The noun מים (water) includes all waters in the world, even water in vessels, unless the noun מים comes versus ארץ (land); then it is only talking about water that is on land.

ימים (seas) and נחלים (rivers) come as proper nouns.

And in its precise meaning, the word ימים are the great spaces that God created on the third day of Creation (and according to Rabbi Yehuda, it was only the Mediterranean Sea) and נחלים (rivers) are also deep places that attract and flow.

And in its broad meaning, the noun נחלים also includes bodies of water that attract but do not flow. And the noun ימים also includes bodies of water that flow but do not attract.