>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.