by ACOE. This section requires permits in navigable waters of the U. S. for all structures such as riprap and activities such as dredging. Navigable waters are defined as those subject to the ebb and flow of the tide and susceptible to use in their natural condition or by reasonable improvements as means to transport interstate or foreign commerce. The ACOE grants or denies permits based on the effects on navigation. Most activities covered under this act are also covered under Section 404 of CWA.

Fish and Wildlife Coordination Act (16 U.S.C. 661-666). This act applies to any Federal project where the waters of any stream or other body of water are impounded, diverted, deepened, or otherwise modified. Project proponents are required to consult with FWS and the appropriate state wildlife agency. These agencies prepare reports and recommendations that document project effects on wildlife and identify measures that may be adopted to prevent loss or damage to wildlife resources. The term "wildlife" includes both animals and plants. Provisions of the Act are implemented through the NEPA process and Section 404 permit process.

National Wild and Scenic Rivers Act (16 U.S.C. 1271-1287). This act is administered by a variety of State and Federal agencies. Designated river segments flowing through Federally managed lands are administered by the land managing agency (e.g., U. S. Forest Service, Bureau of Land Management, and the National Park Service). River segments flowing through private lands are administered by the Resources Agency in conjunction with local government agencies. The Act prohibits Federal agencies from activities that would adversely affect the values for which the river was designated. Caltrans consults with the managing agencies during the NEPA process on projects that affect designated rivers or their immediate environments. This early consultation reduces potential conflicts with wild and scenic river values that are protected by the Act.

Executive Order 11988 Floodplain Management (May 24, 1977). This order directs all Federal agencies to avoid the long-term and short-term adverse impacts associated with floodplain modification and to avoid direct or indirect support of floodplain development whenever there is a practicable alternative.

Executive Order 11990 Protection of Wetlands (May 24, 1977). This order establishes a National policy to avoid adverse impacts on wetlands whenever there is a practicable alternative. The U. S. Department of Transportation (DOT) promulgated DOT Order 5660.1A in 1978 to comply with this direction. On Federally funded projects, impacts on wetlands must be identified in the environmental document. Alternatives that avoid wetlands must be considered. If wetland impacts cannot be avoided, then all practicable measures to minimize harm must be included. This must be documented in a specific Wetlands Only Practicable Alternative Finding in the final environmental document. An additional requirement is to provide early public involvement in projects affecting wetlands. The Federal Highway Administration (FHWA) provides technical assistance in meeting these criteria (FHWA Technical Advisory 6640.8A) and reviews environmental documents for compliance.

Memorandum of Understanding (MOU) with Fish and Wildlife Service (November 1988). This MOU establishes procedures for the early and continuous coordination of transportation project development activities between Caltrans and FWS.

MOU with the Department of Fish and Game (December 1990). This MOU ensures that State transportation projects are planned, designed, constructed and maintained to protect fish and wildlife resources in conformance with CEQA and CESA.

Memorandum of Agreement (MOA) between FHWA, ACOE, EPA, FWS, DFG, and Caltrans (May 1991), Early Mitigation Planning for Transportation Improvements in California. This MOA establishes a process to identify and evaluate valuable natural resources and habitat at the earliest stages of transportation improvement planning. It provides a framework to implement coordinated mitigation planning at the beginning of the project development process leading to an agreement on mitigation strategy for guidance during project design.

Planning Guidelines for Standard Approaches to Mitigation Site Monitoring and Maintenance - under November 1988 MOU with Sacramento Office of FWS (November 1991). This MOU provides planning guidelines to improve the success of project mitigation within the jurisdiction of Caltrans and FWS.

MOU - NEPA and Clean Water Act Section 404 Integration Process (April 2006). This MOU ensures the earliest possible consideration of environmental concerns pertaining to waters of the U. S., including wetlands, at the transportation project planning, programming, and project development stages by integrating section 404 into the NEPA process.

Caltrans' purpose and vision is to promote the State's economic vitality and enhance the quality of life for the people of California by providing for mobility of people, goods, services, and information while protecting the environment and addressing social needs.

Transportation projects are planned and constructed to avoid or minimize impacts to biological resources whenever practicable.

Caltrans evaluates and plans for mitigation of adverse impacts to natural resources during the early stages of transportation planning and decision making.

Caltrans works closely with resource agencies and FHWA in the development and implementation of mitigation for project impacts necessary to satisfy State and Federal laws while ensuring that mitigation necessitated by impacts to sensitive resources is a reasonable expenditure of highway funds.

If impact avoidance is not possible, the first consideration is to minimize impacts on-site.

If mitigation on-site is not practical, off-site compensation may be required. Off-site mitigation may include land acquisition and habitat improvement. The following is to be considered:

• avoid purchasing or improving habitat on small isolated sites;
• if possible, achieve compensation in advance of project impacts;
• develop mitigation banks when appropriate opportunities exist; and
• consider Conservation Easements before considering right of way purchase.

Caltrans provides for monitoring and sustained maintenance and operation of mitigation sites.

When possible, Caltrans turns over mitigation sites to responsible public or private resource organizations for long-term management.

Caltrans maintains a mitigation site inventory providing information on costs and performance success.

The District Environmental Offices independently administer and perform all biological functions for the District, with assistance or review by the Environmental Program on request.

