Metrolink train 603 heading from Oceanside to Los Angeles struck the trio on tracks under the Alicia Parkway overcrossing at 6:06 a.m., agency spokeswoman Angie Starr said. The group included two young women and a young man, authorities said.
The dead were identified late Thursday as Daniel Akins, 22, of Mission Viejo, and Anastasia Bolton, 17, of Del Mar, sheriff's Lt. Colin Murphy said.
The woman who was injured may have been sleeping on rocks near the track, said county sheriff's spokesman Jim Amormino. She suffered moderate injuries that were not life-threatening, and called 911 to report that she and her companions had been struck by a northbound train, Amormino said.
"She said she heard the train coming and jumped out of the way and it nicked her arm and leg," Amormino said. "It's possible they were sleeping on the tracks but there was no evidence they were drinking at the scene."
It was not immediately clear why the three were on the tracks.
"They definitely were not homeless," Amormino said.
Amormino initially said the three were 18 or 19 years old, but later said they might be older. They were not immediately identified.
The women, who had met on Facebook, spent Wednesday evening at nearby Laguna Beach and were planning to go to a friend's house in Mission Viejo when they were hit by the train, Amormino said.
Authorities also searched a car in a nearby parking lot. Amormino said the victims had parked there and walked to the tracks.
Starr said the train's crew and 67 passengers were not hurt.
The train was going about 90 mph and was being pushed by its locomotive, a tactic called "cab forward" that the agency uses to avoid having to turn the trains around when switching directions. The engineers sits in the cab and has all the normal controls and a horn, she said.
"The horn had nothing to do with this incident," she said. "People were on the tracks, the train wouldn't be able to slow down fast enough."
Accident investigators will study the train's events recorder and footage from a camera on the train, Starr added.
Starr said the passengers on the train were put on another train and continued their journey. However, tracks in the area were closed for the investigation, delaying other trains. Buses were taking other passengers between Laguna Niguel and Irvine stations.
In addition, Amtrak said its Pacific Surfliner service between Irvine and San Diego was temporarily suspended and three trains were canceled while other routes were truncated.
Hours after the accident, investigators scoured the section of track in a concrete-lined cutting that runs under the Alicia Parkway overcrossing.
Yellow plastic sheets covered parts of the rail line, and portions of the victims were carried more than 500 feet along the tracks, Amormino said.
A pair of aqua sneakers and some clothing also lay on the tracks.
Starr said Metrolink has had problems systemwide with people going onto tracks, including in the area some 50 miles southeast of downtown Los Angeles.
"There's been quite a bit of trespassing in this whole region. We have been looking at all our highly dangerous crossings," she said.
Keith Ball, 46, who lives nearby, said his family was bothered by teenagers who gathered in a small park next to the tracks to party. Ball said his barking dog awakened him at about 3 a.m. Thursday and he heard laughter and loud talking from the park.
"It's been going on all summer," Ball said. "It's a problem. They really need to come down here and patrol this area more."