The seal was then blindfolded with a stocking mask, and released to search for the submarine.
Scientists have discovered that a seal uses its whiskers to detect the watery trail of a swimming fish.
They say it is the first time that an animal has been shown to hunt in this way.
The animal's highly sensitive whiskers are able to detect miniscule vibrations as fish swim by, allowing the seal to catch food in dark or murky waters.
"We found that a seal was able to follow a hydrodynamic trail using its whiskers," co-researcher Bjorn Mauck of the University of Bonn, Germany, told BBC News Online. "This is the first time that an animal has been shown to do this."
Mini submarine
The team simulated the water movements generated by a large fish using a propeller-driven miniature submarine.
They trained Henry - a male harbour seal - to locate the submarine in his pool of muddy seawater.
The seal was then blindfolded with a stocking mask, and released to search for the submarine.
The researchers found that Henry was able to locate the craft by the hydrodynamic trail left behind it, in 256 of 326 trials.
He could find and follow the submarine, even from a distance of about 40 metres (131 ft).
But when Henry's whiskers were covered with a stocking, he failed to spot the vibrations in the water.
Hydrodynamic information
The team repeated the experiments with another male harbour seal - Nick - in an outdoor pool filled with clear fresh water.
Again, the seal was able to locate the trail in 37 out of 45 trials (82.2%), while he never detected the trail when his whiskers were covered.
The question of how marine mammals track down their prey in dark or murky waters has long puzzled biologists.
Dolphins, porpoises and other toothed whales use echolocation, which is similar to the sonar used on ships.
The whales generate sound waves, which bounce or echo back to them when the waves hit an object such as a fish. They can use this information to catch food, avoid obstacles, and tell where they are.
The new study shows that for seals hunting in the dark, the movements generated as fish swim through the water are a vital information source.
Herring alert
Until now, the accepted view was that this faculty was only important to seals at short distances, when it was very close to its prey.
The researchers believe seals might be able to detect the water movements left by a swimming herring from more than 180 metres (196 yards) away.
Dr Mauck said the seal's highly sensitive whiskers acted like the lateral line of a fish.
This network of sensory receptors located along the head and sides of fishes detects water and pressure changes in the surrounding water.
The precise mechanism of how the seal detects water disturbances with its whiskers is not clear. But the German researchers think the whiskers of a swimming seal vibrate with characteristic frequencies. This might allow the seal to detect tiny modulations to the vibrations, when it crosses a hydrodynamic trail.