Sheriff Roger Massey would not say how the car went down a boat ramp into Clinton Lake, killing the 6-year-old, 3-year-old and toddler inside.
Massey said authorities know what the motive was, but he would not provide details other than to say it did not involve life-insurance money.
Maurice Lagrone Jr., 28, and Amanda Hamm, 27, were each charged with three counts of first-degree murder for each death, Massey said.
They were arrested separately Tuesday and were being held on $5 million bail each, reports CBS News Correspondent Drew Levinson.
Deputies arrived at the lake in central Illinois on Sept. 2 within five minutes of receiving a 911 call from Hamm saying her children were in the water. The two suspects were on the lakeshore when rescuers arrived and Hamm was crying hysterically, according to one eyewitness.
Neither the couple nor investigators have ever offered a public explanation for why the couple was at the lake. Authorities have said the suspects were not launching or removing a boat, and it was not clear if they were in the car when it went in the water. The couple never spoke to reporters or returned messages for comment.
The sheriff said the car went in front first and the rear end was in 4½ feet of water when rescuers arrived.
Immediately after the deaths, Massey said they were being investigated as an accident. Within a day, he started calling them "the incident."
Lagrone initially was charged with driving under the influence. That charge was dropped last month, and Massey said Wednesday that investigators do not believe drugs or alcohol were a factor.
Asked how authorities decided the deaths were not an accident, Massey said investigators several times sent the car back into the water to see how it would sink.
"Our purpose is to disprove an accident," Massey said.
The siblings were Christopher Hamm, 6, Austin Brown, 3, and Kyleigh Hamm, 23 months. Lagrone was not the father of any of the children.
The case drew parallels to the 1994 case of Susan Smith, who was convicted of drowning her children in a South Carolina lake. Smith at first alleged that a man carjacked her and took her two young sons. She later admitted rolling her car into a lake with the children strapped into car seats.
Massey said he did not believe either Hamm or Lagrone had an attorney yet. They are scheduled to make their first court appearance Thursday morning.
Clinton, a town of 7,500, is about 140 miles southwest of Chicago.