Skip to Content


Notice of Intent To Prepare a Draft Environmental Impact Statement/Environment Impact Report (DEIS/DEIR) for a Permit Application for the Proposed San Elijo Lagoon Restoration Project, City of Encinitas, San Diego County, CA

Document Details

Information about this document as published in the Federal Register.

Document Statistics
Document page views are updated periodically throughout the day and are cumulative counts for this document including its time on Public Inspection. Counts are subject to sampling, reprocessing and revision (up or down) throughout the day.
Published Document

This document has been published in the Federal Register. Use the PDF linked in the document sidebar for the official electronic format.

Start Preamble


United States Army Corps of Engineers, Los Angeles District, Regulatory Division, Defense.


Notice of Intent (NOI).


The United States (U.S.) Army Corps of Engineers (Corps), in conjunction with the County of San Diego Department of Parks and Recreation (County Parks), is preparing a joint Environmental Impact Statement/Environmental Impact Report (EIS/EIR) for the proposed San Elijo Lagoon Restoration Project (SELRP). The Corps will be lead agency under National Environmental Protection Act (NEPA) and County Parks will be the lead agency under the California Environmental Quality Act (CEQA). The development of the EIS/EIR and associated technical studies are being completed to determine the Agency Preferred Alternative, which would improve and/or restore wetland functions and services within the San Elijo Lagoon. Given the complexity of the alternatives analysis and range of potentially significant issues, the appropriate environmental document was determined by the Corps and County Parks to be a combined EIS/EIR, respectively. The Corps and the County Parks have agreed to jointly prepare the EIS/EIR to optimize efficiency and avoid duplication. The EIS/EIR is intended to be sufficient in scope to address federal, state, and local requirements for environmental analysis and permitting.

Implementing the Agency Preferred Alternative would require a Department of the Army permit pursuant to Section 404 of the Clean Water Act, which regulates the discharge of dredged, excavated, or fill material in wetlands, streams, rivers, and other waters of the U.S. and the potential impacts on the human environment from such activities. To be authorized by the Corps, the Agency Preferred Alternative must also comply with the Section 404(b)(1) Guidelines (40 Code of Federal Regulations [CFR] Part 230) and may not be contrary to the public interest.

Federal agencies coordinating in the development of the EIS include the U.S. Fish and Wildlife Service (Service), National Marine Fisheries Service (NMFS), and Environmental Protection Agency (EPA). State agencies coordinating in the development of the EIR include Department of Fish and Game (CDFG), California Coastal Commission (CCC), San Diego Regional Water Quality Control Board (RWQCB), State Water Resources Control Board, California Department of Transportation (Caltrans), and San Diego Association of Governments (SANDAG).

The EIR/EIS is currently evaluating three alternative restoration designs, the No Project/No Action alternative, and associated maintenance and long-term management and maintenance measures. In addition, alternatives are being evaluated to determine if project phasing is necessary to maintain adequate habitat for sensitive aquatic species, including light footed clapper rail (Rallus longirostris levipes) and potentially western snowy plovers (Charadrius alexandrines nivosus) and California least terns (Sterna antillarum browni) . The study area encompasses approximately 960 acres within and adjacent to the Reserve, but final project size may vary, depending on the outcome of the alternatives analysis. Additional details and alternative designs are provided in Section 4. Should the project receive a permit, it is anticipated that construction of the SELRP would begin in fall 2014. The study area boundaries for the SELRP are generally defined to include publicly owned parcels where restoration activities could occur.

Start Further Info


Comments and questions regarding scoping of the Draft EIS/EIR may be addressed to Ms. Michelle Mattson, Senior Project Manager, U.S. Army Corps of Engineers, Los Angeles District, Regulatory Division, Carlsbad Field Office, Attn: CESPL-2009-00575-MLM, 6010 Hidden Valley Road, Suite 105, Carlsbad, CA 92011 or comment letters can also be sent via electronic mail to The project title “San Elijo Lagoon Restoration Project, CESPL-2009-00575-MLM” should be included in the electronic mail's subject line and the commenter's physical mailing address within the body of the letter. Michelle Mattson can be reached at (760) 602-4835. Comments and questions can also be sent to Ms. Megan Hamilton, County of San Diego Department of Parks and Recreation, 5500 Overland Avenue, Suite 410, San Diego CA 92123 or via electronic mail to Megan Hamilton can be reached at (858) 966-1377.

