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Last Updated: Tuesday, April 15, 2008 1:10 PM

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Chapter 3 - Wetlands

3-1 INTRODUCTION

This chapter will describe the responsibilities of the District Biologist, the definition of wetlands, how and why wetlands are regulated, and the general procedures that should be implemented by the biologist when dealing with wetland impacts.

3-2 BIOLOGIST'S ROLE

The Caltrans District Biologist acts as the liaison between Caltrans and resource and regulatory agencies, such as the U.S. Army Corps of Engineers (ACOE), that are responsible for approving actions that affect habitats described as wetlands. The District Biologist is responsible for being aware of the regulatory procedures required for identifying wetlands. In addition, the biologist must have a basic understanding of wetland ecology in order to determine the extent of potential impacts and to design appropriate mitigation or compensation activities.

The District Biologist is a member of the Project Development Team (PDT) with varied responsibilities that frequently go beyond the environmental analysis process. With regard to wetlands, the overall processes that involve the biologist are listed below.

  • Perform field reviews of the project, as needed, to determine whether wetlands are present.
  • Map or delineate the wetlands and other waters of the United States and submit a report to the ACOE and the Natural Resources Conservation Service (NRCS) documenting results and requesting verification of the determination.
  • Provide mapping to the Project Manager and discuss methods to avoid, minimize, or mitigate (compensate for) potential impacts to wetlands.
  • Coordinate with resource and regulatory agency staff to discuss potential project impacts and methods to avoid, minimize, or mitigate potential impacts to wetlands. Where possible, written agreement is obtained from agency staff regarding proposed methods.
  • Confirm implementation of avoidance, minimization, and mitigation activities during and/or prior to construction of the transportation project.
  • Where required, monitor or provide monitoring oversight for habitat mitigation activities.
  • Report monitoring results to resource and regulatory staff as required.

3-3 WETLANDS DEFINED

Executive Order 11990 - Protection of Wetlands (1977), calls for no net loss of habitats referred to as wetlands. Wetlands are driven by hydrology. The presence of water near the soil surface results in soil and plant characteristics that are not found in uplands (mostly dry) or aquatic (almost always wet) areas. Wetlands are generally found in transition zones between upland and aquatic habitats.

For the regulatory process, the ACOE and U.S. Environmental Protection Agency (EPA) jointly define wetlands as follows: "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" (EPA, 40 CFR 230.3 and ACOE, 33 CFR 328.3).

Caltrans recognizes this definition and uses it in the assessment of biological impacts of transportation projects. The EPA, ACOE, U.S. Fish and Wildlife Service (FWS) and the California Department of Fish and Game (DFG) work together in reviewing and approving the permits most frequently required for projects which will impact wetlands. The Regional Water Quality Control Board (RWQCB) may also have a role in its capacity of providing Section 401 certification.

The following wetland types are commonly found in California:

Freshwater

These areas may be permanent or seasonal, inland or coastal. This category includes riparian, or streamside areas, marshes, seeps, montane mountain meadows, and vernal pools. In some cases, wetlands may also occur within riparian settings above the wettest portions of the streambed. Areas subject to saltwater influence in coastal settings support vegetation adapted to brackish conditions. Alkaline conditions may support vegetation similar to that found in areas influenced by saltwater.

Saltwater

Coastal marsh, subject to full tidal action, occurs along the coast of California.

3-4 REGULATORY AGENCIES

The term "regulatory agency" is typically used to describe agencies such as the ACOE and the DFG which issue wetland related permits or agreements.

The following table provides a summary list of the agencies that regulate activities in wetlands (Cylinder et al. 1995).

