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.

This volume addresses general issues related to biological resource management, such as complying with Federal and State environmental laws, describing the existing biological environment and how the project alternatives affect that environment, the general procedures that should be implemented by the biologist when dealing with wetland effects, a summation of the laws, documentation, and processing requirements of the Federal and State Endangered Species Acts, and biological habitat mitigation and monitoring. Project specific issues that vary from the information provided herein may require consultation with Headquarters or other District staff and require management approval.

Volume 3 of the Standard Environmental Reference (SER) should be used with other project planning and development guides and references including Volume 1 of the SER, especially Chapter 14 and Chapter 15, and the Project Development Procedures Manual.

This guidance:

• 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 effects 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, prior to undertaking any actions that may affect the environment.

In 1973, Congress passed the Federal Endangered Species Act (FESA). FESA provides a means whereby the ecosystems upon which endangered and threatened species depend may be conserved and provides a program for the conservation of such endangered and threatened species. A similar California Endangered Species Act (CESA) was passed in 1985 to provide a means to conserve, protect, restore, and enhance any endangered or threatened species and its habitat.

In response to public concern over the loss of wetlands, in the mid-1970s the U.S. Army Corps of Engineers (USACE) 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 effects to wetlands whenever there was a practicable alternative.

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

National Environmental Policy Act (42 U.S.C. 4321 et seq.). On January 1, 1970, the National Environmental Policy Act of 1969 (NEPA) was signed into Law. NEPA established a national environmental policy intentionally focused on Federal activities and the desire for a sustainable environment balanced with other essential needs of present and future generations of Americans.

NEPA established a mandate for Federal agencies to consider the potential environmental consequences of their proposals, document the analysis, and make this information available to the public for comment prior to implementation. While NEPA established the basic framework for integrating environmental considerations into Federal decision making, it did not provide the details of the process for which it would be accomplished. Federal implementation of NEPA was the charge of the Council on Environmental Quality (CEQ), which interpreted the law and addressed NEPA's action forcing provisions in the form of regulations and guidance. NEPA requires, to the fullest extent possible, that the policies, regulations, and laws of the Federal Government be interpreted and administered in accordance with its environmental protection goals. NEPA also requires Federal agencies to use an interdisciplinary approach in planning and decision making for any action that adversely effects the environment.

NEPA requires, and FHWA and Caltrans are committed to, the examination and avoidance of potential effects to the social and natural environment when considering approval of proposed transportation projects. In addition to evaluating the potential environmental effects, we must also take into account the transportation needs of the public in reaching a decision that is in the best overall public interest. The project development process is an approach to balanced transportation decision making that takes into account the potential effects on the human and natural environment and the public's need for safe and efficient transportation.

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

• Section 9 lists those actions that are prohibited under the Act. Take of a listed species in accordance with the Act is prohibited. There are two processes, Section 7 and Section 10, whereby take is allowed when it is incidental to an otherwise legal activity.
• 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 7 allows for incidental take of a listed species for activities funded or carried out by Federal agencies if the take is incidental to, and not the purpose of, an otherwise lawful activity (economic development or land or water use activities).
• 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. Specifically, section 10(a)(1)(B) permits the incidental take of a federally listed species by private interests and non-Federal government agencies if the take is incidental to, and not the purpose of, an otherwise lawful activity and is accompanied by a Habitat Conservation Plan. Also, section 10(a)(1)(A) allows take for scientific research purposes or to enhance the propagation and survival of the species.

Migratory Bird Treaty Act (16 U.S.C. 703-711). This treaty with four international conventions (with Canada, Mexico, Russia and Japan) makes it unlawful at any time, by any means or in any manner, to pursue, hunt, take, capture, or kill shared migratory bird resources. Each of the conventions protect selected species of birds that are common to both countries (e.g., they occur in both countries at some point during their annual life cycle). The law applies to the removal of nests (such as swallow nests on bridges), eggs, and feathers. This law is of particular concern when birds nest on bridges, buildings, signs, and ferry dock structures.

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 (U.S.) 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 USACE regulating the discharge of dredged or fill material into waters of the U.S. (including special aquatic sites such as wetlands). The purpose of the permit is to prevent water quality degradation and to prevent the overall loss of waters of the U.S. Implementing regulations by USACE are found at 33 CFR Parts 320-330. Guidelines for implementation are referred to as the Section 404 (b)(1). Guidelines were developed by the Environmental Protection Agency (EPA) in conjunction with USACE (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 effects.

Section 10 of the Rivers and Harbors Act (33 U.S.C. 401 et seq.). Section 10 of the Rivers and Harbors Act requires a permit for creating obstructions (including excavation and fill activities) to the navigable capacity of waters of the U.S. 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 USACE 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. 661-667 (e)). 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 possessing outstandingly remarkable scenic, recreational, geologic, fish and wildlife, historic, cultural, or other similar values, shall be preserved in free-flowing condition, and that they and their immediate environments shall be protected for the benefit and enjoyment of present and future generations. Rivers flowing through Federally managed lands are administered by the land managing agencies (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 undertaking 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.

