What does Genesis 3:9 mean?

Previous verses revealed the first consequence of human sin: shame and guilt. The combination of knowledge, disobedience, and human frailty led to an overpowering urge to be covered and to hide from God. Prior to this, the nakedness of Adam and Eve was nothing to be ashamed of. Their minds were pure and innocent, so there was no reason to be embarrassed or self-conscious. The immediate result of having their eyes opened to good and evil was that the man and woman understood their own evil and the goodness they had lost.

Adam had never hidden from God before. God had never had to ask where the man was. It's not that God did not know, of course. God's question here is no different from any other parent who asks a question to their child, when they already know the answer. God wants Adam to answer, to reveal himself to God, and to confess.

It should be noted that the Hebrew word for "you," both here and in verse 11, is singular. In other words, at this moment, God is not calling to Eve, or challenging her actions. He is not asking "where are you [two]?" He is specifically asking, "where are you, [Adam]?"

Adam, right from the beginning, is treated as the one ultimately responsible for the fall of mankind (Romans 5:12).