John 3:5 says by water and by Spirit. In my understanding of the word water here it doesn't mean actual water as in John's baptism for repentance as John said he must decrease and Jesus increase. Jesus was now that living water (word) who now had the power and authority to forgive sin. When Jesus was actually water baptized by John it was for the fulfillment of Gods righteousness in Him as Jesus received Gods power and authority at that time.There is nowhere in scripture that says the 12 Disciples or even Paul was water baptized, but only baptized in Christ by the word for repentance and then received the Holy Spirit before they could start their journeys.
Acts 1
1 The former treatise have I made, O Theophilus, of all that Jesus began both to do and teach,
2 Until the day in which he was taken up, after that he through the Holy Ghost had given commandments unto the apostles whom he had chosen:
3 To whom also he shewed himself alive after his passion by many infallible proofs, being seen of them forty days, and speaking of the things pertaining to the kingdom of God:
4 And, being assembled together with them, commanded them that they should not depart from Jerusalem, but wait for the promise of the Father, which, saith he, ye have heard of me.
5 For John truly baptized with water; but ye shall be baptized with the Holy Ghost not many days hence.
6 When they therefore were come together, they asked of him, saying, Lord, wilt thou at this time restore again the kingdom to Israel?
7 And he said unto them, It is not for you to know the times or the seasons, which the Father hath put in his own power.
8 But ye shall receive power, after that the Holy Ghost is come upon you: and ye shall be witnesses unto me both in Jerusalem, and in all Judaea, and in Samaria, and unto the uttermost part of the earth.
Acts 2:38 Then Peter said unto them, Repent, and be baptized every one of you in the name of Jesus Christ for the remission of sins, and ye shall receive the gift of the Holy Ghost.