Coastal Zone Management Act (16 U.S.C . 1451-1465). This act preserves, protects, develops, and where possible, restores or enhances, the resources of the Nation's coastal zone for this and succeeding generations. This act encourages public, state, and federal agencies to participate, coordinate, and cooperate to benefit and manage the coastal resource

Marine Mammal Protection Act (16 U.S.C. 1361-1407). This act establishes a Federal responsibility to conserve marine mammals with management vested in the Department of Interior and the Department of Commerce. With certain specified exceptions, the Act establishes a moratorium on the taking and importation of marine mammals as well as products taken from them, and establishes procedures for waiving the moratorium and transferring management responsibility to the States. The law authorized the establishment of a Marine Mammal Commission with specific advisory and research duties.

Executive Order 11990 Protection of Wetlands (May 24, 1977). This EO establishes a National policy to avoid adverse effects 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, effects on wetlands must be identified in the environmental document. Alternatives that avoid wetlands must be considered. If wetland effects 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.

Executive Order 12962 Recreational Fisheries (June 9, 1995). This EO directs all Federal agencies to the extent permitted by law and where practicable, and in cooperation with States and Tribes, to improve the quantity, function, sustainable productivity, and distribution of U.S. aquatic resources for increased recreational fishing opportunities. In addition a National Recreational Fisheries Coordination Council as well as a Recreational Fishery Resources Conservation Plan were created to increase benefits to recreational fisheries.

Executive Order 13112 Invasive Species (February 3, 1999).This EO requires Federal agencies to work cooperatively to prevent and control the spread of invasive plants and animals. On August 10, 1999, FHWA issued implementing guidance on EO 13112. On October 22, 1999, Caltrans issued a memo to implement the FHWA guidance (found in SER Policy Memo Section). The guidance provides that a NEPA analysis for an action include an analysis of the probability of the action to cause or promote the introduction or spread of invasive species. If analysis indicates that disturbances caused by the action have the potential to promote the introduction or spread of invasive species, all feasible and prudent measures must be taken to minimize this likelihood.

California Environmental Quality Act (P.R.C. 21000 et seq.). CEQA establishes State policy to prevent significant, avoidable damage to the environment by requiring changes in projects through the use of alternatives or mitigation measures. CEQA applies to actions directly undertaken, financed, or permitted by State lead agencies. Regulations for implementation are found in the State CEQA Guidelines published by the Resources Agency. These guidelines establish an overall process for the environmental evaluation of projects that is similar to that promulgated under NEPA. The Guidelines make provisions for joint NEPA/CEQA documents.

California Endangered Species Act (Fish and Game Code 2050 et seq.). This act establishes the policy of the State to conserve, protect, restore, and enhance threatened or endangered species and their habitats. CESA mandates that State agencies should not approve projects that would jeopardize the continued existence of threatened or endangered species if reasonable and prudent alternatives are available that would avoid jeopardy. There are no state agency consultation procedures under CESA. For projects that affect both a state and federal listed species, compliance with the Federal Endangered Species Act (FESA) will satisfy CESA if the Department of Fish and Game (DFG) determines that the federal incidental take authorization is "consistent" with CESA under F&G Code Section 2080.1. For projects that will result in a take of a state only listed species, Caltrans must apply for a take permit under Section 2081(b).

Native Plant Protection Act (Fish and Game Code 1900-1913). California's Native Plant Protection Act (NPPA) requires all State agencies to utilize their authority to carry out programs to conserve endangered and rare native plants. Provisions of NPPA prohibit the taking of listed plants from the wild and require notification of the DFG at least 10 days in advance of any change in land use. This allows DFG to salvage listed plant species that would otherwise be destroyed. Caltrans is required to conduct botanical inventories and consult with DFG during project planning to comply with the provisions of this act and sections of CEQA that apply to rare or endangered plants.

California Wild and Scenic Rivers Act (P.R.C. 5093.50 et seq.). This act preserves certain designated rivers in their free-flowing state. These rivers must possess extraordinary scenic, recreational, fishery, or wildlife values. The Resources Agency is responsible for coordinating activities of State agencies that may affect these designated rivers.

Section 1602 of the Fish and Game Code. Under this section of the Fish and Game Code, Caltrans and other agencies are required to notify DFG prior to any project that would divert, obstruct or change the natural flow, bed, channel, or bank of any river, stream, or lake. Preliminary notification and project review generally occur during the environmental process. When an existing fish or wildlife resource may be substantially adversely affected, DFG is required to propose reasonable project changes to protect the resource. These modifications are formalized in a Streambed Alteration Agreement that becomes part of the plans, specifications, and bid documents for the project.

