Greek lexicons do not think it is speculation that water refers to the Holy Spirit:
1. Brown: For the final future of their nation the prophets hoped for an eschatological sprinkling with God's purifying water which would cleanse both land and people, set idolatry aside and put a new Spirit in their hearts (Isa. 44:3; Ezek.26:25ff.; Zech 13:1f.). Here water has become a picture for the Spirit of Yahweh who brings cleansing and eradicates wickedness (NIDNTT 3:989, Water).
2. Vine: Some regard the kai, "and," in John 3:5, as epexegetic, = 'even,' in which case the water would be emblematic of the Spirit, as in John 7:38 (cp. 4:10, 14) (Vine's Expository Dictionary of Old and New Testament Words, water, page 1214).
3. Wuest: One of the basic rules of interpretation is to ascertain just what the Word of God meant to the one who recorded it, and to the one who received it at the time it was written. Another rule of interpretation is to take into consideration the other uses of the same term in other places. Our Lord was talking to a man who was learned in the Old Testament scriptures. He would be expected to use Jewish phraseology in a case like this. In John 7:37, 38, He uses the word "water" as referring to the Holy Spirit. When speaking to the Samaritan woman who as a Samaritan was familiar at least with the Pentateuch, He uses the word "water" in such a way that we are led to believe that He referred to the Holy Spirit, because He speaks of the water which He will give, as a spring of water leaping up into life eternal. In neither place does He explain the symbol, John finding it necessary to do so in 7:39, and for the reason that he is writing for Gentile believers. Nicodemus, as a Jewish theologian, is supposed to have been familiar with Isaiah 44:3, where water is a type of the Holy Spirit, and also with Isaiah 55:1, where the prophet says, "Ho, every one that thirsteth, come ye to the waters." These considerations lead the writer to incline to the interpretation that the word "water" here was used by Jesus as a symbol of the Holy Spirit as He does in the case of the Samaritan woman and also when He spoke at the great day of the feast. The Greek word translated "and" has other uses than merely that of a connective. It has an emphatic or ascensive use, and is at that time translated by the word "even". Thus, the translation here could read, "Except a man be born of water, even of the Spirit, he cannot enter into the kingdom of God." Another consideration pointing to this interpretation and translation is the fact that when Jesus recurs again to the new birth in verse 6 and 8, He does not refer to water at all, but only to the Spirit. Evidently seeing the blank look on the face of Nicodemus, our Lord adds the words "even of the Spirit," thus explaining the symbol to this theologian of the Old Testament who should have understood it (Word Studies in the Greek New Testament 3:56, 57, Jesus and Nicodemus, #2).
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