The killing ignited a diplomatic firestorm between Ottawa and New Delhi, with Canadian Prime Minister Justin Trudeau last September publicly linking Indian intelligence to Nijjar's death.
India dismissed the charges as "absurd" and responded furiously, briefly curbing visas for Canadians and forcing Ottawa to withdraw diplomats.
Canadian broadcaster CBC, citing documents submitted in a Western Canadian court, said the three arrested men are faced with first degree murder and conspiracy charges. They are accused of being shooters, drivers and spotters on the day Nijjar was killed.
CBC said police were also investigating possible links to three more murders, including of an 11-year-old boy in Edmonton. Police are reportedly set to hold a press conference later Friday.
Nijjar, who immigrated to Canada in 1997 and became a Canadian citizen in 2015, advocated for a separate Sikh state carved out of India.
He was wanted by Indian authorities for alleged terrorism and conspiracy to commit murder.
In June last year, he was shot dead by two masked assailants in the parking lot of a Sikh temple near the west coast city of Vancouver.