Sara Krueger, 23, and Scott Warner, 26, became subjects of an intense search in the San Francisco Bay Area after officers conducting a welfare check at Krueger's Napa apartment found the child's body in her bed on Saturday, Lt. Debbie Peecook said.
A few hours earlier, witnesses had seen Krueger and Warner leaving the apartment with luggage, police said.
Someone who spotted the couple at a restaurant near a Bay Area Rapid Transit station Sunday in the city of El Cerrito alerted police, and BART officers detained them, Peecook said. BART police Lt. Gil Lopez said they were detained without incident at the station in El Cerrito, about 30 miles south of Napa.
They were questioned and booked on suspicion of murder with special circumstances and assault on a child resulting in death. Peecook said she didn't know whether they have retained an attorney.
The child, whose name was not released, showed signs of having been sexually assaulted and blunt force trauma, investigators said.
Her biological father, who is serving time at San Quentin State Prison, was notified of her death.
The property manager at Krueger's apartment building told the Napa Valley Register (http://bit.ly/1ejqZQx ) that in recent months, police visited the mother's residence for several disturbances, including late-night noise, slamming doors and neighbors reporting possible physical abuse of the child.
Warner "moved in about 10 months ago, and it all went downhill from there," Elizabeth Chechourka said.
"Management sent a letter to them about 2 1/2 weeks ago saying, 'The authorities know about you, and you need to shape up or you're gonna lose your housing,'" she added.
Peecook said Napa officers had made several welfare checks at Krueger's home, most recently last week, but none of the visits resulted in an arrest.
She said she didn't know whether Napa County Child Protective Services had visited the apartment in response to any neighbors' complaints.
A family friend who often baby-sat the girl was baffled by news of the girl's death and her mother's arrest.
"Never saw her raise a hand to the girl. It was like pulling teeth getting her to somewhat discipline her," Kindra Kunkel told reporters.
"This is not Sara; this is not the Sara I know," said Kunkel. "She fought so hard for her little girl."