1Now there was a man of the Pharisees named Nicodemus, a ruler of the Jews. 2This man came to Jesus by night and said to him, “Rabbi, we know that you are a teacher come from God, for no one can do these signs that you do unless God is with him.” 3Jesus answered him, “Truly, truly, I say to you, unless one is born again he cannot see the kingdom of God.” 4Nicodemus said to him, “How can a man be born when he is old? Can he enter a second time into his mother’s womb and be born?”
Nicodemus thought of 2 distinct kinds of birthing.
5Jesus answered, “Truly, truly, I say to you, unless one is born of water and the Spirit, he cannot enter the kingdom of God. 6That which is born of the flesh is flesh,
The first kind is physical as a baby is being born of flesh. This is a physical reality. This happens when a person comes out of his mother's womb.
and that which is born of the Spirit is spirit.
The second kind is a spiritual event happening in the spiritual reality.
7 Do not marvel that I said to you, ‘You must be born again.’ 8The wind blows where it wishes, and you hear its sound, but you do not know where it comes from or where it goes. So it is with everyone who is born of the Spirit.”
Born of the Spirit is a distinct event separate from being born of water.
It happens when the Holy Spirit functions as the Paraclete and dwells in the person by connecting with that person's spirit.