Agency Regulation Authority
U.S. Army Corps of Engineers Clean Water Act, Section 404 Regulates placement of dredged or fill material into waters of the United States.
Rivers and Harbors Act of 1899 Section 10 Regulates work in navigable waters of the United States.
U.S. Environmental Protection Agency Clean Water Act Enforcement of regulations, may veto ACOE permit.
CEQA, NEPA Commenting authority.
U.S. Fish and Wildlife Service Fish and Wildlife Coordination Act Reviews/comments on Federal actions that affect wetlands and other waters, including Section 404 permit applications.
Endangered Species Act ACOE must consult with FWS if endangered species on site.
CEQA, NEPA Commenting authority.
National Marine Fisheries Service Fish and Wildlife Coordination Act Reviews/comments on Federal actions that affect coastal waters, including Section 404 permit applications.
Endangered Species Act ACOE must consult with NMFS if endangered marine species on site.
CEQA, NEPA Commenting authority.
California Department of Fish and Game California Fish and Game Code Sections 1600-1607 Regulates activities resulting in alteration of streams and lakes.
CEQA, NEPA Commenting authority.
Regional Water Quality Control Boards Clean Water Act, Section 401 Issues water quality certification; certification required for Section 404 permits.
Clean Water Act, Section 401 Regulates discharge of waste into waters of the United States.
CEQA, NEPA Commenting authority.
California Coastal Commission Coastal Act of 1976 Issues all coastal development permits.
Coastal Zone Management Act of 1976 Issues notice that work is consistent with state coastal management plan.
CEQA, NEPA Commenting authority.
San Francisco Bay Conservation and Development Commission McAteer-Petris Act of 1965 Regulates work within the bay, certain creeks, and a shoreline band of 100 feet inland from line of highest tidal action.
State Lands Commission Public Trust Doctrine May preclude the use of submerged lands and tidelands if this use is inconsistent with public trust.

3-4.1 U.S. Army Corps of Engineers

Wetlands have legal protection in accordance with Section 404 of the Clean Water Act (33 U.S.C. Section 1344). A permit from the ACOE is required for most activities that will impact wetlands.

The term "waters of the U.S." is also discussed in Section 404. Waters are currently described as any areas that might be considered waterways, either for commerce or recreation, even on a limited scale. Wetlands are a subcategory of waters. Frequently, the term "wetlands and other waters of the U.S." is used when describing areas under ACOE jurisdiction. Delineation of waters and wetlands results in "potential jurisdictional areas" which must be verified by the ACOE. Upon verification, these areas are referred to as "jurisdictional areas." Litigation may result in modification of the definition of waters and/or wetlands; therefore, the District Biologist or other user of this handbook must use the latest guidance from the ACOE.

A Section 404 permit is required from the ACOE when a project requires fill or other modification of waters, including wetlands. There are two types of permits issued by the ACOE, individual and general.

Individual Permits

Individual permits are the most complex. They cover projects affecting more than three acres, resulting in potentially significant impacts. The process of obtaining an individual permit usually takes many months. Special Conditions of the permit may include mitigation activities that need to be monitored for a five to ten year period for the most complex and/or controversial projects.

General Permits

There are two types of general permits, nationwide and regional. Nationwide permits cover a wide variety of activities with minimal impacts (less than three acres, 500 feet of lineal stream). Nationwide permits may take two to three months, or more, to obtain. Regional permits are wide ranging, blanket permits used to cover roadside ditch maintenance activities, for example, for a designated geographic area. Regional permits may take months to prepare; however, they save time in the long run for small activities such as routine maintenance.

Initiation of a request for an ACOE permit to affect wetlands involves other resource and regulatory agencies as a part of the interagency review process. The ACOE submits permit applications to the EPA, DFG, National Marine Fisheries Service (NMFS), and FWS for review and comment. Time periods and extent of commenting required by these agencies varies depending upon the permit type. Individual permits are the most lengthy and involved.

Applications for ACOE permits may be prepared and submitted by the Project Engineer, the District Biologist, or others, using information on delineated wetlands and other waters of the U.S. as prepared by the biologist. The Project Engineer provides information on the extent of the construction impacts responsible for proposed fill. The District Biologist is the key liaison with resource and regulatory agency staff regarding the wetland habitat impacts and potential mitigation.

3-4.2 Regional Water Quality Control Board

Section 401 of the Clean Water Act (33 U.S.C. 1341) requires any applicant for a Federal license or permit to conduct any activity that may result in a discharge of a pollutant into waters of the United States to obtain certification from the State in which the discharge originates. As a result, proposed fill in waters and wetlands requires coordination with the appropriate RWQCB that administers Section 401 and provides certification. The RWQCB also plays a role in review of water quality and wetland issues, including avoidance and minimization of impacts. Section 401 certification is required prior to issuance of a Section 404 permit. The Project Engineer may be responsible for this coordination, with assistance from the District Biologist, regarding specific impacts and mitigation.

