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Last Updated: Wednesday, July 2, 2014 7:24 AM

Chapter 2- Natural Environment Study


A Natural Environment Study (NES) describes the existing biological environment and how the project alternatives affect that environment.  The NES summarizes technical documents (e.g., focused species studies, wetland assessments, biological assessments, etc.) related to effects on biological resources in the Biological Study Area (BSA) for use in the environmental document.


To gather information on the biological resources in the BSA, the District Biologist must review the proposed project description and materials, be familiar with the BSA, consider comments received during the project scoping process, and review existing sources of information known about the BSA.

An initial site visit to observe the type of natural communities and their condition in the BSA will help focus the collection of background information.  Background information is used to plan the extent of biological studies needed prior to conducting field investigations.  This initial planning step is necessary to ensure that studies address resources of concern that may be affected by the project while at the same time avoiding lengthy discussions of the local or regional biota.  Biological resources addressed in the NES are limited to those pertaining to the BSA and those likely to be effected by the project. The BSA limits are determined in coordination with the Project Development Team (PDT) (refer to section 2-3.2).

The District Biologist reviews substantive resource issues identified during the project scoping process before initiating biological studies.  From the information obtained in the background research and the comments received during the scoping process, the District Biologist develops a list of sensitive species and habitats that may be present within the BSA, as well as records of any additional biological considerations, such as the presence of invasive species.

Information about biological resources in the BSA is available from a myriad of sources.  Some of the common sources of biological information include:

Environmental documents prepared for nearby projects and documents prepared by resource agencies concerning species potentially found in the study area are also helpful informational resources.  A 10-mile radius from the project site normally provides a useful frame of reference for developing a list of sensitive taxa to be considered during project studies.  As a rule, the biologist considers all species whose range includes the BSA and whose life requirements may be met by the habitat and vegetation that is present within the survey area.


The scoping process identifies many of the issues that require discussion in an environmental document.  The District Biologist supplements this process on an as needed basis, with site visits and interviews with local experts and agency personnel familiar with sensitive resources potentially found in the BSA.

2-3.1 Level of Detail

The level of detail must be sufficient to determine if the project will result in any considerable effects.  The NES describes the project setting in detail that project planners and the public have a clear idea of the nature, distribution, and abundance of resources.  The NES must address whether a sensitive or biologically important resource occurs in the BSA, whether the resource will be affected, and whether the project effects are considerable.

As the sensitivity of the resource increases, the level of detail in the NES will also increase.  Rare, threatened and endangered species, as well as proposed species, candidate species, and some special status resources require a thorough analysis of potential project effects.  A determination of the potential for take of a listed species or critical habitat is required.

2-3.2  Area of Direct, Indirect and Cumulative Effects

The District Biologist coordinates with the PDT to develop the limits of the BSA.  A BSA includes the footprint of the completed project, new right-of-way (ROW) limits, areas needed for utility relocation, construction access roads, driveway realignments, and construction easements.  Within these limits the biologist evaluates biological resources for both direct and indirect effects.  If effects resulting from the project extend beyond the project limits, the effected areas must be included in the analysis

Area of Direct Effect.  The area of direct effect is where construction activity results in the removal of biotic resources and landforms.  The National Environmental Policy Act (NEPA) Regulations define direct effects as those "which are caused by the action and occur at the same time and place." Resources lost under the footprint of the action are obvious direct effects, such as filling a wetland to build a highway.  Less obvious direct effects might be where a natural process has been blocked, such as blocking a migration corridor or disrupting a breeding cycle.

Area of Indirect Effect.  As defined in the NEPA Regulations, indirect effects are those "which are caused by the action and are later in time or farther removed in distance, but are still reasonably foreseeable.  Indirect effects may include growth inducing effects and other effects related to induced changes in the pattern of land use, population density or growth rate, and related effects on air and water, and other natural systems, including ecosystems."

When evaluating an action for indirect social effects, the District Biologist coordinates with the Environmental Planner to determine indirect social changes that may occur from the construction of a project.  The environmental planner determines probable changes likely to occur in the BSA.  The District Biologist evaluates the biological resources that will be affected because of these indirect social effects.

Area of Cumulative Effect A cumulative effect 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 effects can result from individually minor yet collectively significant actions taking place over a period of time."

Effects definitions for FESA and CESA may vary from the NEPA definition. Chapter 4 provides more detail on these definitions.

