Or HaChaim on Genesis 8:2/אור החיים על בראשית ח׳:ב׳

1 ויסכדו מעינות תהום. The wells of the deep closed up. The Torah here hints that the waters beneath the earth had risen in proportion to the rain descending from the heavens. These two phenomena go hand in hand. Our verse alludes to this fact by mentioning the withdrawal of the waters beneath the earth as occurring simultaneously with the cessation of the rain from the heavens. We have pointed out previously that these two types of waters complement each other, enabling growth to occur (Taanit 28).