The presence of fins in their back, the fish-like head and the pearls are possibly the reason for its Water type.
Its secondary type may also originate from the weightlessness one experiences in water, such as the fact that astronauts use water to train for space expeditions.
Source: Bulbapedia/ Palkia
Just saying, I was already thinking of the second reason before I went on Bulbapedia. They just happened to think of it too.