2-3.3 Contacts with Agencies and Individuals

Throughout the development of the NES, the District Biologist contacts individuals and agencies for information or negotiation purposes. A section within the NES discusses the coordination that has taken place and agreements that have been made. Contacts are made primarily to gather information or to negotiate modifications in the project design.

Information.  As needed, the District Biologist will interview individuals who are familiar with the biological resources of the BSA, including local agency and academic personnel who are experts on the biota of the study area.  These experts may provide additional, unpublished information regarding the distribution and importance of resources within the BSA.  A District Biologist should attend the project's public information meetings and workshops to establish contacts with property owners.  Property owners can supply knowledge of prior and current land uses and the ecological character of the area.

Negotiation. These contacts are established for the purpose of project modification to avoid or lessen an effect on biological resources.  These negotiations typically involve State, Federal, and local agencies.  The Project Manager is responsible for determining any project obligations.  Negotiation meetings are frequently followed with a letter confirming the final agreements.  This process is referred to as consultation when threatened or endangered species are involved.  Chapter 4 in Volume III, Endangered Species Act Procedure, discusses this process in detail.


Prior to conducting field surveys, the District Biologist compiles lists of potential sensitive resources  as well as other biological considerations, such as invasive species, likely to occur within the vicinity of the BSA.  The limits of the project are known and delineated on project plans and/or aerial photos.  If possible, the area is surveyed and delineated with survey markers or flagging.

Biological field surveys are conducted to obtain information needed to determine the project's level of effects, including consideration of long-term and short-term effects, and the cumulative effects of the project on the biota in the area.  Prior to collecting biological data, the District Biologist formulates questions and issues that need to be investigated during the field surveys.  Pertinent questions include: 

  • What is the significance of the effected resources on a local or regional scale? 
  • What is the rarity or abundance of the resource in the region and elsewhere? 
  • What is the resilience of the resource?
  • Are there invasive species currently in the BSA and will the action promote the spread of invasive species?

In some cases, where species require a specific survey method protocol or survey permit, it will be necessary to coordinate with resource agencies to obtain approval of the field survey methodology.

The District Biologist walks the project study area to develop an accurate description of the BSA, determines the presence of sensitive habitats and species, observes for any invasive species present, and evaluates the effects of the proposed project on the BSA.  All field surveys to determine the presence of special status species (any species of fish, wildlife, or plant that is officially listed as rare, threatened, endangered, or candidate for rare, threatened, or endangered species listing under the state or federal Endangered Species Acts, or of local importance) are conducted at the appropriate blooming or active period for each resource.  A determination of the presence of some sensitive resources may require sampling over more than one season.  Some listed species require handling in order to determine their presence in the project vicinity.  The District Biologist must obtain the required permits for handling these species or hire a qualified consultant who possesses the required permits prior to conducting the field surveys.

If the BSA is too large to adequately survey, the District Biologist will use aerial photos and maps to investigate the total area.  The biologist then conducts meandering transects that traverse the BSA, being sure to investigate areas of potential sensitivity found from the pre-survey information search and aerial photo interpretation.

Field safety is extremely important when conducting field surveys.  It is the responsibility of the District Biologist to become familiar with Caltrans’ Safety Manual and Surveys Manual.  For example, as discussed in the Surveys Manual biologists must use the buddy system during field surveys, as well as provide a trip itinerary or study plan to their supervisor, wear appropriate clothing, and consider other safety precautions.

Guidelines were set forth May 22, 2002, in a memorandum signed by Caltrans’ Right of Way, Environmental and Legal programs which describe the responsibilities Right of Way and Environmental Planning & Engineering have in obtaining permission to enter upon property (see Policy Related Memos; Right of Entry Guidelines for Environmental Work).  The guidelines require written permission from the property owner in situations where the work performed could be considered to cause substantial interference or be invasive or damaging in nature, ie., boring, trenches, digging with hand tools, cutting vegetation, or any activities affecting any site improvements.  However, an informational letter may be sent to the property owner in those situations where entry does not interfere with the property owner’s use, or is clearly non-invasive in nature, such as walk-on visual inspections, taking photographs, etc.  The letter will inform the owner or lessee of the purpose and effect of such entry together with the approximate time of the entry and further advise the property owner or lessee to contact an identified person only if they have objections to such entry or have specific instructions they wish to have observed during such entry (personal contact before entering, closing livestock gates, instructions concerning dogs, etc.).  It is important that the District Biologist coordinate with the District ROW Unit for assistance to determine any actions that might be necessary prior to survey work on private property.  Obtaining Rights of Entry (ROE) could be a time consuming process and it is important that requests for ROE be coordinated in the initial planning phases of the project.  Environmental and Right of Way staffs are encouraged to work together to make this process successful.   

