There is obviously more than one baptism, as
Hebrews 6 says not laying again the foundation of "baptisms" ... plural. Baptism by water, and baptism in the spirit.
It is very important to note that Jesus' earthly ministry did not begin until he was baptized by John, and then the Holy Spirit descended upon Him. Jesus was baptized by water, and by the Holy Spirit, as an example for all believers.
For the apostles, there is no record of how they themselves were baptized, so we know it was not a simultaneous experience (both water and spirit occurring at the same time). No doubt they were baptized unto Jesus during the earthly ministry of Jesus, and later went on to be spirit baptized on the Day of Pentecost, (obviously because the Holy Spirit could not come upon them until the time appointed).
Today, we know that being baptized in water, and receiving the baptism of the Holy Spirit can be a single event with both water and spirit baptism happening together, or they can take place separately, but regardless.... if one wants to be a part of the body of Christ, a baptism of both water, and spirit is necessary to truly become part of the body of Christ, according to the doctrine of the apostles, and exampled by Jesus himself.