Water and Spirit in John is not about baptism, the NT example of baptism was not yet established. This is seen in Jesus saying to Nicodemus, "Are you the teacher of Israel and do not understand these things" Jesus expected Nicodemus to understand what He was saying. It is a reference to Ezekiel 36:24-27:
'For I will take you out of the nations; I will gather you from all the countries and bring you back into your own land. 25I will sprinkle clean water on you, and you will be clean; I will cleanse you from all your impurities and from all your idols. 26I will give you a new heart and put a new spirit in you; I will remove from you your heart of stone and give you a heart of flesh. 27And I will put my Spirit in you and move you to follow my decrees and be careful to keep my laws.
John 4:14 -but whoever drinks the water I give them will never thirst. Indeed, the water I give them will become in them a spring of water welling up to eternal life."
John 7:38,39 - Whoever believes in me, as Scripture has said, rivers of living water will flow from within them." By this he meant the Spirit, whom those who believed in him were later to receive. Up to that time the Spirit had not been given, since Jesus had not yet been glorified.
John 3:5 "
Jesus answered, Verily, verily, I say unto thee, Except a man be born of water and of the Spirit, he cannot enter into the kingdom of God."
Jesus speaks of one new birth that consists of two elements: 1) water 2) Spirit
Later in John 3:23-24 we can easily see that Jesus means by "born of water" "
After these things came Jesus and his disciples into the land of Judaea; and there he tarried with them, and baptized. And John also was baptizing in Aenon near to Salim, because there was much water there: and they came, and were baptized." So 'born of water' in the immediate context of John 3 refers to water baptism as performed by John. John's baptism would be how one was born again before John's baptism was replaced by Christ's baptism of the great commission beginning in Acts 2. You cannot go to a remote text, [as in John 4 or elsewhere], where "water" is being used figuratively and then import that figurative meaning into the text of John 3:5. The 'water" of John 3:5 is literal just as 'water' in John 3:23 is literal...literal water and literal spirit compose the new birth.
Two points:
(1) from the context of John 3 we see Nicodemus had not experienced the new birth. Why? "But the Pharisees and lawyers rejected the counsel of God against themselves, being not baptized of him." Luke 7:30. Pharisees as Nicodemus rejected John's baptism and doing so they rejected the new birth. And anyone that rejected John's baptism would accountable themselves for that rejection.
Some claim John 3:5 refers to some baptism with the Holy Ghost. If that were the case then Nicodemus NOT being born again would be the Lord's fault and accountability for failing to "spirit baptism" Nicodemus. Yet water baptism has been commanded to men to obey and those that do not will be held accountable for their own decision and not what the Lord failed to do.
(2) John's baptism was later replaced by Christ's baptism of the great commission (Matthew 28:19-20; Mark 16:15-16) as to how men would be born again. With the Bible being its own best commentary, we can again easily see what Jesus meant by "born of water":
John 3:5--------------Spirit++++++++++++++
water>>>>>>>>>>>in the kingdom
1 Cor 12:13-----------Spirit++++++++++++
baptized>>>>>>>>>>>in the body
Titus 3:5-----------Holy Ghost+++++++++
laver of water>>>>>>>>>saved
Three "born again" verses that have "water" equivalent to "baptized" which is equivalent to "laver of water". The Bible is truth and does not contradict itself going from one verse to another.
Lastly:
John 3:5-----------
born of water and of the Spirit>>>>>>>>>>>>>>enter into the kingdom
Matthew 7:21------
he that doeth the will of the Father>>>>>>>>>>>enters into the kingdom
Since there is just one way to be saved (enter the kingdom) then there has to be some definite connection between being "
born of water and of Spirit" and "
doing the will of the Father". Therefore being born again is a matter of "doing" on the part of man. God has commanded men to be water baptized and those that "do the will of the Father" in submitting to, obeying this command are the ones who are doing the will of the Father and are born again. There is no example in the NT gospel of one being born again by NOT doing the will of the Father.