Matthew notes (Matthew 3:6) that John was baptizing in the Jordan river, but he does not record the question put by the Pharisees and recorded in John’s Gospel: ‘Why baptizest thou then, if thou be not that Christ, nor Elias, neither that prophet?’ (John 1:25). John’s answer, here however, apparently takes that question into account, when he says, ‘I indeed baptize you with water’, wording which seems to acknowledge such a question.
When does Christ baptize with the Holy Spirit? Paul teaches that every believer in the New Testament church has been baptized by one Spirit into the body of Christ (1 Corinthians 12:13). This baptism must therefore take place at the very beginning of the Christian life in order to include all. But John tells us that the Spirit was not yet given during the earthly ministry of Christ (John 7:39), because Christ had not yet been glorified, and he would only send his Spirit from heaven after he returned to heaven and his work of redemption was complete. For this reason the disciples were instructed to tarry at Jerusalem until they received power from on high (John 14:16, 26; Luke 24:49; Acts 1:8). On the day of Pentecost the New Testament church was inaugurated and received the Spirit for the first time. At that time there were special visible tokens given to indicate this and Christ baptized all who believed who were present in Jerusalem, but from then on, the baptism of the Spirit takes place at conversion for each individual believer.