Frequently Asked Questions

Semipalmated Plovers at San Elijo Lagoon (Photo: C. Mayne)

Section A:
Questions about the Needs and Goals of Restoration

A1) Why is San Elijo Lagoon Restoration needed? 
The present pattern and extent of circulation is insufficient to maintain a healthy system. Salt marsh plants, like cordgrass, are overgrowing the mudflats. Mudflats are the primary source of food for many animals, especially waterfowl that spend the winter here and those that use the Reserve as a resting/refueling area during migration. At present, there are only 35 acres of mudflats. It is estimated that without restoration, all mudflats will be functionally gone in five years.
In addition, the existing sediments within the lagoon have excessive concentrations of nutrients. These nutrients accumulated during the years that the lagoon received untreated and lightly-treated sewage from surrounding communities. Although these nutrients are not inherently unhealthy, they can cause excessive plant growth (eutrophication) and overproduction of organic detritus, which leads to depletion of oxygen in the sediment and bottom waters (anoxia). These characteristics do not generally indicate a healthy system. Improved circulation and removal of high-nutrient sediments will help reverse this increasing trend toward eutrophic events.

 A2) Why are we losing mudflats?
Prior to development around and across San Elijo Lagoon, the inlet periodically closed and broke open again. Salt marsh vegetation cannot withstand prolonged periods of submersion and the high water behind the closed inlet provided a natural barrier to the lower extent of the vegetation.  San Elijo Lagoon no longer opens naturally and we manually maintain an open inlet most, or all of the year. Without periodic flooding, the vegetation is growing out onto the lower mudflats. Also, the vegetation itself increases siltation, elevating the level of the substrate and exacerbating the problem.
A3) How will San Elijo Lagoon be restored?
Circulation will be improved by widening, deepening, and straightening the channels; grading selected areas; breaching the dike in the East Basin, and lengthening the span under the I-5 bridge. Water quality will be improved by removing and burying high-nutrient sediments. Mudflats will be restored and habitat diversity increased by sculpting the topography of the lagoon bottom. Bottom topography and circulation are related, and improved circulation will help maintain the newly created habitat diversity. 
A4) What will happen when global warming causes sea level to rise? Won’t the new mudflats be flooded?
We have built resiliency into our plan based on our best estimate of the likely range of seawater rise over the next 50 years. We have provided stepping stones for species. Areas of Central Basin will be higher than at present. As seawater rises, subtidal and intertidal species will move upward into these areas. Also, the tidal salt marsh will migrate into East Basin as the fresh water marsh moves upstream.
A5) How do we know the plan will work? 
The effects of the final plan have been estimated using scientifically accepted models which have proven successful in several similar restorations in Southern California (e.g. Bolsa Chica, Batiquitos, and San Dieguito). These models are only as good as the input data. We are unique in having over 25 years of data on which to base our models. Nevertheless, we expect that some adjustments will be necessary. We are prepared to monitor the results closely and make any adjustments needed to fulfill restoration goals (“adaptive management”). We have budgeted funds for this.
 A6) Who will pay for the restoration? How much will it cost? 
We estimate restoration will cost approximately $120 million. This essential restoration project is funded by Transnet tax revenue, the voter-approved, regional half-cent sales tax. This funding includes funding for an endowment to maintain the inlet opening, monitor the recovery of the system, and complete any adaptive management (post-restoration fine-tuning) needed to meet our restoration goals. No individual, corporate or foundation donations will fund this project. 
A7) How will we measure the success of the restoration? After restoration activities have concluded, how long will it be before our goals of a fully functioning saltmarsh system have been achieved?
Circulation improvement will be measured by the increase in “tidal prism” (the amount of water that moves in and out of the estuary during a tidal cycle), and by the residence time (the average amount of time a water parcel stays in the estuary). Water quality will be assessed by periodic physical, chemical and biological measurements. Ecological success will be measured by the persistence of various habitat types (such as mudflats, vegetated salt marsh and subtidal areas), by the diversity of species supported by these habitats and by the health of our endangered species populations. These elements are the key factors of an efficiently functioning estuarine ecosystem. 
The physical and chemical goals of the restoration are to improve tidal circulation and water quality; these will have been accomplished when the Restoration project is complete. The re-population of new and disrupted habitats by native plants and animals will take longer. We expect the natural recovery of salt marsh plants to be 1-3 years; the return of mobile species such as birds will follow. During the recovery period, adaptive management will allow us to make modifications to ensure achievement of our goals. We expect the transition to a fully functioning system to be on the order of 3 to 5 years. 

