About this permitting pathway

Programmatic Biological Opinion for the East Alameda Conservation Strategy. The Conservation Strategy addresses 19 focal species: nine state and/or federally listed species and ten non-listed special status species. The Conservation Strategy provides a framework for long-term conservation and management of these species and the habitats that support them. The Conservation Strategy includes measures to protect all 19 focal species as if they are currently listed as endangered and threatened under the Act and or California Endangered Species Act.

This purpose of the programmatic document is to streamline section 7 consultations on projects that implement the Conservation Strategy for eight federally listed species. It does not evaluate the effects for non-federally listed focal species or the federally threatened California coastal steelhead (Oncorhynchus mykiss) focal species.

This Programmatic BO is issued to the Army Corps for permits, enforcement actions or mitigation banks (project(s)) that are under their jurisdiction. Projects that are appended to this Programmatic BO will be provided individual incidental take authorization. Incidental take authorization is not provided in this document. This Programmatic BO will expedite the process for project approval provided all information listed in the Procedures for Appending Projects to the PBO section on page 11 of the PBO, and below on this web page.

The Conservation Strategy and Programmatic BO provide the framework for compensation, mitigation, conservation, and appropriate minimization measures. The Service will track project effects, compensation, and other pertinent information.

Applicable locations

The Conservation Strategy Area encompassing 271,485 acres in Eastern Alameda County, California. The western boundary runs along the Alameda Creek watershed boundary. The northern, southern, and eastern boundaries follow the Alameda County line with Contra Costa County, Santa Clara County, and San Joaquin County, respectively.

Permit documents

Species covered

  • Longhorn fairy shrimp (Branchinecta longiantenna) and its critical habitat
  • Vernal pool fairy shrimp (Branchinecta lynchi) and its critical habitat
  • Callippe silverspot butterfly (Speyeria callippe callippe)
  • California red-legged frog (Rana draytonii) and its critical habitat
  • Central California Distinct Population Segment (DPS) of the California salamander (Ambystoma californiense) (Central California tiger salamander) and its critical habitat
  • Alameda whipsnake (Masticophis lateralis euryxanthus) and its critical habitat
  • San Joaquin kit fox (Vulpes macrostis mutica)
  • Palmate-bracted bird’s beak (Cordylanthus palmatus)

Activities covered

Covered activities include development projects, infrastructure projects, which are not described in detail here, but are listed starting on page 13 of the PBO.

Restoration Projects:

  • Pond and/or Stream Restoration/Enhancement/Construction
  • Fish Barrier Removal and Modification
  • Wetland Construction and Maintenance (if needed)
  • Channel Reconfiguration to Increase Complexity for Floodplain Creation and Recontouring
  • Species/Habitat Conservation/Restoration Projects

Maintenance Projects:

  • Sediment Removal: Flood control channel, basin, stock pond
  • Debris removal: for large trash and woody debris
  • Dams and other Water Impoundments (Existing): Maintenance. New construction or increases in capacity or size are not covered.
  • Vegetation Management: Riparian, native, and control of invasive vegetation (dependent on application)

Certain activities will be covered as part of a long term management plan for conservation areas that are managed for listed species as compensation for project effects. These activities may include but are not limited to: integrated pest management, vegetation management, grazing, species surveys, conservation area enhancement actions, fence installation and maintenance, grazing water supply infrastructure installation and maintenance, and pond maintenance.


Projects that are not covered activities will not be appended to this Programmatic BO and will require individual formal consultation.

Application Tips and Resources

Procedures for Appending Projects to the Programmatic Biological Opinion

The following information is required from the applicant and will be used by the Corps to evaluate whether a project can be appended to this Programmatic BO:

  1. Corps Permit Application including Assessor’s Parcel Number(s), Universal Transverse Mercator (UTM) or Latitude and Longitude coordinates, GIS shape files with metadata, and street address of the project;
  2. Corps-verified jurisdictional determination
  3. Biological Assessment pursuant to 50 Code of Federal Regulations (CFR) 402.12. The Biological Assessment will include at a minimum:
  • Detailed project and compensation maps with listed species occurrences and critical habitat;
  • Baseline conditions for listed species;
  • Construction and compensation details;
  • Conservation measures; and
  • Effects of the project, conservation measures, and compensation on the listed species.

The Corps will make one of the following determinations of effect for a project by reviewing the Biological Assessment and other information provided by the applicant and will take the identified action.

  • No effect. The proposed project will not affect listed species or critical habitat. The Corps will not consult with the Service.
  • May affect but is not likely to adversely affect listed species and or critical habitat. The proposed project effects are expected to be discountable, insignificant, or completely beneficial. Beneficial effects are contemporaneous positive effects without any adverse effects to the species. Insignificant effects relate to the size of the impact and do not ready the scale where take occurs. Discountable effects are those extremely unlikely to occur. Based on best judgment, for these effects a person would not: (1) be able to meaningful measure, detect, or evaluate insignificant effects; or (2) expect discountable effects to occur. The Corps will consult with the Service for concurrence and forward all biological and other pertinent information.
  • May affect and is likely to adversely affect listed species or critical habitat. The proposed project has any adverse effect, either as a direct or indirect result of the proposed action or its interrelated and interdependent actions, and the effects are not: discountable, insignificant, or beneficial. The proposed project may be overall beneficial to listed species, but is also likely to cause some adverse effects. The proposed project anticipates incidental take. The Corps will consult with the Service, requesting that the proposed project to be appended to this Programmatic BO and forward all biological and other pertinent information.

The Service will review the proposed project to evaluate whether it is appropriate to append the project to this Programmatic BO based on the level of effects, avoidance, minimization, and compensation measures. The Service may determine some projects require separate section 7 consultation and will not be appended to this Programmatic BO. If the Service does not concur the project is appropriate to be appended to this Programmatic BO, the Service will notify the Corps in writing. Applicants who have had consultation initiated by the Corps prior to the date of this Programmatic BO may continue with that consultation or may request their project be appended to this Programmatic BO.