Charts break it into sections, and locals use every one of them. Outer, Middle, and Inner Harbour handle the ships, the floatplanes, and the ferries. North of the Johnson Street Bridge lies the Upper Harbour, running up to the Point Ellice Bridge with the small notch of Rock Bay in its northeastern corner; the Sail and Life Training Society keeps its topsail schooner Pacific Swift up here. Beyond that is Selkirk Water, crossed by the Selkirk Trestle - a Canadian National Railway structure now carrying the Galloping Goose Regional Trail. Then comes the Gorge Waterway, three kilometres of narrows reaching northwest past paddling clubs and the Gorge Waterway Discovery Centre to the Craigflower Bridge, where Highway 1A joins View Royal to Saanich between an 1856 manor house and the oldest surviving schoolhouse in Western Canada. Past that bridge, it becomes Portage Inlet.

A predecessor of the Point Ellice Bridge stood at the head of the Upper Harbour, and on a spring afternoon in 1896 it gave way. A streetcar packed with roughly 143 passengers - far more than it was meant to carry, most of them heading across to celebrate Queen Victoria's birthday - was crossing when the span failed beneath it and dropped the car into the water. Fifty-five people died, twelve of them children, killed by the fall or drowned in the harbour their families had crossed a hundred times without incident. Inadequate maintenance and the absence of meaningful safety standards were both found to have contributed. It remains one of the worst transit disasters in British Columbia's history and, on that day, the greatest single loss of life the city has ever suffered.

For generations the Gorge was where Victoria went swimming. There was a tall diving platform at Curtis Point, and on hot days the narrows filled with people. By the 1930s that was over - the water had grown too polluted to swim in, and the city turned its back on a waterway it had been using for pleasure since before anyone alive could remember. Recovery took most of a century. Sustained cleanup work has brought swimmers back to the Gorge in recent years. The region's larger wastewater problem persisted far longer: as late as 2006 the Capital Regional District's municipalities were discharging around 129 million litres of screened but untreated sewage into the Strait of Juan de Fuca every day. That finally ended in December 2020, when the McLoughlin Point treatment plant came online.

Despite the modest land area draining into it, Victoria Harbour is a genuine estuary, fed by a scattering of small freshwater tributaries - Colquitz Creek, Craigflower Creek, Durrell Creek, water from Elk and Beaver lakes, Swan Lake, Blenkinsop Lake, and the Thetis Lakes. One of them, James Bay Creek, now runs entirely in culverts beneath landfill, a buried stream under a busy downtown. The biological payoff sits upstream. Portage Inlet holds about 70 hectares of eelgrass, the nursery habitat that quietly underwrites a great deal of coastal life, and the inlet and Gorge together may support the largest colony of Pacific oysters on the west coast. Pacific herring spawn in these same waters, which is to say that a functioning estuary is operating a few minutes' drive from a provincial legislature.

This is still a working harbour. Ogden Point takes cruise ships and break-bulk cargo; Fisherman's Wharf houses the fishing fleet and its famous float homes; barge docks at Rock Bay move asphalt and cement; the Coast Guard station sits on Shoal Point; and floatplanes come and go from Ship Point while the Black Ball ferry runs south to Port Angeles. It is also a harbour that likes an occasion. The Swiftsure race has gone out into the Strait of Juan de Fuca and back every year since 1930. The Vic-Maui, a long haul to Lahaina, has run in even-numbered years since 1968. Since 1991 the Victoria Symphony has played its Symphony Splash concert from a barge in the Inner Harbour on BC Day, with much of the audience listening from kayaks, and the Dragon Boat Festival has filled the same water every year since 1994.