Genesis 1:9

"Let the waters gather:" They were spread over the face of the whole earth and he gathered them in the Okiyanus (the Ocean), which is the largest of all the seas.

And the Lord said, Let the lower waters which remain under the heavens be gathered together into one place, and the earth be dried, that the land may be visible. And it was so.

"and He said" - according to my opinion, this passage is attached to one that precedes it, for the firmament was not made until the earth became dry, and as proof: "On the day which Hashem, G-d, make earth and heaven" - behold, on one day they were made. Now revealing a hidden thing and gathering that which is scattered is not creation [per se] (beri'ah). The meaning is then, "G-d had already said, let the waters be gathered", and there are hundreds of similar usages in the Torah. In parashat Bereshit alone I will give you two witnesses. The first: "And He placed there [in the Garden] the man whom He had formed", while afterwards, "And Hashem, G-d, caused to grow [from the ground every tree...]" - but before [placing] man had He caused it to grow. The second witness: He commanded man not to eat from the tree of knowledge, and afterwards it is written, "And Hashem, G-d, formed from the ground..." - rather, its explanation is, "He had already formed". According to this explanation, the words, "and G-d saw that it was good" [verse 10] refers to the second day, and "Let the earth bring forth grass" is the beginning of the third day.

The explanation of "let them be gathered" is: "let them join together", and likewise: "[and all the nations] shall be gathered to her [Jerusalem] Jeremiah 3:17

LET THE WATERS UNDER THE HEAVEN BE GATHERED TOGETHER. The deep, which is water and sand, was like turbid waters, and He decreed concerning the waters that they be gathered together in one place, surrounded on all sides, and He further decreed concerning the sands that they rise up until they be seen above the waters and that they become dry, so that there be a stretch of dry land suitable for settlement thereon. And so it is written: To Him that spread forth the earth above the waters. Or perhaps G-d’s decree was that the earth be spherical, partly visible and mostly submerged in the waters, as the Greeks imagine in their proofs, apparent or real. Thus there were two decrees, that is, two matters done by the Will of G-d that are contrary to their natural inclination. For in view of the heaviness of earth [which would cause it to sink] and the lightness of the waters [which would cause them to rise], it would have been natural that the pillar of the earth be in the center and that the waters should cover it, thus surrounding it from all sides. Therefore, He said, Let the waters under the heaven be gathered together, that is to a lower place, and then He said, And let the dry land appear. He gave them names as they assumed these forms, for at the beginning their collective name was “the deep.”

ויאמר אלוקים יקוו המים... אל מקום אחד, we already explained on verse 2 that the means employed to achieve this was the ruach, the wind. This is the reason why we were told already in verse 2 that “G’d’s wind (spirit) hovered over the expanse of the deep, something which occurred by making the rakia. (between heaven and earth) Now the water above the earth were concentrated in one region, location.

ותראה היבשה, a reference to the earth which had already been created at the same time as the heaven, before the light had been created, as I explained on verse 2.. It does not matter whether this occurred spread over a short period or over a long period.

יקוו המים; this does not mean that the waters should dry up, as many people interpreted it. These people said that the process would be achieved by a substantial part of the oceans freezing and turning to ice such as the polar regions, and that this would be caused by forces in the celestial regions. אל מקום אחד. The waters should not deviate from this location. As a result they became much higher than the surrounding land mass without crashing down on earth as our senses would have us think would be the case. This is why David tells us in Psalms 104,9: גבול שמת בל יעברון, “You have set them limits which they must not cross.” The meaning is that the waters must not flood the earth.”

ויאמר אלוקים יקוו המים מתחת השמים, the words מתחת השמים refer to the waters beneath the rakia, known as shamayim.