I regret to say I do not know of a book or website that focuses specifically on extracting moral lessons from stories in the Bible, but I can point you to a Protestant source that helps to explain the Christian perspective and lessons to be learned from the miracles performed by Jesus.
One important lesson to be learned from the account of Peter walking on the water to meet Jesus is that although he literally stepped out in faith, he soon became fearful and began to sink – his faith was short-lived:
Peter’s exercise of faith does not end in failure. Although he is sinking in fear, he calls out to the Lord, “Save me!” God loves to hear our cry for help. It means we know we can’t save ourselves. Peter helplessly cries out to the only one who can help him. The disciple’s experience reminds us that a lapse of faith is merely a stumble. The Lord is near to raise us back safely to our feet when we call to Him for help. Source: https://www.gotquestions.org/Peter-walking-on-water.html
Linked to this is the meaning behind Jesus walking on the stormy Sea of Galilee to meet his disciples already in the boat:
When the disciples saw Jesus walking on the lake, they thought He was a ghost. They cried out, because they all saw Him and were terrified (Mark 6:48–50). And this brings us to the second significant point of this miracle. Jesus always comes to us in the storms of life... The point is this: fear and faith cannot live in the same heart, for fear frequently blinds the eyes to the presence of the Lord. Source: https://www.gotquestions.org/walking-on-water.html
Other important lessons can be learned from the incident when Jesus was in a boat with the other disciples and a storm arose. The disciples were afraid for their lives, but Jesus quelled the storm:
The apostles’ lack of faith reminds us that even those who lived and walked with Jesus, saw His miracles, and heard His message still found it difficult to be 100 percent faith-filled all the time. In that way, the disciples were a lot like us. If Jesus was able to rescue the apostles from the storm, He is also able to rescue us from the storms of everyday life: sickness, job loss, marriage problems, and even the sting of death (1 Corinthians 15:55). The Lord never promised we will never see a storm in life (as a matter of fact, He has told us to expect trouble, John 16:33). Rather, He has promised that He will be with us in the storm. He will never leave His children alone in the midst of trouble; with perseverance they will overcome (Deuteronomy 31:8; James 1:12). Source: https://www.gotquestions.org/calming-the-storm.html
The “moral of the stories” found in the Bible regarding the various miracles has a specific application to Christian faith. Faith in Christ is never misplaced. If Jesus can command the elements and calm the wind and the waves with one word, He can calm the storms of life as well.
Allow me to leave you with a link to an article that lists all the miracles of Jesus and points to their spiritual significance:
The vast majority of miracles recorded in the Gospels were miracles of healing. While those who received the healing were relieved of their physical ailments, the stated purpose of the miracles is rarely ever the simple alleviation of physical suffering. The miracle of healing always points to a greater truth, namely, that Jesus is the Son of God with authority. When He casts out demons, His authority over them is emphasized. When He heals on the Sabbath, His authority as Lord of the Sabbath is emphasized. Likewise, many of the miracles emphasize Jesus’ authority over nature. Source: https://www.gotquestions.org/miracles-of-Jesus.html