The aquashuttle was the shuttle-type assigned to Constitution-class vessels; typically armed with phasers. This vehicle is capable of travelling through a planets atmosphere; is transporting across water like a boat, and is additionally submersable.
In 2269, Captain Kirk, Commander Spock, Dr. McCoy and Lt. Clayton transported down to the planet Argo to study its formation aboard an aquashuttle assigned to the USS Enterprise.
The shuttle was attacked by a sur-snake, and eventually destroyed. During the final moments, McCoy and Clayton were thrown clear. Kirk and Spock, however, were not as fortunate, and were taken down in the shuttle, by the sur-snake.
Five days later Commander Scott, whilst travelling aboard a scouter gig, discovered Kirk and Spock near the remains of the destroyed aquashuttle. (TAS: "The Ambergris Element")