Former Canadian Armed Forces reservist Patrik Mathews, 27, and Brian Lemley, 33, of Elkton, Md., entered their pleas during separate arraignments on charges including transporting a firearm and ammunition with the intent to commit a felony.
William Bilbrough, a 19-year-old pizza delivery driver, pleaded not guilty to charges including conspiracy to "transport and harbor certain aliens."
Federal authorities believe the three men are members of a white supremacist group called “The Base.”
In a court filing, Justice Department prosecutors said Lemley and Mathews discussed "the planning of violence" at last month’s gun rights rally in Richmond, Va.
A closed-circuit television camera and microphone installed by investigators in a Delaware home captured Mathews talking about instigated trouble at the rally with the hopes that it would spiral into a “full-blown civil war,” according to prosecutors.
Bilbrough, the only defendant in the case who isn't facing firearms-related charges, allegedly participated in early discussions with Lemley and Matthews about traveling to Richmond. But prosecutors say he has since tried distance himself from the group.
The trio was arrested last month as part of a broad investigation into The Base. A grand jury in Maryland handed up the 12-count indictment on Jan. 27, nearly two weeks after their arrest.
Mathews and Lemley also were indicted last month in Delaware on separate but related charges.
FBI agents arrested Mathews, Lemley, and Bilbrough as part of a broader investigation of The Base. Authorities in Georgia and Wisconsin also arrested four other men linked to the group.
Fox News’ Louis Casiano and The Associated Press contributed to this report.