2-4.1 Mapping

The District Biologist maps the survey area as early as possible during field investigations to provide base maps for subsequent biological work and a preliminary assessment of effects.  Mapping should be at a scale large enough to show vegetation types and important biological features such as habitat for sensitive species, wetlands unique plant assemblages, and the presence of state listed noxious species.  Vegetation community map units must be selected on the basis of a recognized classification system  and referenced appropriately in the NES.  The current standard for vegetation classification is “A Manual of California Vegetation” published by the California Native Plant Society in conjunction with DFG.  This manual should be used as a basis for the habitat descriptions and the vegetation map.  If another vegetation classification system is used, the report must reference the system and provide the justification for its use.

District Biologists should use a combination of aerial photo interpretation and ground truthing to delineate vegetation types.  Descriptive information for each mapping unit includes the distribution of the unit within the study area, an estimate of total acreage, the dominant plant species, and the relative sensitivity of the vegetation type.  All plant and animal taxa encountered during site visits should be listed by vegetation type in an appendix to the NES.  The biologist will identify each species observed to the extent necessary to determine whether it is threatened or endangered.  In addition to identifying species, the biologist will identify natural communities whose status is being tracked by the CNDDB.

There may be times when it is appropriate for a biologist to do more than map and calculate the area of the vegetation communities in a BSA.  A biologist may need to develop a detailed discussion of communities in the BSA when communities of state or local significance, such as oak woodlands or wetlands, will be effected.  Information on the degree of canopy cover, tree density, species frequency, and functions and values of specific habitats may be necessary in order to evaluate and develop mitigation.  Collecting a greater level of detail will assist the biologist in developing mitigation that appropriately offsets the project effects.  By discussing effects to these vegetation communities in greater detail within the NES, any associated mitigation costs or project scheduling adjustments can be included in the early planning stages of the project.  Investigation of specific habitat or community characteristics will help ensure that proposed mitigation matches project effects.

2-4.2 Waterways, Wetlands, and Jurisdictional Areas

Caltrans biologists identify, delineate, and discuss effects to riparian and aquatic communities, including rivers, streams, lakes, wetlands, and other waters of the United States to satisfy the requirements of Executive Order 11990, Section 10, of the Rivers and Harbors Act (33 U.S.C. 401 et seq.), Section 404 and Section 401 of the Clean Water Act (33 U.S.C. 1251-1376), National Wild and Scenic Rivers Act (16 U.S.C. 1271-1287), NEPA, the California Environmental Quality Act (CEQA), Sections 1601-1603 of the Fish and Game Code, and the California Wild and Scenic Rivers Act (P.R.C.5093.50 et seq).

Streams, Rivers, and Lakes.  Caltrans is 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 under Sections 1602 of the Fish and Game Code.  Preliminary notification and project review generally occurs during the environmental process.  When an existing fish or wildlife resource may be adversely affected, DFG is required to propose reasonable project changes to protect the resource.  These modifications are formalized in a Streambed Alteration Agreement (e.g. 1602 agreement).  The District Biologist must identify in the NES those areas that may pertain to Section 1602 of the Fish and Game Code.

Wetlands and Other Waters of the United States. As discussed in greater detail in Chapter 3 of Volume III, Waters of the U.S. and the State, to determine the presence of a wetland, the District Biologist uses the U.S. Army Corps of Engineers (USACE) and U.S. Environmental Protection Agency (EPA) joint definition:  "Those areas that are inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances do support, a prevalence of vegetation typically adapted for life in saturated soil conditions."  Wetlands generally include swamps, marshes, bogs, and similar areas.

A District Biologist will use the procedures described in the USACE Wetlands Delineation Manual (January 1987) to make the wetland determination.  The wetland determination requires the identification of three criteria: 

  1. Presence of wetland hydrology;
  2. Hydric soils; and
  3. A prevalence of hydrophytic vegetation.  An in-depth discussion of wetland identification and report format is included in Chapter 3 of Volume III, Wetlands.

When wetlands occur in the BSA, the NES will include a Wetland Assessment.  The purpose of an assessment is to map the wetland area and discuss the functions, values, and potential effects on wetlands.  For most projects, the discussion of wetland issues is included entirely within the NES.  In cases where the discussion of wetland issues is lengthy and/or project effects are significant, a separate Wetland Assessment will be prepared, summarized within the NES, and included in the NES as a technical appendix.