3-4.3 California Department of Fish and Game

Wetlands may also be subject to jurisdiction of the DFG in accordance with DFG Code Sections 1600-1607. The DFG regulates activities that would alter the flow, bed, channel or bank of streams and lakes by issuing Streambed Alteration Agreements, a type of permit. In riparian areas their jurisdictional limits are usually delimited by the tops of the stream or lake banks, or the outer edge of riparian vegetation, whichever is wider. Wetlands under jurisdiction of the ACOE may or may not be included in the area covered by a Streambed Alteration Agreement obtained from the DFG.

Caltrans must contact the DFG regarding any potential Section 1600-1607 impacts independent of their role as reviewer on ACOE Section 404 permits. The DFG contacts for Section 1600 are best facilitated by coordination with the District Biologist.

3-4.4 California Coastal Commission

When a project will require fill in wetlands within the coastal zone, Caltrans must obtain a permit from the California Coastal Commission (CCC) or the city or county with coastal permit jurisdiction. The CCC oversees implementation of the California Coastal Act (CCA) and the Federal Coastal Zone Management Act (CZMA). The coastal zone is generally defined as the distance from the ocean shoreline 1,000 yards inland, or more in some locations. The District Biologist and the Project Engineer may share coordination with the CCC, when needed.

3-4.5 San Francisco Bay Conservation and Development Commission

Projects affecting wetlands within the limits of San Francisco Bay may require a permit from the San Francisco Bay Conservation and Development Commission (BCDC). The BCDC has jurisdiction over all areas of San Francisco Bay subject to tidal action up to the mean high tide line, or a line five feet above mean sea level in marshlands. The area 100 feet inland from the mean high tide is also within jurisdiction. The BCDC is responsible for Federal implementation of the CZMA within the limits of San Francisco Bay, rather than the CCC. The Project Engineer is usually the key contact for this agency. The District Biologist provides analysis of wetland impacts and may work directly with agency staff on mitigation requirements unique to the BCDC.

3-4.6 State Lands Commission

The State Lands Commission (SLC) manages submerged lands, tidelands, and swamp and overflowed lands owned by the State. Despite the fact that most of these lands have been conveyed to the private sector, submerged lands and tidelands are still subject to the public trust, even if filled. Permits from the SLC or land use leases with conditions to protect the purposes of the public trust may be required.

3-5 RESOURCE AGENCIES

The term "resource agency" is typically used to describe agencies such as the FWS, NMFS, and the EPA, which protect natural resources but do not issue wetland-related permits.

3-5.1 U.S. Environmental Protection Agency

The mission of the EPA includes protection of human health and safeguarding the natural environment. The EPA has the right to challenge an ACOE permit approval. Section 404 (b) (1) of the EPA and ACOE guidelines for Section 404 of the Clean Water Act (ACOE, EPA 1993) involve assurance that the proposed activity does not violate water quality standards. It requires that the applicant provide an alternatives analysis to show that the alternative least damaging to waters of the United States has been selected.

3-5.2 Natural Resources Conservation Service

Caltrans may be required to coordinate with the NRCS, formerly the Soil Conservation Service, when a proposed transportation project may affect agricultural lands where farmers have been growing commodity crops in areas that were drained, filled, or otherwise altered wetlands prior to 1985. The Food Security Act of 1985 (referred to as "Swampbuster") ended the NRCS approval of the draining of wetlands for commodity crops. The NRCS administers the Act, as amended by the Food, Agriculture, Conservation, and Trade Act of 1990 and the Federal Agriculture Improvement and Reform Act of 1996.

In 1994, the NRCS signed a Memorandum of Agreement (MOA) with the ACOE which makes the NRCS responsible for wetland delineations on prior converted croplands and farmed wetlands that receive agricultural subsidies through the Federal government. Agricultural land is defined as land that is intensively used and managed for the production of food and fiber. Examples are cropland, hayland, and pastures, including native pastures and rangeland, orchards, vineyards, areas which support wetland crops, other lands used to produce or support the production of livestock, and small tree farms. The NRCS may use the procedures for delineating wetlands as described in the National Food Security Act Manual, Third Edition (NRCS 1996). Linear projects such as roadway improvements may be excluded from the NRCS involvement.

When the NRCS is involved, the District Biologist is responsible for contacting the NRCS, submitting the wetland delineation report to the appropriate NRCS field office, and requesting verification. In some cases, the ACOE may take the responsibility for the NRCS verification, or provide evaluation of an "other waters" determination. It is best to obtain guidance from the NRCS regarding responsibility of all aspects of the determination.

