A federal judge in California is scheduled to release a decision this week that will outline what the Navy must do to protect whales and other marine mammals from the loud blasts of its sonar equipment.

U.S. District Judge Florence-Marie Cooper’s ruling in the closely watched case, expected by week’s end, will not only affect Navy training exercises scheduled for the waters off Southern California over the next year but could also clarify how closely the military must follow environmental laws.

With marine scientists increasingly convinced that sonar can frighten, confuse, and sometimes injure or even kill sea creatures — especially the acoustically sensitive whales — and with America at war, the issue has become contentious and the stakes high.

“This case is really about whether the Navy has to follow the law,” a lawyer who has argued the case for the Natural Resources Defense Council and has taken the Navy to court on several other sonar-related issues, Joel Reynolds, said. “Is the military bound by environmental laws, or does national security trump them?”

Mr. Reynolds said the council and other environmental groups, later joined by the California Coastal Commission, support the Navy’s need to train sonar operators. The problem, he said, is that the Navy is unwilling to make the operational changes necessary to avoid harming whales during such training.

Vice Admiral Samuel Locklear, commander of the U.S. 3rd Fleet in San Diego, said that the Navy already has 29 procedures in place to avoid harming marine mammals, and that what the council and other groups are seeking would cripple sonar training.

“We have developed a range off the coast of California where our men and women can train in a realistic manner,” he said. But if the court follows the advice of the plaintiffs, he said, “we would basically have to close down the majority of the Southern California range. That means we would not be able to practice the art of antisubmarine warfare in a fully integrated way. … Our national security is at stake here.”

The waters off Southern California are some of the most fertile in the world — home to many varieties of fish and 35 species of marine mammals, including at least six types of endangered whales. They are also a favorite sonar training and testing area for the Navy, which has major bases nearby and underwater ranges it considers perfect for teaching young sailors how to detect submarines.

The conflict that Judge Cooper will try to resolve involves balancing both interests.

Midfrequency active sonar, which sends out blasts of sound as a way to locate objects underwater, has been used by navies worldwide since the end of World War II.

In the mid-1990s, marine researchers began to connect sonar with mass strandings of whales, particularly the deep-diving beaked whale. A 2000 stranding in the Bahamas during a U.S. Navy sonar exercise provided the first conclusive evidence that the sounds were driving some whales ashore and to their deaths.

Sonar-related strandings have been confirmed off the Canary Islands and Spain since then, and other incidents have been reported off Hawaii and Washington state. Scientists can confidently establish a sonar-caused stranding only when the animal is discovered soon after death, and those situations are rare.

The California standoff began in late 2006, when the Navy announced it would conduct 14 training operations off Southern California between early 2007 and early 2009.

The exercises would involve extensive use of midfrequency active sonar and typically would last two weeks or more. Under the Navy plan, the sonar would be used throughout thousands of square miles of ocean and would be permitted near Channel Islands National Park off Santa Barbara.