The aquashuttle was the shuttle-type assigned to Constitution-class vessels; typically armed with phasers.
In 2269, Captain Kirk, Commander Spock, Dr. McCoy and Lt. Clayton transported down to the Argo to study its formation aboard an aquashuttle assigned to the USS Enterprise.
The shuttle was attacked by a sea-monster, native to Argo, which possessed a similar skeletal structure as a Denebian whale. The shuttle is destroyed and McCoy and Clayton are thrown clear, Kirk and Spock were not as fortunate, and were taken down in the shuttle, by the sea-monster.
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")