Section B:
Questions About the Final Restoration Plan

B1) The plan adopted is a Modified Alternative Plan 1B Reduced.” What are the main modifications, and why?
The most significant modifications address maintaining suitable habitat for the Ridgway’s Rail (Rallus obsoletus levipes), formerly the Light-footed Clapper Rail, (Rallus longirostris levipes). These modifications were necessitated by events that were not foreseen at the start of the planning process.
The first event was the appearance of California cord grass (Spartina foliosa) in the Reserve (2005); this is a salt marsh species not known to grow here in the past. Since then, cord grass has spread throughout the Central Basin. Cord grass is the preferred habitat for the Ridgway’s Rail, and, since the appearance and spread of the grass, our Rail population has expanded rapidly.
The second event was the recent revision of the relationships among the subspecies of the former Clapper Rail. Genetic information has split the Clapper Rail into three separate species. The three west coast subspecies are now recognized as one distinct species, the Ridgway’s Rail, which is an endangered species. San Diego birds, which used to be an endangered subspecies of a secure, widespread population, are now recognized to be an endangered subspecies of an endangered species. This has significantly elevated the threat level for our birds and made both the Rails and the cord grass an important consideration in the Restoration Project.
As a consequence, the dredging and excavation methods to be employed in the Central Basin have been modified to minimize disruption. A series of dikes will be constructed along the main lagoon channel and the channel connecting to the ocean. These temporary dikes will control water elevations and turbidity to allow for sufficient dredging, while minimizing environmental impacts. These dikes will control flooding of the Central Basin and provide refugia to endangered species like the Ridgeway Rail.
Cord grass that must be removed will be maintained in a nursery and replanted later in the project. The amount of restored mudflat has been reduced and the amount of cordgrass habitat expanded from that proposed in the original plans. Instead of using a floating dredge to modify the topography, swamp cats (extra wide-track minimum-impact equipment specially designed to work in wetlands) will be used to micro-contour the mudflat area by pushing material into the main channels where the dredge will pick it up and remove it. 

B2) What are the positive and negative aspects of the final plan?

The final plan will not centralize the inlet (plan 2a), and its lateral position will continue to impede water flow in and out of the estuary and to need annual excavating. Reconfiguration of channels will increase the exchange of fresh and sea water, improve water quality and extend the tidal influence further east, but circulation will not reach our original goals of a residence time less than four days throughout the estuary.

However, the final plan will maximize habitat diversity, restoring mudflats and protecting cordgrass and maintaining them an estimated 50 years; it will provide buffer zones which existing habitats can occupy under predicted sea level rise; and the excavating, which will remain annual, will be less expensive in the long-term than the less frequent, but more extensive dredging and excavating required by a central inlet.

The plan includes a bridge and trail system across the lagoon, connecting the Nature Center and the 'Pole Road'.

B3) If you reduce the pickleweed won’t you decrease habitat for the endangered Clapper Rail (now Ridgeway’s Rail) and Belding’s Savannah Sparrow?

As explained above (B1) the final plan has been modified to ensure quality habitat for the Ridgway’s Rail. Belding’s Savanah Sparrow both nests and feeds in the pickleweed, so reducing the amount of pickleweed may reduce the population somewhat. However, there is evidence that the Belding’s Savannah Sparrow population in the Reserve is not at its maximum sustainable density, so habitat loss may be offset by density increase. While these are two species of special concern, the restoration plan attempts to balance the needs of all species over the long term.

B4) Why are you removing the berm in the east basin? Wasn't it built to promote Least Tern nesting? What will happen to the American White Pelicans and other birds that use the seasonal lake east of the berm?

The present berm was designed to flood the area to the east to provide foraging habitat for winter waterfowl. The salt pan and two islands east of the berm were constructed as Least Tern nesting areas; these were not successful due to our inability to control predation and plant growth.

The berm will be breached on both ends, creating an island in the middle to act as refugia for species during high tides and flood events. This island will be vegetated and therefore will not be specific for Terns or Plovers. The salt pans will remain isolated from the tides, except the most extreme king tides, but will be seasonally inundated by rain and flooding events. This will maintain the evaporative function of the area and maintain the winter ponds and summer salt pan.

