A grand jury returned the 17-count indictment alleging Rachelle Lynette Carlock, 31, Ella Louise Sanders, 56, and Eric Reginald Robinson, 43, planted bombs at the courthouse May 4 and at a San Diego FedEx building April 25.
Neither early-morning bombing caused any injuries.
The indictment portrays Carlock and Sanders as planning the bombings, with Robinson in a supporting role, The San Diego Union-Tribune reported.
U.S. Attorney Karen Hewitt said the most serious charges were conspiracy to use a weapon of mass destruction and using a weapon of mass destruction. Each carries a life sentence upon conviction.
The indictment followed a massive FBI investigation that started after the courthouse was bombed, the Union-Tribune said.
Officials would not say how the defendants know each other. They also would not discuss motive.
Hewitt said prosecutors leveled the weapon-of-mass-destruction charges because the pipe bombs had the potential to kill numerous people and significantly damage structures.
The charges will be heard by San Diego federal Judge Margaret McKeon.