Also in the point of water, when ever someone has a Dive ino Heart, they fall through loads of water before landing on the stations.
NOTE- LONG PARAGRAPH AND SPOILERS BELOW
If Sora is "Sky," Riku "land" and Kairi "sea" then it make sense that these three act is the bases for all worlds.
Every world has three things, a Sky, Land, and Sea. Kairi has established that "there are many worlds, but they share the same Sky" This, as was said by twilight_dragon, shows that the Sky connects all worlds as a sort of interdemsional pathway. This can also be interpreted as being a reference to Sora, and how all worlds share the same "Sora," for Sora has been chosen to protect the worlds, open the Door to Light, etc.
Land is a common feature in all worlds, even in Atlantica which has underwater land features. Land forms the physical core of the world, allowing the people to live about their normal lives. Riku, being the more hard, realistic of the group is symbolic of this land, rooted in his feelings. He however, in the beginning of KH, wants to escape from his land prison, and go out into the ocean. This can be symbolic of his caring for Kairi, "Sea" or his wish to be like Sora, "Sky" anything but the land he is stuck on.
Sea on the other hand, is what this discussion is about. As it has been said, Water (or Sea) plays a part in boundaries, symbolically the boundary of Destiny Islands, the living Paradise, as well as being the boundary of the Realm of Darkness (the beach where Sora and Riku end up after KH2. The resemblance of those two Islands leads one to believe the Realm of Darkness is a sort of Anti-Destiny Islands, perhaps being the headquarters of Darkness, just as Destiny Islands is sort of the headquarters of Light) Water also plays a role (as said) to transporting messages, Kairi's message to Sora, and the King's message to Sora (Interestingly, Kairi's message from Destiny Islands reached Sora at DI's dark counterpart, the realm of Darkness. If this is somehow connected, then the King's message must have been sent from the Realm of Darkness as well (this beach). This leads questions on to why the King was BACk in the realm of Darkness, etc. etc.
Another thing to note on the elements, Sea, Sky, and Land, is that each element is represented in the Dive into Heart. Sora/Roxas first falls through dark black water (or blue, but it doesn't really matter), before landing on solid ground (although glass, could still represent land). The solid ground then breaks apart into doves which fly through the air (Sky) into the distance. Similar how this is in Dive into Heart, Sky, Sea, and Land might also be the main components of a Heart of a World.
The Sea, Sky, and Land also correspond to the Soul, Heart, and Body of a being.
Body being hard, and strong, physical, is Land
Heart being powerful, and the main component, Sky
and the Soul being fluid, Sea.
So in conclusion, the Water is an important part of the three, but not neccesarily a mystery within itself. More like a part of the trio that make up the worlds, just like the Soul, Body, and Heart make up a person.