Let's see how a master exegete, St. Augustine, approaches this problem.
In his day, a prevailing scientific theory was that heavy elements (water and earth) seek their "natural place" toward the center of the earth, and lighter elements (air and fire) seek their "natural place" toward the heavens. So, how can there be “waters above the firmament” (Genesis 1:6-9)? The waters being "above" is not their natural place; how can they stay there?
St. Augustine in The Literal Meaning of Genesis, lib. 2 cap. 4 n. 7 writes:
Taking these theories into account, a certain commentator [St. Basil] has made a praiseworthy attempt to demonstrate that the waters are above the heavens, so as to support the word of Scripture with the visible and tangible phenomena of nature… Hence, from the existence of the air between the vapors that form the clouds above and the seas that stretch out below, our commentator proposed to show that there is a heaven between water and water. This painstaking enquiry is, in my opinion, quite praiseworthy.
ibid. n. 9:
Certain writers, even among those of our faith, attempt to refute those who say that the relative weights of the elements make it impossible for water to exist above the starry heaven. They base their arguments on the properties and motions of the stars. They say that the star called Saturn is the coldest star, and that it takes thirty years to complete its orbit in the heavens because it is higher up and therefore travels over a wider course.
It is true, indeed, that by its own motion, moving over a vast space, it takes thirty years to complete its orbit; yet by the motion of the heavens it is rotated rapidly in the opposite direction…and therefore, it ought to generate greater heat by reason of its greater velocity. The conclusion is, then, that it is cooled by the waters that are near it above the heavens, although the existence of these waters is denied by those who propose the explanation of the motion of the heavens and the stars that I have briefly outlined.
With this reasoning some of our scholars attack the position of those who refuse to believe that there are waters above the heavens while maintaining that the star whose path is in the height of the heavens is cold. Thus they would compel the disbeliever to admit that water is there not in a vaporous state but in the form of ice. But whatever the nature of that water and whatever the manner of its being there, we must not doubt that it does exist in that place. The authority of Scripture in this matter is greater than all human ingenuity.
So, St. Augustine denies a leading scientific theory of his day in favor of the "authority of Scripture," which "in this matter is greater than all human ingenuity." (source).
We have it even better today because modern astronomy has been able to detect, with radio telescope spectroscopy, the chemical signature of water in interstellar gas clouds.
cf. also Galileo Was Wrong: The Church Was Right (vol. 3) by Robert Sungenis, which is devoted to history and Scriptural exegesis; e.g., pp. 560 ff., where he quotes St. Augustine's Literal Interpretation of Genesis to prove that Scripture has more authority than science