Cranes sit on either side of Interstate 5 at the Manchester Avenue exit and orange netting outlines the area where vegetation has been cleared at San Elijo Lagoon. There is hardly any water in the back basins, the lagoon lacks greenery, and if one did not know better, it might look like the lagoon is in trouble.

However, all is as it should be, according to Doug Gibson, executive director and principal scientist of the San Elijo Lagoon Conservancy. The North Coast Corridor Program, also known as BuildNCC, which includes expansion of Interstate 5 and rail work, has officially reached Cardiff-by-the-Sea and the lagoon is currently in Phase 1 of 5 of the restoration phase.

“We have to break things down to simpler elements and sometimes that doesn’t look very good,” Gibson said. “I’m reminding myself this every day. Are we still on the right track and are our goals still on the right track?”

Gibson and his team are overseeing the enhancement and restoration part of this long-term project, which the lagoon group refers to as Reviving Your Wetlands. In addition to coastal rail improvements and interstate expansion to include four express lanes, the lagoon is undergoing an ecological facelift.

According to maps, the preserve will be home to 6 acres of community gardens and 10 acres of open space, which will be managed by the San Elijo Lagoon Conservancy, 150 parking spaces including dedicated recreational parking, interpretive lagoon displays, a Class 1 bike trail connection and four electric vehicle charging stations.

“The coordination of having one contractor doing the highway, the rail and the lagoon is going very well,” said Arturo Jacobo, project manager for the NCC Program for Caltrans.

The conservancy, Caltrans and other agencies took a different approach with this freeway expansion and lagoon restoration by using one company to manage all three projects, therefore having one contractor to serve as contract manager and general contractor.

“The combined efforts and synergy using a single construction management/general contract is working very efficiently,” Keith Greer, principal regional planner for the San Diego Association of Governments, said in an email statement for this story.

According to Jacobo, Caltrans has finished the foundation for the new bridge on the west side and is set to begin the foundation on the east side. Jacobo also said that once the foundations are in, work will speed up.

“Once you are off the ground it goes a lot faster,” Jacobo said.

In the beginning of March, the process of moving sand from the lagoon and depositing it on Cardiff State Beach also began. Gibson recently shot a video to explain how this “beach replenishment process is moving along.” According to Gibson, the process is aiming to widen and replenish the coastline.

“The first week, the dredge was sort of up and down,” Gibson said. “Those initial kinks had to be worked out, and this second week, we started to see this sand accumulation.”

Initially, there was a question as to what could be done with the sand, according to Gibson.

“Our goal wasn’t to build a beach, that’s not what we do,” Gibson said. “We knew we had to get rid of the sediment.”

According to Gibson, trucking it out didn’t seem like the best option because the environmental footprint of that process and the cost involved could have jeopardized the project.

“We’re moving 620,000 cubic yards of sand,” Gibson said. “The most effective way to do that was to bury it on site.”

Gibson said that since the sand from the lagoon is native, it is the sand that should be on the beach and it will protect the infrastructure as well as provide recreational usage. The process of removing the sand from the lagoon and depositing in on the beach will go through May.

“It was one of those things where it just worked out,” Gibson said.

Gibson also said his organization is responsible for making sure the contract (through Caltrans) is abiding by all the permits and to make sure what is being done is the same as what was designed. The lagoon group is also monitoring wildlife and vegetation.

“We couldn’t clear vegetation during breeding season,” Gibson said.

Since that was approaching, the team had to get the vegetation cleared before breeding season, and another issue, according to Gibson, was to make sure the animals that are at the lagoon could handle the construction.

“Before we even did this, we made sure these animals could be packed in tighter,” Gibson said. “They don’t seem to be too flustered.”

Gibson also said that the animals are being monitored by biologists and they are flushing birds to make sure they stay in certain areas.

In addition to what’s being monitored now, Jacobo said after plant establishment has been completed near the end of the three-year project, Caltrans will monitor it for five years as part of the contract.

As for pedestrian access during the project, Gibson said it has been affected.

“There are definitely impacts to certain trails,” Gibson said.

Gibson said the conservancy is trying to allow as much access as possible, but there are cutoffs and certain trails are blocked.

In addition to preserving the habitat, the project is setting up the lagoon’s success for decades to come, Gibson, Jacobo and other officials said.

“SANDAG, Caltrans and the San Elijo Lagoon Conservancy have been working together for the last 10 years to make this vision of a better mobility system, while improving the environment, a reality,” SANDAG’s Keith Greer said.

“We are taking a hit now, but the end result is pretty amazing,” Gibson said.

Meghan Lanigan is a local freelance writer. Letters to the editor and comments are welcome. Comment below or send letters to letters@northcoastcurrent.com. Follow the North Coast Current on Twitter at @nccurrent.