Jesus answered, “Very truly I tell you, no one can enter the kingdom of God unless they are born of water and the Spirit. John 3:5
In order to understand this verse we must look at the whole dialogue.
Jesus replied, “Very truly I tell you, no one can see the kingdom of God unless they are born again.” “How can someone be born when they are old?” Nicodemus asked. “Surely they cannot enter a second time into their mother’s womb to be born!” John 3:3- 4
We see that a person must be born of water and the Spirit. When it refers here to the water it refers to be being physifically born and born of the Spirit is to become a child of God. This is clarified in the following verses John 3:6-8
Flesh gives birth to flesh, but the Spirit gives birth to spirit. You should not be surprised at my saying, ‘You must be born again.’ The wind blows wherever it pleases. You hear its sound, but you cannot tell where it comes from or where it is going. So it is with everyone born of the Spirit.” John 3:6-8
When we continue reading we see clearly that Jesus makes the distinction of being physically born and Spiritually born. Then he describes how the Spirit takes posesion. If we accepted that being born of water refered to water baptism, then we would have to accept that there should be three births and Jesus says they are born again (second time spiritually, not a third one). As humans we are born of water naturally but in order to be children of God we have to be born of the Spirit.
So in this dialogue with Nicodemus Jesus was not commanding us to water baptise he was simply telling us that we do have to be physically born and Spiritually born. When Jesus says flesh gives birth to flesh and Spirit gives birth to spirit, it refers to many verses in the bible about being born of the Spirit in order to become children of God.
Yet to all who did receive him, to those who believed in his name, he gave the right to become children of God—children born not of natural descent, nor of human decision or a husband’s will, but born of God. John 1:13-14
because those who are led by the Spirit of God are sons of God.
At that time the son born in the ordinary way persecuted the son born by the power of the Spirit. It is the same now.
He chose to give us birth through the word of truth, that we might be a kind of firstfruits of all he created. James 1:18
For you have been born again, not of perishable seed, but of imperishable, through the living and enduring word of God.
1 Peter 1:23
If you know that he is righteous, you know that everyone who does what is right has been born of him.
1 John 2:29
No one who is born of God will continue to sin, because God’s seed remains in him; he cannot go on sinning, because he has been born of God.
1 John 3:9
Everyone who loves has been born of God and knows God.
1 John 4:7
Everyone who believes that Jesus is the Christ is born of God
1 John 5:1
for everyone born of God overcomes the world. This is the victory that has overcome the world, even our faith.
1 John 5:4
Being born of God is being born of Spirit because God is Spirit
God is spirit, and his worshipers must worship in the Spirit and in truth. John 4:24
Another example that being of born of water does mean physically born and not water baptism is 1 John 5:6
This is the one who came by water and blood–Jesus Christ. He did not come by water only, but by water and blood. And it is the Spirit who testifies, because the Spirit is the truth.
1 John 5:7
This verse is not refering to water baptism when it says that Jesus came by water its refering that he was physically born. In this letter John was warning Christians about gnosticism (the denial of Jesus’ incarnation). In 1 John 4:2-3 It tells us that Jesus was born in the flesh.
This is how you can recognize the Spirit of God: Every spirit that acknowledges that Jesus Christ has come in the flesh is from God, but every spirit that does not acknowledge Jesus (came in the flesh) is not from God. This is the spirit of the antichrist, which you have heard is coming and even now is already in the world.
1 John 4:2
Jesus did come by water to be human and the Spirit does testify this.
The Word became flesh and made his dwelling among us. We have seen his glory, the glory of the one and only Son, who came from the Father, full of grace and truth. John 1:14
regarding his Son, who as to his human nature was a descendant of David, and who through the Spirit of holiness was declared with power to be the Son of God by his resurrection from the dead: Jesus Christ our Lord. Romans 1:3-4
Jesus had to come through water in order to be human, just like we are born of water because everything born of flesh is flesh and that which is born of Spirit is spirit. We have to be born again of Spirit to see the kingdom of God.
We have been born of water therefore flesh but are we willing to be born of the Spirit in order to be Children of God?