The rather mystical world-view implied by the idea that "the waters are one" relates to Antonio's attraction to the idea of the Golden Carp, which Antonio feels is a pagan idea (as opposed to Catholicism). This religious stuggle - or crisis of faith - is a significant element of Antonio's search for identity.
Antonio hopes to find a "true" religious world-view to believe in and he feels that only one point of view can be true for him. As the story goes on, Antonio encounters the magic, mystical and pagan world-views relating to Ultima and to the Golden Carp and he feels the truth of these each rather deeply. He also has been raised to believe in the Catholic religion and feels that leaving the church would disappoint his mother.
So, the phrase about the waters being one is suggestive of the ideas surrounding the Golden Carp and relates strongly to Antonio's spiritual conflicts.