Objection 1. It would seem that it was not fitting that the gathering together of the waters should take place on the third day. For what was made on the first and second days is expressly said to have been "made" in the words, "God said: Be light made," and "Let there be a firmament made."But the third day is contradistinguished from the first and the second days. Therefore the work of the third day should have been described as a making not as a gathering together.
Objection 2. Further, the earth hitherto had been completely covered by the waters, wherefore it was described as "invisible" [66, 1, Objection 1]. There was then no place on the earth to which the waters could be gathered together.
Objection 3. Further, things which are not in continuous contact cannot occupy one place. But not all the waters are in continuous contact, and therefore all were not gathered together into one place.
Objection 4. Further, a gathering together is a mode of local movement. But the waters flow naturally, and take their course towards the sea. In their case, therefore, a Divine precept of this kind was unnecessary.
Objection 5. Further, the earth is given its name at its first creation by the words, "In the beginning God created heaven and earth." Therefore the imposition of its name on the third day seems to be recorded without necessity.
On the contrary, The authority of Scripture suffices.
I answer that, It is necessary to reply differently to this question according to the different interpretations given by Augustine and other holy writers. In all these works, according to Augustine (Gen. ad lit. i, 15; iv, 22,34; De Gen. Contr. Manich. i, 5, 7), there is no order of duration, but only of origin and nature. He says that the formless spiritual and formless corporeal natures were created first of all, and that the latter are at first indicated by the words "earth" and "water." Not that this formlessness preceded formation, in time, but only in origin; nor yet that one formation preceded another in duration, but merely in the order of nature. Agreeably, then, to this order, the formation of the highest or spiritual nature is recorded in the first place, where it is said that light was made on the first day. For as the spiritual nature is higher than the corporeal, so the higher bodies are nobler than the lower. Hence the formation of the higher bodies is indicated in the second place, by the words, "Let there be made a firmament," by which is to be understood the impression of celestial forms on formless matter, that preceded with priority not of time, but of origin only. But in the third place the impression of elemental forms on formless matter is recorded, also with a priority of origin only. Therefore the words, "Let the waters be gathered together, and the dry land appear," mean that corporeal matter was impressed with the substantial form of water, so as to have such movement, and with the substantial form of earth, so as to have such an appearance.
According, however, to other holy writers [66, 1] an order of duration in the works is to be understood, by which is meant that the formlessness of matter precedes its formation, and one form another, in order of time. Nevertheless, they do not hold that the formlessness of matter implies the total absence of form, since heaven, earth, and water already existed, since these three are named as already clearly perceptible to the senses; rather they understand by formlessness the want of due distinction and of perfect beauty, and in respect of these three Scripture mentions three kinds of formlessness. Heaven, the highest of them, was without form so long as "darkness" filled it, because it was the source of light. The formlessness of water, which holds the middle place, is called the "deep," because, as Augustine says (Contr. Faust. xxii, 11), this word signifies the mass of waters without order.
Thirdly, the formless state of the earth is touched upon when the earth is said to be "void" or "invisible," because it was covered by the waters. Thus, then, the formation of the highest body took place on the first day. And since time results from the movement of the heaven, and is the numerical measure of the movement of the highest body, from this formation, resulted the distinction of time, namely, that of night and day. On the second day the intermediate body, water, was formed, receiving from the firmament a sort of distinction and order (so that water be understood as including certain other things, as explained above (Question 68, Article 3). On the third day the earth, the lowest body, received its form by the withdrawal of the waters, and there resulted the distinction in the lowest body, namely, of land and sea. Hence Scripture, having clearly expresses the manner in which it received its form by the equally suitable words, "Let the dry land appear."
Reply to Objection 1. According to Augustine [Gen. ad lit. ii, 7,8; iii, 20], Scripture does not say of the work of the third day, that it was made, as it says of those that precede, in order to show that higher and spiritual forms, such as the angels and the heavenly bodies, are perfect and stable in being, whereas inferior forms are imperfect and mutable. Hence the impression of such forms is signified by the gathering of the waters, and the appearing of the land. For "water," to use Augustine's words, "glides and flows away, the earth abides" (Gen. ad lit. ii, 11). Others, again, hold that the work of the third day was perfected on that day only as regards movement from place to place, and that for this reason Scripture had no reason to speak of it as made.
Reply to Objection 2. This argument is easily solved, according to Augustine's opinion (De Gen. Contr. Manich. i), because we need not suppose that the earth was first covered by the waters, and that these were afterwards gathered together, but that they were produced in this very gathering together. But according to the other writers there are three solutions, which Augustine gives (Gen. ad lit. i, 12). The first supposes that the waters are heaped up to a greater height at the place where they were gathered together, for it has been proved in regard to the Red Sea, that the sea is higher than the land, as Basil remarks (Hom. iv in Hexaem.). The second explains the water that covered the earth as being rarefied or nebulous, which was afterwards condensed when the waters were gathered together. The third suggests the existence of hollows in the earth, to receive the confluence of waters. Of the above the first seems the most probable.
Reply to Objection 3. All the waters have the sea as their goal, into which they flow by channels hidden or apparent, and this may be the reason why they are said to be gathered together into one place. Or, "one place" is to be understood not simply, but as contrasted with the place of the dry land, so that the sense would be, "Let the waters be gathered together in one place," that is, apart from the dry land. That the waters occupied more places than one seems to be implied by the words that follow, "The gathering together of the waters He called Seas."
Reply to Objection 4. The Divine command gives bodies their natural movement and by these natural movements they are said to "fulfill His word." Or we may say that it was according to the nature of water completely to cover the earth, just as the air completely surrounds both water and earth; but as a necessary means towards an end, namely, that plants and animals might be on the earth, it was necessary for the waters to be withdrawn from a portion of the earth. Some philosophers attribute this uncovering of the earth's surface to the action of the sun lifting up the vapors and thus drying the land. Scripture, however, attributes it to the Divine power, not only in the Book of Genesis, but also Job 38:10 where in the person of the Lord it is said, "I set My bounds around the sea," and Jeremiah 5:22, where it is written: "Will you not then fear Me, saith the Lord, who have set the sand a bound for the sea?"
Reply to Objection 5. According to Augustine (De Gen. Contr. Manich. i), primary matter is meant by the word earth, where first mentioned, but in the present passage it is to be taken for the element itself. Again it may be said with Basil (Hom. iv in Hexaem.), that the earth is mentioned in the first passage in respect of its nature, but here in respect of its principal property, namely, dryness. Wherefore it is written: "He called the dry land, Earth." It may also be said with Rabbi Moses, that the expression, "He called," denotes throughout an equivocal use of the name imposed. Thus we find it said at first that "He called the light Day": for the reason that later on a period of twenty-four hours is also called day, where it is said that "there was evening and morning, one day." In like manner it is said that "the firmament," that is, the air, "He called heaven": for that which was first created was also called "heaven." And here, again, it is said that "the dry land," that is, the part from which the waters had withdrawn, "He called, Earth," as distinct from the sea; although the name earth is equally applied to that which is covered with waters or not. So by the expression "He called" we are to understand throughout that the nature or property He bestowed corresponded to the name He gave.
Source: Summa Theologica (New Advent)