The California High-Speed Rail Authority has selected a tract of former industrial land in Brisbane as the preferred site for a train maintenance yard, a decision the property owner says could thwart long-standing plans to build one of the Bay Area’s largest mixed-use projects there.

For 10 years, Universal Paragon, which owns a 684-acre Baylands property straddling San Francisco’s southern border with Brisbane, has been planning a transit-oriented development that would include 4,434 homes, 7.5 million square feet of commercial space and 300 acres of restored habitat.

Universal Paragon General Manager Jonathan Scharfman said the authority’s decision to “exclusively” study the Brisbane Baylands for a maintenance yard was unexpected and was not made clear until a series of community meetings in late May. While the developer has urged the California High-Speed Rail Authority to consider alternative sites, it has little power to influence a decision.

He emphasized that the Brisbane Baylands site is identified as a “priority development area” by the Association of Bay Area Governments, the regional planning group known as ABAG. Priority development areas, which include old industrial sites like the former Hunters Point Shipyard and the Concord Weapons Naval Station, are transit-rich sites big enough that they have “a unique potential to reduce greenhouse gas emissions,” according to ABAG literature.

“Our focus is to transform a legacy industrial site into productive use for the 21st century,” Scharfman said.

1 of 5 planned facilities

High-Speed Rail Authority spokeswoman Lisa Marie Alley confirmed that Brisbane has been selected for a 75-acre light-maintenance facility, one of five that will be located along the 520-mile route between San Francisco and Los Angeles.

“It could be east of the tracks, west of the tracks, or both,” she said. “We are still going through our technical analysis. There is still a lot of work to be done .”

The Baylands property is just one of hundreds of parcels the High-Speed Rail Authority must take to complete the $64 billion project. Work has started on the first phase of the project, 119 miles of track from Madera to an area near Bakersfield. The authority is taking 150 parcels in the Central Valley alone — either through purchases or eminent domain.

“All large infrastructure projects have impacts like this,” Alley said. “We know that our system will have an impact on people, and any impact on someone’s life is hard. That’s someone’s home. That’s someone’s farm. That’s someone’s business. That’s the worst part of this project, but we know in the long run it will benefit folks.”

The Brisbane Baylands is split into two sections. To the west of the tracks lies the former Southern Pacific rail yards, which closed in the 1980s. To the east is an old landfill, where San Francisco sent its trash until 1967.

Universal Paragon’s current plans call for predominantly commercial development to the east and housing mostly to the west.

Until the authority figures out exactly where it wants to put the Brisbane maintenance facility, it will be hard to know the impact it would have on the development proposal, although putting a 75-acre maintenance facility along the tracks would likely “split up the street network and transportation network and development pattern in such a way that it would be very difficult to plan adjacent uses,” Scharfman said.

The parcel sits to the immediate south of the 20-acre former Schlage Lock manufacturing campus, where Universal Paragon has started building infrastructure for a 1,679-unit housing development. Buildings will start rising on that property late next year.

Taken together, the 6,000 new homes and millions of square feet of commercial space have the potential to create a “Mission Bay 2.0,” according to the developer. While developers of urban “brownfield” sites frequently have to bring public transit in, the Baylands land comes with a Caltrain stop smack in the middle of the site. The end of San Francisco Muni’s T-Third streetcar line is a short walk away.

“It’s a new city — it really is,” said Howard Pearce, the project civil engineer. “It’s a tremendous undertaking. The goal is to get everybody out of their cars, living and working on transit.”

The potential conflict between high-speed rail and transit-oriented development is an uncomfortable one for pro-growth organizations like the Bay Area Council and SPUR, which support both. SPUR Executive Director Gabriel Metcalf said ideally a compromise could be reached where the Baylands property could accommodate both. Scharfman said, “There is zero ambivalence about our record standing in support of regional rail and high-speed rail.”

“It makes sense to me that high-speed rail would be looking at Brisbane because it’s the largest undeveloped area on the track between San Francisco and San Jose,” Metcalf said. ”But if there is a way that we can have that and also have the transit-oriented development we need, that would be ideal.”

Political headwinds

But the potential maintenance yard is not good news for a development project already facing strong political headwinds.

In Brisbane, a town with about 2,000 housing units, a recent survey of 580 residents found that 43 percent support no housing at the Baylands site, while another 28 percent said they would be in favor of fewer than 1,000 units. Only 12 percent said they would support more than 2,000 units. Most residents said they opposed housing there because it would increase traffic and alter Brisbane’s “small-town feel.”

San Mateo County has produced 54,000 new jobs since 2010, but only 3,000 new homes.

Since September, the Brisbane Planning Commission has held 19 hearings or meetings on the plan. Universal Paragon has opened a storefront office in downtown Brisbane, where community outreach manager Xiomara Cisneros talks to largely skeptical residents about the Baylands.

Other potential sites

John Swiecki, Brisbane’s community development director, agreed with Scharfman that the rail authority should look at other sites besides the Baylands. Scharfman suggested existing Caltrain yards in San Jose and San Francisco, as well as Port of San Francisco sites between Pier 80 and Pier 96 on either side of Islais Creek.

The Baylands project is set for a Planning Commission vote later this year.

Land use attorney Tim Tosta said the property owner will have little power to influence plans once the authority identifies land it intends to seize.

“They are just going to have to take it on the chin,” said Tosta, who represented a property owner whose land was taken by the Transbay Joint Powers Authority. “The condemning authority has a right to take the land, and then you fight over the money later.”

Frank Oliveira, whose family owns 200 acres of nut trees in Kings County that the authority is seizing, said once property is targeted, it’s hard to plan for the future.

“They draw the lines on the map where they want to go, and you don’t have much say in the matter,” he said.

J.K. Dineen is a San Francisco Chronicle staff writer. Email: jdineen@sfchronicle.com

Twitter: @sfjkdineen