Dramatic Photos Show Aerial View of California Train Derailment

The train had 214 passengers on board when it struck a tree on the tracks.

The crews are taking the cars off the train tracks before they remove the car that fell in the water, Castillo said, and he estimated the process could take days.

The train had 214 passengers on board when it struck a tree on the tracks and derailed between Fremont and Pleasanton, according to ACE Train, which operates the commuter service between Stockton and San Jose.

Fourteen people were injured, ACE said. Nine people were transported to the hospital, five of them with minor injuries, while the remaining four had injuries that were considered serious but non-life threatening, according to the Alameda County Fire Department.

"Crews had to fight the creek's fast-moving currents to pull riders from the partially submerged rail car,” Alameda County Sheriff's Sgt. Ray Kelly said.

"It was dark, wet, it was raining," Kelly said. "It was very chaotic.”

Castillo said the water temperature was especially cold.

ACE train service has been canceled until further notice, Castillo said, adding that Union Pacific has extensive protocol for making sure tracks are clear, especially during rough weather.

"We are working with our partners to restore service as soon as possible pending a complete investigation and assurance that the tracks are safe,” ACE said.

ABC News' Kayna Whitworth contributed to this report.