Thousand Islands NY fishing report for the week of September 17, 2026. The St. Lawrence has started its fall turnover this week, and that means the muskie season is getting serious. The trollers have been putting in long hours on the shoals with the first real results of the fall, and the smallmouth have moved back onto the shoals in numbers. Cool nights have made the evening walleye bite worth staying out for.
What’s Hitting
What’s hot this week is muskie. The river’s big fish are moving onto the shoals and the drop-offs as the water cools, and trollers working the 40 Acre Shoal, the Clayton and Alexandria Bay shoals, and the channel edges between the islands have reported fish in the 45 to 50-inch class, with the true giants still to come in October. Smallmouth bass from 2 to 5 pounds are stacked on the shoals and the rock drop-offs in 15 to 30 feet, feeding on gobies and perch. Walleye are feeding along the channel edges and the deep weed lines at dusk and after dark. Northern pike are on the weed edges in the bays, and yellow perch are schooling on the flats.
Where to Find Them
Muskie are on the shoals and the drop-offs along the main channel from Cape Vincent through Clayton and Alexandria Bay, with the 40 Acre Shoal, the Clayton shoals, and the Rock Island area the most consistent this week. Smallmouth are on the rock shoals and the drop-offs around the islands in 15 to 30 feet, moving shallower on cloudy days. Walleye are along the channel edges and the deep weed lines off Cape Vincent and around Chippewa Bay at dusk. Pike are on the weed edges in Chippewa Bay, Goose Bay, and the Lake of the Isles.
Tides & Conditions
River water has dropped into the mid to upper 60s and is falling, which is what has the muskie moving and the smallmouth stacking. The river is clear and at a normal early-fall level. Winds have been light out of the north and west most mornings with a comfortable river, and the fall color is starting on the islands.
Tackle & Tactics
For muskie, large trolled crankbaits and jerkbaits like 10 to 12-inch Believers and Jakes run 15 to 30 feet down along the shoal edges at 3 to 4 miles per hour, on heavy trolling rods with 80 to 100-pound braid and a heavy fluorocarbon or wire leader. Casters want large bucktails and rubber baits over the shoal tops with a figure-8 at the boat every cast. Smallmouth want a drop-shot with a goby imitation, a tube, or a Ned rig on the shoals. Walleye want a trolled stickbait or a jig and minnow along the channel edges at dusk. Pike want a large spoon or a spinnerbait along the weed edges.
Local Intel This Week
The Clayton village ramp, the Alexandria Bay municipal ramp, the Cape Vincent village ramp, and the Keewaydin and Wellesley Island state park ramps are the main public launches on the American side. Shore anglers are catching smallmouth and perch from the Clayton and Cape Vincent waterfronts and the Wellesley Island shoreline. Fish are concentrating on the shoals and drop-offs along the main channel. Muskie have a 54-inch minimum on the St. Lawrence and the fishery is catch-and-release by strong local custom; check current NY DEC and Ontario regulations before fishing, and carry a release cradle.
This Week’s Tip
When trolling the shoals for muskie, run your baits along the edge where the shoal drops into deep water, not over the top of it, and vary your speed with S-turns. The fish sit on the break, and a bait that speeds up and slows down as the boat turns triggers follows that a straight troll does not.
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