From the NOVA site I linked to above:

In 1987, an expedition called Operation Deep Scan used a flotilla of 20 sonar-equipped boats to sweep the loch with a curtain of sound; the operation yielded three underwater targets that could not be explained. In the early 1990s, the BBC's Nicholas Witchell helped organize Project Urquhart, the first extensive study of the loch's biology and geology. Although they weren't looking for monsters, the expedition's sonar operators detected a large, moving underwater target and followed it for several minutes before losing it. And during the 1997 expedition featured in NOVA's Loch Ness film, Rines and his longtime colleague Charles Wyckoff detected yet another puzzling underwater target. According to the expedition's sonar expert, marine biologist Arne Carr, it was a moving target, appeared to be biological in nature, and was about 15 feet long—the size of a small whale.