B5) What will become of the 'old settling ponds'?

In Phase I of the Restoration Project this disturbed area will be used as a staging area for the main dredge. When the project is complete the settling ponds will be filled with soft material dredged and excavated from other areas in the lagoon and capped with sand. With some reconfiguration of the boundary berms, these will provide suitable nesting areas for both Least Terns and Snowy Plovers. 

B6) Will restoration impact Cardiff Reef or water quality along the beach? 

Restoration will not impact surfing at Cardiff Reef. We engaged in a year-long surf monitoring program in coordination with The Surfrider Foundation and the resource agencies to insure that these beach replenishment projects do not impact the local reefs. Impacts on water quality along the beach will be short term. Most of the dredging and excavation will be done with the lagoon inlet blocked. When reopened, there is likely to be some deterioration of water quality along the beach, but this will be transient—much like what happens each year when the lagoon mouth is excavated.       

B7) Will the increased exchange of fresh/salt water cause more upstream pollution to be discharged at the beach? Will it destroy the freshwater habitat east of the freeway?

The increased circulation and exchange of fresh and salt water will actually dilute the concentration of pollutants in the discharge water. Also, the healthier marsh means improved functioning of the marsh plants, which break down organic materials and take up excess nutrients and many pollutants.

While increased penetration of salt water east of the freeway may reduce the amount of fresh water marsh in that area, the goal of this project is the restoration and maintenance of a coastal salt marsh, a habitat that is rare in California. Fresh water marshes are relatively abundant.

B8) Will the improved circulation eliminate the need for mosquito control?

Partly. Increased circulation will reduce the standing water in which fresh water mosquitoes breed. This is expected to reduce the need for mosquito control. The fresh water mosquitoes are the vectors for human diseases (West Nile virus, Zika virus, malaria, etc.). However, we also have salt water mosquitoes. These will not be affected by the restoration. While they also produce itchy bites, they do not vector diseases.

B9) Will there be new trails? Will I still be able to walk under the freeway? Will there be improved parking around the Reserve? Will we lose any trails? 

A new trail will connect the Nature Center and the 'Pole Road'. This trail will be connected with two bridges and a berm. The east-west trail under the freeway will remain. Solana Hills Trail will remain. Portions of some trails will be closed during construction. The dike east of I-5 will be breached, and crossing the Reserve at that point will no longer be possible. The I-5 B freeway project includes plans for a footbridge under the freeway connecting north-south that will be built after the freeway construction is finished. 

No additional parking is planned within the Reserve. Parking will be available at a new Park and Ride located at the I-5/Manchester Ave interchange. The Park & Ride will have 150 parking spots (with dedicated recreational parking). A crosswalk across Manchester Ave will provide safe access to Reserve trails.

B10) Will there be any changes to present Reserve regulations? Will there be boating or fishing? Will I be able to let my dog run off leash? Will horses be allowed west of the freeway?

The Restoration Project does not include any changes to present Reserve regulations.  

Section C:

C1) When will restoration start? How long will it last? Can you outline the expected sequence of construction projects?

Phases I of the Restoration Project will start in December 2017 and completed by late 2020. The construction will proceed in 4 phases. Phase I involves clearing vegetation, assembly of the main dredge, creation of dikes, creation of overdredge pit, and beach replenishment. Stay up-to-date via Lagoon Connections, the Conservancy blog for sharing Reviving Your Wetlands—San Elijo Lagoon Restoration Project news and updates with you.

C2) Who will manage the construction?

All three projects in the Reserve (the freeway widening, the railroad double-tracking and the San Elijo Lagoon Restoration) will be coordinated. Each project will have its own dedicated resident engineer, appointed by SANDAG. In addition, there will be one lead resident engineer coordinating all three projects.  For more details see question D1.

C3) Do you plan for unintended consequences?

Adaptive management (rapid response to unexpected outcomes) is critical, and funding is included in our budget. We will monitor the system during and after construction (as we have been doing prior to construction) to identify any unintended consequences and possible solutions.

C4) Are there contaminants in the sediment that will be released by dredging/excavating? Will harmful toxins/pollutants escape onto the beach and ocean?

