John 3:5–6 says, “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. That which is born of the flesh is flesh; and that which is born of the Spirit is spirit.”
We must ask what being “born of water” would have meant to Nicodemus. In his commentary on John, Leon Morris writes:
Nicodemus could not possibly have perceived an allusion to an as yet non-existent sacrament. It is difficult to think that Jesus would have spoken in such a way that His meaning could not possibly be grasped. His purpose was not to mystify but to enlighten. In any case the whole thrust of the passage is to put the emphasis on the activity of the Spirit, not on any rite of the church. (The Gospel according to John (Grand Rapids: Eerdmans, 1995): 215–16)
The emphasis throughout the passage is on the Spirit, with no other reference to water. Verse 6 shows that, as each of us has had a physical birth, so we must have a spiritual birth to enter the kingdom of God.