Praised be Jesus and Mary, now and forever.
Most of the gospel according to John is structured around six signs or miracles. The seventh sign will be Jesus's resurrection. The miracle at the wedding of Cana was the first sign. The second was in yesterday's gospel and the third in today's.
As at Cana today, we hear of water in which Jews wash. At Cana, the water was for the ritual purification of the Jews. This water in the pool at the sheep gate seems to have been used for washing sheep before they were sacrificed in the temple but it was also a place of healing.
An ancient tradition explains that every so often an angel descended into the pool and stirred the waters. Whoever entered it first after the angel was healed. The central figure in today's gospel is a Jew who was ill for 38 years. Before Jesus was born this man was stricken with an illness for committing some sin. As Jesus himself says or indicates when he says to him do not sin anymore so that nothing worse may happen to you. This proves that some illnesses are punishments for sin. Not all are for Jesus said of the man born blind it was not that this man sinned or his parents but that the works of God might be displayed in him.
But as for those illnesses caused by sin, St. John Chrysostom explains even though our soul be afflicted with many ills, we are untroubled, whereas if our body receives even a small injury, we exert every effort to free it from its indisposition because we perceive this with our senses.
For this reason, God often punishes the body because of offenses committed by the soul so that by the chastisement of the inferior part the superior part may seek and obtain a cure.
There is some confusion in the Greek manuscripts about the name of this pool. If it was Bethesda its name can be interpreted as house of mercy. The man who sought who had sinned was suffering for it, and the man who had sinned and was suffering for it sought mercy and healing.
The first reading speaks of a healing water coming out of the temple, and the man sought healing near the temple, but 38 years passed, and while the man saw others healed, he was not healed.
His infirmity prevented him from going down into the water, and he had no man to help him.
The fathers of the Church explained the significance of these events. St. John Chrysostom says God was using that pool to prepare the Jews to accept baptism.
The water healed diseases of the body to prepare the people to believe that water could heal the diseases of the soul as happens in baptism. But it was not water alone that healed but water imbued with the heavenly power which the angel was bringing in the case of the pool.
Around the pool there were five porticoes, one on each of the four sides of the rectangular pool and a fifth that divided it in two. The five porticoes remind the fathers of the five books of the law of Moses. What does it signify that the Jew had no man to help him into the water and be healed? The law of Moses had an infirmity. It condemned sin, but it did not have sacraments to produce grace and heal of sin, and so because of this infirmity, the Jew could not enter the water. A man had to come and help him before he could be healed and this man was God. Jesus came and asked him, do you want to be well? St. Augustine points out that Jesus knew well what the man desired, but he asked in order to make known the man's patient endurance. 
This man waited 38 years like the Jews who were born after the exodus or born during the exodus after they left Egypt. The first generation who had been slaves in Egypt rebelled and so God made them wander in the desert for 38 more years until the rebellious generation had died and the faithful generation had taken his place. This new generation had to wait patiently until the 38 years were completed before they could enter the promised land. It is baptism that enables us to enter the promised land of heaven. 
Bethesda, the pool of mercy, is baptism. There the sheep are washed for we are his people and the sheep of his pasture. But baptism is greater than the pool that prefigured it as St. Chromatius of Aquileia explains. The water was stirred once a year. This water of the Church's baptism is always ready to be stirred. That water was stirred only in one location. This water is stirred throughout the whole world. There an angel came down, here the Holy Spirit. There the water healed only one person per year. Here it saves people daily.
That one delivered the body alone from a malady. This one delivers body and soul from sin. Once Jesus comes there is no longer any need for the water of the five porticoes. There is no longer any need for the ceremonial washing of the Jews. He says to the man, rise, take up your mat, and walk. God's command to rise gives him the power to rise. He is healed. To show that he has been completely healed in an instant, Jesus further commands him to take up his mat and walk.
But when some of the Jews saw him carrying his mat, they complained that he was breaking the Sabbath. Jesus didn't have to tell the man to carry his mat, so by his command he is showing that the Son of Man is Lord of the Sabbath. For his part, the man defends himself from the charge of violating the Sabbath by saying that the man who healed him told him to carry the mat. Who can heal a man in an instant after 38 years of illness except God? And if God did the miracle, doesn't that show that he approves of the command? 
The old precepts are passing away because what they prefigured has come. Besides baptism, there is also another kind of washing for the sheep. This one is accomplished just with words, with no water, and Jesus healed the man using only words.
This is confession, which is for those who have sinned as that man had sinned. So this is the sacrament with which St. Lawrence of Brindisi connects the miracle. Christ's words to the man show what we must do to be healed in the sacrament of confession. St. Lawrence explains, Christ told him to do three things, rise from his mat healed and saved, take up his mat as a sign of his cure and health with all his powers and strength divinely restored, and take his burden upon himself and walk. To walk with a heavy burden, moreover, requires not only health but also sufficient strength. So he says, rise up in your mind and heart from carnal and sensual affections, from vices to virtues, arise, stand up. Second, take up your mat. What used to mean rest and a place of leisure and pleasure has now become a burden to you. Your body, your flesh, your senses have become a burden to you because now you seek to avoid sin instead of consenting to it.
Before the flesh supported you in your life of sin, the flesh ruled over you. But now you must rule over your flesh and your body. So deny yourself and take up your cross. Finally, walk in the way of the Lord's commandments. Do not sin anymore, lest something worse happen to you.
When the man learned the name of the person who had healed him, he lost no time in proclaiming the good news. As Saint Augustine says, he told how he had been healed, but the Jews he told, instead of seeking healing themselves, plotted persecution. He was a grateful and happy Jew.
They were ungrateful and angry Jews. The grace that heals us in the sacraments flows from the heart of Christ, like the water that came from his pierced side on the cross. Christ’s body is the temple, the new covenant of which Ezekiel speaks. And the water flows from the right side of the temple because Christ's right side was pierced. The water grows as time goes on, as the number of people who receive the sacraments grows from one century to another.
At the beginning, it was a trickle. There were not many people in the Cenacle after Pentecost, but soon they became thousands and then millions and now over a billion.
Let us hasten to Jesus in confession to receive the healing water of his grace, and then show our gratitude for all God has given us. 
Praised be Jesus and Mary, now and forever.