No. Sediment analysis indicates contaminant levels in San Elijo Lagoon are well below modern standards for public health.  During construction, the inlet may be blocked off periodically, preventing discharge into the ocean. Minor water quality reduction may occur upon reopening the inlet, but this will be transient—much like what occurs with the annual excavation of the inlet.

The soft, surface sediments do contain high levels of nitrate and phosphate. These are not a health issue but adversely impact the functioning of the estuary. Removal and burying these sediments will reduce the nutrient input and improve the water quality in the Reserve. Removing this historical source of excess nutrients is one of the goals of the restoration.

C5) What will be done with the dredge material? What is "soft" material and why is it capped with sand?

Dredged and excavated material may be roughly classified as course material (sand) and fine (soft) material. 

In Phase I an overdredge pit will be created by removing beach quality sand. Approximately 450,000 cubic yards of sand removed will replenish Fletcher Cove and Cardiff State Beach. Approximately 280,000 cubic yards of sand will be placed in an off-shore (S06) borrow site for future beach replenishment. 

“Soft” material is finer than sand and more easily transported by currents. Soft material has elevated concentrations of nitrate and phosphate in later restoration phases, dredged lagoon sediment (soft material) will go back into the overdredge pit. A sand cap will ensure this material stays buried in the pit. The sand cap will be allowed to settle and is expected to revegetate as low marsh.

Sand will also be used to fill the 'old settling ponds' in the Central Basin, creating potential Least & Tern nesting habitat and it will be used to elevate some areas in anticipation of sea level rise.  

C6) How will you avoid impact on nesting birds, especially endangered species?

Restoration will not overwhelm existing habitat, so birds will have the ability to nest where they feel safe. Studies indicate that sufficient alternate habitat is available for species to move within the lagoon basins or temporarily to other lagoons, if needed. This will be a short-term disruption, and long-term, the wetlands are expected to revive and thrive.

C7) Will restoration impact public access to the Reserve or either the Conservation Education programs or Public Programs held in the Reserve?

We will continue to expand our Conservation Education School Programs and our Events and Tours. The visibility of the restoration will provide unique opportunities to address the ecology of restoration and recovery.

There will be temporary trail closures, visit for current trail information. 


D1) What is the North Coast Corridor (Build NCC) Project?
Build NCC—Highway, rail, environmental, and coastal access improvement projects are underway in the cities of Encinitas and Solana Beach as part of Build NCC, the first package of projects being constructed through the 40-year North Coast Corridor (NCC) Program.
Build NCC includes rail double tracking, extended carpool lanes, new bike and pedestrian trails, and the restoration of the San Elijo Lagoon, with the majority of work beginning in Encinitas. These highway, rail, and lagoon improvements are being constructed simultaneously to minimize impacts to the lagoon and neighboring communities. View the San Elijo Lagoon Construction Staging Maps to see how Build NCC will be integrated.
Each project will have its own dedicated resident engineer. In addition, there will be one lead resident engineer coordinating all three projects. By conducting all operations in the same time period, the length of construction disturbance will be minimized; by sharing access points, habitat disturbance will be minimized. Both will benefit our restoration activities.
D2) When will the freeway widening begin? How long will it take?

In mid-January 2017 the construction phase adjacent to San Elijo Lagoon Ecological Reserve began, and is expected to be complete in 2021. 

D3) Why did San Elijo Lagoon Conservancy not oppose the freeway project?

The area of expertise of the San Elijo Lagoon Conservancy Board is the San Elijo Lagoon. Our credibility as a board is defined by that area, and our comments on the EIR/EIS were restricted. Our goal is to insure that the net impact of the widening on the Reserve is neutral or positive. There are aspects of the proposed widening that will benefit the Reserve and will complement our restoration plan. Chief among these is the doubling of the span of the freeway bridge over the reserve which will enhance the exchange of fresh and salt water, promoting tidal action in East Basin. There were other aspects of the initial plan that would have had serious negative consequences (for instance, the Manchester parking structure, and storm water runoff). We took a strong position against these elements and many of these have been modified accordingly.

D4) How will the freeway widening impact the lagoon? What will happen with the freeway bridge?

