Even though there is no specific command in John’s Gospel concerning the need for baptism, it is significant that John’s Gospel is the only gospel which records that baptism was an important part of Jesus’ public ministry. In John 3:22, the author records that Jesus “baptized” a large number of people, so much so that his ministry of baptism began to eclipse the widely popular ministry of John the Baptist. Even though this verse records that Jesus “baptized,” John 4:2 records that Jesus did not actually baptize anyone himself; rather he authorized his disciples to perform baptism on his behalf. But even though Jesus did not personally conduct baptisms, it is clear from the Gospel of John that baptism in water was important in the ministry of Jesus. This aspect of Jesus’ ministry is something that we do not see in the Synoptics.
The meaning given to baptism in John’s Gospel is also worthy of consideration. Baptism is linked to discipleship in the sense that submission to Jesus’ baptism was the initial formal step by which a person became a disciple of Jesus. This is clear from the wording of John 4:1, which says that “Jesus was making and baptizing more disciples and John.” This link between baptism and discipleship is echoed in the theology of the Great Commission in Matt 28:19, where it is taught that disciples are formally “made” through baptism. Having been baptized, the disciple is then obligated to learn from his or her master, to follow his example (John 13:14–15), by keeping the master’s teaching (John 17:6), and obeying his commandments (Matt 28:20; John 15:10). By keeping the master’s commandments, the disciple remains in the master’s love (John 15:10).
There has been a great deal of debate over whether or not Jesus’ teaching concerning rebirth “by water and spirit” in John 3:5 is a reference to Christian baptism. It is best to take these words spoken by Jesus in his dialogue with Nicodemus as teaching about the need for conversion by the Holy Spirit, with water (as is usual in John’s Gospel) being a metaphor for the Holy Spirit. At the same time, however, this metaphor lends itself to seeing a close connection between physical water and the Holy Spirit. The practice of Gentile proselyte baptism, in which Gentile converts to Judaism were considered to become like newborn children makes it quite likely that the word water would have conveyed the idea of baptism, or at least some kind of ceremonial washing, to a Jewish audience. Ezekiel 36:24–27 also connects the future work of the Spirit with the image of water sprinkled upon Israel in order to cleanse her from her uncleanness.
Since conversion or baptism by the Holy Spirit is paralleled in John 3:15–16, 18 with believing in Jesus, the obvious conclusion that must be drawn is that the new birth (i.e., baptism in the Holy Spirit) begins (for the adult convert) when one confesses faith in Jesus Christ. For the early church, the Christian confession of faith consisted of a public confession of belief in Jesus as Messiah using the formula (in a Jewish context) I believe that Jesus is the Christ (John 20:31), or I believe that Jesus Christ is the Son of God (Acts 8:37), which became in a Gentile context the confession that Jesus is Lord (Rom 10:9). The practice of the early church was that a person’s confession of faith in Jesus would be formally sealed in the act of baptism, which was performed immediately upon confession of faith. The book of Acts records no less than nine instances of converts being baptized immediately (or “at once” according to Acts 16:33) upon confession of faith. These are: the 3,000 converted at Pentecost (Acts 2:38,41); the Samaritans (8:12); the Ethiopian eunuch (8:37–38); the Apostle Paul (9:18; 22:16); the first Gentile converts (10:47–48); Lydia (16:14–15); the Philippian jailer (16:31–33); the Corinthians (18:8); and the twelve disciples of John the Baptist (19:3–5). This indicates that the early church thought of baptism as an integral part of conversion (hence, Peter could teach in 1 Pet 3:21 that “baptism … saves you”). Furthermore, it was the belief of the early church that the eschatological gift of the Holy Spirit was ordinarily received through Christian baptism (Acts 2:38, 41; 5:32; 19:2; 1 Cor 12:13; Tit 3:5), following the model of Jesus’ baptism, in which there was a conjunction of water and the Holy Spirit (Luke 3:21–22). Exceptions to the rule of the conjunction of water and the Holy Spirit in baptism only happened at special stages in God’s plan of salvation, such as at Pentecost (Acts 2:1–4) and upon the conversion of the Samaritans (Acts 8:14–17) and the first Gentiles (Acts 10:44–48).
Because this concept of the conjunction of water and the Holy Spirit in baptism was prevalent in the early church, it is most likely that John’s Christian audience, and non-Christians acquainted with Christian religious practices, would have understood the phrase of water and spirit as having some kind of link with Christian baptism. Thus, Jesus’ teaching in John 3:5 can be understood as an implied call for non-believers to convert to Christianity, i.e., to be baptized and to become disciples of Jesus Christ, similar to the teaching of the early church that is recorded in Mark 16:16: “He who believes and is baptized will be saved.”
In sum, it is best to take the primary reference of the words of water and spirit on the lips of Jesus as referring to conversion by the Spirit, but at the same time this implies the necessity of Christian baptism, because baptism in water and the Spirit were ordinarily viewed in the early church as happening together as part of the process of conversion.