There have been several water rescues already, including one by helicopter, the mayor said. About 500 apartments are in the mandatory evacuation area and almost 200 people have been relocated, Liccardo said. Some were rescued from their homes by boat.
The mayor also expressed concern about a homeless encampment near Coyote Creek, where individuals were reluctant to leave.
Other low-lying areas near Coyote Creek are subjects of a voluntary evacuation order, the mayor said.
Coyote Creek hit a historic crest of 13.6 feet on Tuesday. The flood stage is anything above 10 feet.
On Tuesday, residents scrambled to fortify their homes with sandbags, but it was too late for some people. The flooding had submerged some southern San Jose homes.
Residents watched helplessly as the murky water poured into their homes and one flood victim, Jaunita Wilson saw her belongings starting to float around her apartment.
"That's like a nightmare," she told CNN affiliate KPIX
. "It's kind of like something you can't believe is happening, but it is happening."
Employees from two Santa Clara County facilities have been evacuated due to flooding, the county said. More than 300 social services workers were relocated.
"I cannot say that the worst is over," Liccardo said. "My understanding is that the peak level may continue to rise."
Jose Villalobos Chino, who lives near the creek, had to drive through several inches of water on Tuesday morning.
The water was almost up to his driveway at 9 a.m. when he was told to evacuate, he said.
Villalobos said he was unable to grab any clothes, important documents or other valuables before he left.
Later in the day, the water was up to the windows of cars parked in the street.
More than 2 inches of rain had fallen in San Jose in the past 48 hours, the National Weather Service said. The rain had stopped Tuesday afternoon. But there is a chance of rain this weekend.
The creek was rising because of water coming from Anderson Reservoir.
According to the Santa Clarita Valley Water District website, preliminary readings indicated the reservoir was at 105.5% of capacity on Tuesday afternoon and the water level was almost 4 feet above the top of a spillway.