The 19-year-old Bongiovi, a student a Hamilton College in Clinton, NY, is one of the rocker's four children with wife Dorothea Hurley.
Officers and a volunteer ambulance squad were called to the dorm at about 1:51 am on Wednesday to assist a woman who had possibly overdosed on heroin and was not responsive, according to Town of Kirkland Police Department.
They also arrested a student, Ian S Grant, 21, who, like Bongiovi, is from Red Bank, NJ. A later search of the dorm also turned up additional heroin, marijuana and drug paraphernalia.
Bongiovi was also arrested and charged with possession of a controlled substance and possession of marijuana. She has been released and ordered to return to court.
All of the charges are misdemeanors.
Meanwhile, Hamilton College released a statement saying they were working closely with the authorities.
"In addition to violating state law, the actions alleged to have been committed by the students violate Hamilton College policy," they said.
"The college is cooperating with the police investigation. Our first concern is always for the safety of our students. Out of respect for the privacy of our students and in accordance with federal regulations we do not discuss individual health or disciplinary matters."
The news will come as a huge blow to 50-year-old Bovi, who has a family man image and has been married to his wife Dorothea for 23 years now.