Cybertron's surface is covered by at least a few seas, but these seas are not of water. The Rust Sea, for example, is a sea of, uh, rust. There are chambers deep inside Cybertron which also run with liquid, but they have been confirmed to be not water.
Note:Ratbat and other Transformers who are unfamiliar with water are likely confused; as several humans later managed to exist without environmental protection gear on Cybertron without drying up like old corn. Also, in the very first issue of the Marvel comic, Ironhide mentioned his "water gun", and Bumblebee also seemed familiar with it, commenting on how his levers "love a good swim".
Some Transformers, namely the Aquaspeeders and Stormtroopers, use high-pressure water-cannons as armaments. This is after they apparently re-discovered water, or something.