All that verse indicates is that you need water for a 'water' baptism...In no way does it say that all baptisms are water baptisms...
Matthew 3:11 I baptize you with water for repentance, but he who is coming after me is mightier than I, whose sandals I am not worthy to carry. He will baptize you with the Holy Spirit and fire.
In the Holy Scripture there is no other kind when a baptismal rite is possible. So the Church would not give baptism other than in water. However, when we have evidence of conversion and desire for baptism, but the baptism is physically not possible because of involuntary death, like in the case of St. Dismas the Good Thief, then the person is considered baptized "by desire".