Elsa and Anna found the destroyed ship while they were on their adventure. It was in the Black Sea and not the North Sea, as they were told. It's explained in the movie that their parents were trying to find Ahtohallan, to find the truth about Elsa's powers.
Also, the spirits of the nature were angry because of what King Runeard did. Later in the movie, we learn that going to Ahtohallan was actually the answer to all problems.
So, why did the Water Spirit try to prevent that? Rey Agnarr and Reina Iduna finding Ahtohallan was actually what the Water Spirit and everyone needed to calm down, because Agnarr would probably destroy the dam.