In Acts 16:6 it says that the Holy Spirit has his own will and makes his own decisions. How is that?

Good question…the Father, Son, and Holy Spirit are One God but with 3 distinct manifestations or presences. Jesus had a mind and will of His own when He was here on earth, yet chose to be in agreement with His Father. So the Holy Spirit has a mind and will and is present with us today, other scriptures confirm this:

1 Corinthians 12:11 But all these worketh that one and the selfsame Spirit, dividing to every man severally as he will.

The Holy Spirit can even be grieved or saddened by man’s response to God:

Ephesians 4:30 And grieve not the Holy Spirit of God, whereby ye are sealed unto the day of redemption.

The Holy Spirit is a distinct Person in the Godhead and therefore has all the same attributes that the Father and Son also have. It is nice to know that since the beginning of time all three have been in perfect agreement, and Jesus prayed that we would share in this:

John 17:21 That they all may be one; as thou, Father, art in me, and I in thee, that they also may be one in us: that the world may believe that thou hast sent me.