Authorities responded after the three were hit by train #603 near Alicia Parkway and Via Fabricante at 6:06 a.m.
Authorities ruled out alcohol and drugs as factors, and said the incident was not the result of a suicide pact.
A male victim, 22, and a female victim were declared dead at the scene.
A female victim, 27, from Santa Ana, was transported to a local hospital with non-life-threatening injuries, police said. She sustained injuries to an arm and a leg. She told authorities she heard the train and jumped out of the way.
The Metrolink train, traveling from Oceanside to Union Station in Los Angeles, was heading northbound at 90 mph.
Metrolink Spokesperson Angela Starr said L.A.-bound trains travel in what's called the "push" mode, with the locomotive in the rear, and unless the engineer is blowing the horn, the train is virtually silent.
"They're going fast, and the train more than likely won't be able to stop," said Starr. "In this case, the tracks here, the track speed is 90 miles per hour."
It is unclear whether the engineer saw people on the tracks and had time to sound the horn, but according to Metrolink, it would have been nearly impossible at that speed to stop in time.
There were no injuries to any of the 67 passengers or crew on the train.
Metrolink train service in the area was delayed, and buses took passengers between the Laguna Niguel and Irvine stations.
Metrolink officials stressed that it is illegal to be on the train tracks.
Area residents said with two schools and a park near the railroad, too many kids have access to the tracks.
"Children are on these tracks on a daily basis walking to and from school, taking the shortcut through the parks down here, and to me, it's just felt like it's a matter of time before a tragedy like this would happen here," said Mission Viejo resident Diane Zammit. "I mean, it's very unfortunate, but maybe it's a wakeup call to close down the shortcuts that run right here next to the tracks."
Metrolink officials say the event recorder on the train will reveal more of what happened in the accident, including whether the engineer saw the three people on the tracks and whether he was able to sound train's horn.
The deceased victims were not identified pending notification of next of kin.
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