Common Permits Required for Restoration in the Central Coast Region

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Photo source: UC Davis Graduate Group in Ecology


Restoration and research in the Central Coast Region that involves alteration or impacts to natural and biological resources may require a number of permits from federal, state and local agencies. The permit process helps protect the environment by ensuring compliance with local laws and regulation. By tracking the number and types of permits issued, regulatory agencies can set standards for restoration activity, develop new standards, and protect the environment for current and future generations.[1]

Restoration activities are based on restoration science, which is a multidisciplinary approach combining hydrology, biology, oceanography, and the social sciences to protect the natural environment.[2]

Section 7 and Section 10 Permits

Two agencies are responsible for administering the Endangered Species Act (ESA):the National Marine Fisheries Service (NMFS) and the United States Fish and Wildlife Service (USFWS). Terrestrial and fresh water species are under the scope of USFWS. Marine wildlife and anadromous fish are under the NMFS.[3]

Section 7(a)(2) of the ESA requires that federally funded projects are reviewed and approved by either USFWS and/or NMFS and that they do not jeopardize endangered or threatened species or their habitats. Section 7 permits help meet this provision of the ESA. [4]

Section 10 permits are issued under section 10 of the ESA. Any non-federal activity that may lead to incidental take of an endangered or threatened species is subject to section 10 permitting. Section 10 permits authorize the incidental take of an endangered or threatened species.[5]

General and Individual Permits

General permits (including Nationwide) reduce the regulatory burden and delay of the permitting process and allow private land owners or developers to proceed with plans without a site specific evaluation in advance. Annually, approximately 92% of the permits issued by the Army Corps of Engineers were general permits.[6]

Individual permits take longer to process and are subject to site specific evaluation, public hearing, and public notice. [7]

Examples of general permits include: [8]

  • Placement of aids to navigation approved by, and installed according to, U.S. Coast Guard requirements (nationwide permit 1)
  • Activities related to construction and maintenance of authorized outfall structures and associated intake structures (nationwide permit 7)
  • Stream or river bank stabilization activities necessary to prevent erosion(nationwide permit 13)
  • Minor dredging, that is, dredging of no more than 25 cubic yards of material(nationwide permit 19)
  • Activities associated with restoration, enhancement, or establishment of wetlands and riparian areas where the activities result in net increase in aquatic resource functions and services (nationwide permit 27)

Waste Discharge Permits (WDR)

The Central Coast Agricultural Order, generally referred to as the Ag waiver, is a conditional waiver issued by the Central Coast Regional Water Quality Control Boards (RWQCB). The Porter-Cologne Act of 1969 establishes nine regional water quality control boards and gives each RWQCB the authority to issue conditional waivers to the Waste Discharge Requirement (WDR)for irrigated lands.[9]

The 2012 Ag Waiver outlines a compliance criteria based on a tiered system: Tier 1, Tier 2, and Tier 3.

This tiering system is based on risk assessments or threats posed to water quality. Farms with low risk or threats to water quality are placed in Tier 1 or Tier 2 and have fewer requirements for compliance. Tier 3 farms pose the greatest risk to water quality and have the most requirements.

Risk is assessed by grower and confirmed by the RWQCB.

Federal permitting agencies and the permits they issue

United States Army Corps of Engineers
The USACOE has jurisdiction over navigable waters. Navigable waters waters of the United States are defined in the Code of Federal Regulations (CFR), specifically 33 CFR part 329 as: waters that are subject to the ebb and flow of the tides and/or are presently used, or have been used in the past or may be susceptible for use to transport interstate or foreign commerce.[10]

The following is a list of common permits required for restoration and research. For a full list of permits see Regulatory Program Requirements.

  • Section 10 of the Rivers and Harbors Act of 1899 33 U.S.C. 403: Permit must be acquired to fill or excavate a waterway [11]
  • Section 404 of the Clean Water Act: Permit must be acquired to discharge fill material (e.g. sediment, rock into the navigable waters [12].

National Marine Fisheries Service

  • Endangered Species Act (ESA) Section 7: A biological opinions document must be obtained whenever a project may impact an ESA-listed species or habitat [13].
  • ESA Section 10(a)(1)(A)) and Section 10(a)(1)(B)):If a project may result in take of an ESA-listed species an incidental take permit or a permit for scientific research must be acquired [14].

State permitting agencies and the permits they issue

Regional Water Quality Control Board

  • 401 Water Quality Certification: Required to discharge fill material into a waterway or wetland [15].

California Department of Fish and Wildlife

  • Fish and Game Code (Section 1602): Must notify CDFW of any activity that may modify a river, stream or lake. If CDFW determines that the activity negatively impacts fish and wildlife, a Lake or Streambed Alteration Agreement will be prepared [16].

County and city permitting agencies and the permits they issue

Regional Water Quality Control Board

  • Under the Irrigated Lands Regulatory Program, the Resource Water Quality Control Boards (RWQCB) have the authority to conditionally waive Waste Discharge Requirements (WDR) for runoff from irrigated lands. These conditional waivers are generally referred to as Orders or Agricultural Orders. [17]
  • There are nine RWQCBs. Region 3 is the Central Coast RWQCB and covers the following counties: Santa Clara (south of Morgan Hill), San Mateo (southern portion), Santa Cruz, San Benito, Monterey, Kern (small portions), San Luis Obispo, Santa Barbara, and Ventura(northern portion).[18]

California Coastal Commission

  • Coastal Development Permit: Necessary if work will be conducted within 6 miles of the coast [19]. Central Coast District, Santa Cruz, CA. 831-427-4863.

[ Monterey County Resource Management Agency]

  • Use permits/Coastal Development permit: these permits are required per Title 21 (inland areas) and state regulations for coastal areas.

Navigating the Permitting Process

The permitting process can be time consuming. It is essential to start early, preferably a year prior to the start date of the project. All relevant agencies should be contacted simultaneously to begin the process with each. Process for permitting may differ from agency to agency; therefore, contacting all agencies early on may be beneficial. It is also important to learn about the fee structures of all agencies early in order to plan and develop an accurate budget. Whenever possible, invite the agencies, preferably at the same time, to the project site for an environmental assessment. This is valuable in learning about and addressing the concerns of each agency appropriately and ensuring that response for compliance is inline with expectations.[20].

A complete list of steps for project approval is available here: ANR Guide




See also

California Natural Diversity Database


This page may contain students' work completed as part of assigned coursework. It may not be accurate. It does not necessarily reflect the opinion or policy of CSUMB, its staff, or students.