There were more than 200 people on board the train. Nine people were injured and two of the victims remain hospitalized. All of the injured are expected to survive.
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Service was shut down while investigators cleared the train from the track and debris on Tuesday. Although the train has been removed from the track, all trains going through Niles Canyon Road Wednesday will be moving slowly, so passengers can expect delays.
Shortly after 9:10 p.m., officials said Niles Canyon Road reopened to traffic.
At least 75 people worked non-stop on the tracks where the most seriously damaged train car was pulled out of the water.
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It took nearly 24 hours to move the five car train off the tracks, where the night before a mudslide caused two of the cars to derail. Crews inspected the tracks and repaired them.
But many who were at the scene are still shaken by what happened, including two Alameda County Sheriff's Office deputies.
They were truly the 'first' to respond after the train crashed. "The whole scene itself was kind of surreal,"
They both saw a car submerged in an Alameda County creek when they arrived. Both men immediately jumped into the creek, but were almost swept away by the current.
Then they drove onto the tracks, ran a half a mile, and saw and unforgettable scene.
"Someone had injuries, scrapes, and a little bit of blood on them, people were crying, laying down on the tracks, a lot of shock on people's faces," Alameda County Sheriffs Office Deputy Justin Brannon said.
But they knew they had to get into that submerged first car. "We crawled into the train and because of the steep slope it was on, we had to slide down the walls to the inside of the train while avoiding the windows because the body of the train was still lifted off the ground," Alameda County Sheriffs Office Deputy Anthony King said.
They got two people out and carried them a mile to an awaiting ambulance.
They're humbled by the experience. "Wasn't worried about being a hero or what was going to happen. I wanted to make sure everyone was safe before anything else," Brannon said.
Both deputies are back at work.