What Lord Jesus said to Nicodemus was so profound that it is still missed by many in the pulpits.
John 3:3-12
3 Jesus answered and said unto him, "Verily, verily, I say unto thee, Except a man be born again, he cannot see the kingdom of God."
The word "again" is the Greek word anothen, which means 'born from above' (NT:509). So right there Jesus is indeed pointing to our spirit being born from above (i.e., by The Holy Spirit).
4 Nicodemus saith unto Him, "How can a man be born when he is old? can he enter the second time into his mother's womb, and be born?"
Nicodemus is not completely wrong in think that above, because Lord Jesus does point to being born in the sack of water of woman's womb in the next verse. Nicodemus just didn't understand the being born of The Spirit part.
5 Jesus answered, "Verily, verily, I say unto thee, Except a man be born of water and of the Spirit, he cannot enter into the kingdom of God.
In the above phrase, Jesus contrasts both births, one in the flesh, and the other by The Holy Spirit. Many interpret the "born of water" to mean water baptism, when being baptized of water only, which was John's baptism, is not the same as being baptized by The Spirit.
6 That which is born of the flesh is flesh; and that which is born of the Spirit is spirit.
That above is yet another way Lord Jesus is contrasting the idea of our being "born of water" (through woman's womb), vs. being born of The Spirit.
7 Marvel not that I said unto thee, Ye must be born again.
8 The wind bloweth where it listeth, and thou hearest the sound thereof, but canst not tell whence it cometh, and whither it goeth: so is every one that is born of the Spirit."
In the above wind analogy, Lord Jesus is only pointing to the Spirit birth to our 'spirit' inside our flesh. In verse 6 He made it plain that the operation of the flesh is one thing, and the operation of The Spirit is totally another. And if one does NOT understand that God created man with both a flesh body, and placed a spirit-soul inside that flesh body, then they will be like Nicodemus and be ignorant of how these things are.
9 Nicodemus answered and said unto Him, "How can these things be?"
10 Jesus answered and said unto him, "Art thou a master of Israel, and knowest not these things?
11 Verily, verily, I say unto thee, We speak that we do know, and testify that we have seen; and ye receive not our witness.
12 If I have told you earthly things, and ye believe not, how shall ye believe, if I tell you of heavenly things?"
KJV
How did those like Nicodemus, who was a Pharisee, not receive "our witness", which has to mean Christ's Witness in His Word? What's that about?
Much of this was hinted at in The Old Testament Books also. The Ecclesiastes 12:5-7 Scripture especially was a witness about the different operations between our flesh and our spirit.