- U.S. Army Corps of Engineers (USACE)
- Section 404 Permits. USACE oversees federal waters and is responsible for issuing permits under Section 404 of the Clean Water Act. If a proposed project impacts waters of the United States, the project proponent must seek a permit from USACE. Currently, General Program Permits are being requested from USACE for the Habitat Plan and will be available under the Plan soon.
- National Oceanic and Atmospheric Administration (NOAA) Fisheries
- NOAA Fisheries is the federal agency responsible for managing, conserving, and protecting living marine resources in inland, coastal, and offshore waters of the United States. If a proposed project has the potential to impact federally listed fish species that fall under the jurisdiction of NOAA Fisheries, the project proponent must seek a separate permit from NOAA Fisheries.
- U.S. Fish and Wildlife Service: Sacramento Office
- California Department of Fish and Wildlife (CDFW)
- Section 2081 (b) and (c) Permits. Sections 2081(b) and (c) of the California Endangered Species Act (CESA) allow CDFW to issue an incidental take permit for a State-listed threatened or endangered species only if specific criteria are met. If a proposed project impacts State-listed species not covered by the Plan, the project proponent must seek a separate permit under CESA.
- Lake and Streambed Alteration Agreement. To help meet CDFW’s responsibility for conserving, protecting, and managing California's fish, wildlife, and native plant resources, Section 1602 of the Fish and Game Code requires an entity to notify CDFW of any proposed activity that may substantially modify a river, stream, or lake. If CDFW determines that the activity may substantially adversely affect fish and wildlife resources, a Lake or Streambed Alteration Agreement will be prepared.
- Regional Water Quality Control Boards (RWQCBs)
- Water Quality Certifications. Overseen by the State Water Resources Control Board, nine RWQCBs exercise rulemaking and regulatory activities in California. Proposed projects that discharge waters of the State or into waters of the State must consult with the applicable RWQCB. If an applicant obtains a permit from USACE under Section 404, the applicant must also obtain certification of that permit by the RWQCB with jurisdiction over the project site. Projects in Santa Clara County fall under the jurisdiction of the San Francisco RWQCB (for projects north of Morgan Hill) or the Central Coast RWQCB (for projects south of Morgan Hill). Cochrane Road in Morgan Hill is the dividing line between Region 2 and 3. See attached map here.
- Region 2: San Francisco Bay Region
- Alameda, Contra Costa, San Francisco, Santa Clara (north of Morgan Hill), San Mateo, Marin, Sonoma, Napa, Solano counties
- Region 3: Central Coast Region
- Santa Clara (south of Morgan Hill), San Mateo (southern portion), Santa Cruz, San Benito, Monterey, Kern (small portions), San Luis Obispo, Santa Barbara, Ventura (northern portion) counties