It is really hillarious to see the Christian missionary websites or those people who have an axe to grind against Islam asking Muslims about the miracles of the Prophet Muhammad(P). They believe that the Prophet(P) did not perform any miracles. Predictably, their assumptions are wrong. We will allow the great Imam An-Nawawi to comment on Prophet’s (P) known miracles.
The Prophet Muhammad’s Miracles
The Messenger of Allah (P) possesses many manifest miracles and signs demonstrating [his veracity], reaching thousands and they are well known.
From amongst them was the Qur’an the manifest and clear miracle and brilliant proof, falsehood cannot approach it from before it or behind it. It is a revelation from One Who is All-Wise and Praiseworthy. It incapacitated the most eloquent of people in the most eloquent of times to produce a single chapter that would be comparable to it, even if the whole of creation were to gather for that purpose. All? the Exalted, says
“Say: If the whole of mankind and the jinn gathered in order to produce the like of this Qur’an, they could not produce the like of it, even if they assisted each other.” (Qur’an, 17:88)
It challenged them to this despite their large numbers, their eloquence and their severe enmity, and it challenges them to this day.
As for the other miracles, it is not possible to enumerate them all due to their huge number and renewing and increasing nature. However, I will mention some examples:
The splitting of the moon, water flowing from between his fingers, increasing the quantity of food and water, the glorification of the food, the palm tree yearning for him, stones greeting him, the talking of the poisoned leg [of roasted sheep], trees walking towards him, two trees that were far apart coming together and then parting again, the barren [and therefore dry] sheep giving milk, his returning the eye of Qat?h bin an-Nu`m?to its place with his hand after it had slipped out, his spitting lightly into the eye of Ali when it had become inflamed and its being cured almost immediately, his wiping the leg of `Abdull?bin `At?whereupon he was immediately cured.
His(P) informing of the places of death of the Day of B? saying, “this is the place of such polytheists on the and-such a person”. His informing of his killing Ubayy bin Khalaf, that a group of his nation would traverse an ocean and Umm Har?would be amongst them and this occurred. That all that was drawn together for him of the ends of the earth and displayed to him would be opened for his nation, that the treasures of the Chosroes would be spent by his nation in the Way of All? the Mighty and Magnificent. That he feared for his nation that they would be tempted by the wealth and allurement of this world and that the treasures of the Persians and Romans would be ours and that S?????bin M?k would wear the trousers of Chosroes.
He(P) informed us that Hasan bin `Ali would reconcile between two large warring parties of the Muslims, that Sa’?bin Ab?aqq?would live such that nations would benefit by him and others would be harmed. That an-Naj??ad died on this particular day while he was in Ethiopia and that al-Asw?al-`Ans?ad been killed on this particular day while he was in Yemen.
That the Muslims would fight the Turks who were described as having small eyes, wide faces and small, chiselled noses and that Yemen, Syria and Iraq would be conquered by the Muslims.
He(P) informed us that the Muslims would comprise three armies, an army in Syria, and army in Yemen and an army in Iraq. That they would conquer Egypt, a land whose [unit of land measurement] was the Q?t, that they should deal with their people well for they have protection [being Copts] and ties of kinship [through Haj?(the wife of Prophet Abraham(P))]. That Awa?al-Q??ould come to you from the auxiliaries of Yemen, he would be afflicted with leprosy and it would be healed except for the space of a d?? and he indeed arrived during the rule of `Umar.
He(P) informed us that a group of his nation would always be upon the truth and that mankind would become many in number and that the Ans?would diminish in number and that the Ans?would not be given their due [with regards to distribution of wealth and leadership]. That mankind would keep on asking questions until they would say, “All?created the creation…” 
He(P) informed us that R????f?bin Th?t would live a long life, that Ammar bin Yasir would be killed by the transgressing group, that this nations shall divide into sects and that they would fight each other.
He(P) informed us that a fire would emanate from the land of H?z and the likes of this. All of this occurred exactly as he(P) said it would.
He(P) said to Thab?bin Qays, “You will live being praised… and you will die as a martyr”, and he lived being praised and was martyred at al-Y?m? He(P) said regarding `Uthm? “He would be afflicted by a severe trial.”