Federally funded projects must abide by Federal Executive Order 11990, - Protection of Wetlands (May 24, 1977), which directs "all Federal agencies to refrain from assisting in or giving financial support to projects which encroach upon public or private wetlands unless the agency determines there are no practicable alternatives to such construction and that the proposed action includes all practicable measures to minimize harm."  In accordance with Executive Order 11990, federally funded projects must provide an opportunity for early public involvement for all actions involving wetlands.  For actions requiring a Finding of No Significant Impact (FONSI) or an Environmental Impact Statement (EIS), notices for a public hearing and notices of availability must indicate whether alternatives are located in wetlands.  A Wetlands Finding is necessary for actions requiring a FONSI or EIS.  Federal Highway Technical Advisory T 6640.8A (October 30, 1987) provides guidance for addressing wetland effects.  Guidelines for compliance with these requirements are discussed in Chapter 3 of Volume III, Waters of the U.S. and State.

2-4.3 Plant Survey Techniques

Botanical surveys are conducted to determine effects of a proposed project on rare, threatened, and endangered plants, natural communities, as well as risks for invasive species. Caltrans follows the DFG "Protocols for Surveying and Evaluating Impacts to Special Status Native Plant Populations and Natural Communities."

The purpose of these protocols is to facilitate a consistent and systematic approach to the survey and assessment of special status native plants and natural communities so that reliable information is produced and the potential of locating a special status plant species or natural community is maximized. This universal understanding of the quality and methods is accepted broadly by experts and resource agency reviewers.

2-4.3A Invasive Species (Executive Order 13112)

Executive Order (E.O.) 13112 signed February 3, 1999 requires Executive agencies to work cooperatively to prevent and control the spread of invasive plants and animals. This E.O. was followed by Federal Highway Administration (FHWA) Guidance on Invasive Species dated August 10, 1999. On October 22, 1999, Caltrans issued a memo to implement the FHWA guidance (found in SER Policy Memo Section).  The Guidance states that FHWA will not give final NEPA compliance for an action unless appropriate analysis of the probability of the action to cause or promote the introduction or spread of invasive species has been accomplished.  If analysis indicates that the disturbances caused by the action have the potential to promote the introduction or spread of invasive species, all feasible and prudent measures taken to minimize this likelihood will be identified.

According to the Guidance, it is required that Caltrans use the state noxious weed list to define invasive plants until such time as a National List is developed. The National Invasive Species Council was established in 2001 and maintains a collection of databases related to invasive species throughout the country.  This database source has taken the place of a “national list” and should be used in the evaluation of invasive species in the BSA.

2-4.4 Wildlife Survey Techniques

Given the variety and number of wildlife species and types of habitats found in California, it is impossible to present all of the techniques for surveying each species and type of habitat.  As mentioned previously, all wildlife surveys are conducted during a species active period, such as nesting or migration.  In cases when surveys must be conducted at times that animals are less likely to be observed, a thorough investigation of the animal's potential habitat should be made.  Investigations and careful record keeping should report the presence (e.g., tracks, scat, nests or dens, trails, or any other indicators) that are specific to the animal.  The surveys for wildlife must be commensurate with the magnitude of the project and the importance of potential effects to the expected resource.  Specialized surveys are usually reserved for those instances where a sensitive resource is expected in the BSA.  Surveys for many of the species listed as threatened or endangered must follow a specified protocol established by DFG or FWS and may require a permit (e.g., California red-legged frog survey protocol by FWS).

The DFG Survey and Monitoring Protocols and Guidelines contains specified survey protocols for plants, invertebrates, amphibians, reptiles, birds, and mammals.  The protocols and guidelines available are from various sources and are recommended as tested and reviewed methods for their intended purposes.  These purposes include determining the presence or support for a negative finding (e.g., habitat not suitable) for a particular species or its local status.  In some cases, these protocols and guidelines represent what DFG believes to be the best available methodology.  The FWS has issued Survey Protocols and Other Guidelines for federally listed, threatened, endangered species.  FWS also maintains a list of plants and animals native to the United States that are candidates or proposed for possible addition to the Federal list, as well as other guidance concerning wildlife survey techniques.

