The Nanaimo River begins on the eastern slopes of Mount Hooper, where the drainage divide separates waters flowing east toward the Strait of Georgia from those running west into the open Pacific. The river flows east for most of its 78-kilometer length before turning north into the southern end of Nanaimo Harbour. Two lakes - First and Second - lie along its course, part of a chain of four collectively called the Nanaimo Lakes. Third Lake connects via a short stream, while Fourth Lake is a man-made reservoir on Sadie Creek. Three main tributaries feed the system: the North Nanaimo River descending from south of Okay Mountain, the South Nanaimo River starting at Rheinhart Lake, and Haslam Creek flowing east-northeast to meet the main stem near the fish hatchery. The small community of Cedar is the only settlement along the riverbanks themselves.

In 1931, South Fork Dam was built on the South Nanaimo River, creating a reservoir to supply drinking water to the growing city. The dam is built of unreinforced concrete, and the system it anchors is gravity-fed - water flows downhill through pipelines to Nanaimo without pumps. A second dam at Jump Lake followed in 1974, capable of holding enough water to supply every home in the city for a year. In 2000, South Fork Dam was upgraded to produce hydroelectricity for local use. Nine balancing reservoirs are scattered throughout the city to meet peak demand, the first built at Lost Lake in 1969. Almost the entire South Fork watershed is restricted from public access, privately owned by Timberlands under an agreement with the city to protect the water supply. The river that sustained the Coast Salish for millennia now sustains a modern city of 90,000.

The Nanaimo River canyon is where the river reveals its more dramatic side. WildPlay Element Parks operates a bungee jumping facility here, using North America's first purpose-built, legal bridge designed specifically for the sport. Upstream, rock climbers work routes of varying difficulty on the canyon walls. Along the river's length, deep pools, underwater caves, waterfalls, and rocky beaches draw swimmers throughout the summer. The Nanaimo River Regional Park near the river's mouth preserves some of the last intact riparian zones on the lower river, including old-growth Douglas fir with undisturbed riverbank. These parcels were purchased by The Land Conservancy of British Columbia in 1999 and 2000, eventually transferred to the Nature Trust of British Columbia after the Conservancy sought creditor protection in 2013.

Anglers regard the Nanaimo River as one of the best steelhead rivers in Canada. The Nanaimo River Fish Hatchery, operating since 1979 and run by the volunteer-based Nanaimo River Stewardship Society since 2004, maintains the river's fish populations. The watershed supports pockets of old-growth Douglas fir forest classified as part of the Georgia-Puget Basin Ecoregion - recently ranked the 65th of 77 most significant and threatened places in Canada. Vancouver Island marmots, cougars, wolves, and golden eagles inhabit the mountainous headwaters. A ski hill once operated on Green Mountain near Third Lake from 1963 until vandals damaged the lodge and T-bar in 1984, closing it permanently. On Haslam Creek, a suspension bridge carries the Trans Canada Trail across the water to Timberland Lake - one more thread in a landscape woven together by flowing water.