The first European to enter the harbour was Juan Carrasco, a Spanish naval officer who arrived in 1791 and named the bay Bocas de Winthuysen. Carrasco also named Gabriola Island, Galiano Island, Valdes Island, and Porlier Pass - Spanish names that still mark the landscape despite Spain's eventual departure. Captain James Cook had established British claims when he landed at Nootka Sound on the island's west coast in 1778, and Captain George Vancouver sailed into the Salish Sea in 1792, where he unexpectedly encountered another Spanish expedition led by Jacinto Caamano. The competing claims led to the Nootka Crisis and the Nootka Convention, with Spain relinquishing all claims to Vancouver Island in 1795. But the harbour kept its Spanish geography: Gabriola, Galiano, Valdes - names from a brief imperial moment that left a permanent imprint on the charts.

In 1850, Coal Tyee, chief of the Snuneymuxw First Nations, travelled from his village on the harbour to Fort Victoria carrying coal. Governor James Douglas came to investigate personally. By 1853, the Hudson's Bay Company had built the Nanaimo Bastion to protect its new mining interests, and in 1854, twenty-four English settlers arrived to establish Colvile Town - renamed Nanaimo by 1860. The deep, sheltered harbour proved ideal for exporting the resources that surrounded it: coal, timber, fish, sandstone. Sawmills, canneries, and quarries multiplied along the shore. The Coast Salish, who had built longhouses from the harbour's abundant timber and fished its waters for generations, watched their homeland transform into a colonial industrial port.

Nanaimo Harbour is bigger than it appears from downtown. The Port of Nanaimo encompasses the Inner Harbour, the Nanaimo River estuary, Departure Bay, the waters east of Newcastle and Protection Islands, and the Northumberland Channel between Gabriola Island and Duke Point. Seven named rivers and creeks feed into it, from the major Nanaimo River flowing east from the Vancouver Island Ranges to small urban streams like Departure Bay Creek. BC Ferries operates three routes from within the harbour - to Gabriola Island, to Tsawwassen on the Lower Mainland, and to Horseshoe Bay in West Vancouver. Seaplanes take off from the downtown waterfront, heading for Vancouver and the Sunshine Coast. Freight trains run to the Assembly Wharf. It is a working port that also happens to host Canada's only floating pub, the Dinghy Dock on Protection Island.

In 1967, Nanaimo mayor Frank Ney launched the first annual bathtub race - motorized bathtubs crossing Georgia Strait from Nanaimo to Vancouver. The race moved to the harbour circuit in the mid-1990s, but the spirit of cheerful absurdity survived. The harbour also shelters three intentionally sunken ships that now serve as artificial reefs and scuba diving sites: HMCS Saskatchewan, a 366-foot destroyer scuttled in 1997; HMCS Cape Breton, a 442-foot World War II vessel sunk in October 2001; and the tugboat Rivtow Lion, originally the British wartime vessel HMRT Prudent, sunk in 2005. Parks ring the harbour - from Newcastle Island Marine Provincial Park, the largest, to the waterfront promenades and lagoons that now line a shore built on the industrial remains of the coal era.