Oblivious to what is going on below, the sea otter rolls once more in the kelp, cracks open a sea urchin, and slurps up the jellied innards. From beneath, human divers, using non-bubbling closed-circuit scuba gear, float in wait. They hold a large trap. At the right moment, they spring. Meal interrupted, engulfed safely in a net, this otter has become the latest study recruit.

“We come up from underneath, like a killer whale or a great white,” said Jim Bodkin, a marine biologist with the U.S. Geological Survey. “When they’re disturbed, their response is to dive down into the water. We then dra...