Officials say the homicide investigation began at about 1 p.m. on Saturday when Napa police received an anonymous phone call requesting a welfare check at an apartment in the 2000 block of Wilkins Avenue for a three-year-old girl.
The girl was initially reported by police to be 4-years-old, but authorities confirmed Sunday that she was actually 3-years-old.
When officers arrived, they found Kayleigh Slusher on a bed, already deceased.
According to Napa police Lt. Debbie Peecook, detectives found evidence of foul play, observed signs of blunt force trauma injuries on the child's body, and found preliminary evidence of a sexual assault.
The toddler's mother, 23-year-old Sara Krueger, and her boyfriend, 26-year-old Ryan Scott Warner were not home when police arrived and had been last seen carrying luggage from Krueger's apartment at about 10 a.m. on Saturday.
Lt. Peecook says neither Krueger nor Warner owns a vehicle and police were not been able to reach them on their cellphones.
Regional law enforcement was advised to be on the lookout for the couple.
Police say a citizen saw the couple at a restaurant in El Cerrito, about 30 miles south of Napa, and reported their whereabouts to police.
BART police detained Krueger and Warner at the El Cerrito del Norte BART station at about 11 a.m. Sunday.
Napa police officers picked up the couple and interviewed them about the circumstances surrounding the death of Krueger's daughter.
"At this time, Sara Krueger and Ryan Warner have both been arrested for assault resulting in a child's death, homicide, and special circumstances murder," Lt. Peecook said. "Both will be booked at the Napa County Department of Corrections."
Neighbors at the apartment complex tell ABC7 News that the girl's mother and her boyfriend had both been using drugs.
Anyone with information about the case is urged to contact Napa police at (707) 257-9223.
(ABC7 News contributed to this report)