"There's been no sign of the car."
The car was quickly submerged and washed downstream by the Hawkesbury's strong current.
The incident triggered a massive search of the area, including police divers, boat, PolAir helicopters, paramedics and State Emergency Crews who scoured the banks and water.
Police divers found the four-year-old boy's body just before 3pm, a short distance downstream from the boat ramp.
The vehicle and the boat remain in the water.
The fast current and murky water hindered the efforts of emergency services, police said.
"It is believed the vehicle has been pushed downstream by a strong current," police said in a statement.
A report will be prepared for the Coroner.