End Further Info End Preamble Start Supplemental Information


1. Project Site and Background Information: San Elijo Lagoon is located in the city of Encinitas, San Diego County, California. The lagoon is the terminus of the Escondido Creek and La Orilla Creek watersheds at the Pacific Ocean. The study area is composed of approximately 961 acres, which are separated into four basins or areas (East Basin, Central Basin, West Basin, and Coastal Area). The lagoon provides habitat for resident and migratory species, some of which are sensitive or listed as federally-threatened or endangered under the Endangered Species Act (ESA).

Due to encroachment by development, restricted tidal influence, and the increase of freshwater from the watershed, the San Elijo Lagoon has gradually degraded over time. Tidal influence has been restricted by infrastructure and development at the inlet of the lagoon. The Pacific Coast Highway (PCH), the North County Transit District (NCTD) railroad, and Interstate 5 (I-5) all traverse the lagoon and further modify tidal and freshwater circulation patterns and increased sediment accumulation from the watershed. Freshwater input has increased as a result of residential and commercial land uses in the 77-square-mile hydrologic watershed. Because of these hydrologic changes, lagoon habitat is rapidly transitioning from mudflats to mid-marsh habitat through the rapid expansion of cordgrass (Spartina spp.) and pickleweed (Sarcoconia pacifica) and the East Basin supports large areas of freshwater marsh vegetated primarily by cattails (Typha spp.). The changes have also decreased the quality of water in the lagoon causing elevated bacteria levels and increased the occurrences of beach closures during high flow events.

Mechanical breaching of the ocean inlet is routinely performed to maintain tidal flushing within the lagoon, but benefits are only temporarily realized due to the physical and hydrological changes previously mentioned. If no action is taken to restore the lagoon, functions and services will continue to degrade, further reducing the diversity of estuarine habitats and increasing freshwater wetland and riparian habitats. Sensitive flora and fauna currently dependent on the estuarine conditions will continue to be adversely Start Printed Page 68742affected. The SELRP is an effort to restore estuarine functions and services to the greatest extent practicable in light of permanent constraints. Depending on the restoration alternative chosen through development of the Draft EIS/EIR, the SELRP would improve tidal influence by modifying and maintaining the existing inlet of the lagoon or by constructing a new, permanently open lagoon inlet. Habitat diversity and other wetland functions and services would also be improved by modifying existing tidal channels, grading new tidal channels, and/or by grading areas specified by a range of tide elevations.

The basic project purpose of the proposed SELRP is to restore tidal wetlands; this is a water dependent activity. The overall project purpose of the SELRP is to enhance and restore the physical and biological functions and services of the lagoon by increasing the tidal prism to support a diverse range of habitat types.

The overarching goal of the SELRP is to protect, restore, and then maintain, via and adaptive management the San Elijo Lagoon ecosystem and the adjacent uplands to support a diversity of estuarine and brackish marsh habitats and associated native species of southern California.

This goal can be further refined into three categories of objectives:

1. Physical restoration of lagoon estuarine hydrologic functions,

2. Biological restoration of lagoon estuarine habitats, and

3. Management and maintenance of the lagoon to ensure long-term viability of the restoration efforts.

2. Proposed Action: Three restoration alternatives and the No Project/No Action alternative are being evaluated in the EIR/EIS. All the restoration alternatives are designed to counteract the conversion trend to freshwater habitats and restore a range of estuarine habitat types. Therefore, increasing tidal influence is the primary action being evaluated to restore ecological functions and services. Two alternatives retain the existing tidal inlet and one constructs a new inlet further south. Restoration alternatives evaluate varying degrees of dredging and filling portions of the three basins (West, Central, and East Basin) to restore or create a diversity of estuarine habitat types. Excess sediment from dredging could be discharged on the adjacent beach or in the nearshore zone west of the lagoon, if it is identified as suitable beach sand material. Maintenance and adaptive management strategies are also being evaluated for each alternative (i.e. new inlet channel maintenance would differ from the existing inlet channel maintenance).

Through the EIS/EIR process, an Agency Preferred Alternative will be chosen and a Restoration Plan will be developed. The Restoration Plan will be consistent with the goals and objectives listed above and will fit within the overall management strategies identified in the San Elijo Lagoon Enhancement Plan (County Parks 1996) and the San Elijo Lagoon Action Plan (San Elijo Lagoon Conservancy 1998).