A California Native Species Field Survey Form should be completed and sent to CNDDB when sensitive species are located.  The information requested in the survey form includes the location of the species (e.g., county, landowner, GPS location), habitat description (e.g., plant communities, dominants, associates, substrates/soils, aspects/slope), site information (e.g., overall site, occurrence quality/viability, etc.),  animal information (e.g., number of adults, juveniles, larvae, etc.), and plant information (e.g., phenology). 

A sampling of references that describe wildlife survey techniques is presented.  However, this is not an exhaustive list.  Protocols for conducting wildlife surveys must be chosen carefully to ensure the results are appropriate for the circumstances.  Each biologist must select the methods with which they feel most comfortable.

Brookhout, T. A., editor. 1994. Research and management techniques for wildlife and habitats. The Wildlife Society, Bethesda, MD. 740 pp.

Cooperrider, A. Y., R. J. Boyd, and H. R. Stuart, editors. 1986. Inventory and Monitoring of Wildlife Habitat.
U.S. Department of Interior, Bureau of Land Management, Service Center. Denver, CO., 858 pp.

Davis, D. E. 1990. CRC Handbook of Census Methods for Terrestrial Vertebrates. CRC Press. 375 pp.

Hays, R. L., C. Summers, and W. Seitz. 1981. Estimating Wildlife Habitat Variables. FWS Report
FWS/OBS- 81/47. 111 pp.

Leedy, D. L. and L. W. Adams. 1982. Wildlife Considerations in Planning and Managing Highway Corridors. FHWA Report. FHWA-TS-82-212. 93 pp.

Meese, Robert J., Shilling, Fraser M., Quinn, James F., and California Department of Transportation,
Environmental Division, supervised by Amy Pettler. 2007. Wildlife Crossings Guidance Manual and associated Wildlife Crossings Website.

Nathanson, J. A., M. Lanzafama, and P. Kissam.  2006.  Surveying Fundamentals and Practices, 5/E. 
Prentice Hall.  512 pp.

Ralph, C. J., G.R. Geupel, P. Pyle, T.E. Martin, and D.F. DeSante. 1993. Handbook of Field Methods for
Monitoring Land Birds. Pacific Southwest Research Station Report. PSW-GTR-144. 41 pp.


Technical documents do not include the “determinations of significance,” rather the District Biologist evaluates the effects of the project on the biotic resources in the BSA and reports them in the technical documents.  This evaluation of the direct and indirect effects (as discussed in Section 2-3.2), the long-term and/or short-term effects, and the cumulative effects resulting from the project are used by the PDT in the determination of significance to report in the Environmental Document. 

2-5.1 Evaluating Level of Effects

Per NEPA guidelines, effects are evaluated by assessing the context and intensity.  Context and intensity are defined by the CEQ Regulations (see Vol. 1 of the SER).

CEQA Guidelines has similar approaches to determine the level of effects. 


A brief synopsis of mitigation is discussed in this chapter as it pertains to the NES.  A detailed discussion can be found in Chapter 5 of Volume III, Mitigation and Monitoring.

The District Biologist takes the lead in developing and implementing biological mitigation measures for the proposed action.  Only mitigation measures approved by Caltrans management in conjunction with the resource agencies requesting the measures will be discussed in the mitigation section of the NES.  All approved mitigation measures are included in the environmental documents.  Recommendations from consultants concerning mitigation measures and significance will not be included in the NES, but are discussed in the Official Memo transmitting the consultant document to the Contract Administrator.

Mitigation development is coordinated with the appropriate resource or regulatory agency (USACE, FWS, DFG, NMFS , Coastal Commission, etc.) and all Caltrans programs affected by the proposed measures.  Development of the mitigation plan may involve Design, Construction, Landscape Architecture, Maintenance, Hydraulics, and Environmental.

In some cases the District Biologist must produce a Mitigation Plan, separate from the NES, which outlines measures to avoid, reduce, or offset adverse biological effects associated with transportation projects.  This plan will inform personnel associated with the project of the agreed upon mitigation measures, the goals and objectives to be achieved, procedures for their implementation, and practicable monitoring techniques.

Mitigation measures as defined in the CEQ Regulations (40 CFR Part 1508.20) shall include:

  • Avoiding the effects altogether by not taking a certain action or parts of an action;
  • Minimizing effects by limiting the degree or magnitude of the action and its implementation;
  • Rectifying the effects by repairing, rehabilitating, or restoring the effected environment;
  • Reducing or eliminating the effects over time by preservation and maintenance operations during the life of the action; and
  • Compensating for the effect by replacing or providing substitute resources or environments.

The level of mitigation required will be a consequence of the significance of the effects on the biotic resources.