Or HaChaim on Genesis 1:9/אור החיים על בראשית א׳:ט׳

1And God said, "let gather:" It needs to be known whether these waters are the waters of the depths and [so] when He said, "let the waters be gathered to one place," behold no other waters remained - and this is the opposite of what the verse states (Exodus 20:4), "and in the waters below the earth;" and if [these] waters were others besides the [ones of] the depths, it needs to be known how these waters were different from the waters of the depths, that the verse should refer to them alone. Also, [this would be difficult to say, since] we did not see that the statement specifies to say, "let the 'x' waters gather," but rather just "let the waters gather;" all the waters of the world are [thereby] implied. Also [it needs to be known] why the appearance of the earth is dependent on the gathering of the waters. And also we need to be precise [and understand the use of] the word, appear, since it should have said and 'the dry land be' [substituting 'be' for 'appear'].

2And regarding what I explained on the verse, "In the beginning," that all was created with one statement - except that it was mixed up until God set up each thing on its day; and according to that, from the words of God in this [section] we know that the dry land extended in the water over the expanse of the earth and there was water above and below it; and the firmament divided the waters above the dry land and it lifted half of them with its wings, as it is stated, "let the firmament be within" - and [the] unqualified [use of] within implies [in] the middle - and the remaining half covered the dry land. And it is to those waters that God said, "let the waters gather to one place;" which is the waters of the oceans. And the dry land appeared from the place that it was at the time of its creation - as it acquired its place [to be] there, except it was covered and He [now] decreed about it, that it should appear.

3And maybe the word appear could include that it wasn't visible in the color of the dry lands and its color was like that of the water and there was no [clear] distinction between its border and the border of the sea. And also within the understanding of 'appear' (teraeh) is that it was [now] fitting (reouiah) to what the dry lands need to be fit for, for the needs of the world. ...

4And it also wanted [to teach] by stating, "and appear," that all the time that the waters are below and above the earth, the natural state of the earth is not preserved, since the water will change its [state]. And go and learn from what Maimonides wrote at the beginning of the Laws of Character Traits (Laws of the Foundations of the Torah 4:5) that water transforms the core element of dirt to water; for this [reason], He said, "let the waters gather, etc." and with this "and the dry land appear;" and the explanation [of this] is that it will stay in its [state] to put in motion the reason for its creation. And really its creation already [happened] on the first day in the first statement as explained above. We also end up saying [according to this] that not all of the waters of the world were gathered into the oceans and there are [waters in the] depths below the earth.

5And it is possible that there is no gap between the waters that were gathered and the [waters of the] depths - and [it is] about that portion that has no earth [covering it], that they, of blessed memory, said (Chagigah 12a) that God said to the land, "Enough" that it should not extend from one end [of the world] to the other end - and the waters remained connected to the lower waters.

6After I wrote all that is written [above], a midrash from Pirkei Rebbe Eliezer 5 came to my hands and this is what it says, "On the third day, the earth was flat like a valley and the waters covered over the face of the whole earth and when the words, "let the waters gather, etc." went out from the mouth of the Holy One, blessed be He, the mountains and hills separated over the face of the whole earth and the innards of the earth arose and the waters rolled [back] and gathered, etc." Behold [from here, we see that] when the Holy One, blessed be He said, "let the waters gather," the land was already in existence and these are [in agreement with] our words. And [this is so] even if, according to the words of this [midrash], it appears that it explains [the phrase] "and the earth appear (teraeh)," [that its] explanation is that the dry land will be sand [as a] border for the sea, [so that] when the waters fear (yireh) the dry land, they acquire their [permanent] place - by way of its stating (Jeremiah 5, 22), "that I have placed the sand as a border for the sea," and made the fear of the dry land upon the sea - and [so] the explanation of teraeh (appear) is from the word yirah (fear), and that is what it states, "Do you not fear me?, etc., that I have placed the sand as a border for the sea;" and this is different than our explanation, [since] this is the way of derash (homily) and our way is the way of peshat (straightforward understanding) and the Scripture intends [it] all.

7And Nachmanides, of blessed memory, explained it's stating "and the dry land appear;" that the dirt was mixed with water and God decreed that they should separate one from the other, [so] that the dirt will harden and become dry land. So far [his explanation]. And [the] explanation of [Nachmanides], of blessed memory, needs a guarantor; also the simple meaning of the verse doesn't say this. Also, according to [the] words of [Nachmanides], of blessed memory, there was no need for the waters to gather to one place, but rather that He should say to the dry land that it should appear according to the arrangement mentioned in the words of [Nachmainides] - that the dirt should separate from the water and float up, and that the waters should stay in their place. And it is also implied from the verse that all of the waters that were under the firmament which were adjacent to the earth were gathered to one place; and that is not what is implied according to the words of the master; and also the word, 'appear,' is not exact according to [the] approach of [Nachmanides], of blessed memory. And the correct [understanding] in my eyes is as I have explained: that the land was stretched out within the waters and [there was] water above and water below it; and the Ordainer ordained that the water above the land have the firmament be placed within it and carry up the higher waters on its wings; and the part remaining under the firmament would not remain under all of the firmament equally, but rather, gathered to one place, and this is what it says, "and the waters under the heavens gather to one place" and through this, "and the dry land appear" [is understood] according to its simple meaning.

8And it appears that it can be said that the aspect of all the waters upon the earth - whether the upper one that are above the firmament [or whether] the ones that were gathered to one place - they are in the aspect of 'male waters.' And so, you will find that the germination of seeds is from the waters of the ocean, which are the gathered waters, as they, of blessed memory, said (Taanit 9a) that the rains come form the water of the oceans; and after God brings rain from them, corresponding [waters] come up from the depths, and that is like they, of blessed memory, have said (Taanit 25b), no drop comes down from above for which (two or three) corresponding drops do not come up from below. And the seeds do not grow from the rain waters and not from the waters of the depths [individually], since a male by itself or a female by itself will not give birth. And behold for you their words, of blessed memory, that they said (Pirkei Derabi Eliezer 25) that there are two waters, one male and one female and this is what they wrote [on the verse (Genesis 7:19)], "'and the waters grew very strong;' when the male waters joined with the female waters, they grew exceedingly."