According to St. Ephremn, Commentary on Genesis, when God separated the waters on the earth from the waters in the sky (Genesis 1:6), both bodies of water were sweet, but when God gathered the waters on the ground together and created the seas (Genesis 1:9), the waters on the earth remained salty and those in the sky remained sweet.

He also thinks that the flood waters were from the fresh waters above, that is, those above the sky.