Lind found that the government had presented some evidence to support both charges.
Manning showed no reaction to the rulings, sitting forward in his chair and appearing to listen intently, as he has throughout the trial.
More than two dozen of his supporters also sat quietly in the courtroom, some wearing T-shirts reading, simply, "truth."
"We're disappointed," Jeff Paterson, a board member of the Bradley Manning Support Network, said outside the courtroom. "However, we're very hopeful" that Manning eventually will be found innocent of the charges, he said.
The trial is moving toward closing arguments, possibly next week.
To convict Manning, prosecutors must prove the charges beyond a reasonable doubt; they had to meet a less stringent standard in convincing Lind that the charges should stand.
To convict him of aiding the enemy, the government must prove Manning gave WikiLeaks intelligence with "evil intent" and "actual knowledge" that what he leaked would be seen by al-Qaida members. Prosecutors produced evidence that al-Qaida leader Osama bin Laden obtained digital copies of some of the leaked documents WikiLeaks published. Lind said prosecutors also produced evidence that Manning knew from his training and other military documents, that "it must be presumed foreign adversaries will view" anything posted on the WikiLeaks website.
The government also charged Manning with espionage and theft.
Manning has said he leaked the material to provoke public discussion about what he considered wrongdoing by American troops and diplomats. The material included video of a 2007 U.S. Apache helicopter attack in Baghdad that killed 11 men, including a Reuters news photographer and his driver. A military investigation concluded the troops reasonably mistook the photography equipment for weapons.
Paterson and other critics said the judge's refusal to drop the charges is a blow to whistleblowers.
"The government is equating all leakers with traitors and they're not," Boston College Law School professor Mary-Rose Papandrea said in a written statement. "There are very important differences between those who send information to the enemy with the intent of aiding the enemy and those people who release information to the public with the intent of informing the public debate. It's time for our legal system to draw some clear distinctions between these two categories."
Amnesty International called the charge of aiding the enemy "ludicrous" and said it should be withdrawn.
Lind also heard oral arguments Thursday on defense motions to acquit Manning of five theft counts.
Manning is charged with 22 counts. He has pleaded guilty to reduced versions of nine espionage and computer fraud counts, essentially admitting violations of less-serious military laws, and to a military infraction prohibiting wrongful storage of classified information. He faces up to 20 years in prison for those offenses. Prosecutors accepted one of those pleas, involving a computer fraud charge, but are still trying to convict him of the original charges on the other counts.
Manning chose to be tried by a judge, rather than a jury.