San Francisco plans to build its biggest Navigation Center yet after the Board of Supervisors rejected an appeal from a group of residents to halt the project over worries that the homeless shelter will attract more crime, violence and nuisance to the Embarcadero.

The residents — mostly from South Beach, Rincon Hill and Mission Bay neighborhoods — urged supervisors Tuesday to overturn a unanimous April decision by the San Francisco Port Commission, which granted the city a two-year lease on a 2.3-acre parcel across from Piers 30-32.

But their argument fell flat to the 11-member board.

“This Navigation Center will move forward, and it will have the continued partnership from my office and the city,” said Supervisor Matt Haney, whose district includes the proposed site. “Entire communities are safer when they are inside.”

The city plans to start start building the 200-bed Navigation Center — which is an around-the-clock shelter with intensive on-site services to help guide people into stable housing — this summer. Once the city breaks ground, it will likely take about five months until people can start using the facility, according to the mayor's office.

But there may be a hurdle ahead: The group of residents vowed to sue the city over the project in an attempt to delay the construction, or squash it all together.

“If we take this matter to court, we expect to win, no matter how long it takes,” said Peter Prows, the group’s attorney with the law firm Briscoe Ivester & Bazel.

The proposed Navigation Center has sowed major divisions in the city since it was proposed by Mayor London Breed in March. The proposal set off emotionally charged debate from residents, who opposed the idea of a shelter coming to their neighborhood. Many complained that they were blindsided by the proposal, and said the city rushed the process with little regard for how the Navigation Center would impact the surrounding community.

“I went to more than a dozen community meetings, but it was like speaking into a black hole,” said Judy Dundas, 55, who lives near the proposed site. “Nothing we said was heard.”

Dundas reiterated the residents’ plan to take the case to court.

“Now we’re left with no choice but to pursue expensive litigation,” she said. “We’re going to fight this for as long as we can.”

Despite the intense neighborhood opposition, Breed remained firm on her proposal. As the city’s homeless population reaches record levels, the mayor — who is running for re-election in November — has been under intense pressure to increase resources for those on the streets. Even though the city has built hundreds of new shelter beds and more than $300 million is spent annually on the issue, a recent report showed that the city’s homeless population grew by 17% since 2017.

The new Navigation Center is critical for the mayor, who promised to open 1,000 new shelter beds by the end of 2020. About 400 beds have opened around the city since she took office.

“Our city is in the midst of a homelessness crisis, and we can’t keep delaying projects like this one that will help fix the problem,” she said in a statement. “When we have people suffering on our streets we need to be able to provide them with the care and services they need.”

The residents appealed the port’s decision on the argument that the city skipped a number of critical steps, including proper public outreach and a comprehensive environmental review. The residents also said they worried about how the center would impact the surrounding neighborhoods, from an increase in homelessness, emergency vehicles, crime and drug use.

Prows said he was not surprised by the board’s decision to strike down the appeal. He said he will likely file a lawsuit “within a matter of weeks or a few months.” The goal, he said, is to stop the project completely.

“This is a political decision,” he said outside the City Hall board chamber shortly after the appeal was denied. “The board can make these kinds of political decisions, but the courts will have the last word on this.”

After several community meetings over the past few months, the mayor and Haney struck a few concessions with the residents: Rather than starting at full capacity, the facility will initially open with 130 beds, and gradually ramp up to 200. The city will also start with a two-year lease, instead of four, with the opportunity to extend it if the Port finds the center helped reduce homelessness in the area. Officials also promised uniformed police officers will patrol the center and the surrounding area seven days a week.

While Haney said the outreach process wasn’t perfect, he said the city’s homeless crisis is too dire to forgo an opportunity to create 200 more beds. But, he said, the city also needs to extend those services beyond where they are currently concentrated in the Tenderloin, SoMa, Mission and the Bayview.

He proposed an ordinance earlier this year that would force the city to open up a Navigation Center or other types of homeless services in every district — but critics have questioned the cost effectiveness and viability of that plan.

“There are learnings that should come from this,” he said. “Because this will not be the last Navigation Center we build.”

Shortly before Tuesday’s appeal, Supervisor Aaron Peskin made an announcement that could signal another fight ahead: he’d like the city to support a Navigation Center in his own district, at a proposed site that teeters between the Tenderloin and Polk Gulch.

So far “people are supportive,” he said. “Which is not to say there won’t be detractors.”

Trisha Thadani is a San Francisco Chronicle staff writer. Email: tthadani@sfchronicle.com Twitter: @TrishaThadani