The three-judge panel in the federal appeals court upheld a lower court decision requiring the Navy to take safety precautions to reduce possible harm to whales and other marine mammals when it employs sonar for training exercises off the coast of California.
The court, which handed down its ruling late on Friday, gave the Navy 30 days to appeal the case to the Supreme Court.
Environmental groups that took the Bush administration to court over the matter welcomed the ruling as an important precedent.
"The court is saying that neither the President nor the US Navy is above the law," said Joel Reynolds, director of the Marine Mammal Protection Project at the Natural Resources Defense Council (NRDC).
"The court found that the Navy must be environmentally responsible when training with high intensity sonar, and that doing so won't interfere with military readiness," Reynolds said in a statement.
Environmental groups say the equipment is potentially harmful to marine mammals, citing cases in the Bahamas and Canary Islands where sonar has been linked to mass deaths of whales.
The waters off the coast of Southern California include five endangered species of whales, the NRDC said.
Last month Bush granted an exemption to the Navy over the use of sonar, arguing it was vital for military preparedness exercises which were in the "paramount interest of the United States."
Under the court decision, the Navy must maintain a 12 nautical mile no-sonar buffer zone along the California coast, shut down sonar when marine mammals are spotted within 2,200 yards (meters) and avoid whale habitats among other measures.