The Natural Resources Defense Council has filed suit against the Navy for using mid-range active sonar in Navy training exercises, and thus injuring, killing, and beaching several species of marine mammals and other marine wildlife, without going through the appropriate procedures of the Marine Mammals Protection Act and the Endangered Species Act.
The Navy has been stonewalling on this topic for years. One of the incidents that features prominently in their case took place in Haro Strait, right next to San Juan Island, in May 2003 when the USS Shoup steamed through the strait with its mid-range sonar blasting. Haro Strait is a significant habitat for several threatened and endangered species, and the Navy was apparently oblivious to the fact that there would be tons of witnesses to this particularly egregious exercise. There were several boatloads of eco-tourists in close proximity, as well as more people on the shore, who could hear the active sonar with their own ears and witness the marine life behavior. There was listening equipment in the strait that is used for studying marine mammals. There were lots of amateur camcorders and other recording equipment.
The NRDC's lawsuit specifically quotes from a research report by the Office of Naval Research supporting the correlation between mid-range active sonar and injury to marine mammals. I looked this morning, however, and was unable to find the report on the ONR web site. I'll keep looking, though; if it's available I'm sure it makes for fascinating reading, and would be particularly damning for the Navy.
10:22:37 AM 
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