How and when did the water come into being?

Most of the ancient creation myths have a record of primordial waters. This is seen in the Enûma Eliš (Apsû) and in several Egyptian creation myths. In the Egyptian myths, this water is deified as Nu.

Of course Genesis shares this same idea and imagery as you have already picked up on. Like the other creation stories in the Levant, Genesis also implies that the waters always were and that they acted as the medium from which creation was fashioned. The creation of man is most often compared to a potter fashioning a pot in ancient creation stories (and Genesis.) Since the potter does not create both the clay and the pot, it would make little sense for the creator of the world to create the vessel (mankind) and the creative medium (the waters). Just as the clay is simply there and need only be harvested by the creator before he begins fashioning the pot, the same is true of the waters - they are just simply there and need only be harvested before being used as a creative medium. While this may seem troublesome to modern readers, Creation ex nihilo is a modern novelty that came about in the 2nd century AD.

This is not to say that there was not some idea of Creation ex nihilo prior to the 2nd centruy in that Amun is though to have created Nu in one Egyptian creation myth. The logical extension of this is creation ex nihilo, but this is more coincidental than anything. This myth arose from an attempt to establish the supremacy of Amun in the New Kingdom period of Egypt, not out of a realization that matter had to have a beginning. This was just not philosophically realized until the Greek philosophers got a hold of it. The earlier Mesopotamian writers just didn't think about this and the problem of time necesitating a beginning simply didn't matter to them. Attempting hermeneutic gymnastics to conclude that The Bible records the creation of these waters would be an exercise in eisegesis.

The waters were created in the first line of genesis.

In hebrew text, 'the heavens' is spelled the same as 'the two waters'. Therefore, god the spirit hovers to the surface of waters, because 2 waters have been created.

According to the dogmas of the larger denominations, the creation story isn't literal chronology. And the question is nonsensical.

Here's why -- the question is takes the thought from verse 2 out of context.

Firstly, it's out of the context of any Christian or Jewish dogma. The accounts of creation are held by most Christians (the large denominations) to be largely symbolic of God's creative effort and personality. They're not a detailed, literal, chronological retelling of everything God did in precise sequence. A good indicator of this, even outside any particular tradition, is that simple fact that there are two creation stories in Genesis.

And those two creation stories do NOT agree. In the first story, humans are the last-made creature. In the second story (Genesis 2:4-25), man is first, then the garden, then animals, and woman last. Thus, the larger Christian denominations (and most Jews) are in agreement that Genesis is not a literal, chronological account of creation.

Secondly, it's taken out of the immediate literal context. There's more to Gen. 1:2 than wind sweeping over waters. And the full content of Gen. 1:2 is in the context of a larger thought that begins in the previous verse.

(1) In the beginning, when God created the heavens and the earth — (2) and the earth was without form or shape, with darkness over the abyss and a mighty wind sweeping over the waters—

So, even if I were defending a creationist viewpoint (I'm not), it's clear from the two verses combined that the earth and heavens already exist in a primitive, chaotic state. (What the author means by "earth" and "heavens" is debatable.)

Also notable, "the waters" (referring to the sea) in biblical language is almost always a metaphor for chaos. The "wind" in Genesis 1:2 is sweeping over the "primordial chaos." We can extrapolate then that first creation story illustrates the point that God creates (from nothing) by bringing order out of chaos. (That is, a chaos which He creates for the purpose of bringing about an ordered creation.)

The creation story in Genesis chapter 1 was not regarded as a literal story by some of the early Christian Church Fathers, who regarded it as an allegory. For example, Origen (De Principiis, Book 4.1.16):

.as even these do not contain throughout a pure history of events, which are interwoven indeed according to the letter, but which did not actually occur. Nor even do the law and the commandments wholly convey what is agreeable to reason. For who that has understanding will suppose that the first, and second, and third day, and the evening and the morning, existed without a sun, and moon, and stars? and that the first day was, as it were, also without a sky? And who is so foolish as to suppose that God, after the manner of a husbandman, planted a paradise in Eden, towards the east, and placed in it a tree of life, visible and palpable, so that one tasting of the fruit by the bodily teeth obtained life? and again, that one was a partaker of good and evil by masticating what was taken from the tree? And if God is said to walk in the paradise in the evening, and Adam to hide himself under a tree, I do not suppose that any one doubts that these things figuratively indicate certain mysteries, the history having taken place in appearance, and not literally...

