John Calvin Commentary 2 Peter 3:5

"For this they willfully forget, that there were heavens from of old, and an earth compacted out of water and amidst water, by the word of God;" — 2 Peter 3:5 (ASV)

For this they willingly are ignorant of. By one argument only he refutes the scoff of the ungodly: namely, that the world once perished by a deluge of waters, even though it consisted of waters (Genesis 1:2). And as the history of this was well known, he says that they willingly, or of their own accord, erred.

For those who infer the perpetuity of the world from its present state deliberately close their eyes, so as not to see such a clear judgment of God. The world undoubtedly had its origin from waters, for Moses calls the chaos from which the earth emerged 'waters'; and furthermore, it was sustained by waters. Yet it pleased the Lord to use waters for the purpose of destroying it.

Therefore, it appears that the power of nature is not sufficient to sustain and preserve the world, but that, on the contrary, it contains the very element of its own ruin, whenever it may please God to destroy it.

For it should always be remembered that the world stands by no other power than that of God’s word, and that therefore, inferior or secondary causes derive their power from Him and produce different effects as He directs them.

Thus, the world stood through water, but water could have done nothing by itself; on the contrary, it obeyed God’s word as an inferior agent or element. Then, as soon as it pleased God to destroy the earth, the same water obeyed, becoming a ruinous inundation.

We now see how egregiously those err who stop at the bare elements, as though there were perpetuity in them and their nature were not changeable according to God’s command.

By these few words, the petulance of those who arm themselves with physical reasons to fight against God is abundantly refuted. For the history of the deluge is an abundantly sufficient testimony that the entire order of nature is governed by the sole power of God (Genesis 7:17).

It seems strange, however, that he says the world perished through the deluge, when he had previously mentioned the heaven and the earth.

To this I answer that the heaven was then also submerged—that is, the region of the air, which lay open between the two waters. For the division or separation mentioned by Moses was then disrupted (Genesis 1:6); and the word heaven is often understood in this sense.

If anyone wishes for more on this subject, let them read Augustine on the City of God, Book 20.