California Desert Native Plant Act (Food and Agriculture Code 80001-80006). This act protects California desert native plants from unlawful harvesting on both public and privately owned lands. This act also provides the people of this state with the information necessary to legally harvest native plants so as to ultimately transplant those plants with the greatest possible chance of survival. This act is applicable only within the boundaries of the Counties of Imperial, Inyo, Kern, Los Angeles, Mono, Riverside, San Bernardino, and San Diego.

Senate Concurrent Resolution No. 17: Oak Woodlands. Passed in September 1989, this resolution requests State agencies to preserve and protect native oak woodlands and to provide for replacement plantings whenever Blue, Engelmann, Valley or Coast Live Oak are removed from native woodlands. For purposes of this measure, "oak woodlands" means a five-acre circular area containing five or more oak trees per acre.

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, USACE, EPA, FWS, DFG, and Caltrans (1990), 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.

FHWA Policies (23 CFR § 771.105)

FHWA has built a framework of policies and procedures to help meet its social, economic, and environmental responsibilities while accomplishing its transportation mission. It is FHWA policy that:

• To the fullest extent possible, all environmental investigations, reviews, and consultations be coordinated as a single process, and compliance with all applicable environmental requirements be reflected in the environmental document required by this regulation.
• Alternative courses of action be evaluated and decisions be made in the best overall public interest based upon a balanced consideration of the need for safe and efficient transportation; of the social, economic, and environmental effects of the proposed transportation improvement; and of national, state, and local environmental protection goals.
• Public involvement and a systematic interdisciplinary approach be essential parts of the development process for proposed actions.
• Measures necessary to mitigate adverse effects be incorporated into the action.

Caltrans' Policies

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

Caltrans evaluates and plans for mitigation of adverse effects 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 effects necessary to satisfy State and Federal laws while ensuring that mitigation necessitated by effects to sensitive resources is a reasonable expenditure of highway funds.

If avoidance of effects is not possible, the first consideration is to minimize the effects 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 the project;
• Develop mitigation banks when appropriate opportunities exist; and
• Consider Conservation Easements before considering right-of-way (ROW) purchase.

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

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

The District Environmental Offices independently administer and perform all biological functions for the District, with assistance or review by the Division of Environmental Analysis 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 effects to resources which are sufficiently serious to stop or severely delay a project. In addition, biologists develop study schedules that estimate the time needed to complete biological surveys, coordinate with resource agencies, and write reports. The biologist provides 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 effects. When there is a potential for adverse effects, the biologist works with the Project Manager and project team to determine if the project can be modified to avoid the effects. After making necessary project adjustments, if there are still effects that require mitigation, the biologist works with the project team to develop feasible mitigation measures. Affected functional units, such as Landscape Architecture, Construction, and Maintenance, should be consulted if they are not currently active members of the project team. Personnel from other resource and regulatory 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 summarizes all of the biological studies, effect 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 effect analyses required for listed, proposed, and candidate endangered and threatened species.

The biologist insures that all biological commitments are recorded in the Environmental Commitments Record (ECR) which becomes part of the Resident Engineer (RE) Pending File. The ECR will also alert the RE that the biologist would like to be notified of the pre-job conference. Throughout development of the draft Plans, Specifications and Estimate (PS&E), the biologist should review 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 effects 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 USACE 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.

Oversight Responsibilities: Frequently, the biologist is responsible for overseeing consultant prepared documents. The biologist’s oversight includes the review of consultant prepared natural resource studies to assure that these documents meet all Federal and State laws and regulations, Agreements and Understandings (MOU’s), Executive Orders, as well as Caltrans and FHWA policies. A consultant prepared document is essentially a Caltrans document, therefore, the biologist often provides a large amount of input to the consultant in preparation of these documents. This oversight includes determining the environmental consequences of activities and proposing prudent, feasible, and cost effective strategies and alternatives to avoid or minimize adverse effects of the Department activities. The biologist must also ensure that the mitigation selected is appropriate for approval by the Project Development Team. The biologist and Contract Manager (CM) are the point of contacts between the consultant and Caltrans. It is the biologist responsibility to do the following:

• Review draft reports and return comments to the consultant (review may be performed by the biologist, staff specialists, and external agencies with special expertise or regulatory responsibility.
• Accept final reports.
• Authorize the consultant to contact others within Caltrans.
• Arrange, or request consultant to arrange, interagency meetings.
• Guide the consultant in the day-to-day conduct of work specified under the contract.

Only the CM (not the biologist) can authorize changes to the contract work scope or budget. Depending on the situation, a contract amendment or supplement may be required before these changes can be approved

The Division of Environmental Analysis at Headquarters is responsible to:

• Provide training to districts under the Capitol Skills Development Program and, as needed, for specific regional needs;
• Provide assistance and expertise to districts for the development and processing of biological studies;
• Develop and maintain natural resource sections of the Standard Environmental Reference;
• Prepare and analyze proposed legislation;
• Develop and propose departmental policy to ensure conformity with laws and regulations and to promote uniformity in addressing biological issues;
• Act as a liaison and provide 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 instruction, 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.