The Lake County sheriff's Marine Unit and Patrol Division responded to the crash at about 5:15 p.m. Tuesday. The collision occurred on Lake Marie, which is part of the Chain O'Lakes.
Sarina Vootkur, 16, from Lake Forest, and Elle Kim, 13, from Long Grove, Illinois, were killed in the crash.
Vootkur was driving the WaveRunner near the channel to Grass Lake when a boat operated by a 55-year-old Antioch man approached the same area, the sheriff's office said.
Witnesses told police that the WaveRunner was traveling at high speed directly at the boat, leading to a crash.
The girls on the WaveRunner, who were wearing life vests, were knocked unconscious and thrown into the water, investigators said.
The occupants of the boat immediately pulled the girls from the water, rendered aid and called 911. Both girls were taken to Advocate Condell Medical Center in Libertyville, where they later died.
The medical examiner said both girls died from blunt force injuries from the crash.
It is unknown if Vootkur had a boating safety certificate, which is required in Illinois for anyone born after June 1998. The training involves an eight-hour course and is certified by the Department of Natural resources.
Investigators said there was no sign that either the driver of the boat or the WaveRunner were impaired.
No other injuries were reported.
The crash remains under investigation by the Lake County Sheriff's Office Marine Unit and Illinois Conservation Police.