The physical birth -- common to all mankind -- was automatically discounted by Christ in His response to Nicodemus.
Christ was revealing the absolute necessity of the New Birth, which is (1) supernatural, (2) spiritual, (3) unseen with the human eye, (4) necessary to enter into the Kingdom of God, and (5) enables one to see the invisible Kingdom of God (as presently constituted).
It is when we come to John 3:5 that a huge number of misunderstandings and misinterpretations arise. "Born of the Spirit" means born of God, born from above, and born again. This is the totally supernatural effect of believing on the Lord Jesus Christ and being saved (John 1:12,13). But what does "born of water" mean?
If people would go back to the Old Testament and see what it says about the New Birth (and Nicodemus should have know this but either forget it or ignored it) they would realize that the New Birth is not produced through water baptism. It is the "water" of the Word of God, as well as the "water" of the Holy Spirit that Christ was talking about (since water is used as a metaphor in this connection).
EZEKIEL 36: THE FUTURE REDEMPTION AND RESTORATION OF ISRAEL
24 For I will take you from among the heathen, and gather you out of all countries, and will bring you into your own land [Israel].
25 Then will I sprinkle clean water upon you, and ye shall be clean: from all your filthiness, and from all your idols, will I cleanse you.
26 A new heart also will I give you, and a new spirit will I put within you: and I will take away the stony heart out of your flesh, and I will give you an heart of flesh.
27 And I will put my Spirit within you, and cause you to walk in my statutes, and ye shall keep my judgments, and do them.
While this is addressed to Israel, it is also a part of the New Covenant, and the outpouring of the Holy Spirit on the day of Pentecost (30 AD) and which will again happen after the Second Coming of Christ.
But when Jesus referred to this while addressing Nicodemus, He also made it a reality for the Church Age. The Church was born on the day of Pentecost, when about 3,000 Jews were given the GIFT of the Holy Spirit and saved by grace. And ever since every sinner who was saved received the gift of the Holy Spirit.
And it is only after a sinner receives the gift of the Spirit that He is "born of the Spirit". But the "water" is the Word of God -- indeed the Gospel -- and Peter made this clear in his first epistle (1 Pet 1:23-25), but called the Gospel the "incorruptible seed" which produces the New Birth.
23 Being born again, not of corruptible seed, but of incorruptible, by the Word of God, which liveth and abideth for ever.
24 For all flesh is as grass, and all the glory of man as the flower of grass. The grass withereth, and the flower thereof falleth away:
25 But the Word of the Lord endureth for ever. And this is the Word which by the Gospel is preached unto you.
If the Christian Church was started on the day of Pentecost then how can you explain these passages:
Acts 21:
20 And when they heard it, they glorified the Lord, and said unto him, Thou seest, brother, how many thousands of Jews there are which believe; and they are all zealous of the law:
Acts 3:
12 And when Peter saw it, he answered unto the people,
Ye men of Israel, why marvel ye at this? or why look ye so earnestly on us, as though by our own power or holiness we had made this man to walk?
13
The God of Abraham, and of Isaac, and of Jacob, the God of our fathers, hath glorified his Son Jesus;
25 Ye are the children of the prophets, and of the covenant which God made with our fathers, saying unto Abraham, And in thy seed shall all the kindreds of the earth be blessed.
Acts 11:19
Now they which were scattered abroad upon the persecution that arose about Stephen travelled as far as Phenice, and Cyprus, and Antioch, preaching the word to
none but unto the
Jews only.
---Paul was chosen by Jesus to be a vessel and given revelation which were unknown to the Jews.
Acts 9:
11 And the Lord said unto him, Arise, and go into the street which is called Straight, and enquire in the house of Judas for one called Saul, of Tarsus: for, behold, he prayeth,
15 But the Lord said unto him, Go thy way: for he is a
chosen vessel unto me, to bear my name before the Gentiles, and kings, and the children of Israel:
16 For I will shew him how great things he must suffer for my name's sake.
Romans 16:25
Now to him that is of power to stablish you according to
my gospel, and the preaching of Jesus Christ,
according to the revelation of the mystery, which was kept secret since the world began,
Ephesians 2
11 Wherefore remember, that ye being in time past Gentiles in the flesh, who are called Uncircumcision by that which is called the Circumcision in the flesh made by hands;
12 That at that time ye were without Christ,
being aliens from the commonwealth of Israel, and strangers from the covenants of promise, having no hope, and without God in the world:
13 But now in Christ Jesus ye who sometimes were far off are made nigh by the blood of Christ.
14 For he is our peace, who hath made both one, and hath broken down the middle wall of partition between us;
15 Having abolished in his flesh the enmity, even the law of commandments contained in ordinances; for to make in himself of twain one new man, so making peace;