In general, a tornado occurring over water. Specifically, it normally refers to a small, relatively weak rotating column of air over water beneath a Cb or towering cumulus cloud. Waterspouts are most common over tropical or subtropical waters.
The exact definition of waterspout is debatable. In most cases the term is reserved for small vortices over water that are not associated with storm-scale rotation (i.e., they are the water-based equivalent of landspouts). But there is sufficient justification for calling virtually any rotating column of air a waterspout if it is in contact with a water surface.