Matthew Brendan Warner, 30, faces one count each of murder, assault on a child causing death, torture, oral copulation or sexual penetration with a child 10 years old or younger and aggravated sexual assault of a child, Deputy District Attorney Julie Kramer said in a news release.
According to the criminal complaint, the murder and sexual assault happened on Friday.
Deputies with the Santa Clarita Valley Station said Warner and his girlfriend came to the station Friday night and reported their baby girl, Ellorah, missing from their home.
Ellorah's body was discovered the next morning in the front cab of a Nissan pickup truck in a parking lot in the 23630 block of Newhall Avenue, about a half-mile from where the child lived. Warner was arrested on suspicion of murder.
The baby's maternal grandmother, Nan Allison, said neighbors saw Warner leave their apartment complex with a bundle. She says he later told his girlfriend, Tawni Wallis, that their baby was missing.
Wallis was not arrested and will likely not face any charges. Detectives say Wallis is distraught, but cooperating in the investigation. She left court Tuesday without speaking to the media.
Allison, Wallis' mother, stopped to tell Eyewitness New what she would say to Warner.
"I would tell him that when a man, but then I don't consider him a man, has a child he should be that child's protector until the day he as a father dies, and the idea that a three-week-old child should have to worry about defending herself against her 30-year-old father is abhorrent to me," Allison said.
The criminal complaint lists "revenge" as a motive for the alleged crimes.
"I am not going to address that. It was behind closed doors. I have my opinions, but I am not going to say anything about that," Allison said.
Warner's mother, Victoria Law-Thomson, says even though her son had a history of drug addiction she does not believe he would have done anything to harm his infant daughter.
"I still believe in you. I just wish you'd reacted different. I think you made some really idiotic choices," Law-Thomson said.
The coroner has yet to determine an exact cause of death.
Meanwhile, Allison says her daughter is "inconsolable."
"I hope that every minute of the rest of his existence he is burdened with guilt over what he's done," Allison said.
Warner was under post-release community supervision stemming from a 2012 conviction for unlawful driving or taking of a vehicle with priors.
Arraignment was scheduled for Tuesday but was continued to Feb. 18. Bail was set at $2.25 million. If convicted of all charges, Warner faces a maximum penalty of life in prison.
A candlelight vigil was held at 6:30 p.m. Tuesday for baby Ellorah at Old Orchard Park. Friends of the Wallis family have set up a GiveForward.com account to help with funeral expenses. You can donate here: www.giveforward.com/fundraiser/kqg7/baby-ellorah.