The train itself and its passengers were not in any immediate danger, but rescue crews had to decide whether to evacuate the train or risk sending it back to departing station in Santa Clarita.
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Metrolink spokesman Scott Johnson told Eyewitness News that the Antelope Valley Line train 215 originated at Union Station in Los Angeles and was heading toward Lancaster.
As the train passed through the Via Princessa Station in Santa Clarita, heading toward Acton, a section of ground near the tracks was washed out by the flood waters.
One passenger said she and other riders noticed a little water along the roads, but then quickly saw the flood waters wash over the pavement and along the train's route.
Johnson said the train then tried to head back to the station, but another portion of tracks was also affected by the flood waters.
MORE: Flash floods cover roads in mud, damage homes, cause train delays in Acton
Another passenger said once the train stopped and the erosion continued, it felt like the train started leaning to one side.
"It was like tilting, and it was scary," Neomi Smith said.
The train sat on the tracks for more than an hour while officials evaluated their options and the condition of the tracks.
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L.A. County Fire Department personnel helped several passengers with medical issues during the waiting period, while sheriff's deputies had to deal with several unruly passengers.
"It was crazy. Some lady opened two windows. I think she almost opened the door," a young passenger said.
Violet Richard, a passenger who was helped off the train by fire personnel,
"My legs are shaking at that point now because we can't go nowhere, so I'm like, 'What is there to do?' I started to ask the people that was outside, the policeman, everybody - 'Hey, what's going on? What are we going to do?" she said.
Passenger Danny Lozano said one woman jumped over him to pull open a window. He said he told her to stay calm and that the train would move again soon.
Eventually by about 7:30 p.m. they decided to send the train back to the Via Princessa Station with the passengers.
MORE: Southern California forecast - get the latest weather
Anyone who needed to go to other parts of Acton, Palmdale or Lancaster would be given an alternate form of transportation.
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Stations along the corridor would be affected, according to Johnson, with at least 1,000 people total on about four trains being delayed as the train moved back.
While the train was stranded between tracks, Johnson said there were no safe areas to detrain passengers unless they had an urgent need to get off in which case firefighters helped them out.
Johnson added that the tracks issue would continue to affect Friday morning commutes, especially for people in Lancaster and Palmdale.
Train service was expected to continue Friday from Union Station to Via Princesa, but trains were not expected to travel past there to the three additional stations through Friday.
In a press release, Metrolink said the Antelope Valley Line trains 200 and 202 between Lancaster and Union Station were canceled for Friday morning. The first train set to operate in the line will be train 204 leaving from Lancaster at 5:19 a.m.
Metrolink will also operate the line's 285 train, which makes limited stops between Palmdale and Union Station.
Commuters were advised to check Metrolink's Twitter feed for the latest information.