The birth “of water and the Spirit” spoken of is obviously baptism. But it is not any baptism at all, but that which contains, beneath the visible sign, the invisible reality, if such an expression be permissible: the Spirit—and Jesus shows the contrast between the power of the spirit and that of the flesh (that is, as always in John’s terminology, human nature in itself, left to its creaturely infirmity). It is important to clarify the characteristic mark given here of the Spirit within us: his power by its very nature eludes our understanding.
We cannot, anymore than Nicodemus could, deny Jesus’ supernatural character: it thrusts itself on our notice by its effects, but our attempts at a human explanation of these are fruitless:
“The wind (In Greek, the same word means “wind” and “Spirit”) blows where it will, and thou hearest its sound, But dost not know where it comes from or where it goes.”
Nicodemus’s answer shows that his doubt, though lessened, is not yet resolved:
“How can these things be?”
Now he is clearly aware that the matter in question is quite different from what he thought; but is he not held back by just that inevitable necessity of giving up those traditions of thought and habits of mind common among devout Jews of the time? Hence Jesus’ almost bitter retort: just now Nicodemus called him “teacher,” but of the two speakers, it is officially he who can claim the title by right; but here is the “teacher in Israel” admitting he cannot understand even the most ordinary elements of the Kingdom of God.
12. If I have spoken of earthly things to you, and you do not believe, how will you believe if I speak to you of heavenly things?
13. (And no one has ascended into heaven except him who has descended from heaven; the Son of Man.)
By this transition we pass from baptism, which confers the gift of the Spirit on men, to the work of salvation, worked by the Son of Man, the source of baptism and the cause of the outpouring of the Spirit. Baptism and the Life resulting from it in us take place on earth: the death and resurrection of the Son of Man ascending to heaven are events in heaven (cf. in the Apocalypse, the lamb sacrificed in heaven [Ch. 5]). (Louis Bouyer, The Fourth Gospel [trans. Patrick Byrne; Athlone, Ireland: St. Paul’s Publications, 1962], 79-80)
