Back to nature Habitat restoration has replaced landfills, military buildings and weeds from other parts of the world with thriving native flowers, trees and animals. And some endangered species have been revived along the way.

Back to nature Habitat restoration has replaced landfills, military buildings and weeds from other parts of the world with thriving native flowers, trees and animals. And some endangered species have been revived along the way.

The wry look on Lew Stringer’s bearded face should have been a giveaway, but there really wasn’t anything about the inconspicuous bush he was gesturing toward that seemed special.

“This is a Franciscan manzanita,” said Stringer, the associate director of natural resources for the Presidio Trust, pointing to a large, green, ground-hugging plant.

This particular manzanita species was thought to be extinct outside of nurseries until 2009, when one was discovered growing in the Presidio of San Francisco and later moved to a secret location.

The careful nurturing of the last remaining wild manzanita of its kind is part of a wider experiment — one of the most ambitious ever undertaken — to engineer and rebuild a wild ecosystem in an urban setting that over its 200 years as a military base had been paved over, polluted, pocked with landfills and overrun by weeds.

Twenty-five years after the U.S. Army turned the Presidio over to the National Park Service, the 1,491-acre former military base has been largely transformed, fulfilling a vision that seemed, early on, to be little more than a fantastical dream.

Many of the old military buildings have been restored and rented out, making the Presidio economically self-sufficient, but the most remarkable changes have been to the natural landscape.

Over the past three decades, a shoreline lagoon and a historic, natural lake have been restored. Hundreds of thousands of native plants — some of them endangered — have been planted. Indigenous wildlife has returned, and an ancient creek ecosystem was freed from underground pipes, exposing hidden streams and ponds that once quenched the thirst of American Indians.

Map: Habitat restoration sites in the Presidio

“It is a place where you have this incredible evolution of biological diversity in the form of plant life,” said Stringer, as he took in the sweeping view from Inspiration Point of the green hillsides dotted with red-roofed buildings sloping down to San Francisco Bay. “We have the most diverse plant community in all of San Francisco of indigenous native plants that still exist — over 150 species of wildflowers, grasses and small things.”

The grand plan began in 1994 when the Park Service took over the land and, two years later, created the Presidio Trust to preserve and enhance the interior 80% of the park, including 262 acres of historic forest planted by the Army in the 1880s. The Park Service maintains the remaining 20%, mostly along the northern and western edges that include Crissy Field and Baker Beach.

The work required an understanding of history, including what the Presidio was before Europeans arrived, but also what it became in the more than 240 years since the Spanish first erected adobes in the windswept dunes that covered most of what would become the city.

A picture of Inspiration Point from the 1940s shows a sparsity of vegetation. The restored hillside hosts rare plants such as the Presidio clarkia and is thick with native grasses. | Left: courtesy Presidio Trust, right: Mark Lundgren / The Chronicle

The idea was to restore the land where possible while preserving scattered patches of remnant native landscapes. So far about 100 acres have been restored, while another 23 remnant acres are under stewardship.

The Presidio Trust, in collaboration with the Park Service and the Golden Gate National Parks Conservancy, began by restoring 11 acres of coastal sand dunes in Lobos Creek Valley at the southwestern edge of the park. A boardwalk was constructed to open the site to the public.

Coastal habitat off Battery Caulfield Road, near 15th Avenue in the Richmond District, also was restored, as were dunes at Baker Beach, where invasive European dune grass and ice plant — introduced by the Army to stabilize coastal bluffs — were ripped out and replaced with natives such as American dune grass, yellow sand verbena and dune tansy.

The creation of Crissy Field Marsh has been the biggest project. It was also the start of an undertaking still in progress almost 20 years later.

The resurrection of the marsh, completed in 2001, was an attempt to restore a portion of what once was a 200-acre wetland that extended from the Golden Gate past what is now the Palace of Fine Arts. It was once a hunting and fishing ground for the Yelamu tribe of Ohlone Indians.

The original lagoons and marshes had been used as a dump and in 1915 were filled in to make room for the Panama-Pacific International Exposition. Crissy Field was later covered with asphalt and warehouses and used as an Army airfield.

“This was 40 acres of asphalt and chain-link fence. Now it’s tidal marsh and dune habitat,” said Michael Chassé, a natural resource management specialist for the Golden Gate National Recreation Area who has worked on the project since the beginning.

“Some of the plants you see here are from the original planting, but a lot of these plants have just regenerated on their own,” he said as he stood in the dunes recently explaining to students how seeds, including invasives like cord grass and Algerian sea lavender, float in on the tides.

MacArthur Meadow in 2016, with new channels dug for the three tributaries of the Tennessee Hollow watershed, compared with MacArthur Meadow in November 2019. | Left: courtesy Presidio Trust, right: Mark Lundgren / San Francisco Chronicle

The marsh was the first piece in a comprehensive effort to daylight the 270-acre Tennessee Hollow watershed, three tributaries that drain through a bowl-shaped valley into the marsh and out to the bay.

The watershed, named by the U.S. Army after a regiment of volunteers from Tennessee that camped in the area in 1898, had been an important source of fresh water for the 193 Spanish residents who founded El Presidio de San Francisco on July 26, 1776.

The creeks, one of which is seasonal, start near the southeast corner of the park and come together at MacArthur Meadow, where restoration started in 2016. It runs under the Lovers’ Lane bridge, which marks the historic trail that once led from the Presidio to Yerba Buena Cove, site of the frontier settlement that eventually became San Francisco.

After running through another restored area across the street and then dipping back underground below the Presidio YMCA parking lot, the waterway reappears at Thompson Reach, named in honor of famed Army nurse Dora Thompson. In 2006, the creek, which was recently named Petlanuc after the historic Yelamu village, was freed from underground pipes — 77,000 tons of landfill debris had to be removed.

