Park water at the top, closed until 2027
The Kootenay rises on the northeast side of the Beaverfoot Range and runs southeast through a marshy valley in Kootenay National Park, where the Vermilion River, the larger of the two at their meeting, joins near Kootenay Crossing. Do not plan to fish it there for now. Parks Canada has closed every waterbody in Yoho and Kootenay national parks to watercraft and angling until March 31, 2027 to slow the spread of aquatic invasive species, whirling disease among them. The ECCC gauge at Kootenay Crossing still reports, but the fishable B.C. river starts outside the park.
Below the park the river picks up the Palliser, runs through a gorge at the White River confluence, and comes out into the Rocky Mountain Trench at Canal Flats, where it passes within 2 kilometres of Columbia Lake, the source of the Columbia. In 1889 the Baillie-Grohman Canal, with a single lock, was cut across that gap for steamboats. Kootenay Fly Shop in Fernie calls this upper section, down through the logging town of Canal Flats, a wilderness float with good river camping.
Down the Trench past Fort Steele
From Canal Flats the river meanders south over a broad valley floor of glacial sediment. It takes the Lussier near Skookumchuck, then the St. Mary and the Wild Horse at Fort Steele, where the 1863 Wild Horse gold rush brought thousands of miners, then the Bull River at the settlement of the same name before slowing into Lake Koocanusa, the 130-kilometre reservoir behind Libby Dam in Montana. The Elk joins inside the reservoir. Kootenay Fly Shop notes that the Kootenay and the Elk are the two rivers in the region you can float easily in a drift boat, and that the East Kootenay rivers all drain into it.
Why this reach is open in April
Region 4 closes every stream from April 1 to June 14, but the 2025-2027 synopsis exempts the Kootenay from Koocanusa Reservoir upstream to the White River. On that reach you may fish from April 1 to October 31 and keep one trout or char a day, with no trout under 30 cm and no bull trout under 75 cm. From November 1 to March 31 all trout and char are catch and release, and burbot are catch and release everywhere upstream of the Montana border. Single barbless hooks are required in all Region 4 streams all year. Upstream of the White River, including its tributaries, the season is June 15 to October 31 and the river is Class II classified water, which means a daily classified licence for non-residents. Region 4 also closes bass, pike, walleye, perch and white sturgeon to fishing, and kokanee may not be kept from streams.
The Kootenay below Kootenay Lake is a different fishery, with its own rules from Corra Linn Dam to the Columbia, including a walleye quota below Brilliant Dam; this guide is about the East Kootenay reach.
A glacial river, read backwards
On most rivers you wait for the water to come up; on the Kootenay you wait for it to go down. Kootenay Fly Shop says the river fishes best in March and April and again after the glacier melt slows and it clears, from about mid-September to mid-November. ECCC's long-term monthly means at Fort Steele show why: about 40 cubic metres per second in March, 85 in April, 376 in May, 629 in June and 371 in July, then 166 in August, 108 in September, 84 in October and 67 in November. The 1,400 to 3,900 cfs range on this page, roughly 40 to 110 m3/s, is the level of those spring and fall windows; no shop quotes a specific number. On September 24, 2026 the gauge read 87.7 m3/s, about 3,100 cfs, right in the fall window.
Kokanee, bull trout and big streamers
The reason people fish the Kootenay in November is the bull trout. Kootenay Fly Shop says they grow large here because kokanee spawn and die in the system, and it describes the fall and spring streamer fishing as some of the best anywhere. The bulls also run from the Kootenay up the Elk and into the Wigwam in early summer to spawn in late fall, so the fish in this river are the same ones people chase in the tributaries. With a 75 cm minimum, almost every bull trout goes back; land them fast and keep them wet.
The shop's broader hatch notes for the area cover what the cutthroat and rainbows eat when the water allows: midges late in winter, blue-winged olives on cool fall days, caddis through the summer and October caddis in the fall. Early and late in the year, though, this is mainly a streamer and nymph river.