Under the law God had given through Moses, Jewish people like Nicodemus entered into a covenant relationship with God by virtue of their physical birth into the nation (there was more to it than that, of course, but that was where it began). With the coming of Christ, covenant relationship no longer came through the flesh—it came through birth of the Spirit (John 1:12-13).
This is exactly what John the Baptist brought to Israel—the opportunity to be born from above. He showed up in the wilderness and was baptizing many people in connection with Christ and His coming kingdom. The Jewish leaders were suspicious and sent out a deputation to question the authority behind him baptizing (v. 19-28). Despite John’s testimony, they remained skeptical and rejected John and his baptism (Matthew 21:24ff). John then baptized Jesus who, through His disciples, baptized more people than John (3:22-26, 4:1-2).
In the middle of all of this, John (the writer of the gospel), wants to tell us the story of one of those Jewish leaders who came to Jesus at night. McGuiggan notes that, “Nicodemus wants to talk with Jesus about the kingdom. Jesus talks about water and Spirit.”
There was a reason for this. Nicodemus was part of the group that rejected the baptism from heaven (Matthew 21:24ff) so many others had embraced. By doing so, they had rejected God’s purpose for themselves (Luke 7:30). Nicodemus had the credentials of flesh, but not those of faith. Like the woman at the well, he wanted to talk about theology, but Jesus wanted to talk about obedience. (Theology that doesn’t become biography isn’t worth much).
But it simply can’t be true that dipping a penitent person in water can be that important, can it? It can’t really make a difference in where we stand with God, can it? Jesus seemed to think it did and made it His principle talking point with Nicodemus.
But it’s just water—there’s nothing magical about it. That’s absolutely true, but it’s also true that God has chosen the foolish things of the world to shame the wise. Furthermore, it is foolish as well as futile to try to evaluate the spiritual through the lens of the natural. We can’t deduce empirically how the Spirit works any more than we can see the wind. We only see its results. To deny that the Spirit works through water is to puts us at odds with Jesus and Scripture (Titus 3:3-5; 1 Peter 3:21-22).