The Charleston (W.Va.) Daily Mail reported that all three face charges of felony possession of marijuana with the intent to deliver.
The report added that the Monongalia County sheriff's department spotted the three acting suspiciously when they left an apartment complex Tuesday night. The three were later pulled over for speeding.
After smelling a strong odor of marijuana, deputies searched their vehicle and found individually wrapped bags of marijuana.
Stewart told the newspaper the players will retain their scholarships through the end of the school year, pending the legal process.
It is the first major disciplinary action taken by Stewart since he was hired in January to succeed Rich Rodriguez, who left West Virginia to coach at Michigan.