Jesus is referring to water baptism when he says born of water in John 3:5. When someone repents and is water baptized they become a child of God. They are a babe in Christ. They are born again as in a spiritual birth. A baby is inside birth water and comes out from the birth water to begin a new life and they are an innocent baby free from sin. A sinner goes into/inside the water and comes out from the water to begin a new life, having by faith been washed by the blood of Christ, and they are free from their past sins.
Why would Jesus have in mind physical birth in John 3:5? That is what Nicodemus thought (John 3:4). Jesus was talking about entering the kingdom. That is a spiritual kingdom not physical.
“I say to you, unless one is born again” Born AGAIN.
Jesus answered, “Most assuredly, I say to you, unless one is born of water and the Spirit, he cannot enter the kingdom of God” UNLESS one IS BORN OF WATER.
Would He be needing to remind Nicodemus about his own birth? Is Jesus more concerned with physical birth for Nicodemus or for anyone else who has already been physically born? Or is He more concerned with a SPIRITUAL birth? If Jesus wanted to say that one must be born once biologically (of birth water) and then again from the Spirit, would He not have made it clearer such as saying, “born of the womb and the Spirit” or “born of flesh and the Spirit”?
In verse 6 He says “That which is born of the flesh is flesh, and that which is born of the Spirit is spirit.“ If born of water in John 3:5 is referring to birth water (it’s not), then why didn’t Jesus say “born from their mother’s womb”, as He did in Matthew 19:12?
To my knowledge, the Bible never uses the words “born of water” to describe amniotic fluid. Jesus said “water” and that is exactly what He meant, else what did John mean later in this same chapter when he wrote that John baptized at Aenon because “there was much water there (v 23)?
In an article on "Baptism and Remission" in Baptist Quarterly (July, 1877, pg. 309), Wilmarth said:
"Christ Himself, in His early Judean ministry 'made and baptized disciples.' His preaching at the outset was of similar purport with that of John. It is natural to suppose that His baptism (in connection with repentance and faith) was, like John's, in order to remission. We are confirmed in this by our Savior's words to Nicodemus, who came to Him during that early period to learn more fully, no doubt, of the kingdom which Christ and John were preaching. Christ said to him, "except a man be born of water and of the Spirit he cannot enter into the kingdom of God;" i.e. Baptism and Renewal by the Spirit are the conditions of true citizenship in the kingdom of God on earth. Unquestionably, Remission was one of the blessings of that kingdom." [1]
In Wall's History of Infant Baptism (Vol. I, pg. 443) we find:
"All the ancient Christians (without the exception of one man) do understand that rule of the Savior, John 3:5, 'Verily, verily, I say unto thee, Except a man be born of water and of the Spirit, he cannot enter the kingdom of God'; of baptism. [1]
"I had occasion in the First Part to bring a great many instances of their sayings: where all that mention that text, from Justin Martyr down to St. Austin (Augustine) do so apply it. Neither did I ever see it otherwise applied in any ancient writer. I believe Calvin was the first that ever denied this place to mean baptism. He gives another interpretation, which he confesses to be new." [1]
Philip Schaff:
"In view of the facts that John baptized, that Christ Himself was baptized, that His disciples (4:2) baptized in His name, it seems impossible to disconnect water from baptism. Calvin's interpretation arose from doctrinal opposition to the Roman Catholic over-evaluation of the sacrament, which must be guarded against in another way" (footnote on John 3;5, Lange's Commentary, Vol. III, 127). [1]
In his Notes on John 3:5, Albert Barnes said:
"Be born of water. By water, here, is evidently signified baptism. Thus the word is used in Ephesians 5:26; Titus 3:5)." [1]
Adam Clarke said:
"Baptism in water, into the Christian faith, was necessary to every Jew and Gentile that entered into the kingdom of the Messiah" (Commentary on John 3:5). [1]
A professor at Southern Baptist Theological Seminary say to a large class: "If you have not been tampered with, you will admit that the water in John 3:5 refers to baptism."[1]
The same professor said to a second year Greek class studying the book of Galatians, that Paul's statement in Galatians 3:26,27 shows that "in New Testament days it was understood that a person was not in fellowship with Christ until after he was baptized." After some discussion on the statement, he said, "I don't make it (baptism) essential to salvation." I believe in the first statement he spoke as a Greek scholar, but in the latter statement he spoke as a Baptist preacher! [1]
Scholarship admits that "water" in John 3:5 refers to baptism. Of course, it has been true all along; it doesn't take "scholarship" to make it so. But it is obvious that anybody who tries to argue that it means something else is inconsistent with both the "scholars" and the word of Christ. "Let God be true, but every man a liar" (Romans 3:4). [1]
Case Notes:
Cooper , James E. The New Birth of Water, Biblical Insights, 2 Feb. 2005 [1]