That completed project was the first solid evidence that the ambitious habitat restoration plans for the park could work.

“We were able to show that we were actually able to do this,” said Terri Thomas, the Presidio Trust’s former director of conservation and research, who oversaw the project. “People had daylighted creeks, but nobody really trusted that we could do it. At that time we were really just a bunch of volunteers.”

Six years later, El Polin Spring — the main, central tributary — was daylighted and the area turned into a people-friendly wetland, complete with riparian plants, ponds and preserved historic cobblestone channels. A pedestrian path and boardwalk now loop around the whole ensemble.

El Polin, a drinking water source for Native Americans for thousands of years, is one of the most important historical locations in the Presidio. It is where archaeologists discovered the foundations of adobes dating to 1810 and where the family of Marcos Briones, a colonial soldier and a founder of El Presidio de Monterey, is believed to have lived.

El Polin Spring in the initial stages of restoration, when tarps were laid to kill non-native weeds and grasses. Replanting on the site began in 2008. The right side of the slider shows the area as it looks in November 2019. | Left: courtesy Presidio Trust, right: Mark Lundgren / The Chronicle

The last piece of the Tennessee Hollow project is planned within the next year, when an underground drain is removed, creating a brackish, 6-acre wetland known as Quartermaster Reach that will connect to Crissy Field Marsh. It will be the first time an entire urban watershed has been restored from its headwaters to its mouth.

Large as it is, Tennessee Hollow is just one of dozens of habitat restoration projects in the park undertaken by staff, contractors and volunteers.

The rehabilitation of Mountain Lake, which had become a filthy pond teeming with invasive species, including thousands of discarded goldfish that grew into 3-foot carp — reached its final stages the past few years. The spring-fed lake, where Spanish explorers camped in 1776, is now home to natives like the three-spined stickleback fish, western pond turtles, freshwater mussels and chorus frogs that sing in the evening.

The lake was dredged and the water filtered and cleaned before it was returned to the lake. Its north and east arms have been restored as wetland habitat. It is the first time an ancient lake ecosystem in an urban area had been restored roughly to the way it was before Europeans arrived.

Time Machine To see before-and-after photos of projects and sites in the Presidio, visit the Presidio Time Machine at https://timemachine.presidio.gov Natural resources — by the numbers 100 Acres of native plant zones restored so far 798,683 Plants planted 4,227,104 Exotics/invasives removed, in gallons 263,442 Volunteer hours Source: Presidio Natural Resources

On the western side of the Presidio, new dunes were created from ancient sand excavated from Golden Gate Park when the underground parking garage was built at the museum concourse.

That new habitat, located behind what is now the Landmark apartment building, gave restoration managers space to help endangered species like San Francisco Lessingia — a flowering plant down to about 300 individuals in the 1980s — grow and recover their populations. Lessingia now numbers in the hundreds of thousands each season.

Another large project is the replacement of 60,000 Monterey pine, cypress and eucalyptus trees planted by the Army. The plan is to remove the trees as they reach the end of their lives and put in a canopy of different-aged trees that is easier to manage. The flammable, invasive blue gum eucalyptus trees that make up 42% of the park’s 300-acre historic forest are being replaced by the less volatile mountain gum.

The trees and native plants are nurtured in the Presidio Native Plant Nursery, near Fort Scott. But a large number of new plants have sprouted on their own, as invasive plants were removed and suitable habitat restored.

Overall, biologists have reported a more than tenfold increase in the number of native plants in the Presidio, including at least six species that are endangered or threatened.

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Those include that well-hidden Franciscan manzanita, which was presumed extinct in the wild until a motorist, who happened to be a biologist, spotted it in 2009 after it was exposed during the Doyle Drive rebuild project.

The remnant shrub was relocated, but is no longer alone. Many cuttings have been planted in the rocky serpentine hills, and biologists are trying to expand the genetic diversity and revive the species using sprouts from Franciscan manzanitas collected decades ago at the old Laurel Hill cemetery and kept alive in botanical gardens.

Left, Thompson Reach being prepared for restoration work. Landfill had been removed and the creek daylighted out of the pipe it had flowed through. A few years later, it was on its way to filling in with willows and the other native plants. | Left: courtesy Presidio Trust, right: Mark Lundgren / The Chronicle

Other rare plants making a comeback are the endangered Presidio clarkia — also once thought to be extinct — and the Raven’s manzanita, which was rediscovered in the 1950s after being gone for half a century.

With the plants come the wildlife — butterflies, hummingbirds and a variety of migratory birds now frequent the park. Earlier this year, a colony of silver digger bees appeared in the western dunes after not being seen for almost a century. A nesting pair of Western bluebirds was spotted a few years ago at Lobos Creek Dunes shortly after they were restored — the first sighting in 70 years. Western chorus frogs have settled in several locations after being gone for many years.

Coyotes were first spotted in the Presidio in 2000, apparently after crossing the Golden Gate Bridge. There are now so many of them that biologists have begun fitting them with GPS tracking collars. In 2017, 300 checkerspot butterfly caterpillars were released near El Polin Spring, where they hadn’t been seen in nearly 40 years, and have spread across the park.

Stringer said the Presidio is now a climate-resilient “botanical wonderland of rare and endangered species” that is closer than ever before to the coastal ecosystem that existed before San Francisco emerged out of the wilderness.

“We found that if you get the ingredients right, it’s not that hard,” he said. “It just takes energy, resources and people willing to be there for a long time to tend it. We’re just creating the ideas. Now people can reference them and say, ‘Hey, this is working.’”

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