San Bernardino County sheriff's spokeswoman Cindy Bachman says a dive team is preparing to re-enter the aqueduct Friday morning to search for the missing child who is about 2 years old.
Authorities are still investigating why the Hesperia family's vehicle crashed into the aqueduct.
They suspended the search late Thursday night after clearing the most probable areas of the aqueduct.
The MAIT investigation is ongoing, and the cause of the collision remains under investigation.
Around 7:30 p.m., the San Bernardino Fire Department tweeted the vehicle had been found submerged and the dive team was "making entry for rescue".
Paramedics pronounced the boy's mother, 31-year-old Christina Eileen Estrada, dead at the scene. A 2-year-old was pulled from the water and also rushed to the hospital as first responders administered CPR, according to San Bernardino County Fire Department spokesman Jeremy Kern.
The Volkswagen Beetle struck a guardrail before plunging into the aqueduct, which crosses under the main street in the Mojave Desert city 65 miles northeast of Los Angeles.
Authorities believe there may have been a fourth victim in the auto and were continuing their search for the potential missing child in the water Friday morning.
Elijah was doing well at Loma Linda University Medical Center, said his uncle, Steven Abbott.