Conservancy gives update on San Elijo Lagoon restoration

Restoration work will continue in the San Elijo Lagoon, as a new phase in the efforts is set to begin this summer.

Doug Gibson, executive director and principal scientist of the San Elijo Lagoon Conservancy, updated the community about restoration efforts at the lagoon in a recent lecture at MiraCosta College in Cardiff on May 25.

In August, the Conservancy is slated to complete the first phase of lagoon restoration, which began last December and has included:

  • Over-dredge pit and beach sand placement
  • Starting Central Basin excavation and dredging
  • Beginning excavation of the East Basin
  • Adding water control features
  • Removing vegetation and salvage from the Central Basin
  • Removing vegetation started in the East Basin

The second phase, which is slated to begin in August and be completed by next February, includes:

  • Completing channel excavation in the Central and East Basins
  • Completing channel dredging in the Central Basin
  • Initiating channel dredging in the East Basin
  • Initiating planting and irrigation in the Central and East Basins
  • Removing vegetation from the West Basin
  • Installing culvert at the south end of the West Basin
  • Progressing construction surveys

The conservancy is also planning two additional phases to be completed by April 2020 to maximize restoration efforts at the lagoon.
Gibson said the conservancy’s goal is to enhance and restore the functions of the lagoon by promoting a diverse range of native intertidal and transitional habitats. The conservancy also wants to help flourish the number of marine life and bird species at the lagoon and maintain recreational and educational opportunities.

During its restoration efforts, the conservancy is also monitoring surf; marine environments; bird nesting and usage; topography; water quality; bacteria levels; beach sand quantities and profiles; and sediment in the water, inlet and ocean.

Gibson said that added infrastructure has changed the way water moves throughout the lagoon. The Conservancy has opened the inlet to help the water flow. During the first 10 years of the inlet being open, there has been better water quality in the lagoon, Gibson said.

“We have about four miles of crisscrossing,” he said. “What that’s done to the lagoon is sort of change the way water moves throughout it. We’ve taken some steps from the conservancy in terms of trying to advance the progress of the lagoon by keeping the inlet open predominantly. Because we can’t go back to that natural condition ... we need to get water in and out. What we’ve realized, after we kept the inlet open, we saw dramatic increases in water quality.”

However, there hasn’t been any further improvement after those initial 10 years, and now there is a high amount of nutrient sediment. Gibson said secondary treated sewage was dumped into two locations the lagoon for 30 years, and the City of Escondido dumped its sewage down the creek. The Conservancy is now working to remove some of that sediment.

“In order to move forward, we knew we had to remove some of our past sins,” he said. “I try to explain it’s not contamination or hazardous waste. Really what we’re left with is this high nutrient sediment because the inlet wasn’t open... and nutrients were binding to the sediment and settling out. That’s great for plants but really bad because... that’s where we get these really wide swings of oxygen. If we want to improve above our plateau where we’re at now, we need to remove some of that high nutrient sediment and get it out of the interaction with the water column.”

On April 13, the Conservancy conducted an unscheduled inlet closure due to a natural build up of sand and decreased tidal velocity, likely due to the railroad berm that was being used to build the new rail bridge. Gibson said water quality tests showed dissolved oxygen levels dropped rapidly, and on the third day of the closure, oxygen levels were at zero for extended periods of time. Fish began moving to the surface for air, and Conservancy staff went out and saved hundreds of fish that had been trapped, Gibson said.

The inlet was re-opened five days later, at which point dissolved oxygen levels return to normal after the first tidal flush.

Gibson said the Conservancy is committed to restoring the lagoon and helping it thrive.

“This is what we’re here for,” he said. “We want to ensure this lagoon is restored, and when it’s done we’re going to measure it over the next 40 years to ensure that we did what we said we were going to do.”

For more information about the San Elijo Lagoon Conservancy and its restoration efforts, visit