Our Conservation Projects

San Elijo Lagoon
Restoration

To revive our wetlands, restoring the San Elijo Lagoon is a crucial step.

Keeping our lands healthy means increasing tidal circulation – a natural process that modern infrastructure has nearly halted.

Mudflats are a key habitat for many animals – especially waterfowl. Currently, we only have 35 acres of mudflats. Without restoration, all mudflats are estimated to be functionally gone in 5 years.

Our project, called Reviving Your Wetlands – San Elijo Lagoon Restoration, includes new mudflats and tidal dredging in the East + Central + West Basins. As one of the largest restoration project in California, the half-cent Transnet, rather than donations, fund this $120 million undertaking.

New trails will connect our communities, and these paths will also provide more educational opportunities for Nature Collective visitors of any age.

Healthier waters, greater wildlife diversity, and new trail connections are all in store!


“Reviving Your Wetlands is one of the first projects to address our future conditions. How is sea-level rise going to impact this lagoon? What steps can we take to leave the stepping stones for other species?” 

Doug Gibson, Executive Director | Principal Scientist

Photo Gallery

The Restoration, Step By Step

• Clear vegetation from the work area 🗸
• Create an overdredge pit by removing beach quality sand and transporting the sand via a series of pipes to Cardiff State Beach (300,000 cubic yards) and Fletcher Cove Beach (146,000 cubic yards) 🗸
• Construct a series of water control features along the main lagoon channel and inlet to regulate water elevation and turbidity 🗸
• Sculpt channels wider to increase tidal circulation 🗸
• Dredge channels deeper to increase tidal circulation and transport dredged materials via a series of pipes to the overdredge pit 🗸
• Create new transitional mudflat areas in preparation for sea level rise 🗸
• Create new avian nesting areas for snowy plovers and least terns
• Construct pedestrian bridges at the north and south ends of a new trail that will head west across the lagoon connecting the  Nature Center Loop Trail with Solana Beach side trails.
• Restore habitat by planting and irrigating plants for an establishment period
• Monitor the overdrege pit for conversion back to salt marsh
• Remove all water control features to open the lagoon to natural tidal circulation
• Remove all restoration project equipment
• Remove ESA fencing

 

• Clear vegetation from the work area 🗸
• Sculpt wider channels to increase tidal circulation 🗸
• Dredge deeper channels to increase tidal circulation and transport dredged materials via a series of pipes to the overdredge pit 🗸
• Create new transitional areas, including mudflats, low, mid, and high marsh, and a upland refugia island in preparation for sea level rise 🗸
• Restore habitat by planting and irrigating plants for an establishment period
• Remove all restoration project equipment
• Remove ESA fencing

• Clear vegetation from the work area 🗸
• Dredge deeper channels in inlet to increase tidal circulation and transport dredged materials to the avian nesting area in the Central Basin 🗸
• Sculpt and dredge a new channel to increase tidal circulation and transport dredged materials via a series of pipes to the overdredge pit
• Install rock slope protection to prevent erosion of the western embankment of the lagoon inlet, absorb storm surges in preparation for sea level rise.
• Install a culvert at the south end to allow tidal circulation past the berm
• Remove water control feature to open the basin to natural tidal circulation
• Remove all restoration project equipment
• Remove ESA fencing

• Rios West (Pole Road) Trail reopens
• New connector trail to nature center opens
• New connector tunnel to Harbaugh Seaside Trails opens

• Solana Hills Trail reopens
• East/west trail connector under Interstate 5 reopens
• North/south connector trail under Interstate 5 opens

Update May 17, 2019

Stakeholders in this
Important Project:

1. The Needs and Goals of Restoration

The current tidal circulation is insufficient to maintain a healthy lagoon. Weak tides allow salt marsh plants, like cordgrass, to overgrow the mudflats. Mudflats are the primary source of food for many animals, especially endangered. At present, there are only 35 acres of mudflats. Without restoration, all mudflats would be gone in five to ten years.
In addition, the existing sediments within the lagoon have too many nutrients. These nutrients accumulated during the years that the lagoon was not managed, poorly connected to the ocean, and received wastewater from surrounding communities. These nutrients are not inherently unhealthy; they are the same as the fertilizers you would add to your garden at home. But, in a lagoon, they can cause excessive plant growth which combined with poor tidal circulation creates a perfect environment for bacteria to thrive. Poor tidal circulation means water sits in the lagoon for too long and bacteria decomposition depletes the oxygen in the water, which can lead to die offs of the fish and invertebrates in the lagoon, which causes a ripple effect through the entire community.