3-5.3 U.S. Fish and Wildlife Service

The mission of the FWS includes working to conserve, protect, and enhance fish and wildlife and their habitats for the continuing benefit of the American people. According to the Fish and Wildlife Coordination Act, all Federal agencies are required to contact the FWS, NMFS, and the state's wildlife agency regarding activities that affect, control, or modify waters of any stream or other bodies of water. The DFG is the state wildlife agency in California. These consulted agencies review applications for permits issued under Section 404 and provide comments to the ACOE about the environmental impacts of the proposed project.

3-6 EARLY COORDINATION AND AGREEMENTS

3-6.1 Early Coordination

It is important to identify potential wetland impacts as early in the environmental process as possible. Early notification to the Project Manager allows time for investigation of design modifications to avoid or minimize potential impacts to wetlands. If impacts cannot be avoided, and have been reduced to the minimum level practicable, wetland mitigation proposals to compensate for those impacts must be developed by the District Biologist and others on the Project Development Team, and evaluated as part of the environmental impact analysis process.

3-6.2 NEPA/404 Memorandum of Understanding

Caltrans has implemented early coordination with the State and Federal agencies involved in the wetland regulation process. In 1993, Caltrans signed a Memorandum of Understanding (MOU) with the Federal Highway Administration, Federal Transit Administration, EPA, ACOE, FWS, NMFS, and the Arizona and Nevada Departments of Transportation. The objective of the MOU is to integrate the National Environmental Policy Act (NEPA) and the Clean Water Act, Section 404. Referred to as the NEPA/404 integration process, the MOU commits these agencies to ensuring the earliest possible consideration of environmental concerns pertaining to waters of the U.S., including wetlands.

Early stage planning meetings allow for full discussion of project alternatives to avoid wetlands. These alternatives may need to be discussed in the environmental document as a Wetlands Only Practicable Finding (WOPAF). Section 404 permit applications also require an alternatives analysis.

3-7 WETLAND DELINEATION

As stated in Section 3-3, Caltrans follows the wetlands definition agreed to by the EPA and ACOE. Although the DFG and FWS have their own definitions, they rarely play a role in the wetland delineation and assessment process.

The ACOE publishes guidance regarding the standard procedures required to delineate wetlands that may be under ACOE jurisdiction (Env. Lab. 1987). In 1994, the EPA, NRCS, and ACOE agreed to use the 1987 ACOE Wetland Delineation Manual for non-agricultural lands (CFR Vol. 59, No. 12, pp. 2920-2924 Jan. 19, 1994). The procedure describes a three-parameter approach that includes presence of hydrophytic vegetation, wetland hydrology, and hydric soils. All three parameters must be present, under normal circumstances, for an area to be designated as a wetland under jurisdiction of the ACOE. Such wetlands are referred to as jurisdictional wetlands. In order to obtain a Section 404 permit, Caltrans must provide the ACOE with a delineation of potential jurisdictional areas, including wetlands.

The delineation must be made by a qualified biologist. A qualified biologist is one who has successfully completed an ACOE approved training course in wetland delineation in accordance with the currently approved methodology. Biologists who have not completed the training should be supervised by a qualified biologist when preparing wetland delineations. The biologist takes site information and background materials to prepare what is commonly referred to as a Wetland Delineation Report. For clarification of the fact that this report covers wetlands and other waters of the U.S., it might more accurately be referred to as the Wetlands/Waters Delineation and Assessment Report.

This report is submitted to the ACOE as a part of the Section 404 permit application package. It also serves as a technical report for the environmental document, in conjunction with the Natural Environment Study (NES) described in Chapter 2 of this handbook. If the wetland impacts of a project are very small, their discussion may be included as a part of the NES. In this case, a separate Wetland Delineation Report would be prepared and submitted to the ACOE for the permitting process. Materials to include in these reports will be discussed in the following section. If the wetland impacts are large or controversial, it is more convenient to prepare a report separate from the NES. The NES covers non-wetland impacts that would not necessarily be of interest to the ACOE in review of a Section 404 permit application.

3-8 WETLANDS ASSESSMENT

Delineation of wetlands is only the first phase of determining potential impacts. The biologist must also analyze the impacts with respect to the proposed loss of wetland functions and values. Proposed mitigation or compensation actions must also be developed. In order to do this, the functions and values of the wetland habitat must be evaluated to determine the degree of impacts resulting from the proposed transportation project. In this manner, appropriate mitigation plans may be developed to replace those functions and values.

