We say that rain on Shabbos is a sign of Hashem's blessing. Salt is also a sign of Hashem's blessing. Originally in Genesis water covered the earth. So that we the Jewish people would prepare a holy place for Hashem to reside among us. Water is a cleansing agent.
Water is a purifier.
The water encompassing the earth as a covering purifies and hides our destructive, chaotic past. In other words, water covered our errors. Water stood between G-d as judge and our failings. G-d separated these waters. Certain water was gathered unto the Heavens with G-d and certain water remained covering the earth symbolically as a covering for mankind's failings.