Opponents of a 200-bed Navigation Center planned for the Embarcadero filed a lawsuit against the project Wednesday in an attempt to stop the city from building the homeless shelter in their neighborhood.

The lawsuit, filed in Superior Court in Sacramento County, comes just a few weeks after the San Francisco Board of Supervisors turned down an appeal by the residents against the project. The city has since fenced off the area where it plans to build the Navigation Center, though it is unclear whether construction has actually started.

The residents, mostly from South Beach, Rincon Hill and Mission Bay, have opposed the project since Mayor London Breed proposed it in March. At several emotionally charged hearings — including one where Breed was shouted down from the podium— the residents argued that the facility would attract more homeless people, crime and blight to their neighborhoods.

Last month, the group was unsuccessful in trying to persuade the supervisors to overturn a unanimous April decision by the San Francisco Port Commission to grant the city a two-year lease on its 2.3-acre parcel across from Piers 30-32. The residents, who formed a group called Safe Embarcadero for All, vowed to bring the matter to court if the appeal didn’t go their way.

“The board can make these kinds of political decisions, but the courts will have the last word on this,” said the group’s attorney, Peter Prows, as he stood outside the board chamber shortly after the appeal was denied last month.

The lawsuit makes arguments that are similar to those in the appeal: that the city failed to get the necessary approvals from the State Lands Commission, the agency that oversees waterfront development. It also argues that the city did not go through a proper environmental and design review and seeks a restraining order to halt the development from progressing until the lawsuit is decided.

John Coté, a spokesman for City Attorney Dennis Herrera, said “all appropriate land use laws were followed.”

“San Francisco has a homeless crisis on its hands. The city is ready to put roofs over people’s heads and get them indoors,” he said in a statement. “Rather than trying to shift the problem to someone else’s backyard, everyone needs to do their part.”

Navigation Centers are around-the-clock shelters with intensive on-site services that help guide people into stable housing. They are meant to be temporary structures, often built on land slated for development.

Many of the city’s homeless find Navigation Centers to be more comfortable and flexible than the city’s traditional shelters, which often have wait lists that stretch more than 1,000 people every night. But the Navigation Centers have also started filling up long before sunset every day — increasing the urgency in City Hall to find space to build more.

S.F. Homeless Project This month, beginning July 28, The Chronicle will again join with other Bay Area news outlets in the SF Homeless Project, a media collaboration exploring causes and solutions to our regional homelessness crisis. July 28: We answer your questions on homelessness and offer a guide to ways you can help. July 29: The Chronicle assesses the effectiveness of a San Francisco program that offers homeless people a bus ticket home. July 29-31: Our Fifth & Mission podcast tackles the issue of homelessness. July 30: San Francisco Mayor London Breed and an expert panel discuss homelessness at the first of two public events. July 31: The Chronicle presents an in-depth report, “24 Hours of Homelessness.” Aug. 8: San Jose Mayor Sam Liccardo and an expert panel discuss homelessness in front of a live audience. To submit questions, purchase tickets to the public events and find all our reporting on this topic, go to: http://www.sfchronicle.com/homelessness Supported by Cisco

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Creating more shelter beds is a difficult and costly endeavor. Both the mayor and several supervisors say finding sites to hold the facilities has proved to be challenging.

The lawsuit represents the latest obstacle for Breed as she attempts to fulfill her promise of opening 1,000 shelter beds by the end of 2020. Since announcing her goal in October, she has added 286 beds across the city. There are 304 more in the pipeline — 200 of which are planned for the Embarcadero site.

Despite losing the appeal last month, Prows said Wednesday that he was confident the group will win the lawsuit and stop the project. It is unclear whether the suit will delay the project, but Prows said he hopes a judge will consider as early as Friday the requested restraining order to prevent the city from breaking ground.

The case was filed in Sacramento County because it involves the State Lands Commission and because “San Francisco County would not be a neutral venue,” the lawsuit says.

Supervisor Matt Haney, whose district includes the proposed site, said he was frustrated by the lawsuit and hopes that it does not delay the project further. The mayor originally wanted to open the site by this summer. Now, unless the lawsuit gets in the way, the earliest the site could realistically open would be this winter.

“It’s important that the neighbors stay closely involved with this Navigation Center but, candidly, this isn’t the kind of involvement I hoped for,” Haney said Wednesday. “The board rejected the appeal unanimously. ... I don’t know what else they want at this point.”

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