Our Conservation Projects

San Elijo Lagoon

Wetlands Revived

Tidal flow is improved. Enhanced wetland habitats and new trail connections are benefiting nature and community!

This is one of the largest wetland restorations in California. With restoration nearly complete, we are monitoring now and through the next 50 years — ensuring that what we designed is working as sea levels rise and our climate changes.

Our project, called Reviving Your Wetlands – San Elijo Lagoon Restoration – includes new mudflats and tidal dredging in the East + Central + West Basins. The half-cent Transnet tax, rather than donations, funded this $120 million undertaking. Mudflats are a key habitat for many animals – especially waterfowl. Without restoration, we would have lost these vital habitats— now restored and enhanced for sea level rise.

Keeping lagoon lands and waters healthy means increasing tidal circulation – a natural process that modern infrastructure had nearly halted. But wider bridge spans, and enhanced tidal channels, are now delivering tidal flow farther and deeper into San Elijo Lagoon.

New trails connect our communities! These paths provide more experiences for Nature Collective visitors of all ages.

Reviving Your Wetlands addresses our future conditions. We restored the lagoon for enhanced water flow and anticipated sea-level rise. And we took actions to leave the stepping stones for current and future species. 

Doug Gibson, Executive Director | Principal Scientist

Photo Gallery

2021 Restoration, Step By Step

  • Crews will continue periodic irrigation, planting, and invasive plant removal through summer 2024.
  • We will monitor the overdredge pit for conversion back to salt marsh habitat.
  • Crews will continue periodic irrigation, planting and invasive plant removal through summer 2024.
  • East/West trail connector under Interstate 5 reopens
  • North/South connector trail under Interstate 5 opens
  • Late 2021: The I-5 Project Completes
  • Crews will continue periodic planting and invasive plant removal through summer 2024.

Updated June 2021

Stakeholders in this
Important Project:

1. 50-Year Restoration Monitoring Plan

We measure success of the restoration project in two broad categories. First, that we caused no negative environmental impacts; and second, that we measurably improved the wetland ecosystem. We have many difference specific monitoring requirements that help us determine if we meet these two criteria for success.

We can think of the project as taking place in two general areas. First is the wetland itself; and second is the local coastal marine environment where the project provided beach nourishment sand.

Within the wetland we monitor 13 key variables to make sure we caused no negative impacts and that the wetland ecosystem is improved. We compare measurements we take within San Elijo Lagoon to measurements in San Elijo from before the restoration and we also compare measurements in San Elijo Lagoon to the same measurements at three other “reference” wetlands in Southern California. These other wetlands were chosen by independent experts as the best indicator wetlands in Southern California. In short, measurements in San Elijo Lagoon have to be as good or better to San Elijo Lagoon before the restoration and measurements in San Elijo Lagoon have to be better than at least one of the indicator reference wetlands for many years in a row for the project to be determined a success.

Within the marine environment, we monitor for five years to see if there are any detectable impacts from the beach nourishment component of the project. The project was intentionally designed to place less sand on the beach than would cause any impacts. The monitoring is a rigorous check of those assumptions to make sure that we are also protecting the valuable costal resources offshore the lagoon.

We measure the habitat types in the lagoon by acreage to make sure we have desirable amounts of each important habitat type. We also measure how thick the vegetation cover in these habitat types is, so that we do not have underperforming habitat areas. Two special habitat types we pay attention to are eelgrass – an underwater plant that is a strong indicator of high quality aquatic habitat – and cord grass – a low marsh plant that is a strong indicator of high quality habitat for the federally endangered California Ridgeway’s Rail.

You can experience these habitats and plants firsthand along the trail over the pedestrian bridges and toward the nesting island. Look into the main channel, when on the pedestrian bridge, to see if you can spot the patches of eel grass. Try and identify the large areas of cord grass along the Pole trail and see if you are lucky enough to spot a federally endangered California Ridgeway’s Rail!

We measure the diversity and abundance of birds, fishes, and invertebrates in many different areas of the lagoon.

We measure the water quality continuously at multiple locations in the lagoon channels.

We host an annual presentation that describes the monitoring activities and results each year. We will post the annual reports (see the lower section: Learn About Restoration Project. All the data from the monitoring activities will be posted.

2. The Needs and Goals of Restoration

The tidal flow in and out of San Elijo Lagoon was restricted. This resulted in poor water quality when compared to a system with increased tidal flow.

Looking at the lagoon with sea level rise now and in the future, without action, we would be losing many of the valuable habitats that already existed in the wetland. The restoration project enabled us to increase the flow of water in and out of the lagoon and to modify the topography of the wetland to increase its resilience against sea level rise.

The biggest part of the restoration was making the channels in the lagoon wider and deeper, and extending them farther into the East basin. Overall, these changes now allow up to three times as much water flow in and out of the lagoon, twice a day, with each tide cycle.

As sea level rises, areas within the lagoon will begin to transition to new habitat types. San Elijo Lagoon has areas that have been designed to provide a ramp for survival as the sea level rises, gradually changing to higher and higher elevations. So, plants have adjacent locations they can grow in as the sea level rises.

The monitoring component of the project is how we determine if the plan is working. Each year we collect numerous measurements in the lagoon to track how it is functioning compared to how the wetland functioned in the past, and in comparison, to other well-functioning wetlands in Southern California.

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.

Already we see strong signals of a healthy salt marsh than before the restoration project. We have 10 years to achieve broad measures of success across all of our measurements we take within the lagoon.

If you are interested in helping indigenous habitats grow and thrive, we host opportunities to volunteer your time and passions in the removal of invasive species, and the propagation, maintenance and monitoring of lagoon-specific plant species that will better connect wildlife corridors and the indigenous flora that so many animals depend on. Visit naturecollective.org/volunteer to sign up for these weekday activities. You can also sign up for our monthly e-newsletter on this volunteer site.


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 Restoration Stories

Wetland Revived | The Natural Observer
Bridging Coastal Communities
Nest-Ready Refuge
Growing up with the Lagoon
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You are a Nature Hero
Digging in Deeper
A Career in Conservation Begins
Welcome, President Circle Chair
THANK-uary Heroes + Leonard Family Foundation
Today is Giving Tuesday! Give to Nature.
Is Nature in Your Holiday Giving?
Pacific Flyway Conservation Grant Award
Ecosystems in Action
Tar Ball Removal Update
Tar Ball Monitoring + Removal
Opening the Outdoors + Field Trips Resume
Underwater Meadows of Life
lmproving WildLife + Batiquitos Lagoon
Bird Counts are Back!
Nurturing an Environmental Leader
Welcome, Ramona School Children!
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Lagoon Views


The Beginning of Finishing Touches + Lagoon Restoration


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Greening + Lagoon Restoration
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Your Year-End Gifts Are Matched!
Giving Tuesday Begins! Nature Needs Your Support.
Your Holiday Gifts Are Matched!
Final Donor Tiles Available + Harbaugh Seaside Trails
Next Gen Science
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Shaping Emerging Leaders
In AWE of You! Gala Funds Nature for All
Brush Fire Extinguished + San Elijo Lagoon
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The Science Behind Tea Time + San Elijo Lagoon
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Be In AWE! Gala Auction Underway
Bidding Begins! Join AWE Auction
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