You need to read the passage in context to understand it.
You are just snipping bits out.
John 3:3-10
3. Jesus answered and said to him, “Amen, amen, I say to you, no one can see the kingdom of God without being born from above.”
- or born again; it involves a rebirth, a second birth
4. Nicodemus said to him, “How can a person once grown old be born again? Surely he cannot re-enter his mother’s womb and be born again, can he?”
- Nicodemus is thinking of physical birth
5. Jesus answered, “Amen, amen, I say to you, no one can enter the kingdom of God without being born of water and Spirit.
- Jesus is telling Nicodemus this is a different kind of birth, a birth of water and Spirit. He is not saying there are two births, one of water and one of Spirit, but that the new birth, the rebirth, is by water and Spirit.
6. What is born of flesh is flesh and what is born of spirit is spirit.
- the natural birth is of the flesh, but the rebirth is of the spirit (but is effected by water and spirit)
7. Do not be amazed that I told you, ‘You must be born from above.’
8. The wind blows where it wills, and you can hear the sound it makes, but you do not know where it comes from or where it goes; so it is with everyone who is born of the Spirit.”
9. Nicodemus answered and said to him, “How can this happen?”
- Nicodemus hasn’t understood
10. Jesus answered and said to him, “You are the teacher of Israel and you do not understand this?”
- Nicodemus is a scholar – he should have understood the words of Ez 36:25-27
I will sprinkle clean water upon you to cleanse you from all your impurities, and from all your idols I will cleanse you. I will give you a new heart and place a new spirit within you, taking from your bodies your stony hearts and giving you natural hearts. I will put my spirit within you and make you live by my statutes, careful to observe my decrees.
You see water and spirit.
Moreover Nicodemus should have understood that on previous occasions when God makes a new start he does so with water and Spirit:
1. At creation – Gen 1:1-2
In the beginning God created the heaven and the earth. And the earth was without form, and void; and darkness was upon the face of the deep. And the Spirit of God moved upon the face of the waters.
2. With the flood (Gen 7/8) God used water to cleanse the earth, then as the water subsided Noah sent out a dove “And the dove came in to him in the evening; and, lo, in her mouth was an olive leaf plucked off: so Noah knew that the waters were abated from off the earth. “ (Gen 8:11). The dove is a symbol of the Holy Spirit (cf Mt 3;16)
3. When God brought the Israelites out of Egypt to make them his people under the Siniai covenant he took them through the waters of the red sea and protected them by a pillar of cloud and fire (the Holy Spirit) – see also 1Cor 10:2
4. Jesus, the new Adam, is baptised in water and after that the Holy Spirit descends on him (Mt 3:13-16)
You see, each time water and spirit.
Immediately after this conversation with Nicodemus Jesus and his disciples go baptising with water. A co-incidence? I think not.
So where does that leave
Jesus answered, “Amen, amen, I say to you, no one can enter the kingdom of God without being born of water and Spirit (Jn 3:5)
Clearly baptism with water.