Fowey was already a working harbour at the Norman invasion. The Domesday Book records manors at Penventinue and Trenant; a priory was established nearby at Tywardreath; the prior granted Fowey a town charter. The natural deepwater harbour, formed when meltwaters at the end of the last ice age flooded a river valley to make a tidal inlet navigable for seven miles, let merchants trade with continental Europe. Their ships were also useful to the king. During the Hundred Years' War, a band of privateers called the Fowey Gallants received royal licence to seize enemy vessels, which they did with enthusiasm, sometimes drifting into outright piracy. The French got their revenge in 1457, sacking the town. Place House by the church was defended successfully and afterwards strengthened. Around 1540 a small castle was built on St Catherine's Point to guard the harbour entrance. The defences worked: when a Dutch fleet attacked in 1667, Fowey beat them off.

Most of Fowey sided with the Royalists when the English Civil War began. In 1644 the Earl of Essex brought a Parliamentary army down through Lostwithiel and occupied the peninsula around Fowey. The Royalists arrived in August and surrounded him. King Charles I himself rode out from Lostwithiel to look at the situation and walked along Hall Walk above Polruan, the high path on the eastern shore where you can still walk today and see the same view. A musket shot from somewhere across the river came close to killing him. On the night of 31 August the Parliamentary cavalry forced their way through the Royalist lines and got away towards Saltash, leaving their foot soldiers to be evacuated from Fowey by sea. Essex escaped, but most of his men surrendered near Golant a few days later. They were marched to Poole. Most died along the way. The river that had carried Cornish wool and tin for six centuries had become a battlefield exit.

After the medieval boom, Fowey's fortunes faded. Trade went to Plymouth. Fishing and smuggling took over. Then, in the nineteenth century, came china clay. The white kaolin clay quarried from the moors around St Austell needed deepwater ports for export, and Fowey had the harbour. The Lostwithiel and Fowey Railway opened in the 1860s, the quays at Carne Point grew, and Fowey became the world's leading china clay port. Joseph Treffry built rival facilities at Par. Charlestown opened around 1800. Fowey held its share by virtue of the natural anchorage. During the Second World War the town served a different cargo: the main port for loading ammunition for the US 29th Division as they prepared for D-Day on Omaha Beach. A munitions siding at Woodgate Pill, just north of town, had originally been built for the Great War. It saw the Americans through. The china clay trade survives today, with ships still loading at Carne Point, the only freight traffic on the otherwise mothballed branch line up to Lostwithiel.

Sir Arthur Quiller-Couch, known to literature as Q, settled in Fowey in 1891 and stayed for fifty-three years. He was professor of English literature at Cambridge, edited the Oxford Book of English Verse, and lived in The Haven on the Esplanade, writing fiction and influential criticism that shaped a generation of undergraduates. Kenneth Grahame visited him and got married in the parish church in 1899. The Fowey estuary became part of the river world Grahame would draw in The Wind in the Willows nine years later. Daphne du Maurier first came to Fowey as a young woman, then made it her home. She rented Menabilly, the great house above Polridmouth Cove, and it became Manderley in Rebecca, the novel that won her global readers and a 1941 Best Picture Oscar for Hitchcock's film adaptation. She also wrote Jamaica Inn here, The Birds, Don't Look Now. Mabel Lucie Attwell, the illustrator whose round-faced children appeared on a million postcards, lived in Fowey and died here in 1964. The du Maurier Festival each May, in the month of her birth, still draws readers to the harbour she made famous.

Mary Bryant was born in Fowey in 1765 and transported as a convict to New South Wales, where she became one of the first to escape from the new colony, rowing a stolen boat with her husband, two children, and seven others over three thousand miles to Timor. Antony Hewish, born in Fowey in 1924, shared the 1974 Nobel Prize for Physics for his work on pulsars. Hugh Peters, the seventeenth-century preacher who urged the execution of Charles I, was born here. John Whitehead Peard, called Garibaldi's Englishman for his service in the Italian campaigns of 1860, came from Fowey too. The actress Dawn French lived above the harbour for years. The town today holds about 2,244 souls at the 2021 census, plus an aquarium in the centre which features an exceptionally rare albino bull huss. Ferries cross the river to Polruan for foot passengers and Bodinnick for cars, the same routes used in Charles I's time, the same routes the Gallants would have known.