The two were recovered from the North Edisto River after the car was found near a rural boat landing, Orangeburg County Sheriff Larry Williams said.
County Coroner Samuetta Marshall identified them as 18-month-old Ja'van T. Duley and 2-year-old Devean C. Duley, both of Orangeburg. She would not speculate on a cause of death until autopsies are completed Tuesday.
The boys' mother, whose name was not immediately released, was being held Monday on a charge of leaving the scene of an accident, Williams said.
He said the Highway Patrol was notified about 6:15 a.m. Monday about an accident and a woman who needed help getting her children out of the car.
The children were still strapped in their child seats when divers found them and recovered their bodies about 45 minutes after being called to the scene.
"Early in the investigation, the state patrol felt there was not enough indicators to substantiate that there was an automobile accident," Williams said. "We are looking into all possibilities as to what happened."
The woman, who did not have a cell phone, had walked some distance down the country road by the boat landing and flagged down a passing motorist to call the Highway Patrol.
"She showed some emotion, but I can't say she was overly distraught," the sheriff said. "Through her statements, there are some things we think are not believable."
Williams said authorities were attempting to contact the children's father, who did not live with the family.
The sheriff said investigators are considering how a traffic accident could have happened at the boat ramp, about 20 yards upstream from a main road that crosses the slow-moving river. A mobile home, a house and mechanic's shop are a short distance away.
Local residents said they were suspicious.
Shakeyia Baxter said the main road was heavily traveled in the mornings and would have been especially busy on Monday — the first day of school. Baxter stopped by the boat ramp, which is littered with empty beer cases and discarded soda bottles, on her way home from work at a McDonald's to tuck silk flowers into a sign that warns of high levels of mercury in the fish.
"My heart goes out to them," said Baxter, a 30-year-old mother of two. "I would have been doing everything I could to get those kids out of that car seat."
Orangeburg is about 35 miles south of Columbia, the state capital.
The incident was reminiscent of the deaths of two other toddlers in South Carolina.
In 1994, in a case that made headlines worldwide, Susan Smith left her 3-year-old and 14-month-old sons strapped in their car seats as she rolled her car into a lake in Union County in the northwest part of the state.
She was convicted in their deaths and is serving a life prison term.
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