Arno C. Gaebelein in The Gospel of John (Neptune: Loizeaux Brothers, 1965) writes, Water here is figurative of the Word of God as it is also in the thirteenth chapter, in connection with the feet washing of the disciples, and in Ephesians 5:26: The washing of water by the Word. Then there are three passages which show conclusively that the Word of God is meant: I Corinthians 4:15, for in Christ Jesus I have begotten you through the Gospel, James 1:18, Of His own will begat He us with the Word of Truth, and I Peter 1:23. In the last named passage Peter writes: Being born again, not of corruptible seed, but of incorruptible, by the Word of God, which liveth and abideth forever. This Petrine statement is sufficient to silence the view that water baptism is an agent in the new birth. . . . The Spirit of God uses the Word of God to bring about the new birth. Faith cometh by hearing and hearing cometh by the Word of God. The Word believed and accepted, the Holy Spirit accomplishes by His power the new birth, and the new nature, the eternal life is received
Arthur W. Pink in the Exposition of the Gospel of John (Grand Rapids: Zondervan, 1975) writes, If then the Lord Jesus used the word water emblematically in John 3:5, to what was He referring? We answer, The Word of God. This is ever the instrument used by God in regeneration
James Montgomery Boice in The Gospel of John, Vol. 1 (Grand Rapids: Baker Books, 2005, paperback edition) writes, Water is also a metaphor for the written Word of God, the Bible. Thus, Ephesians 5:26 says that Christ gave himself for the church to make her holy, cleansing her by the washing with water through the word. In I John the same author who composed the fourth Gospel distinguishes between the witnesses to Christ on earth of the Spirit, the water and the blood (I John 5:8). Since he then goes on to speak of Gods written witness to the fact that salvation is in Christ, in this context the Spirit must refer to Gods witness within the individual, the blood to the historical witness of Christs death, and the water to the Scriptures. Psalm 119:9 declares, How can a young man keep his way pure? By living according to your word. Jesus said, You are already clean because of the word I have spoken to you (John 15:3)