Pamela Ayn Austen
Water and Spirit
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5. Jesus answered, “Truly, truly, I tell you, no one can enter the kingdom of God unless he is born of water and the Spirit.
Water in Scripture represents God's grace, and before the Holy Spirit is given to us, we must humble ourselves before God and receive his grace and forgiveness. This is the water and the Spirit from which we are born into the Kingdom of God.
We are born into the Spirit and into the Kingdom of God in just this way: we confess our sins before the Lord and ask for his forgiveness and salvation; and he, by his grace, forgives us and washes us clean of our sins; and then he gives us the gift of his Holy Spirit. We are born again, not of flesh, but of the spirit, and we are born into the fellowship of God's children.
I heard a pastor once claim that the water Jesus speaks of here is the water of the amniotic fluid within the womb, and that a person must be born physically before he can be born spiritually, but that's just not true. Jesus said, "The flesh profits nothing; it is the Spirit that gives life." Jesus spoke in parables and he used symbolism to represent spiritual things; and water is the spiritual symbol of grace. And throughout all of Scripture, we're told that we are saved by grace; and Jesus sends us the Holy Spirit to lead us into all truth and to seal us for the day of the Lord. To show that water here is not actual water but spiritual water (grace), in the next story in John, Jesus asks the woman at the well for water, and then says to her, "Whoever drinks this water will thirst again; but whoever drinks the water that I give will never thirst. The water that I give will become in them a spring of water gushing up to eternal life." 4:13-14
John the Baptist first came preaching and baptizing people in water, requiring them to repent of their sins. Only after John's water baptism, or rather, God's symbol of his grace, did Jesus come bringing our baptism into the Holy Spirit. So we have water and the Spirit here: Grace and the Holy Spirit. John and Jesus together picture the birthing of sinners into God's spiritual kingdom through Water and Spirit.
At the wedding in Cana, Jesus told the servants to fill the jars with water, and only afterward did he turn it into wine, with water being the symbol of our preparation to receive the Lord's Spirit. Our preparation to receive Jesus is by our repentance and faith in him, and thereby, we are shown grace. That is the first step toward receiving eternal salvation. The water must come first; and so our humility and repentance must also come first.
Scripture says, "Prepare the way of the Lord, make his paths straight." Isaiah 40:3 We must prepare for the Lord to come into our lives, and we must make a straight path for him by repenting of our hardness of heart and lack of faith. We all commit many sins, and we can't repent of them all at once with any degree of success, but there is one sin we must repent of before Jesus will come into our heart and life, and that sin is a lack of faith in Jesus, and all that Jesus said about himself and the Father. We must repent of our lack of faith before Jesus will respond to us and give us his Holy Spirit and eternal life.
When the Roman soldier pierced Jesus's side with a sword, after Jesus had died on the cross for us, both water and blood came out of him. Within Jesus's body was housed all that we need to be saved and have eternal life. Within Jesus was both the water, which is God's grace, and the blood of atonement, which enables the Holy Spirit to be given to us. Within Jesus's body was our entire eternal salvation; and by our faith, the Father gives us all of his Son, and all we need to live with God forever.
So that is how we are born again: through the water of God's grace, and the gift of his Holy Spirit. First comes the water of grace, and then comes the Holy Spirit. First comes baptism in water, and then comes the baptism of the Holy Spirit. First came John the Baptist, then came Jesus. First came water, then came wine.
See also my article about what water symbolizes here.