There is a sense in which water is used as a symbol with plenty of different meanings in this excellent book. Not only does the water relate to the water in which the golden carp swims, but it also relates to Catholicism. Water is given extra importance, however, by the way in which it also is linked to the dreams and visions that Antonio experiences throughout the novel. Consider, for example the following description of these visions and how water is used as a metaphor to describe them in Catorce (chapter fourteen):
Strange scenes swirled in my ocean of pesadilla, and each one seemed to drown me with its awful power.
Water then is both linked to the two rival religious beliefs and philosophies that are presented in the novel as it is to the magical power that Antonio inherits and his ability to experience visions and see things that are beyond him and distant to him.
You can find the quote where Ultima helps Tony find a way to resolve his conflict about his mother's (Los Luna) and father's (Marez)way of life.
Ultima uses the surnames of Tony's parents (Marez & Luna) to describe how the water cycle on earth works. Her words show that the waters of the moon and the waters of the ocean are related and you can't have one without the other.
Interestingly, the author's mother's last name was Mares (a variant of Marez) and she hailed from a place named Puerto de Los Luna.