"Water and the Spirit," so closely followed by "that which is born of the flesh is flesh and that which is born of the Spirit is spirit" (and the fact that this is an explanation of "born again") makes it seem clear that "born of water" means the first birth and "born of the spirit" is the second birth.
Unborn babies live in the amniotic sack, also called “bag of waters,” until just prior to birth. They swim in it when still small enough to have room.
Unborn babies live in water for the entire pregnancy, and even breathe water in the later months.
It is certain that the idea of babies living in water before birth was widely known from the earliest of ancient times.* The amniotic fluid itself is clear. It can be mixed with some blood when it emerges, but this mixing happens after it breaks. A good bit of blood will be seen if the mucous plug which seals the uterus breaks free at the same time. This is called the “bloody show” and usually happens prior to the breaking of water. Even when mixed with the bloody show, it will generally be pretty obvious that the blood is a separate thing. It would be barely mixed in any case and not blended. It comes out in a big whoosh, as if a water balloon broke up in there. It is much like that. It is a bag of fluid which breaks, usually under the pressure of early contractions.
Therefore, “born of water” is a very natural term for physical birth. Add to this the fact that John had already contrasted physical birth with spiritual birth in the very first chapter (where the physical circumstance of blood is associated with physical birth), and I think the case is even stronger for interpreting John 3:5 as a contrast between physical birth and spiritual birth.
Which were born, not of blood, nor of the will of the flesh, nor of the will of man, but of God. (John 1:13.)
Of course, "the will of the flesh" and "the will of man" obviously indicates how the whole process of physical birth gets started.
However you interpret it, this passage must be reconciled with John 3:16; 3:18; 5:24, etc.--which would all be contradicted if it supported the idea of baptismal regeneration (as some claim).
Ed
*Note: Speaking of water, Gregory Nazianzen wrote "And this which comes to the aid of our first (physical) birth, makes us new instead of old, and like God instead of what we now are; recasting us without fire, and creating us anew without breaking us up."
Oration 40 (on Holy Baptism.)
In the Jewish Talmud, Rabbi Eliezer wrote "a fetus inside the womb is like a nut placed inside a bladder of water. If you press your finger on the bladder, the nut recedes." (Niddah 31)
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