An earlier mandatory evacuation that included 14,000 residents near a creek that appeared to have breached now only covers about 3,800 residents, said David Sykes, director of the emergency operations center.
That means nearly 1,100 structures are still under the mandatory evacuation order, down from 4,000, officials said. Sykes said the figures don't include two additional areas recently cleared for re-entry.
San Jose officials said they are working to lower water levels in some flood units and identify homes that can be reoccupied.
On Tuesday, residents scrambled to fortify their homes with sandbags, but it was too late for some. The flooding had submerged some southern San Jose homes.
"You were able to see the water coming but you couldn't stop it. You feel so powerless," resident Peter Miskin told CNN affiliate KGO
Miskin and his partner, Gary Johnson, and a friend tried to save anything they could.
"It was so fast we managed to evacuate the dogs, medications and passports. Everything else stayed," said Miskin.
KGO reported that hundreds of people were still waiting to return home after Coyote Creek dropped below flood stage.
Officials continued to pump waters back into the creek channel in the area of three mobile home parks, according to Assistant Fire Chief Robert Sapien.
"We can say at this time, we are pretty dry in all three parts," Sapien said.
Asked by reporters where residents can dump contaminated trash, Sapien said the officials will deliver dumpsters to several areas on Friday. He urged residents to take caution when handling the trash and use gloves and frequently wash their hands.
"We're going to ask that people presume that the flood waters were contaminated," he said.
Sykes said officials are watching a storm expected for the weekend.
The National Weather Service is calling for showers from Saturday through Monday. But CNN meteorologist Judson Jones said any rainfall is still a concern because of receding floods water and the saturated ground.