In 1670, French missionaries François Dollier de Casson and René Bréhant de Galinée became the first Europeans to winter at what is now modern day Port Dover. Earthen remains and a plaque mark the spot near the fork of the Lynn River (Patterson's Creek to many older Port Doverites) and Black Creek where they and seven Frenchmen built a hut and chapel.
By 1794 the first settlers, a group of United Empire Loyalists, had established a hamlet known as Dover Mills (named for the English port of Dover) which was razed to the ground by the Americans in the War of 1812. Subsequent reconstruction took place closer to the mouth of the Lynn River, where a harbour had been in use since the early 1800s. In 1835, merchant Israel Wood Powell registered a village plan for Port Dover. Improvement to the harbour during the next fifteen years made Port Dover a principal Lake Erie port. Shipyards, tanneries, and Andrew Thompson's woollen-mill contributed substantially to local economic growth. In 1879, Port Dover became an incorporated village with a population of 1,100.
Port Dover in the 20th century became a fishing village and tourist destination. Port Dover's fishing industry at one time hosted the largest freshwater fishing fleet in the world that employed many of the town’s citizens and continues to be important to the community.
From 1906 to 1993, the town was home to Thomas A. Ivey and Sons, one of Canada's largest wholesale florists and rose-growers, and Port Dover's largest employer. In 1974, Port Dover was incorporated as Ward 2 of the former city of Nanticoke.
In the summer, Port Dover is busy with thousands of tourists who come to swim in Lake Erie and enjoy the town and surrounding area. Port Dover’s business district is dominated by small shops that cater to the tourist trade with many bars and restaurants that depend largely on the increased traffic during the summer months.
The Port Dover Yacht Club has occupied land purchased from W.F. Kolbe and Co. at the fork of the Lynn River and Black Creek since September 1938. The P.D.Y.C. welcomes visitors every summer from around the Great Lakes region and beyond.
Port Dover has celebrated Canada Day with a parade every year since July 1867. The day starts off with the annual Soap-box Derby, the Boat Parade at the harbour, a Calithumpian Parade down Main Street and a fireworks display after dark.
Since 1981, there has been a tradition of motorcycle enthusiasts gathering in the town for Friday the 13th. Chris Simons and approximately 25 friends, through word of mouth, got together at the old Commercial Hotel. It was in November and it was Friday the 13th. They decided they should do it every Friday the 13th. On June 13, 2008 an estimated 150,000 bikers and spectators converged on Port Dover for Friday the 13th.