The new construction will include a longer bridge span over the lagoon which will complement our efforts to improve circulation between Central and East Basin. Most of the habitat disruption due to the freeway construction will occur on the CalTrans berm. This is nesting habitat for the California Gnatcatcher and CalTrans has mitigated the loss by purchasing a 5-acre parcel adjacent to the Reserve. This parcel is excellent sage-scrub habitat and includes several rare plants. Freeway activities adjacent to the reserve will result in trail closures. Visit for current trail information.

D5) How will the double-tracking of the railroad influence the restoration?

A narrow strip of land east of the railroad berm (now degraded habitat and tidal ponds) will be filled to accommodate the double tracks. This land belongs to the railroad and is not in the Reserve. However, Railroad construction will require mitigation. As one part of this, San Elijo Lagoon Conservancy was able to negotiate an underpass connecting the main Reserve (Rios trail) with the Harbaugh Seaside Trails property.  The underpass will be opened on completion of this segment of the railroad.

D6) Will there be any changes to the railroad trestle that spans the lagoon?

The bridge span will not change significantly, but new concrete support piers will improve water exchange beneath the bridge.

Section E:
Questions About CEQA/NEPA Process

E1) What is CEQA/NEPA? 
CEQA, the California Environmental Quality Act, and NEPA, the National Environmental Protection Act, are state and federal regulations that help ensure that large projects have negligible environmental damage, or that that damage is mitigated. Although CEQA and NEPA are separate acts, their requirements are similar and the two processes often proceed together. Our final environmental document is a joint document for both.

CEQA: A state act that requires state and local agencies to identify the significant environmental impacts of their actions and to avoid or mitigate these impacts, if feasible. An EIR (Environmental Impact Report) is the document that informs the general public and decision makers of potentially significant environmental effects of a proposed project. The County of San Diego Parks and Recreation Department prepared the EIR for this project. For more information on CEQA, refer to

NEPA: A federal act that requires all federal agencies to assess environmental impacts of their proposed actions prior to decisions about issuing permits or spending federal dollars. An EIS (Environmental Impact Statement) is a requirement of NEPA. It discusses the purposes and needs of the project and the environmental impacts. It considers a reasonable range of alternatives and summarizes comments from stakeholders and the general public. The Army Corps of Engineers prepared the EIS for this project. For more information on NEPA, refer to

E2) What has been the review process to date? 

In 2011 a series of meetings were held to inform the public that plans to restore San Elijo Lagoon were under way, to introduce a broad range of alternative strategies, and to allow members of the public to input their thoughts and concerns about the project. On the basis of public comment and numerous additional studies, one of the initial alternatives was eliminated and two were refined, and the required environmental impact reports (EIS/EIR) were prepared for the remaining alternatives. Alternatives and their EIS/EIRs were released to the public at a second series of meetings in the summer of 2014. Information presented at the final series of public hearings was much more specific and the discussion more focused. Public input was accepted during the subsequent 45 days. These comments provided a multi-faceted view of the project and its potential impacts and this helped us develop the best plan for the community.

All public comments were reviewed and, where appropriate, modifications to the alternatives were made. Additional comments from the resource agencies further refined the alternatives and we began the federally mandated analysis that would choose the preferred alternative - known as the Least Damaging Practicable Alternative (LEDPA).  

E3) Who is the “project applicant”? Who are the “lead agencies” and the “stakeholders”? 

San Elijo Lagoon Conservancy is the project applicant. It is unusual for a non-profit organization to take this responsibility.

There is one lead agency for CEQA and one for NEPA. In our case these are the County of San Diego and the Army Corp of Engineers.

Typically, the stakeholder group consists of those government agencies that must issue permits for the restoration to go forward. San Elijo Lagoon Conservancy also invited interested (but non-permitting) local government and nongovernment agencies to be part of this group. A complete list may be found at

E4) Who made the final decision?

Legally, the final decision was made by San Elijo Lagoon Conservancy. Practically, however, the decision was a collective one involving the Conservancy, the lead agencies, and the other stakeholder groups.

E5) Where can I read the final plan for myself?

The final plan is available at




Click on questions to advance to the answers.

A) Questions About the Needs and Goals of the Restoration

B) Questions About the Final Restoration Plan

C) Questions About Construction

D) Questions Concerning  the Interstate 5 Expansion and the Railroad Double-Tracking

E) Questions About CEQA/NEPA Process



San Elijo Lagoon Conservancy
(760) 436-3944 x713
restoration [at] sanelijo [dot] org