Prior to the 1880’s, the inlet periodically closed and broke open again each year. Once roads were built across the lagoon, the inlet could no longer open easily. High water behind the closed inlet allowed sediment that would have washed out to sea to accumulate on the mudflats, raising their elevation. The raised mudflats are now converting to cordgrass habitat.

Circulation will be improved by widening, deepening, and straightening the channels. Habitats will be improves and made resilient to sea level rise by grading selected areas to specific elevations to create mudflats, low,mid,and high-marsh, and transitional zones for sea level rise.

Breaching the dike in the East Basin, and widening the span under the I-5 bridge will allow salt water east of the freeway and allow the eastern portion of the wetland to convert from a freshwater wetland to a saltwater wetland.
Water quality is improved by removing and burying high-nutrient sediments and reducing the time water stays in the lagoon between tides with the new channels.

We have built resiliency into our plan based on our best estimate of the likely range of seawater rise. The restoration project is built to handle up to 3 feet of sea level rise over the next 50 years. We have provided stepping stones for species by raising areas of the lagoon with low slopes to higher elevations. As seawater rises, subtidal and intertidal species will move upward into these transitional areas. Also, the tidal salt marsh will migrate into the East Basin as the fresh water marsh moves upstream.

The effects of the final plan have been estimated by models used in similar restorations in Southern California (e.g. Bolsa Chica, Batiquitos, and San Dieguito). Nevertheless, we expect that some adjustments will be necessary. We are monitoring the results closely and will make any adjustments needed to fulfill restoration goals (this is called “adaptive management”).

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.

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 needed to meet our restoration goals. No individual, corporate or foundation donations fund this project.

The physical goals of the restoration are to improve tidal circulation and water quality; these will be accomplished when the Restoration project is complete in 2020. 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. More information will be available in summer 2019.

2. The Final Restoration Plan

The significant last minute modification was to maintain suitable habitat for the Ridgway’s Rail (Rallus obsoletus levipes), formerly the Light-footed Clapper Rail, (Rallus longirostris levipes). Since restoration planning began, cord grass 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. Ridgway’s Rail are an endangered subspecies of an endangered species so protecting both the Rails and the cord grass was a new and important consideration in the Restoration Project. Consequently, the dredging and excavation methods were modified to minimize disruption. We control water elevations and turbidity to allow for sufficient dredging, while minimizing environmental impacts and providing 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.

The final plan will not move the inlet location (plan 2a), and its existing position will continue to impede water flow in and out of the estuary and need annual excavating. But, the reconfiguration of channels will greatly increase the exchange of fresh and sea water, improve water quality and extend the tidal influence further east.

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 and expensive dredging and excavating required by a central inlet. The project includes significant enhancements to the trail system in the lagoon so the reserve can be enjoyed by all.

The Manchester trail was unsafe access from Manchester. It is being replaced with dedicated lagoon parking, safe crosswalks, and a suspension foot bridge under the I-5.

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. 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.

The settling ponds along the pole road will be filled with sand to provide suitable nesting areas for both Least Terns and Snowy Plovers.

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. Most of the dredging and excavation will be done with the lagoon inlet blocked.

The increased circulation and exchange of fresh and salt water will dilute the concentration of pollutants exiting the lagoon. Also, the healthier marsh means improved functioning of the marsh plants, which break down organic materials and take up excess nutrients and pollutants. Water quality at Cardiff Reef State beach will improve after the restoration project.

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.

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.).

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.

A new trail will connect the Nature Center Loop Trail and Rios Ave West. This trail will be connected with two bridges and a berm. The east-west trail under the freeway will be improved and reopen at the completion of the Interstate 5 project. Solana Hills Trail will be improved and reopen at the completion of the Interstate 5 project. The Dike Trail east of I-5 will be removed. The Interstate 5 project includes plans for a footbridge under the freeway connecting north-south that will be accessible at the completion of the project.

