Officials said the burns were from scalding hot bath water. The girl was taken to Victor Valley Community Hospital on Saturday with third-degree immersion burns to nearly 30 percent of her body, according to authorities.
Hospital nurses grew suspicious about the burns and called detectives.
Authorities determined that the girl's father, Bryan Escalante, and his girlfriend, Vanessa Poindexter, were believed to be responsible for the burns. They were arrested and booked at Central Detention Center in San Bernardino on Saturday.
The District Attorney's Office filed one count of willful cruelty to a child on both suspects. Poindexter was also charged with one count of torture.
The couple's neighbor, Robbie Winter, said he doesn't believe the charges.
"I'm really shocked about that. I would not believe that, they're really good parents and it's sad because they just had a baby, they were celebrating one of their kid's birthdays. It's shocking really," he said.
Winter said he was home late Friday night when Escalante came over, pounding on the front door.
"He was in a panic and stuff, he told me his little girl got burned by hot water. So he asked me to watch the kids," he said.
The four other children in the home, including an 11-day-old infant, were taken into custody by county family services.
The 3-year-old girl was transferred to a burn center in Northern California and underwent surgery on Monday. She was said to be in critical but stable condition.
Escalante is being held on $100,000 bail, while Poindexter is being held on $500,000 bail.
