The children were the last three to be found of the five who walked away from a group home in the Linda Vista area.
Despite the chopper and heavy police presence throughout the area, it was a neighbor who found the remaining three children just before 9 p.m. Tuesday.
According to San Diego police, the children were reported missing from the San Diego Center for Children, in the 3000 block of Armstrong Street, at about 9:30 a.m. They did not have permission to leave.
Police say the children swam across the San Diego River to reach the Morena area.
Two of the children were discovered about 4 p.m. at the Old Town Trolley Station. Police saw the three others, who ran south down the train tracks.The children are age 10-12, all know each other and are considered "at-risk."
Police officers and dog teams are searching the nearby area, including nearby parks, canyons and shopping centers, for the children. Police are also working with MTS officials because they believe the children might have gotten on the trolley.
The Center for Children "provides evidence-based therapeutic, educational, foster care and transition services to children and families struggling with mental, emotional and behavioral disorders," according to the nonprofit organization's website.
Center administrators issued a statement, which read in part:
The safety and wellbeing of the children in our care is our number one priority. As reported by SDPD, five youth left the facility without permission this morning. As the youth left the property we immediately contacted San Diego Police Department per our safety protocols. We have worked closely today with the authorities to locate the youth for safe return.