The thesis of this work focused upon the breaking up of "the fountains of the great deep" as the cause of the flood, as described in Genesis 7:11, and it presented a model of the earth's structure with ample stores of water within subterranean chambers to cause the Noachian flood. The waters of the present day oceans, Burnet believed, were insufficient to have caused the deluge, which Burnet regarded as world wide in its effects.
Burnet estimated the volume of the subterranean waters required to flood the world at the equivalent of about 9 oceans. His book attracted much interest and attention, having many supporters, but also some powerful opponents among the dignitaries of the Anglican Church. An English translation was printed 1684-1689.
In the first edition, Burnet seems to have argued that the 'firmament' of Genesis 1 was the crust of the earth, but this was dropped in later editions. His contemporary, Robert Hooke, also supposed the firmament of Genesis 1 could be identified with the crust of the earth.
Burnet laid great stress on 2 Peter 3:5-6,
For this they are willingly ignorant of, that by the word of God the heavens were of old, and the earth standing out of the water and in the water,His theory was founded on this and other scriptures alluding to waters within the earth. Referring to the verses quoted above, Burnet interpreted the words "willingly ignorant" as meaning that men were "deliberately ignorant" about the waters within the earth, that were the main source of the flood waters, and he argued that the divine knowledge of the earth's interior structure revealed in scripture had been deliberately suppressed.
Whereby the world that then was, being overflowed with water, perished.
Conventional dogma at the time claimed there was a fiery abode for the souls of the wicked inside the earth, which probably seemed to conflict with Burnet's ideas, which may account for some of the opposition his theory encountered from fellow theologians.
Burnet reasoned that as the materials of the primeval earth precipitated from the initial chaos, they were sorted according to their densities. Heavy rocks and metals formed the core with a liquid layer above; terrestrial materials and air were eventually precipitated to form a perfectly smooth, featureless surface, like that of an egg. Thus the original earth was smooth and beautiful, without faults and wrinkles, such as it exhibits today. Burnet wrote:
In this smooth Earth were the first scenes of the world, and the first generation of Mankind; it had the Beauty of Youth and bloooming Nature, fresh and fruitful, and not a Wrinkle, Scar or Fracture in all its body; no Rocks nor Mountains, no hollow Caves, nor gaping Channels, but even and uniform all over.The climate also was like a perpetual spring, and there were no seasons in the antediluvial world. In contrast, our present world is but a ruin, he said, and shows the effects of the collapse of the crust into subterranean cavities during the flood.
The flood itself was the result of natural causes, Burnet argued, which culminated in the destruction of the world; when the flood waters had retreated into internal caverns, the earth had become "a gigantic and hideous ruin ... a broke and confused heap of bodies."
The book was translated into many languages, and had a considerable influence in Europe for about a century. In 1692 Burnet published Archaeologiae Philosophicae: sive Doctrina antiqua de Rerum Originibus, in which he argued for allegorical interpretations of the 6 days of Genesis and the story of the fall of man. This provoked so much opposition and clamor from his enemies among the clergy that the king was obliged to remove Burnet from his post as clerk of the closet.