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.

The restoration project doesn’t include any changes to present Reserve regulations.

3. Construction

The Restoration Project started in December 2017 and will be completed by June 2020. Stay up-to-date via our blog for sharing Reviving Your Wetlands—San Elijo Lagoon Restoration Project news and updates with you.. View Blog

Nature Collective (formerly San Elijo Lagoon Conservancy) is the co-permittee with Caltrans.

The restoration is part of Build NCC – the highway, rail, environmental, and coastal access improvement projects underway in North County San Diego. 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.

All three projects in the Reserve (the freeway widening, the railroad double-tracking and the San Elijo Lagoon Restoration) are coordinated. For more details, see below.

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

No. Sediment analysis indicates contaminant levels in San Elijo Lagoon are well below modern standards for public health. During construction, the inlet will 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.

The dredged material stays in the lagoon. A 10-acre wide 40 foot deep overdredge was created in the lagoon by removing beach quality sand from underneath the top layer of fine lagoon sediments. Approximately 450,000 cubic yards of sand was removed and replenished Fletcher Cove in Solana Beach, CA and Cardiff State Beach in Cardiff-by-the-Sea, CA. The dredged lagoon sediment from widening and deepening the lagoon channels was used to fill up the the overdredge pit.

Most of the lagoon is outside the limits of the restoration project. Prior to construction, avian biologists walk through work areas and safely flush birds into the protected areas of the lagoon. With the birds safely removed, all vegetation is removed from the work areas. With no vegetation to hide in, birds decide on their own to stay in the protected part of the lagoon and out of the construction zone.

We’ll 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 thenaturecollective.org/thingstodo for current trail information.

4. Interstate

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 constructed through the 40-year North Coast Corridor (NCC) Program.

Build NCC includes rail double-tracking, extended carpool lanes, new bike + 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 under construction 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.

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

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 ensure that the net impact of the freeway 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 stormwater runoff). We took a strong position against these elements and many of these have been modified accordingly.

The new construction will include a longer bridge span over the lagoon which will complement our efforts to improve circulation between Central + East Basins. 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 an excellent sage-scrub habitat and includes several rare plants. Freeway activities adjacent to the Reserve will result in trail closures. Visit thenaturecollective.org/thingstodo for current trail information.

5. Expansion & The Railroad Double-Tracking

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, the Nature Collective 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.

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

6. CEQA/NEPA Process

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. More info on CEQA

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. More info on NEPA

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).

San Elijo Lagoon Conservancy (aka the Nature Collective) is the project applicant. It’s 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 above.

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.

The final plan is available here.

The present pattern and extent of circulation can’t maintain a healthy system. Salt marsh plants, like cordgrass, are overgrowing the mudflats. Mudflats are very important habitats that provide feeding and resting areas for many animals, especially waterfowl that spend the winter here, plus those that rest + refuel during migration. Currently, we only have 35 acres of mudflats. Without restoration, all mudflats are estimated to be functionally gone in five years.

Additionally, 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.

The present pattern and extent of circulation can’t maintain a healthy system. Salt marsh plants, like cordgrass, are overgrowing the mudflats. Mudflats are very important habitats that provide feeding and resting areas for many animals, especially waterfowl that spend the winter here, plus those that rest + refuel during migration. Currently, we only have 35 acres of mudflats. Without restoration, all mudflats are estimated to be functionally gone in five years.

Additionally, 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.

 

Learn All About Our Restoration Project

Environmental Impact Report (EIR)
Environmental Impact Statement (EIS)
Mitigation Monitoring and Reporting Program (MMRP)
Findings Regarding Significant Effects Pursuant to State CEQA Guidelines Section 15091
Statement of Overriding Considerations
Appendices A-F
Appendices G-N
Appendices O-R

Read More About Conservation on Our Blog

We are Nature Collective
Flowing Tides + New Trail Beginnings
Swimming Mule Deer & Dredging Spring Updates
Stabilizing San Elijo Lagoon Inlet
Coastal Views of Lagoon Restoration