John 3:3-7
3 Jesus answered and said unto him, Verily, verily, I say unto thee, Except a man be born again, he cannot see the kingdom of God.
4 Nicodemus saith unto him, How can a man be born when he is old? can he enter the second time into his mother's womb, and be born?
5 Jesus answered, Verily, verily, I say unto thee, Except a man be born of water and of 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.
7 Marvel not that I said unto thee, Ye must be born again.
The Grace New Testament Commentary - John 3:5-6
3:5-6 There are three main views of "born of water and the Spirit." The baptismal regeneration view is contrary to John's Gospel and the entire NT, since believing, not baptism, is the sole condition of eternal life. The symbol of regeneration view understands the expression born of water and the Spirit to refer to the life-giving work of the Holy Spirit parallel to "born of the Spirit" in v 6. Water is an OT figure for the life-giving work of the Spirit (Isa 44:3-5). While possible, there is a simpler understanding. The third view is that by born of water refers to physical birth (and to amniotic fluid) and that born of the Spirit refers to spiritual birth (regeneration). Two facts support this view. First, v 6 is parallel to v 5 and serves to explain it and it speaks of both physical and spiritual birth. Second, Nicodemus was clearly thinking about physical birth (v 4). While it is possible that Jesus would speak of spiritual birth only in v 5 (the symbol of regeneration view) and then talk of both physical and spiritual birth in v 6, it is more natural to take both verses as dealing with physical and spiritual birth.
Thomas Constable's Expository Notes on the Bible - John 3:5
3:5 The definite article translated "the" before "Spirit" is absent in the Greek text. The English translators have inserted it to clarify their interpretation of "spirit" (Gr. pneuma) as the Holy Spirit. A more literal translation would be simply "born of water and spirit."
The construction of the phrase being born of water and the Spirit in the Greek text indicates that the preposition "of" governs both water and Spirit. This means that Jesus was clarifying regeneration by using two terms that both describe the new birth. He was not saying that two separate things have to be present for regeneration to take place. It has but one Source. Jesus' criticism of Nicodemus for not understanding these things (v. 10) indicates that what He taught about the Source of regeneration was clear in the Old Testament.
The only view that seems to be consistent with all of these factors is as follows: The Old Testament often used "water" metaphorically in order to symbolize spiritual cleansing and renewal (Num. 19:17-19; Isa. 55:1-3; cf. Ps. 51:10; Jer. 2:13; 17:13; Zech. 14:8). God's "spirit" (or "Spirit") in the Old Testament represents God's life (Gen. 1:2; 2:7; 6:3; Job 34:14). God previously promised that He would pour out His Spirit on people like water (Isa. 32:15-16; Joel 2:28-29). The result of that outpouring would be a new heart for those on whom the Spirit came (Jer. 31:31-34; Ezek. 36:26). Thus the revelation that God would bring cleansing and renewal like water, by means of or affected by His Spirit, was clear in the Old Testament.
Another popular view is that "water" refers to the written Word of God, and "spirit" refers to the Holy Spirit. This figurative use of "water" does exist in the New Testament (cf. Eph. 5:26), but it is uncommon in the Old Testament. It is unlikely that Nicodemus would have associated water with the Word of God, and it would have been unfair for Jesus to rebuke him for not having done so. This view, like the former one, also specifies two separate entities. But again, the Greek text implies only one as the source of regeneration.
Some commentators take the "water" as an allusion to water baptism, and the "spirit" as referring to the Holy Spirit. According to this view spiritual birth happens only when a person undergoes water baptism, and as a result experiences regeneration by the Holy Spirit. Some advocates of this view see support for it in the previous reference to water baptism (1:26, 33). But Scripture is very clear that water baptism is a testimony to salvation, not a prerequisite for it (cf. John 3:16, 36; Eph. 2:8-9; Titus 3:5). In addition, this meaning would have had no significance for Nicodemus. He knew nothing of Christian baptism. Furthermore, Jesus never mentioned water baptism again in clarifying the new birth to Nicodemus.
Ruckman Reference Bible - John 3:5
3:5 Christ changes "born again" (vs. 3) to "born of water and of the Spirit" in answer to Nicodemus' question in verse 4. "Born of water" is obviously a reference to the first birth, the physical birth, just as it is in Genesis 1:20, Isaiah 48:1, and Proverbs 5:16-18. That is why Jesus says that "born of water" is "born of the flesh" in verse 6. It has no reference to baptism of any kind.