This subject is dealt with, in impressive detail and in a scientific manner, by Morris and Whitcombe in their famous book 'The Genesis Flood'.
They draw attention to the mention of waters 'above the firmament' Genesis 1:7 and I agree that it is very likely that it was a protective canopy of water vapour around the earth - at a distance.
Other protective measures can be seen in the asteroid belt (between Mars and Jupiter) which may well be a capturing point for harmful missiles, in the existence of the gas giant planets (Jupiter, Saturn, Uranus and Neptune) which may well have a protective gravitational effect - maybe the reason for the cluster of asteroids - and in what is termed the 'Oort' cloud, which is believed to be a very large cloud of icy particles circling the solar system beyond Pluto.
The magnetic field around earth is well documented in its protective effect from solar wind which conveys radiation and high velocity particles from the Sun's combustion.
The water canopy would have protected from cosmic radiation and if it is the case that the judgement of God removed this protection then the rapid shortening of human lifespan on earth may well be due to the removal of this protection. Genesis 5 and Genesis 11 contrast the longevities of humans on earth before and after the Flood and it is clear that there was a rapid and permanent reduction in lifespan due to the Flood.
Not only would there be a lack of protection from radiation, there would have been a disastrous change in climactic conditions. What may well have been a humid, temperate and moderate climate, globally - one highly conducive to longevity - might well have become what we experience today, almost immediately after the Flood's recession.
Thus it would be the case that God's judgement was twofold - the removal of the protective layer and the flooding of the earth to remove all flesh. (Except that flesh which was under subjection to faith and, thus, had a provision provided during the judgement of Flood.)
It is worth remarking that anyone could have followed Noah's example and could have built a suitable vessel. They did not need to worry about animals - Noah looked after that - they just had to save themselves in a very much smaller vessel than the ark. But none did. Jesus said they 'were eating and drinking, marrying and giving in marriage, until the day Noah entered the ark' Matthew 24:38.
After the Flood it is clear that the water took time to soak into the earth and Noah had to remain in the ark until it did so, Genesis 8:13,14. There was, presumably, much greater oceanic volume afterwards, than prior to the Flood.
The earth's crust contains truly enormous amounts of water, dispersed widely throughout the planet. It is secreted in sedimentary rock, in aquifers below ground and it floods every mine ever dug below ground. See more information on Wikipedia - Aquifers
The topography of the seabed indicates vast fractures across both the Atlantic floor and the Pacific floor. It would be reasonable to suppose that the weight of water had this effect. 'The fountains of the deep were broken up' may refer to this. Genesis 7:11. This disruption would enable vast quantities of water to gravitate to subterranean levels.
So Morris and Whitcombe suggest - and I agree - that, as to the question posed, the water came from a canopy of water vapour above the earth and it is now visible in the oceans and also to be found below ground, wherever and whenever the earth is penetrated to any depth.