Functions. Functions are the physical, chemical, and biological attributes of a wetland without regard to their importance to society. Examples of functions include flood flow alteration, wildlife habitat, and groundwater discharge.

Values. The term values may be used to describe those functions that are generally regarded as beneficial to society. Recreation and uniqueness are examples of values. All or part of society may not value some functions. Nutrient removal and transformation, for example, may not be considered a value if that function leads to algal blooms and noxious odors.

Caltrans uses the functions and values described in the Wetland Evaluation Technique (WET) (Adamus et al. 1987). The WET manual describes the following functions and values:

  • Groundwater recharge
  • Groundwater discharge
  • Flood flow alteration
  • Sedimentation stabilization
  • Sediment/toxicant retention
  • Nutrient removal/transformation
  • Production export
  • Wildlife habitat (aquatic and terrestrial)
  • Uniqueness/heritage
  • Recreation

The WET Manual describes a detailed methodology for analyzing these functions and values. The results describe habitat values as low, medium, or high, without regard to habitat size. The model is based primarily on wetland systems from the southern and eastern regions of the United States.

Although the complex methodology described in the manual may be used, experience has shown that informed professional judgment, applied to the identified functions and values, accomplishes the same result in California wetlands. These results are obtained in significantly less time than implementing the full methodology. The District Biologist is responsible for interpreting and understanding the functions and values and using their best professional judgement to determine potential impacts.

3-9 WETLAND DELINEATION AND ASSESSMENT REPORT FORMAT

The following outline represents one way to present the project information in a report format. This outline may be adapted to meet the needs of a particular project.

  1. Summary
  2. Introduction
    1. Description of Project
    2. Purpose of Assessment
  3. Project Setting
    1. Vegetation community
    2. Hydrology
    3. Soils
  4. Methodology
    1. Pre-survey investigations
    2. Field survey
  5. Results
    1. Summary table of wetland impacts
    2. Wetland functions and values
      1. Description of existing functions and values
      2. Potential impacts
  6. Discussion
    1. Avoidance and minimization recommendations
    2. Mitigation recommendations
  7. References Cited
  8. Personal Communications Cited
  9. Appendices
    1. Project maps showing proposed ACOE jurisdictional areas (1:100 scale map preferred)
    2. Data Forms - Wetland Delineation
    3. National Wetlands Inventory (NWI) map, where available

3-10 WETLAND MITIGATION

In accordance with Section 404 requirements, Executive Order 11990 - Protection of Wetlands (1977), and the U.S. Fish and Wildlife Service Mitigation Policy (1981) unavoidable impacts to wetlands must be compensated. The District Biologist works closely with the Project Development Team to design a suitable creation or restoration project that will replace the wetland functions and values affected by the transportation project. The District Biologist is usually responsible for monitoring the wetland mitigation report and submitting annual monitoring reports to the ACOE. The processes involved are described in detail in Chapter 5, Mitigation and Monitoring.

3-11 REFERENCES

ACOE, EPA, 1993. Federal Register Vol. 58, No. 163, August 25, 1993, pp. 45008-45038. Dept. of Defense, Dept. of the Army, Corps of Engineers, 33 CFR Parts 323 and 328; Environmental Protection Agency, 40 CFR Parts 110, 112, 116, 117, 122, 230, 232, and 401, Clean Water Act Regulatory Programs.

Adamus, P.R., E.J. Clairain, Jr., , R.D. Smith, and R.E. Young. 1987. Wetland Evaluation Technique (WET): Volume II: Methodology, Operational Draft Technical Report Y-87-1, U.S. Army Engineer Waterways Experiment Station, Vicksburg, Miss.

Cylinder, P.D., D.M. Bogdan, E.M. Davis, and A.I. Herson. 1995. Wetlands regulation - a complete guide to federal and California programs. Solano Press Books, Point Arena, CA. 363 pp.

Environmental Laboratory, 1987. Corps of Engineers Wetlands Delineation Manual, Technical Report Y-87-1, U.S. Army Engineer Waterways Experiment Station, Vicksburg, Miss.

Natural Resources Conservation Service, 1996. National Food Security Act Manual, 3rd Edition. 180-V-NFSAM.

U.S. Fish and Wildlife Service, 1981. U.S. Fish and Wildlife Service Mitigation Policy. Federal Register Vol. 46, No. 15, January 23, 1981, pp. 7644-7663 (as corrected in the Federal Register of February 4, 1981).