A. Christian Baptisms are Trinitarian.
The first and most obvious distinction is that valid Christian baptisms are Trinitarian. John the Baptist viewed himself as simply one preparing a way for Christ (as Matthew 3:3 and Luke 3:4-6 remind us), by drawing us away from our attachment to sin. Acts 19:1-7 makes it abundantly clear that John's Baptism is a preparatory Baptism, to bring people to repentance and to prepare them for Christ and His Baptism - it's not the equal to a Christian Baptism. And the Baptism of Jesus Christ is "in the name of the Father, and of the Son, and of the Holy Spirit," as Matthew 28:17 tells us. This distinction is important, because it's modeled after Jesus' own Baptism, where the Holy Spirit proceeded from the Father to the Son (Matthew 3:16-17 lays this out beautifully).
B. Both Christian Baptisms in Water and "in the Spirit" impart the Holy Spirit, but in Different Ways.
But there's a second, related distinction. A Christian Baptism actually bestows the Holy Spirit. Just as in Jesus' Baptism, the Holy Spirit descended like "like a dove" onto Christ (Matthew 3:16), a valid Christian Baptism does the same. After all, here's how John distinguished his Baptism from the Christian Baptism he knew was coming. Of Jesus, he said, "I am baptizing you with water, for repentance, but the one who is coming after me is mightier than I. I am not worthy to carry his sandals. He will baptize you with the Holy Spirit and fire" (Matthew 3:11). Mark's Gospel, which records it (in Mark 1:8) simply as "I have baptized you with water; He will baptize you with the Holy Spirit," makes it clear that "the Holy Spirit and fire" are not two distinct things, but interrelated: the fire is the Fire of the Holy Ghost. Additionally, the Book of Acts (in particular) makes it clear that the Holy Spirit and fire are in addition to water, not in place of water. Shortly before Pentecost, Jesus reminds them of this promise: "John baptized with water, but in a few days you will be baptized with the Holy Spirit" (Acts 1:5). In Acts 2, at Pentecost, the Holy Spirit descends upon them and they're filled with this fire.
Here, though, is where a lot of Christians get confused. Since the Baptism of the Holy Spirit occurs at Pentecost, does that mean that Trinitarian water Baptisms don't bestow the Holy Spirit? After all, the Disciples at this moment aren't undergoing a water Baptism: in fact, we can surmise that since during Jesus' public ministry, they baptized more than John the Baptist himself (John 4:1-2), that they'd already been Baptized themselves. They'd also already received the Holy Spirit in various forms (e.g., John 20:21-23). But the full Baptism in the Holy Spirit takes place as a separate event.
The Apostles, however, clearly think that both water Baptisms and Baptisms in the Holy Spirit impart the Holy Spirit, but in different ways. Peter said to the crowd at Pentecost, "Repent and be baptized, every one of you, in the name of Jesus Christ for the forgiveness of your sins; and you will receive the gift of the Holy Spirit" (Acts 2:38). Later, though, in Acts 8:14-17, we hear:
Now when the apostles in Jerusalem heard that Samaria had accepted the word of God, they sent them Peter and John, who went down and prayed for them, that they might receive the Holy Spirit, for it had not yet fallen upon any of them; they had only been baptized in the name of the Lord Jesus. Then Peter and John placed their hands on them, and they received the Holy Spirit.So Baptism "in the name of Jesus" (that is, a Trinitarian Baptism; it's being distinguished from the Baptism of John here) actually imparts the gifts of the Holy Spirit; but there's a separate rite which bestows the Holy Spirit in a distinct and powerful way through the laying on of hands (which Acts 8:18-19 makes clear also actually imparts the Spirit). Hebrews 6:2, like much of the New Testament, draws a distinction between these two events, as well.
C. What This Means for Baptism and Confirmation
What occurred at Pentecost is what we now call Confirmation, and the Catechism makes clear it's the same gift of the Holy Spirit as occurred upon that day (CCC 1302). Catholics and Eastern Orthodox follow the Biblical practice of considering water Baptism and Confirmation as distinct things, although sometimes they're received at the same time, as is the norm in the East (CCC 1290). This variance also seems to have been the norm in New Testament times: some people seem to receive everything at once, while others receive one and then the other. In a few unusual cases, Confirmation has preceded Baptism. A guy called St. Paul seems to have received them in reverse. In Acts 9:17-18, Ananias lays hands on him and fills him with the Holy Spirit, and then Paul gets up and is Baptized. Likewise, in Acts 10:44-46, the Holy Spirit descends upon a group of Gentiles listening to Peter speak. Peter calls this a Baptism in the Holy Spirit in Acts 11:16, and his response at the time was to command them to be Baptized in water (Acts 10:47-48).
D. Why Have Both?
So why have two forms of Baptism - Baptism in water and Baptism in the Spirit - if both bestow the Holy Spirit? The answer is easy enough. Baptism is intended for us. It does two things: it cleanses us from sin, and it enters us into the Body of Christ, the Church. Confirmation, in contrast, is intended for others: we're given these gifts to build up the Body of Christ and to draw others into it. 1 Corinthians 12 and various other places through the New Testament (and other early Christian writings) enumerate these spiritual gifts and their purpose.
In fact, this distinction seems to explain the two times Confirmation and Baptism occurred in reverse order. Peter is talking to a group of Gentiles who he's not sure he's even able to Baptize. Ananias has gone to Saul, a notorious persecutor of Christians. The Holy Spirit, by descending upon these people, signals to Peter and Ananias that it's ok to Baptize them.
E. What's the Biblical Support for the Power of Water Baptism?
So here are some of the Biblical passages which support the notion that water Baptisms actually cleanse us from sin, something which many Protestants question today:
* As mentioned, even after Paul has received the Holy Spirit in Acts 9:17-18, he's told to get up and be Baptized. But this Baptism is not merely symbolic. As Paul recounts in Acts 22:16, this was to "wash [his] sins away." At least some Protestants have come to the strange conclusion that this was not a water Baptism, but it clearly is. It occurs after the Baptism with the Holy Spirit, so it can't be held to be the same thing. Likewise, we know from Acts 8:36-38 that this involved literal water.
* In Galatians 3:27, Paul tells us that "all of you who were baptized into Christ have clothed yourselves with Christ."
* St. Peter, in 1 Peter 3:20-22, compares the waters surrounding Noah's Ark to Baptism. Of the Ark, he says:
In it only a few people, eight in all, were saved through water, and this water symbolizes Baptism that now saves you also-not the removal of dirt from the body but the pledge of a good conscience toward God. It saves you by the resurrection of Jesus Christ, who has gone into heaven and is at God's right hand-with angels, authorities and powers in submission to him. * HEBREWS 10:22 TELLS US TO "draw near to God with a sincere heart in full assurance of faith, having our hearts sprinkled to cleanse us from a guilty conscience and having our bodies washed with pure water."
* Paul says that Jesus "loved the Church and gave Himself up for Her to make Her holy, cleansing
