“Except a man be born of water (physical birth for you are in a sack of water inside the womb) and the Spirit you cannot enter in. Jesus said, “You must have a physical birth (womb of water) and a spiritual birth. There is no mention of water baptism here. The reference “of water” is associated with the physical birth that all men must have first. Look at verse 6 where Jesus talks of a fleshly birth (from the womb). There are two births being discussed: physical (“flesh is flesh”) and the spiritual birth.
I don't think there is a separation of two births being discussed here and the teachings of the Apostles and disciples later in the New Testament seems to indicate that they did not understand it this way either.
Phillip certainly preached Baptism with water otherwise the eunuch would not have requested it.
Act 8:36 And as they went on their way, they came unto a certain water: and the eunuch said, See, here is water; what doth hinder me to be baptized?
Peter certainly preached Baptism with water and felt it important enough he would not allow it to be withheld.
Act 10:47 Can any man forbid water, that these should not be baptized, which have received the Holy Ghost as well as we?
If water Baptism is not important why would Peter bother with it on those who had already received the Holy Spirit?
The early Church didn’t understand it that way either.
Justin Martyr refers to the washing of baptism by water as a source for remission of sins.
"Since at our birth we were born without our own knowledge or choice, by our parents coming together, and were brought up in bad habits and wicked training; in order that we may not remain the children of necessity and of ignorance, but may become the children of choice and knowledge, and may obtain in the water the remission of sins formerly committed, there is pronounced over him who chooses to be born again, and has repented of his sins, the name of God the Father and Lord of the universe; he who leads to the layer the person that is to be washed calling him by this name alone."
Justin Martyr,First Apology,61(A.D. 110-165),in ANF,I:183
Irenaeus sees the washing and purifying of lepers in the Old Testament as a type of the water baptism and references the very verse we discuss to support it, thus plainly seeing the water as real water baptism not a reference to the physical birth.
" 'And dipped himself,' says [the Scripture], 'seven times in Jordan.' It was not for nothing that Naaman of old, when suffering from leprosy, was purified upon his being baptized, but [it served] as an indication to us. For as we are lepers in sin, we are made clean, by means of the sacred water and the invocation of the Lord, from our old transgressions; being spiritually regenerated as new-born babes, even as the Lord has declared: 'Except a man be born again through water and the Spirit, he shall not enter into the kingdom of heaven.' "
Irenaeus,Fragment,34(A.D. 190),in ANF,I:574
Tertullian declares salvation is not attainable unless we are baptized and references the very verse we discuss to support it, thus plainly seeing the water as real water baptism not a reference to the physical birth.
" When, however, the prescript is laid down that 'without baptism, salvation is attainable by none" (chiefly on the ground of that declaration of the Lord, who says, "Unless one be born of water, he hath not life' "
Tertullian,On Baptism,12:1(A.D. 203),in ANF,III:674-675
Cyprian also sees baptism as necessary even beyond laying on of hands and reception of the Holy Spirit and he also references the very verse we discuss to support it, thus plainly seeing the water as real water baptism not a reference to the physical birth.
"[W]hen they come to us and to the Church which is one, ought to be baptized, for the reason that it is a small matter to 'lay hands on them that they may receive the Holy Ghost,' unless they receive also the baptism of the Church. For then finally can they be fully sanctified, and be the sons of God, if they be born of each sacrament; since it is written, 'Except a man be born again of water, and of the Spirit, he cannot enter into the kingdom of God.'...
- nly baptism of the holy Church, by divine regeneration, for the kingdom of God, may be born of both sacraments, because it is written, 'Except a man be born of water and of the Spirit, he cannot enter into the kingdom of God.' "
Cyprian,To Stephen,71:72(A.D. 253),in ANF,V:378,385
Finally the Council of Carthage declares that one cannot enter the kingdom of heaven without baptism and the baptism they refer to is a water baptism which is necessary for the spirit to operate.
"And in the Gospel our Lord Jesus Christ spoke with His divine voice, saying, "Except a man be born again of water and the Spirit, he cannot enter the kingdom of God."[8] This is the Spirit which from the beginning was borne over the waters; for neither can the Spirit operate without the water, nor the water without the Spirit...Unless therefore they receive saving baptism in the Catholic Church, which is one, they cannot be saved, but will be condemned with the carnal in the judgment of the Lord Christ."
Council of Carthage VII(A.D. 258),in ANF,V:566
Ambrose makes the following interesting arguments against your interpretation of the water representing the physical birth.
First he argues that Paul refers to the baptism by water as a burial with Christ, so Paul certainly understood baptism by water as something other than referring to the physical birth you apply it to.
"And that the writer was speaking of baptism is evident from the very words in which it is stated that it is impossible to renew unto repentance those who were fallen, inasmuch as we are renewed by means of the laver of baptism, whereby we are born again, as Paul says himself: 'For we are buried with Him through baptism into death, that, like as Christ rose from the dead through the glory of the Father, so we, too, should walk in newness of life.' "
Ambrose,Concerning Repentance,2:8(A.D. 390),in NPNF2,XI:346
In this second of the two arguments Ambrose identified the water of baptism with one of the witnesses. The physical birth you try to associate it with is not a witness, so the two must be different and your interpretation must be wrong.
"Therefore read that the three witnesses in baptism, the water, the blood, and the Spirit, are one, for if you take away one of these, the Sacrament of Baptism does not exist. For what is water without the cross of Christ? A common element, without any sacramental effect. Nor, again, is there the Sacrament of Regeneration without water: 'For except a man be born again of water and of the Spirit, he cannot enter into the kingdom of God.' "
Ambrose,On the Mysteries,4:20(A.D. 391),in NPNF2,XI:319
So we see the Phillip did not understand the water to represent the physical birth, Peter like wise did not, nor did Paul and neither did many in the early Church.
Conversely it would be interesting to know the earliest reference to this interpretation. I believe this interpretation is a modern invention of men, but I would like to know just who came up with it first if you have a verifiable reference.