John 3:1 Now there was a man of the Pharisees, named Nicodemus, a ruler of the Jews; 2 this man came to Jesus by night and said to Him, “Rabbi, we know that You have come from God as a teacher; for no one can do these signs that You do unless God is with him.” 3 Jesus answered and said to him, “Truly, truly, I say to you, unless one is born again he cannot see the kingdom of God.” 4 Nicodemus said to Him, “How can a man be born when he is old? He cannot enter a second time into his mother’s womb and be born, can he?” 5 Jesus answered, “Truly, truly, I say to you, unless one is born of water and the Spirit he cannot enter into the kingdom of God. 6 That which is born of the flesh is flesh, and that which is born of the Spirit is spirit.”
The phrase “of water and the Spirit” has been interpreted in various ways. Calvin notes that “water” has most commonly been understood to signify baptism, but disagrees with that opinion. I take the view of Calvin:
[Jesus] employed the words Spirit and water to mean the same thing, and this ought not to be regarded as a harsh or forced interpretation; for it is a frequent and common way of speaking in Scripture, when the Spirit is mentioned, to add the word Water or Fire, expressing his power. We sometimes meet with the statement, that it is Christ who baptizeth with the Holy Ghost and with fire, (Matth. iii. 11; Luke iii. 16,) where fire means nothing different from the Spirit, but only shows what is his efficacy in us. As to the word water being placed first, it is of little consequence; or rather, this mode of speaking flows more naturally than the other, because the metaphor is followed by a plain and direct statement, as if Christ had said that no man is a son of God until he has been renewed by water, and that this water is the Spirit who cleanseth us anew and who, by spreading his energy over us, imparts to us the rigor of the heavenly life, though by nature we are utterly dry. And most properly does Christ, in order to reprove Nicodemus for his ignorance, employ a form of expression which is common in Scripture; for Nicodemus ought at length to have acknowledged, that what Christ had said was taken from the ordinary doctrine of the Prophets.
By water, therefore, is meant nothing more than the inward purification and invigoration which is produced by the Holy Spirit. Besides, it is not unusual to employ the word and instead of that is, when the latter clause is intended to explain the former. And the view which I have taken is supported by what follows; for when Christ immediately proceeds to assign the reason why we must be born again, without mentioning the water, he shows that the newness of life which he requires is produced by the Spirit alone; whence it follows, that water must not be separated from the Spirit.—John Calvin, Calvin’s Commentaries Volume XVII, Commentary on the Gospel according to John Volume I (Baker Books, 2009), 111–112.
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