Police do not yet have a motive for the shooting, but the investigation has focused on a feud between two Turkish families.
Details on the charges were not available, and the names of the three were not released, in line with Dutch privacy laws.
Police spokeswoman Gerda Preusting said investigators had seized a weapon and ammunition in a raid on the family's home in the town of Veghel, 60 miles south of Amsterdam.
The father and two siblings were to be held in separate jail cells until they appear before a judge Friday, said spokeswoman Desiree Leppens of the district attorney's office.
The 17-year-old turned himself in Tuesday shortly after four students and a teacher were wounded at his high school.
Police said the suspect had targeted a youth who had been romantically involved with the suspect's sister. His target, 19, was one of the two people critically wounded.
After the shootings, investigators broadened their probe to include the alleged shooter's 35-year-old father, who allegedly drove his son to school before the shooting and later took him to the police station, where the youth surrendered and handed in his gun.
Police did not say why the 15-year-old sister had been arrested.
On Wednesday, a brother of one victim told reporters that the two families had a long-running feud, and that his family had feared an attack for months.
Newspapers, citing witness accounts, reported Thursday that the suspect seemed driven by a desire to avenge his sister's honor. But the Dutch newspaper De Telegraaf quoted the suspect's mother as saying her son wasn't aggressive.
"He was tormented and pushed to breaking point," she said. "He wouldn't normally hurt a fly."