District Environmental Offices have the ultimate responsibility for the quality and timeliness of all biological studies, regardless of who prepares the studies.

Initial Planning Stage. The biologist provides the project planners with information on biological resources that potentially exist in the project area. The biologist uses a literature search and field visits to provide information on biological resources that might be affected by proposed actions. The biologist may do additional studies to better advise the planners if the potential exists for impacts to resources which are sufficiently serious to stop or severely delay a project. In addition, biologists may be requested to develop study schedules that estimate the time needed to complete biological surveys, coordinate with resource agencies, and write reports. The biologist may also be requested to provide an estimate of what mitigation may be required if a certain action is carried out.

Project Development Stage. Once project alternatives are selected for further study, the biologist is responsible to determine the potential biological resource impacts. When there is a potential for adverse impacts, the biologist works with the Project Manager and project team to determine if the project can be modified to avoid the impacts. After making necessary project adjustments, if there are still impacts that require mitigation, the biologist works with the project team to develop feasible mitigation. Affected functional units, such as construction and maintenance, should be consulted if they are not currently active members of the project team. Personnel from the resource agencies may also be a part of these discussions because of the status of the resources.

Some projects may require permits or agreements. The groundwork for these documents should be developed during the initial stages of the environmental document. Caltrans and the appropriate resource agency should reach an agreement on the requirements to obtain those permits or agreements. These conditions can then be incorporated into the environmental document and become an integral part of the project.

The biologist prepares the Natural Environment Study (NES). The NES details all of the biological studies, impact analyses, and agreed to mitigation measures. The generalist uses the NES to complete the Biological Section of the environmental document. If consultation for endangered species is required, the biologist may need to develop a Biological Assessment that focuses only on those studies and impact analyses required for listed, proposed, and candidate endangered and threatened species.

The biologist insures that the memo from the Environmental Office to the Resident Engineer's (RE) Pending File includes all biological requirements identified during the environmental process. This memo will also alert the RE that the biologist would like to be notified of the pre-job conference. Prior to project advertisement, the biologist should review the draft Plans, Specifications and Estimate (PS & E) to assure that all biological commitments are included in the contract and there is sufficient funding to accomplish those commitments.

Construction Stage. The biologist is often requested to participate in the pre-job conference to clarify biological issues and constraints for the RE and staff and to ensure the contractor's consideration of biological issues during construction. A major role of the biologist during construction is to be available for consultation. The biologist may be requested to field review a project when a change order that will modify the impacts on resources is being considered, or when there is a resource identified that was overlooked during environmental review.

The responsibilities of the biologist during construction can range from occasional consultation to daily monitoring. A frequent requirement of endangered species consultation is that a qualified biologist be present during a phase of construction that has the potential to harm a species. Permits issued by ACOE and coastal zone permitting agencies may require regular or periodic monitoring of construction activities by a biologist if sensitive resources are involved. In some cases, the biologist may be required to oversee the construction phase of a mitigation site.

The RE has the ultimate responsibility for the construction site and for ensuring the contractor's compliance with applicable laws, permits, and contract plans and specifications. Authority for directing the contractor's work must be delegated to the biologist by the RE.

Post Construction Stage. After construction the biologist is responsible for monitoring the success of any biological mitigation that was a condition of construction. A major component of habitat replacement is annual monitoring of any plantings and recommending corrective measures, if appropriate. This monitoring requirement, generally established in the regulatory permit, may last until the habitat reaches a certain stage, which will vary for different habitats, plantings, and conditions. Annual monitoring requirements will usually be determined in negotiations between Caltrans biologists and resource and regulatory agencies. The monitoring requirements are subject to final approval by the Project Manager.

Agency or Developer Funded Projects. Agency or developer funded projects are not technically Caltrans projects but they ultimately become a part of the highway system. The District Director delegates authority to a Caltrans Project Manager to oversee Caltrans' interest in these types of projects. It is up to the Project Manager to consult with specialists to ensure that the information gathered is pertinent to obtain proper approvals and permits from resource agencies. When FHWA funds or approvals are involved in the project, the Project Manager should ensure that the information gathered will meet the needs of FHWA to complete agency coordination. When there is no FHWA action, the Project Manager should ensure that any agreements the local agency makes toward permits and approvals are achievable and acceptable to Caltrans. The appropriate method to meet these goals is to involve the specialists at all stages of the process. The Project Manager is responsible for accepting or rejecting recommendations made by specialists. The difference between agency or developer funded projects and Caltrans' projects is that the biologist usually has a more active role in the development of Caltrans' projects.

The Environmental Program at Headquarters is responsible to:

• provide assistance and expertise to districts for the development and processing of biological studies;
• develop and maintain natural resource handbooks and manuals;
• prepare and analyze recommendations on proposed legislation;
• develop and propose departmental policy to ensure conformity with laws and regulations and to promote uniformity in addressing biological issues;
• provide liaison and assistance to districts in resolving issues with State and Federal agencies;
• identify, manage, and perform research on environmental topics to produce information for statewide application;
• identify need, develop, and provide or conduct training in technical biological areas;
• identify need, develop methodology, and initiate procedure to capture cost and estimate future resources required for biological measures (e.g., mitigation site monitoring, mitigation banks, endangered species, etc.); and
• develop, gather, and disseminate information, technical data, processes, procedures, etc. which may improve the biological program or assist district biologists.