Marquez had no role in the attack, but prosecutors said the guns and bomb-making materials he bought that the couple planned to detonate linked him to the killings.
"While there currently is no evidence that Mr. Marquez participated in the Dec. 2 attack or had advance knowledge of it, his prior purchase of the firearms and ongoing failure to warn authorities about Farook's intent to commit mass murder had fatal consequences," U.S. Attorney Eileen Decker said.
Authorities previously said Marquez had legally purchased the high-powered guns.
The FBI investigated the rampage as an act of terrorism and said the Muslim couple was radicalized before they met online and communicated privately about “jihad and martyrdom” before they married.
President Barack Obama said he was briefed on the investigation Thursday and reiterated the federal government's commitment to find answers to all the unknowns in the case.
Marquez had deep ties with Farook that extended to a family connection. The two grew up next door to each other in Riverside and then became related through marriage.
Both men were witnesses at the wedding of Farook's brother, Raheel, to a Russian woman in 2011, according to Riverside County marriage records.
Last year, Marquez married the sister of Raheel Farook's wife. That made Marquez and Raheel Farook brothers-in-law and gave Marquez and Syed Rizwan Farook a sister-in-law in common.
A lengthy affidavit outlined evidence against Marquez, including statements he gave investigators over 11 days after he waived his rights to remain silent and be represented by a lawyer.
Four years ago, Marquez said, he and Farook planned to toss pipe bombs into the cafeteria at the community college they attended and then shoot people as they fled.
He said they also planned to throw pipe bombs on a busy section of freeway that has no exits, bringing traffic to a halt and then picking off motorists. Marquez would shoot from a nearby hillside, targeting police, as Farook fired at drivers from the road.
As part of the plan, Marquez bought two assault rifles — in November 2011 and February 2012. He said he agreed to buy them because "Farook looked Middle Eastern."
Authorities previously said Marquez had legally purchased the guns Farook and Malik used. But the charges allege that Marquez lied by signing paperwork that said the guns were for himself or a family member.
Those plans may never have come to light if not for the Dec. 2 terrorist attack.
Marquez faces an additional immigration charge for a sham marriage.