He(P) said about a person amongst the Muslims who had just fought a severe fight that “He would be from amongst the denizens of the Fire”, and later he committed suicide. Wabis?bin Ma`b?came to him in order to ask him(P) about righteousness and sin upon which he(P) asked, “Have you come to ask about righteousness and sin?”
He(P) said to `Ali, az-Zub? and al-Miqd? “Go to the garden of Khakh for indeed there is Dha`in?4] who has a book with her”. They found her there but she initially denied having the book and then took it out from within her braids.
He(P) said to Ab?????r? when Satan had stolen some dates, “Indeed he shall return” and he did. He said to his wives, “The most prolific of you in giving charity will be the quickest of you to join me” and it was so.
He(P) said to ‘Abd????h bin Sal? “You will remain upon Islam until you die”.
He(P) supplicated for An?that his wealth and sons increase and that he should live a long life and it was so. He lived for more than one hundred years and not one of the Ans?was richer than he and one hundred and twenty of his children had already been buried before the arrival of al-H?aj [to Basr???. This is detailed further in Sah?al-Bukh? and others.
He(P) supplicated that Islam be strengthened through `Umar bin al-Khatt?or Ab????hl, and All?strengthened it through `Umar(R). He supplicated against S?????bin M?k and the feet of his horse sank into the earth and he was thrown off, he called out asking for safe conduct and was granted it, then he asked the Prophet(P) to make a supplication for him.
He(P) supplicated that All?remove feeling the bitter cold and heat from `Ali and so never did he feel cold or hot. He supplicated for Hudhayfah, the night that he sent him to spy on the Confederates, that he not feel the cold and he did not until he had returned. He supplicated for Ibn `Abb?that All?grant him understanding of the religion and it was so. He supplicated against `Utb?bin Ab?ahb, that All?cause a dog from amongst his dogs to overcome him and he was killed by a lion at az-Zarq?7]
He(P) supplicated for the descent of rain when they asked him to at the time of drought. There was not a single cloud in the sky, and then when he had supplicated, the clouds gathered like mountains and it rained until the next Friday. It rained so much that they had to come back and ask him to supplicate and stop the rain, so he supplicated and the rain stopped and they walked out into the glaring sun.
He(P) supplicated for Ab????lh?and his wife, Umm Sulaym, that he blessed them in the night they had spent together and she became pregnant and gave birth to `Abd????h. He had nine children and all of them were scholars.
He(P) supplicated for the mother of Ab????ra?h(R) that she be guided and Ab????ra?h left to find her performing the ritual bath because she had accepted Islam. He supplicated for Umm Qays bint M????n, the sister of `Ukkash?that she live a long life and we do not know of another woman who lived as long as she did. This was reported by al-Nas? in the chapter concerning washing the deceased.
On the Day of Hunain he threw a handful of dirt at the disbelievers and said, “May the faces be disfigured”, and All? the Exalted, vanquished them, filling their eyes with dirt. He once went out to one hundred of the Qur?h who were waiting to do something horrible to him and he put dirt on their head and went on his way without their seeing him.
 Referring to the hadith, “the people would continue asking until they say, ‘this is All?Who created everything but who created All?'” (al-Bukh? and Muslim)
 The meaning of severe trial is his being imprisoned in his house and his being killed by the transgressors.
 The garden of Khakh is a place falling between Makkah and Madinah. Refer to al-Bukh?, no. 3983 and Muslim, no. 2494 and Tafs?Ibn Kath?[4/344]
 Dha`?h is the woman with whom Hasib al-Balta`ah(R) sent a letter to the people of Makkah in order to inform them of the plans of the Messenger of All?P) to fight them. It was concerning this that the first verses of Surah al-Mumtahinah were revealed.
 Zayn?bint J?h(R) was the most prolific of them in giving charity and was the first to die. Refer to Muslim, no. 2452
 Sah?al-Bukh?, no. 1982
 This is how it is in all of the printed editions; perhaps the author means `Ut?ah bin Ab?ahb for this description fits him. As for `Utb? he accepted Isl?in the year of the Conquest of Makkah.