Our Conservation Projects

San Elijo Lagoon

Wetlands Revived

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

This is one of the largest wetland restorations in California. With restoration 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 the San Elijo Lagoon Restoration – includes new mudflats and tidal dredging in the East + Central + West Basins of San Elijo Lagoon Ecological Reserve. 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.

San Elijo Lagoon Restoration 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

1. 50-Year Restoration Monitoring Plan

We measure the success of the restoration project in two broad categories. First, we caused no adverse environmental impacts, and second, we measurably improved the wetland ecosystem. We have many different 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 replenishment sand.

We monitor 13 key variables within the wetland to ensure we caused no adverse impacts and improve the wetland ecosystem. We compare measurements we take within San Elijo Lagoon to measurements in San Elijo from before the restoration. We also compare measurements in San Elijo Lagoon to the exact measurements at three other “reference” wetlands in Southern California. Independent experts chose these other wetlands as the best indicator wetlands in Southern California. In short, measurements in San Elijo Lagoon have to be as good or better than 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 noticeable impacts from the beach replenishment component of the project. We intentionally designed the project to place less sand on the beach than would cause any effects. The monitoring is a rigorous check of those assumptions to ensure that we are also protecting the valuable coastal resources offshore the lagoon.

We measure the habitat types in the lagoon by acreage to make sure we have desirable amounts of each critical habitat type. We also measure how thick the vegetation cover in these habitat types is so that we do not have underperforming habitat areas. In addition, we pay special attention to two particular habitat types. Eelgrass is an underwater plant that strongly indicates high-quality aquatic habitat. California cord grass is 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. When on the pedestrian bridge, look into the main channel to see if you can spot the patches of eelgrass. Try and identify the large areas of cordgrass 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 lagoon areas.

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. When available, we will post the annual reports (see the lower section: Learn About Restoration Project. All the data from the monitoring activities will be posted. Visit our YouTube page.

2. The Needs and Goals of Restoration

Tidal flow in and out of the Lagoon was restricted. The restriction resulted in poor water quality compared to a system with increased tidal flow.

As sea-level rise continues in the future, without our action, we would lose many of the valuable habitats that already existed in the wetland. The restoration project increases water flow in and out of the Lagoon and modifies the wetland’s topography to increase its resilience against sea-level rise.

The most significant part of the restoration was making the channels in the lagoon wider and deeper and extending them farther into the East basin. This change allows up to three times more water to flow in and out of the lagoon twice a day with each tide cycle.

As sea level rises, areas within the lagoon will transition to new habitat types. We designed areas of San Elijo Lagoon 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 restoration plan is working. Each year we collect numerous measurements in the lagoon to track how it is functioning compared to how the wetland performed in the past compared to other well-functioning wetlands in Southern California.

Adaptive management (rapid response to unexpected outcomes) is critical and included in our budget. As we did before and during construction, we will continue to monitor the system after construction to identify any unintended consequences and possible solutions.

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

If you are interested in helping indigenous habitats grow and thrive, we host weekly and monthly volunteer opportunities. Visit naturecollective.org/volunteer to sign up.


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:

Photo Gallery

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
Welcome All to Your Restored Wetland
Nest-Ready Refuge
Growing up with the Lagoon
Find Your Passion
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!
Are Ridgway’s Rails Travelers?
Give Love: In Memory and In Honor
Cardiff Beach Living Shoreline Gets More Sand: June 1-8
Life + Livelihoods + Your Volunteerism
Escondido to Ithaca: Carol’s Watershed Journey
Saving Dunes and Bluffs + Carlsbad
California Trails + Greenways Award Announced for Harbaugh Seaside Trails
Spring Break Hike with Friends
Wildflower Hour
Join Earth Day Hero Challenge
Your Nature Journey Continues!
Enhancing Wildlife Corridors + Agua Hedionda Lagoon
Pole Trail News + Views
A Rare Succulent in Bloom
Nature At Work | The Natural Observer
Beyond Strawberries | The Natural Observer
Thank You + Nature Love
2021 Board of Directors
Colors on the Pole Trail
THANK-uary Hero + Union Bank Foundation
THANK-uary Heroes + Leonard Family Foundation
Support the Healing Power of Nature
Your Gift Protects Your Home Away from Home
Discovery Kits for Nature’s Kids
Grateful in Nature + Giving Forward
Finn Brings Nature Closer
A Family Hiking Tradition
Fields of Dreams
Big Habitat Help for Little Peeps
Peace on the Trails
Their Winding Path Leads On
The Summer of Nature Love
For the Love of Birds + Nature
Marine Protected Area Ambassadors
Grassroots Style
Growing Up + Working Outdoors
Flowering After Fire
Natural Connector
June + Your Nature Collective Team
Thank You + Spring Giving Heroes
Sand + Soil Elevations for Rising Seas
Join Giving Tuesday Now
May News + Views
Join Earth Day Art Challenge
Working with Nature
Nature Nurtures Her Soul
National Outdoor Science Award
Nature + Essential Services
Inspiring Kids with Nature Joy
Nature Soothes Us Now
More People Need Nature


Lagoon Views


The Beginning of Finishing Touches + Lagoon Restoration


Now Open! Harbaugh Seaside Trails
Bake Sale for the Birds
An Encinitas Love Story
Nature’s Family Playground
Season of Giving Back
Greening + Lagoon Restoration
THANK-UARY + Matching Gift Foundation
Leading By Example
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
Visiting Jimmy’s Bench
Shaping Emerging Leaders
In AWE of You! Gala Funds Nature for All
Brush Fire Extinguished + San Elijo Lagoon
Nature Collective’s AWE Auction + 2 Days Left!
Stopping Sea Lavender + Agua Hedionda Lagoon
The Science Behind Tea Time + San Elijo Lagoon
Escondido Charitable Foundation + More Kids Outdoors
Be In AWE! Gala Auction Underway
Bidding Begins! Join AWE Auction
Art + Nature at Harbaugh Seaside Trails
Your Impacts + Your Gifts
Welcome, Vista Unified School District!
Coming “Dune” This Fall + Lagoon Restoration
Your Gifts + Loving Nature
Opening the Outdoors + The San Diego Foundation
Cord Grass Nursery + Lagoon Restoration
New Trail Underway + Lagoon Restoration
Summer Camps Grow Youth Leaders
Grant Award + Harbaugh Seaside Trails
Encinitas New Trail Celebration
We are Nature Collective
Cardiff State Beach Awarded One Of Nation’s Best Restored
Mudflats Are Coming Into View