There was a glint in Michael Boland’s eyes as he watched cars zooming along the Presidio Parkway over an ugly panorama of broken asphalt, weeds and construction debris behind a chain-link fence next to Crissy Field.

The chief of park development and visitor engagement for the Presidio Trust was excited as he envisioned what the vacant lot was about to become — a picturesque lagoon surrounded by walking trails, vivid greenery and a spectacular view.

The long-anticipated ecological transformation of the northeastern side of the Presidio is set to begin Monday when the first of 90,000 cubic yards of soil is delivered for the 14-acre park planned above the eastern tunnels of Presidio Parkway, the boulevard that in 2015 replaced Doyle Drive, the 1.6-mile segment of Highway 101 leading to the Golden Gate Bridge.

The soil will be used to create a greenway from the Presidio’s Main Post to Crissy Field, connecting them for the first time since Doyle Drive was built in the 1930s.

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But the Tunnel Tops project is only half of an ambitious bid to sculpt the Presidio’s northern waterfront into a lush green wonderland. The mostly empty lot next to the tunnels will be excavated starting in September in the culmination of a 25-year effort to surface and restore the springs and streams that once quenched the thirst of Ohlone Indians and early Spanish colonial settlers in San Francisco.

The spot where Boland stood will be converted over the next year into Quartermaster Reach, which will include a 7-acre lagoon that will enlarge the 20-acre tidal pool known as Crissy Marsh and connect it to the Presidio’s mostly restored Tennessee Hollow freshwater creek system. It will mark the first time anyone can remember that an entire urban watershed has been restored from its headwaters to its mouth, in this case San Francisco Bay.

“We are finally able to tie the two most important parts of the park together — the Main Post and Crissy Field,” said Boland, who has been working since before the Presidio Trust was created on converting the former military base into the country’s only urban national park. “Doyle Drive cut the park in two, and now we’re able to stitch those parts together in a way that will create a single continuous experience.”

The Tunnel Tops and Quartermaster Reach projects are the biggest pieces of an intricate plan by the Presidio Trust, the Golden Gate National Parks Conservancy and the National Park Service to turn the 1,491-acre Presidio into a place teeming with wildlife.

Much of the work has taken place in a 278-acre bowl-shaped valley known as Tennessee Hollow — named by the U.S. Army in 1898 in honor of the 1st Tennessee Regiment, which camped there before leaving to join the Spanish-American War.

The Tennessee Hollow watershed had been well known since the Spanish founded El Presidio de San Francisco and drank from its source, El Polin Spring. It was once the primary freshwater source for a 200-acre wetlands system that extended from the Golden Gate past what is now the Palace of Fine Arts.

Then humans got in the way. The sprawling wetland, long used as a dump, was filled in completely in 1915 to make room for the Panama-Pacific International Exposition. It was later covered with asphalt and warehouses, and used by the Army as an airfield.

The three tributaries that make up the watershed didn’t fare any better. The Army funneled the creeks into culverts and planted nonnative ivy, eucalyptus and ice plant over the riparian habitat, choking out native plants.

The Presidio Trust has been trying to undo that damage since 1994, when the Army turned the land over to the National Park Service and the trust took charge of the interior 80% of the park.

Crissy Marsh, which was completed in 2001, was the first restoration undertaking in the Tennessee Hollow project. The next one, in 2005, brought the long-buried creek at Thompson Reach out of an underground pipe and exposed it to daylight. That required the removal of 77,000 tons of debris from a former Army landfill.

A few years later near the southern border of the park, the area around the historic freshwater source at El Polin Spring, nearly forgotten out of neglect, was transformed with thousands of native riparian plants and newly dug ponds re-creating a wetland. Between 2013 and 2017, most of the creek system downstream was dug out and restored to as close as possible to its natural condition.

The plan now is to dig a huge basin about 10 feet deep from Mason Street, which runs along Crissy Field, to the south underneath Presidio Parkway to Thompson Reach, which connects to MacArthur Meadow, where the three Tennessee Hollow tributaries converge.

An 850-foot-long underground drain would be removed, and the existing Crissy Marsh would flow into the newly created reach through two 36-foot-wide box culverts placed under Mason Street, which will be closed for six months while the work is being done.

“We’d be standing in water right now,” said Boland, looking up at the elevated portion of Presidio Parkway, just east of the tunnels. He expects them to be surrounded by water at high tide by this time next year.

“When people drive into the Presidio, they will come out of the tunnel over water,” he said. “This whole area will be tidal. We want the bay to flow in and out every day.”

Quartermaster Reach will be designed to include mudflats, channels, sandy undulating hills and gently sloping dune swales. Forty species of upland scrub, marsh and dune grasses will be planted, including some reintroduced species that are known to have existed in the area only because of the extensive records kept since Russian explorers visited in 1816.

Genevieve Bantle, project manager for the Presidio Trust, said specially designed shell arrays will be placed in the water so native Olympia oysters can be introduced. She said dozens of fish, birds, crabs and small invertebrates are expected to live and feed in the new wetland, and many are likely to migrate upstream.

The Tennessee Hollow trail will circle the new lagoon, allowing hikers to go from the headwaters at El Polin Spring through wet meadows, past a brackish marsh to the bay shore.

It is hoped that the expansion of Crissy Marsh into Quartermaster Reach will improve hydrology enough that dredging of the outlet channel to the bay will no longer be necessary. Now, the outflow isn’t strong enough to scour things out and prevent occasional blockages.

Kristen Ward, wetland ecologist for the Golden Gate National Recreation Area, said she believes the channel will still need to be dredged. The water volume would have to more than double for the lagoon to fill and drain naturally without assistance, she said, and there just isn’t enough space available to expand it that much.

“It wasn’t designed to fix that problem,” Ward said. But “we’re providing a much more natural tidal system that will improve water quality, increase habitat for birds and wildlife — and it might help.”

All of which will add to the already stunning view from the Tunnel Tops, where native grasses will rustle in the breeze amid mostly native trees, shrubs and gardens.

When the Tunnel Tops are complete in the fall of 2021, visitors will stroll on decomposed granite on a “cliff walk” along the sculpted bluffs, taking in views of the Marin Headlands and the Golden Gate Bridge. Down steps toward Mason Street, there will be a sprawling new children’s learning center next to the renovated Crissy Field Center and a 3-acre outdoor “playscape.”

The project is being designed by James Corner Field Operations, which transformed New York’s High Line from train trestle into ultra-popular pedestrian park.

“It’s a project to give life to these tunnel tops,” said Greg Moore, former president and now special adviser to the Golden Gate National Parks Conservancy, which raises money and supports the parks in the GGNRA.

“It’s going to create such fantastic new landscape that will allow people to enjoy the park in a completely new way,” Boland said, “and that will be an incredibly powerful experience.”

Peter Fimrite is a San Francisco Chronicle staff writer. Email: pfimrite@sfchronicle.com Twitter: @pfimrite