If GOD said that he created the HEAVENS and the Earth, why do you not think that HE created the water in the heavens when he created Heaven?
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Though I'm not sure if the question is about God creating the "water in the heavens" or about God creating "water in the heavens." I'll take a stab at the question that I think is more interesting (to me).
I'm assuming (without attempting to prove—for that is a different question) that any given passage of the Bible was written at least for one particular audience in the past, and may also have been written for an audience in the future. Either way, it definitely has a message for the original audience. I don't consider this too precipitous of an assumption.
God Speaks to People in Terms that They Can Understand
I don't think that the Bible is intended to be used as a science textbook. This is not to say that it contains errors or is not reliable, but attempting to scrutinize words for scientific detail may not be a productive way to understand the text.
The Genesis account was meant to be understood by the ancients (~1500 B.C.). They did not, as a whole, see the world as we see it. There were many physical principles that they did not understand, and they didn't necessarily seek answers to "Why does this work this way?" They just accepted whatever the explanations were, as odd as they may sound to those of us who've studied chemistry or physics. For these people, the Bible was not meant to provide them with extensive facts and knowledge of geology, biology, physics, etc., but rather to help them come to know God.
For example, Leviticus 11:3-6 describes rabbits as "chewing their cud." Rabbits aren't ruminants, as we define "chewing the cud." Is the text incorrect? No. Rabbits will eat chew undigested portions of their own feces, which appears similar to cattle, sheep, and other ruminants. To the ancients, they would be put in the same category. The text was definitely meant to be understood by these people, and they weren't looking for the same type of details that we do. God intended (in part, at least) to give them a sensible means to distinguish between animals that they could and couldn't eat.
What are the Waters Above?
Here's a plausible explanation:
What color is water (in lakes and ponds)? Blue(-ish). When the ancients looked up, what color did they see? Blue. Where did the rain come from? The sky?
Would it be reasonable for an ancient to think that there was water up above? The atmosphere is not devoid of moisture (e.g. clouds). God gathered the water under the heavens so that dry land would appear. Could the "water" have been in gaseous form before this event? What does it mean to gather liquid water together? If it was liquid before it was gathered, where did it go after it was gathered? The earth is said to be coved with/made of water in Genesis 1:2.
What does this mean? Some of the details are cryptic. Does this mean the account is flawed or meaningless? It need not be. If God is describing something that cannot be understood by his audience (because it's outside their realm of experience), it could be reasonable to conclude that the account is maintaining some aspect of the character of what God actually did without describing in full detail how he did it.
Rather than attempt to extract scientific details from the description in the text, it might be more productive to focus on what God wanted those people to understand. In addition to ex nihlo creation, God moves, separates, gathers, etc. everything he has made. He is completely sovereign over the elements just as he is sovereign over living things. God is frequently described like a carpenter or some other workman when it comes to the creation (e.g. Is 40:12, Job 38:1-11).
There are some theories about what the pre-flood world was like, and among them, some say that a water vapor canopy over the earth could explain things like extreme longevity or how the flood happened.
This might be what's referred to as "the waters above the heavens."
Science now believes that the Earths water was supplied from above. This would appear to be in concert with the Genesis account where our atmosphere separates the waters and explains this question.