Jose Maria Cuatro Jr., 28, and Ursula Elaine Juarez, 25, are charged with one count each of murder and torture in the case.
The boy's father is also charged with one count each of assault on a child causing death and the newly added count of sexual penetration with a child under 10 -- the indictment alleges that act occurred on the same day the boy was attacked -- and one count of child abuse under circumstances likely to cause death.
The inquiry began as an investigation into the accidental drowning of the boy.
But in the six months since Noah's death, investigators have said the child was not only murdered but tortured as well.
MORE: Details emerge about Noah Cuatro's history in foster system
Eva Hernandez, Noah's great-grandmother, took care of the boy after Los Angeles County's Department Child and Family Services removed him from his parents.
Attorney Brian Claypool represents Noah's family. They expect to file a civil suit against the county for allegedly not doing enough to protect the boy.
DCFS workers returned Noah to his parents against Hernandez's warnings, then overruled a social worker's recommendation and a court order to once again take Noah away from his parents due to safety concerns.
"Once DCFS got that removal order, the family and myself believed that Noah should have been immediately removed, and had he been removed, he'd be alive today," Claypool said.
The two defendants are scheduled to return to court for an arraignment Feb. 19.
Cuatro, who could face a maximum of 47 years to life in state prison if convicted as charged, was ordered to remain jailed in lieu of $4 million bail.
Juarez is being held on $3 million bail and could face up to 32 years to life in prison, according to the Los Angeles County District Attorney's Office.