3. Issues: A number of potential environmental issues will be addressed in the EIS/EIR for each alternative. Additional issues may be identified during the scoping process, but issues initially identified as potentially significant or that are believed to be of local concern are as follows:

  • Geology and Soils: Permanent impacts through the removal of sediment accumulated in the lagoon and on-going impacts resulting from as-needed maintenance activities.
  • Coastal Processes: Temporary impacts during construction, permanent impacts depending on tidal inlet location, and on-going impacts resulting from as needed maintenance activities.
  • Hydrology: Temporary impacts during construction, permanent changes in water circulation, and on-going impacts resulting from as-needed maintenance of the tidal inlet and/or interior dredging.
  • Water & Aquatic Sediment Quality: Impacts during construction, including turbidity, and potential impacts resulting from as-needed maintenance activities.
  • Aquatic & Terrestrial Biological Resources: Temporary and permanent impacts to existing species.
  • Cultural & Paleontological Resources: Impacts to archaeological resources, human remains, and sacred sites.
  • Land Use: Temporary or permanent impacts to beach use depending on inlet location.
  • Recreation: Temporary impacts to existing trail use during construction and potential on-going impacts resulting from as-needed maintenance activities.
  • Visual Resources: Temporary impacts during construction and permanent impacts associated with changes in vegetation communities and regular tidal flooding.
  • Transportation and Traffic: Impacts during construction and potential on-going impacts resulting from as-needed maintenance activities.
  • Air Quality/Greenhouse Gas Emissions: Impacts during construction and on-going impacts resulting from as-needed maintenance activities.
  • Noise: Impacts during construction and on-going impacts resulting from dredging or other construction equipment during as-needed maintenance activities.
  • Hazards and Hazardous Materials: Impacts during construction and on-going impacts resulting from as-needed maintenance activities.
  • Public Services and Utilities: Impacts during construction and on-going impacts resulting from as-needed maintenance activities.

4. Alternatives: Since 1996, various interested parties have devised restoration concepts and considered alternative configurations of infrastructure that traverse the lagoon. Through an intensive process, four conceptual alternatives have been identified to be carried forward for engineering refinement and environmental evaluation:

  • Alternative 1A—Intertidal Alternative (existing inlet)
  • Alternative 1B—Habitat Diversity Alternative (existing inlet)
  • Alternative 2A—Habitat Diversity Alternative (inlet relocated south)
  • No Project/No Action

There are common design features that would be implemented in each alternative, such as micro-grading and the use of short cobble-blocking structures at the inlet. The range and characteristics of the alternatives addressed in the EIS/EIR will be more fully developed based on input from the scoping process and specialized hydrological and biological technical studies that are underway.

5. Scoping Process: The Corps and County Parks will jointly conduct a series of public scoping meetings to receive public comments regarding the appropriate scope and content for the SELRP Draft EIS/EIR and to assess public concerns. Additionally, a public hearing will be held during the public comment period once the Draft EIS/EIR is released. Participation in the public meetings by federal, state, and local agencies; Native American Tribes; and other interested organizations and persons is encouraged. Parties interested in being added to the electronic mail notification list for any projects associated with the SELRP can register at​regulatory/​ under the Public Notice tab, Distribution List registration. This list will be used in the future to notify the public about scheduled hearings and availability of future public notices.

Parties interested in obtaining additional information about the SELRP can also visit​restoration. Start Printed Page 68743

A series of public scoping meetings will be held on the following dates and locations:

1. Carlsbad: November 15, 2011 at 1 p.m., U.S. Fish & Wildlife Service, Conference Room 1, 6010 Hidden Valley Road, Suite 101, Carlsbad, California 92011.

2. Encinitas: November 29, 2011 at 6 p.m., City of Encinitas Community Center, 1140 Oakcrest Park Drive, Encinitas, CA 92024.

3. Solana Beach: December 1, 2011 at 6 p.m., City of Solana Beach Council Chambers, 635 South Highway 101, Solana Beach, CA 92075.

Comments on the proposed action, alternatives, or any additional concerns should be submitted in writing. Written comment letters will be accepted through December 18, 2011.

The following permits and consultations are expected:

  • Corps CWA Section 404 Permit
  • RWQCB CWA Section 401 Water Quality Certification
  • Service Section 7 Consultation
  • National Historic Preservation Act Section 106 consultation
  • CDFG Section 1600 Streambed Alteration Agreement
  • CCC Development Permit
  • State Lands Commission Lease
  • U.S. Coast Guard Navigation Permit (new inlet only)
  • State Department of Parks and Recreation Encroachment Permit

6. Availability of the DEIS/DEIR: The Draft EIS/EIR is expected to be published and circulated by fall 2012, and public meetings will be held after its publication.

Start Signature

Dated: October 26, 2011.

Mark Cohen,

Deputy Chief, Regulatory Division, Corps of Engineers.

End Signature End Supplemental Information

[FR Doc. 2011-28741 Filed 11-4-11; 8:45 am]