When I wanted to create a devastated area of my campaign world, I developed a historic event in which an insane high priest realized his army was losing the war. He tried to perform a ritual in which the whole world would be destroyed ("If I can't have it, no one shall"). The Good Cleric leading the other army realized what was happening, and cast a counter ritual, sacrificing her own life, to contain the destruction to one area. Thus came into being Umade's Barrens, and Saint Ilyria was born.
Perhaps some sea-dwelling race had an ultimate enemy who decided to rid the world of them. His method of doing so might be to cast a spell, or use an artifact, that would destroy the ocean. Notice that I don't care exactly how it happened. "A ritual" or "an artifact" is enough for me. If my PCs ever try to delve into the question more deeply, then they'll discover that such magic is no longer achievable; or that the only way to learn the ritual is to visit hell itself, or somesuch...