Objection 1. It would seem that the firmament does not divide waters from waters. For bodies that are of one and the same species have naturally one and the same place. But the Philosopher says (Topic. i, 6): "All water is the same species." Water therefore cannot be distinct from water by place.
Objection 2. Further, should it be said that the waters above the firmament differ in species from those under the firmament, it may be argued, on the contrary, that things distinct in species need nothing else to distinguish them. If then, these waters differ in species, it is not the firmament that distinguishes them.
Objection 3. Further, it would appear that what distinguishes waters from waters must be something which is in contact with them on either side, as a wall standing in the midst of a river. But it is evident that the waters below do not reach up to the firmament. Therefore the firmament does not divide the waters from the waters.
On the contrary, It is written (Genesis 1:6): "Let there be a firmament made amidst the waters; and let it divide the waters from the waters."
I answer that, The text of Genesis, considered superficially, might lead to the adoption of a theory similar to that held by certain philosophers of antiquity, who taught that water was a body infinite in dimension, and the primary element of all bodies. Thus in the words, "Darkness was upon the face of the deep," the word "deep" might be taken to mean the infinite mass of water, understood as the principle of all other bodies. These philosophers also taught that not all corporeal things are confined beneath the heaven perceived by our senses, but that a body of water, infinite in extent, exists above that heaven. On this view the firmament of heaven might be said to divide the waters without from those within--that is to say, from all bodies under the heaven, since they took water to be the principle of them all.
As, however, this theory can be shown to be false by solid reasons, it cannot be held to be the sense of Holy Scripture. It should rather be considered that Moses was speaking to ignorant people, and that out of condescension to their weakness he put before them only such things as are apparent to sense. Now even the most uneducated can perceive by their senses that earth and water are corporeal, whereas it is not evident to all that air also is corporeal, for there have even been philosophers who said that air is nothing, and called a space filled with air a vacuum.
Moses, then, while he expressly mentions water and earth, makes no express mention of air by name, to avoid setting before ignorant persons something beyond their knowledge. In order, however, to express the truth to those capable of understanding it, he implies in the words: "Darkness was upon the face of the deep," the existence of air as attendant, so to say, upon the water. For it may be understood from these words that over the face of the water a transparent body was extended, the subject of light and darkness, which, in fact, is the air.
Whether, then, we understand by the firmament the starry heaven, or the cloudy region of the air, it is true to say that it divides the waters from the waters, according as we take water to denote formless matter, or any kind of transparent body, as fittingly designated under the name of waters. For the starry heaven divides the lower transparent bodies from the higher, and the cloudy region divides that higher part of the air, where the rain and similar things are generated, from the lower part, which is connected with the water and included under that name.
Reply to Objection 1. If by the firmament is understood the starry heaven, the waters above are not of the same species as those beneath. But if by the firmament is understood the cloudy region of the air, both these waters are of the same species, and two places are assigned to them, though not for the same purpose, the higher being the place of their begetting, the lower, the place of their repose.
Reply to Objection 2. If the waters are held to differ in species, the firmament cannot be said to divide the waters, as the cause of their destruction, but only as the boundary of each.
Reply to Objection 3. On account of the air and other similar bodies being invisible, Moses includes all such bodies under the name of water, and thus it is evident that waters are found on each side of the firmament, whatever be the sense in which the word is used.
Source: Summa Theologica (New Advent)