There are two general theological beliefs about John 3:5 and being born by water.
1. The water is baptism. One must be baptised for the remission of sins and then one also has to activate the Holy Spirit within himself by becoming a disciple of Christ.
2. The water is the natural water of childbirth. This refers to verse 6 when Jesus says that what is born of the spirit is spirit and what is born of the flesh is flesh. Also, it refers to what Nicodemus asked Jesus: How can a man enter a second time into his mother's womb?
I tend to agree with number two because of the question by Nicodemus and because of Jesus' statement in verse 6.
I did notice in another post of your that you believe we must be baptized in the Jordon River.
This cannot be correct.
When Jesus gave the command for the Apostles to go into all the world and teach and baptize in
Matthew 28:19 it was impossible for others in different regions to make the trip to Israel.
Jesus would never give a command contradicting the Covenant made with Abraham.....
that he would be the father of many nations.
John 3:3-6
3Jesus answered and said to 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? He cannot enter a second time into his mother’s womb and be born, can he?”
5Jesus answered, “Truly, truly, I say to you, unless one is born of water and the Spirit he cannot enter into the kingdom of God. 6“That which is born of the flesh is flesh, and that which is born of the Spirit is spirit.
Matthew 28:19
19“Go therefore and make disciples of all the nations, baptizing them in the name of the Father and the Son and the Holy Spirit,