We need to be aware that when we read the next five chapters of John's Gospel, (13-17) we are reading about Jesus alone with his apostles in the upper room of a house, preparing to celebrate the Passover. No one else is there. He says some of the most intimate and personal things to them in these next chapters.
In fact, right away Jesus does something which would be shocking to them: he washes their feet. Why is this shocking? In this culture, the duty of foot-washing, especially of important guests, fell to a slave. This is why Peter doesn't want Jesus to wash his feet. It would be completely humiliating for Jesus, if Jesus had an ego. He's trying to tell us something, and later he will make it even more clear.
What about the water? The washing seems pretty important. I think there are two things going on here. The first is that Jesus and his apostles introduced a new baptism, which was greater than the one given by John the Baptist. Remember, John the Baptist said this: "I baptize you with water in keeping with repentance, but one will come after me, who will baptize with the Holy Spirit, and with fire." So, I think John's baptism was perhaps one where you confessed sins and promised to do better--which we can see if we go back to read that part--but the forgiveness of all sins, and the gift of the Holy Spirit, comes with Christian baptism. (See also Acts 2:37-41.) In any case, this foot-washing may well have been the Christian baptisms for the apostles. We don't have any verses in any of the Gospels describing their baptisms. (You may also want to take a look at Mark 16:16, to understand the link between baptism and the forgiveness of sins.)
Secondly, whenever priesthood in Israel was transferred from one to the next, there was a ceremonial washing, much like a baptism. Now, this is going to be a little bit different, because Jesus remains the great high priest, and when he dies, he won't stay dead, so he isn't so much passing on his priesthood, as he is sharing it.
With Judas Iscariot of course, he didn't receive the benefit of the forgiveness of sins, because he had a bad will, as the one who intended to betray Jesus. It is true for us as well: the only way not to receive the forgiveness of sins and the grace by which it comes, is to knowingly refuse it. We can think of Michael Corleone, near the end of The Godfather, serving as a Godfather to his sister Connie's baby. Normally doing so is a renewal of one's own baptism, as the person renounces sin and Satan, on behalf of the child. But obviously the man who was orchestrating multiple murders was not renouncing sin! So Judas wasn't fooling anyone, at least not Jesus.
You'll notice St. John sometimes takes a moment to explain what something means. Not all the Gospel writers do this, or at least not quite as often. One of the reasons is that the leaders of the Church came to St. John near the end of his life, to ask him to write this Gospel. The other three, Matthew, Mark, and Luke, had been known. This Gospel is special, because St. John was very close to our Lord, as one of his closest friends on Earth. I think it's fair to say that St. John's Gospel was used especially to spread the message of Jesus beyond the borders of Israel.
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