Superior Court Judge Ethan Schulman had denied a request from neighbors who oppose the Navigation Center to freeze construction.
The opponents who formed a group Safe Embarcadero for All live near the Beale Street site filed their lawsuit earlier this month.
Residents have said they fear there will be more crime and drug-use on the streets of the expensive neighborhood.
They point to the recent attack in which a woman was grabbed by a homeless man as she tried entering the lobby of her condominium as a harbinger of the neighborhood's future if the Navigation Center opens.