Khnum was born in the earliest days of Egyptian civilisation, worshipped from the First Dynasty around 2925 BCE at Herwer in Middle Egypt before his cult migrated south to Elephantine, the island at the First Cataract that marked the traditional southern border of the kingdom. The cataract was a place of terror and wonder, where the Nile narrowed between granite cliffs and plunged through rapids that no boat could navigate except in flood season. The Egyptians believed that the river emerged from two hidden caverns beneath the island, called the Qerti, and that Khnum dwelt at the gate of these caverns, controlling the waters that would rise each summer and transform the valley into a shining lake. His name may derive from the word hnmt, meaning "well" or "spring," or from a root meaning "to join, to unite, to build," for he was the god who joined the parts of the body into a whole and built the cosmos anew each morning.

In the Pyramid Texts of the Old Kingdom, the oldest religious writings in the world, Khnum appears as a craftsman of the gods, fashioning ferryboats and ladders for the dead king's ascent to heaven. But by the Middle Kingdom, recorded in the Coffin Texts, his role had expanded into the creator of life itself. Spell 214 of the Coffin Texts describes him shaping humans on his potter's wheel, moulding their bodies from Nile clay and breathing life into them before placing them in their mothers' wombs. The image was irresistible: the same clay that the flood deposited on the fields, the same silt that made Egypt the Black Land, was the material from which the god shaped mankind. The potter's wheel, a tool known to every Egyptian craftsman, became the instrument of divine creation.

The most vivid myth of Khnum's creative power survives in the Westcar Papyrus, a collection of tales from the Middle Kingdom or Second Intermediate Period that purports to record events from the reign of Khufu, the builder of the Great Pyramid. In the fifth and final story, a woman named Rededjet, the wife of a priest of Ra, is struggling to give birth to triplets who are destined to become the first three kings of the Fifth Dynasty: Userkaf, Sahure, and Neferirkare Kakai. The sun god Ra sends five deities to assist her: Isis, the great enchantress who restored her murdered husband Osiris; Nephthys, the lady of the mansion who guarded the dead; Meskhenet, the goddess of childbirth who decreed the fate of every infant; Heqet, the frog-headed goddess who hastened delivery; and Khnum, who carries the luggage and makes the babies' bodies strong. The gods disguise themselves as musicians, enter Rededjet's house, and deliver the three children one by one. After each birth, Meskhenet declares, "This is a king who will exercise kingship in this entire land," and Khnum makes his body healthy, shaping the royal flesh on his wheel in the celestial realm before the child is born into the world.

By the New Kingdom, Khnum's role in royal birth had become canonical. At Deir el-Bahri, the mortuary temple of Hatshepsut, the female pharaoh of the Eighteenth Dynasty who ruled as king in her own right, the walls depict her divine conception and birth in elaborate detail. The god Amun, king of the gods, falls in love with her mother Ahmose and, disguised as her husband Thutmose I, enters her chamber. Then Khnum appears, moulding the infant Hatshepsut and her ka, the life force that would accompany her through eternity, on his potter's wheel. The goddess Heqet stands beside him, touching the queen with the ankh, the key of life, and the scene is repeated in birth houses across Egypt for a thousand years, from the New Kingdom to the Roman period, proof that every pharaoh, male or female, was shaped by the ram-headed god before they drew their first breath.

The defining legend of Khnum's power over the Nile flood was carved on the Famine Stela, a granite inscription on Sehel Island near Elephantine that purports to record events from the reign of Djoser, the Third Dynasty pharaoh who built the first Step Pyramid at Saqqara. According to the stela, Egypt had suffered seven years of drought and famine. The Nile had failed to rise, the fields lay cracked and bare, and the people were desperate. Djoser, grieving on his throne, summoned his chief lector priest Imhotep, the architect of the Step Pyramid and a man so wise that the Greeks would later worship him as a god of medicine. Imhotep searched the archives of the temple of Thoth at Hermopolis and discovered that the flood was controlled by Khnum, the ram-headed god of Elephantine. He travelled to the island, entered the temple of Khnum called "Joy of Life," purified himself, and prayed. That night Khnum appeared to him in a dream, introducing himself as the creator of mankind who fashioned them on his potter's wheel, and promising to make the Nile flow again. Djoser issued a decree restoring Khnum's temple and granting the god's priests one-tenth of all revenue from Aswan to the Nubian district of Tachompso. The famine ended, and the story was carved in stone during the Ptolemaic Period, more than two thousand years later, a testament to Khnum's enduring reputation as the master of the flood.

At Elephantine, Khnum formed a divine triad with two goddesses: Satet, the archer goddess of the inundation whose arrows were the floodwaters that struck the earth each summer, and Anuket, the goddess of the cataracts whose name meant "the Embracer" and who personified the life-giving waters of the Nile. Together they were the guardians of Egypt's southern frontier, invoked by travellers crossing into Nubia and by sailors navigating the rapids. But Khnum's worship was not confined to Elephantine. At Esna, south of Thebes, he presided over a temple whose hypostyle hall was decorated with some of the most elaborate hymns and astronomical scenes in Egypt. The Great Hymn to Khnum, inscribed on the columns, celebrated him as the creator of all living things: gods, humans, animals, and plants. It described how he shaped the body in anatomical detail, supervised the moment of conception, and initiated the contractions that began the birthing process nine months later. Another hymn declared that "All are formed on his potter's wheel, their speech different in every region but the lord of the wheel is their father too," a remarkable statement of universal creation that included foreigners as well as Egyptians. The temple also recorded the Festival of the Potter's Wheel, celebrated on the first day of the month of Paremhat, when priests offered a potter's wheel to Khnum and hymns were sung praising "the lord of the wheel" who fashioned gods and men, his wheel spun each morning to remake the cosmos.

In the New Kingdom, Khnum was syncretised with Re, the supreme sun god whose barque crossed the heavens each day, becoming Khnum-Ra, the ba or spiritual essence of the solar deity. When Re travelled through the underworld at night, he was often depicted with a ram's head, representing Khnum's protective power in the darkness. The word for ram in Egyptian was ba, the same word used for the spiritual component of the human soul, and this pun reinforced Khnum's role as the animator of life, the force that joined body and spirit at the moment of creation. He was also identified with the creator god Ptah of Memphis and with Atum of Heliopolis, making him one of the principal creator deities of Egyptian religion alongside the most powerful gods in the pantheon.

The worship of Khnum persisted into the Roman period, long after the pharaohs had become a memory. The temple at Esna was expanded under the Ptolemies and completed under the Roman emperors, its columns carved with scenes of Trajan and Commodus making offerings to the ram-headed god. An underground quay connected the temple to the Nile, built by Marcus Aurelius so that the god's processional barque could sail directly to the river. Even after Christianity closed the temples in the fourth and fifth centuries CE, the image of Khnum at his potter's wheel survived in Coptic magical texts and Byzantine amulets, the creator god reduced to a folk memory but never entirely forgotten.