And he preached, saying, "There comes One after me who is mightier than I, whose sandal strap I am not worthy to stoop down and loose. "I indeed baptized you with water, but He will baptize you with the Holy Spirit." (Mark 1:7-8 NKJV)
After this, Jesus and his disciples went out into the Judean countryside, where he spent some time with them, and baptized. (John 3:22 NIV)
The Pharisees heard that Jesus was gaining and baptizing more disciples than John, although in fact it was not Jesus who baptized, but his disciples. (John 4:1-2 NIV)
When the day of Pentecost came, they were all together in one place...They saw what seemed to be tongues of fire that separated and came to rest on each of them. All of them were filled with the Holy Spirit… (Acts 2:1-4 TNIV)
"Repent," Peter said to them, "and be baptized, each of you, in the name of Jesus the Messiah for the forgiveness of your sins, and you will receive the gift of the Holy Spirit. (Acts 2:38 HCSB)
I've participated in churches of different denominations over the years. Most recently, I've served as the Lead Minister of a church. Now that I serve as lead minister, I have people who ask me questions about what kind of church we are. Often, they will ask if we are "Spirit Filled." I struggle with answering this question only because I know my answer will not match their question and I don't want to mislead.
The "Spirit Filled" question has to do with the thought that we need to be baptized in the Holy Spirit, as opposed to water like other churches. Sometimes people in these churches are baptized in water as well. Sometimes they are not. The key, though, is receiving Spirit baptism and seeing evidence of this occurring through Spirit Gifts (usually speaking in tongues).
The question then becomes this: "Was baptism referring to water or Spirit?"
When John (the baptist) performed his baptisms before the work of Jesus, it was a baptism for people who wanted to repent of their sins. The baptism was definitely in water. (He said so above.) He also said that someone would come after him who would baptize with the Holy Spirit. He was referring to Jesus.
Jesus was baptized in the water by John, not to repent of his sins (because he had not sinned) but to "fulfill all righteousness." God wanted Jesus to be baptized in this way to kick off his ministry. God used this moment to confirm Jesus as His Son and to add the Holy Spirit to the picture. The Holy Spirit descended upon Jesus in the form of a dove. For the first time, both water and Spirit were present.
Soon after, Jesus' followers began baptizing people (with water) to signify that they were now following Jesus. The Spirit is not connected to baptism again until after Jesus completed his work on the cross (dying and rising again on the third day, then ascending into heaven). He promised when he left that he would send his Spirit back to them.
This occurred on the day of Pentecost. This time the Holy Spirit descended upon the Apostles in the form of fiery tongues. They immediately started showing signs of the Holy Spirit working in them because they could speak other languages (tongues) that they did not know. Visiting foreigners could hear the Good News about Jesus in their own language!
When sharing the Good News with that crowd, they asked the apostles what they should do. "Repent and be baptized...and you will receive the gift of the Holy Spirit." They told people that day to be baptized in water to receive two gifts: forgiveness of sin and the gift of the Holy Spirit. That pattern continued throughout the rest of the New Testament.
Water and Spirit have both been present in baptisms from that day forward...even to today.