David Turpin, 56, and Louise Turpin, 49, were charged with 12 counts of torture, Riverside County District Attorney Mike Hestrin said. David Turpin also was charged with a lewd act on a child by force or fear of duress.
"This is severe, emotional, physical abuse. ... This is depraved conduct," the prosecutor said.
Of the victims, Hestrin said: "They're relieved. ... Their health is being looked at. They're in good hands. As far as where they're going to end up, I don't know."
The 13 siblings range in age from 2 to 29. Six are minors.
Other charges for the parents include seven counts of abuse of a dependent adult, six counts of child abuse or neglect and 12 counts of false imprisonment.
The Turpins each pleaded not guilty on all counts when they were arraigned Thursday afternoon. A judge set bail at $12 million for each defendant. The Turpins' next court date is February 23.
If convicted of all charges, they could face a maximum sentence of between 94 years and life in prison.
"What we would like the public to know is that our clients are presumed to be innocent, and that's a very important presumption," David Macher, a public defender for David Turpin, told reporters.
When asked about the number of counts and the nature of the charges, Macher said: "It's going to be a challenge."
Allegations of increasing abuse
The allegations cover the time the Turpins have lived in California, but Hestrin said the abuse started while the family lived in Texas.
It "started out as neglect" and became severe, pervasive child abuse, getting worse when the family came west, Hestrin said.
The physical abuse included beatings, chokings, and children being tied up for long periods, Hestrin said.
"Punishment would last weeks or even months at a time," Hestrin said.
The children were fed on a schedule but only the 2-year-old appeared to get enough food, the prosecutor said, adding that he was not charging torture in the case of the toddler.
Besides suffering severe caloric malnutrition associated with muscle wasting, several have cognitive impairment and "neuropathy, which is nerve damage, as a result of this extreme and prolonged physical abuse," Hestrin said.
Pointing to the children's malnourishment, Hestrin said that a 12-year-old has the weight of an average 7-year-old, and a 29-year-old daughter weighs 82 pounds.
David Allen Turpin, 56, and Louise Anna Turpin, 49.
The parents would buy food and apparently let the children see it, but not eat it. This included pies left on the counter, Hestrin said.
The children were allowed to write in journals, and hundreds have been taken into evidence.
Teen escaped and called 911, police say
The Turpins have been in police custody since Sunday after authorities were called to their house in Perris, southeast of Los Angeles.
Investigators arrived at the home, they say, after a 17-year-old girl crawled out of a window at the home Sunday morning and called 911 using a deactivated cellphone she had grabbed from the house.
Hestrin said Thursday that the girl had been working on an escape plan with her siblings for more than two years. The girl initially escaped with another sibling, but that sibling became frightened and returned home, he said.
When police arrived, three of the children may have been shackled to their beds, Hestrin said. The parents unchained two of them, he alleged.
Investigators found the Turpins' children inside a filthy home "in dark and foul-smelling surroundings," the sheriff's department said earlier this week.
The mother was "perplexed as to why" authorities came to her home, Riverside County Sheriff's Capt. Greg Fellows said Tuesday.
"If you can imagine being 17 years old and appearing to be a 10-year-old, being chained to a bed, being malnourished and injuries associated with that, I would call that torture," Fellows said.
Parents 'kept them away from everybody'
The family had lived in Perris since 2014.
Those who tried to speak to the children over the years say they were rebuffed.
In 2015, Kimberly Milligan, a neighbor of the Turpins in California, said she was with her son checking out Christmas decorations on nearby homes. Some of the older Turpin children were putting up a Nativity scene outside their house, and she complimented their decorations.
They seemed "scared to death," she said. "You could tell they were terrified."
Milligan said the children were thin and appeared malnourished.
What could be next for the 13 siblings
The Riverside County Department of Public Social Services is seeking court authorization to provide oversight and care for the 13 siblings "to the extent that's necessary," von Zabern said.
"At this point, we'll be doing a full assessment with medical professionals to better understand needs of the adults as well as the children, and we'll be prepared to provide supportive services as well as engage other agencies in assisting these individuals to be stable," she told reporters Tuesday.
When asked if they would go to live with family members, von Zabern said the practice is to identify relatives who are able to provide care, as long as they pass background checks and are suitable and stable. But at the time of the Tuesday press conference, she said no relatives had come forward.
Of the 13 siblings, the adults are being treated at Corona Regional Medical Center in Corona, and the six children are under care at Riverside University Health System Medical Center in Moreno Valley.
"It's hard to think of them as adults," Mark Uffer, Corona Regional Medical Center CEO, said Tuesday. "When you see them, they're small. They're stable. They're being fed."
CORRECTION: This story has been updated to correct the age of David Turpin. He is 56.
CNN's Sonya Hamasaki, Stephanie Becker, Darran Simon, Ray Sanchez,