Continuing to keep him on a strict "suicide risk," even after a brig medical official said such status was no longer necessary, was "excessive in relation to legitimate government interests," Lind said in her ruling.
Manning was kept alone in a windowless 6-foot-by-8-foot cell 23 hours a day, sometimes with no clothing, and forced while on suicide watch to sleep in only a "suicide smock" that is tear-resistant.
But "dismissal of charges is not appropriate," Lind ruled, saying such an action would be fitting only in the case of "outrageous" military misconduct.
Manning's defense team had asked for the charges to be dismissed or for a 10-for-1 credit for time served for the bulk of his time in Quantico. That could have shaved about seven years from any eventual prison term, The New York Times said.
Manning faces 22 charges, including violating the 1917 Espionage Act and "aiding the enemy," a capital offense. Prosecutors have said they won't seek the death penalty, but if convicted Manning would face life imprisonment.
His military trial is to begin March 6.
Manning, 25, was an Army intelligence analyst who had served in Iraq when he was arrested May 26, 2010, and charged with disclosing more than 260,000 diplomatic cables, more than 90,000 intelligence reports on the war in Afghanistan and a video of a military helicopter attack in Baghdad -- most of it classified.
His arrest came after computer hacker Adrian Lamo told the Defense Department Manning had confided to him in online chats he had downloaded the material and passed most of it to WikiLeaks, a website dedicated to making secret information public.
WikiLeaks and cooperating media outlets published the documents between April and November 2010.
After an outcry over Manning's treatment at Quantico, he was moved to an Army prison at Fort Leavenworth, Kan., where his lawyer said his treatment was better.