The Northeast Margaree River originates in the watershed of the Cape Breton Highlands and flows to join the Southwest Margaree at Margaree Forks, forming part of the 120-kilometre Margaree-Lake Ainslie system that drains a watershed of nearly 120,000 hectares before emptying into the Gulf of St. Lawrence at Margaree Harbour. The upper reaches of the Northeast Margaree are characterized by challenging rapids and chutes, making them suitable for intermediate and advanced paddlers. The gravel bars of the upper river provide spawning grounds for Atlantic salmon, and the icy, clear waters of the upper reaches support both Atlantic salmon and trout populations.

A documented route runs from Portree through Margaree Valley, Margaree Centre, and Doyle Bridge to Margaree Forks, with an optional continuation on the main Margaree River to Margaree Harbour. Shuttle services are available through local outfitters, with access points including Ross Bridge and Big Intervale Bridge on the Northeast River. Upper river water levels are noted as not suitable for canoes after mid-June, making spring the preferred window for paddling the upper sections. The remote upper reaches of the Cape Breton Highlands portion involve little to no quick access points and may require off-trail hiking to reach the river, with paddlers encountering class 2+ rapids through that stretch.

The river passes through a landscape of forested floodplains, hardwood ridges, fertile farms, weirs, and villages with Acadian and Scottish heritage. The Margaree River system holds designation as a Canadian Heritage River, recognized in 1998, and is managed in part by the Margaree-Lake Ainslie Canadian Heritage River Society. The river is well known for Atlantic salmon fishing, and the main stem is restricted to fly-fishing only with barbless hooks under Nova Scotia government regulation — paddlers should be aware of active fishing activity, particularly during salmon runs.

Guided multi-day packraft trips covering approximately 40 kilometres are offered by at least one local outfitter, typically running in May and June. Canoe rentals with shuttle arrangements are also available within the river system, with shuttles generally needing to be booked at least 24 hours in advance and departing before mid-morning.