I think that the waters of Aquaria were already there, but that the creator has created a lot of new life, but certainly not everything.
Reason why I'm thinking this is because the Sunken City looks a big... destroyed, meaning that he doesn't have the skill to make anything right, as seen by futile attempts to make mother. And thus the waters were already there.
And of course as seen in the intro, he fell into the water, so there already was water, to strengthen that, how else would he have powers over the sea and not the land? Certainly the rock landing in the ocean had something to do with it. Or otherwise the origin of the rock might be the reason, but we don't know a single thing about that.