Genesis chapter 1 gradually came to be seen as a literal account, which means that we try to put a modern reading into an ancient text. The English translations we usually see were written by later theologians who believed in a literal creation account, then we add our own modern biases.

The first three words of Genesis are: "בראשית ברא אלהים" (B'reishit bara Elohim), which is often translated as, "In the beginning, God created..." There is no definite article and the grammar is complex, if not confusing. Linguists struggle to agree on how it should be translated, but there is some agreement as to how it should not be translated. Leon R. Kass says in The Beginning of Wisdom, page 27, that the translation “In the beginning” is incorrect. Kass cites Robert Alter (Genesis Translation and Commentary), who treats the first (and second) verse not as a declarative sentence but as a subordinate clause: “When God began to create heaven and earth, and the earth was welter and waste and darkness over the deep and God's breath hovering over the waters, God said ...” Read as a literal creation account, this interpretation appears to mean that the earth and the primeval waters were pre-existing.

As to the stage of the universe at this time, logic says, with the benefit of modern science, that the earth was a cold and lonely rock floating through empty space until day three, when the sun, moon and stars were created. Although the temperature ought to have been at absolute zero, Genesis 1:2 tells us that the waters were liquid (even if we suppose they were not pre-existing, they should have been frozen). All these issues disappear if we return to looking at this creation account purely as an allegory.

The literal read:

So this was before creation, so where does water come from?

Not if you read verse one first "In the beginning God created the heaven and the earth." By creation of earth water was also created.

Why it exist before the first day?

Verse 1 to 5 as day one.

And if there is face of water, there seems to me should be some gravity somewhere, what's the stage of universe at this time?

God uphold the universe. He is a God of order and laws – thus all natural laws is a part of the creation. Gravity is one part. The exact state is not described.

Adding as a note:

Chapter two is a more in detail account of some of the events. Not chronological but nor contradicting chapter 1.

Say i.e. Genesis 2:18-22:

And the Lord God said, It is not good that the man should be alone; I will make him an help meet for him. And out of the ground the Lord God formed every beast of the field, and every fowl of the air; and brought them unto Adam to see what he would call them: and whatsoever Adam called every living creature, that was the name thereof. And Adam gave names to all cattle, and to the fowl of the air, and to every beast of the field; but for Adam there was not found an help meet for him. And the Lord God caused a deep sleep to fall upon Adam, and he slept: and he took one of his ribs, and closed up the flesh instead thereof; And the rib, which the Lord God had taken from man, made he a woman, and brought her unto the man.

• And the Lord God said, It is not good that the man should be alone; I will make him an help meet for him.

This is an ingress. But instead of jumping directly to the creation of Eva we are told that off all creatures this far created there was no mate for man, and as such woman is created.

Genesis 1 and 2 are two different accounts/tales. It was not like they had bibles with chapters and verses. In Genesis 2 we are (therefore) told how animals were created. As it say "And out of the ground …" and not "And then out of the ground …" it can be interpreted both as and and and then, – but as Gen 1:26 is rather clear on the matter one can conclusively say it is and in the sense of "and" and not "and then".

Does verse 20 "And Adam gave names to all cattle, and to the fowl of the air, and to every beast of the field;" contradict verse 19 because had had already named them there "and whatsoever Adam called every living creature, that was the name thereof."?

Well, you see, when two atoms of hydrogen love an atom of oxygen very much...

When I was a literalist (and it seems you are looking through those glasses) my interpretation was that when God created the heavens and the earth (Gen. 1:1, "In the beginning, God created the heavens and the earth."), that would have included the waters. Since the waters and the lands and the waters above the heavens and the waters on the earth were not separated yet, then it is a bit difficult to nail down the dimensionality of it all, but simply because we cannot conceive of a world where there is little boundary between gaseous and liquid state that does not means that it could not exist. Of course, fog exists, so it is quite possible that water was originally created as a liquid suspended in air.

You might be reading too much into "over". To say that God is literally and exclusively "over" something is as nonsensical as saying he is literally and exclusively "under" something. Time and space are never literal in such a context.