The Baitfish Connection for Fall Muskies

The Baitfish Connection for Fall Muskies

A muskies fall hunt for baitfish can make them easier to target if you know what to look for and the most likely places to find it. (Photo courtesy of St. Croix Rods)

Muskies hunt baitfish with great aggression as temperatures cool in the fall. Make the most of this treasured time.

It’s nosecret that fall can be the best time of year to score especially large muskies wherever you chase them. Overall angling pressure has subsided a bit, as the woods become busier than the lakes and rivers with hunters trying to tag a buck.

Still, some of the best hunting to be had is for predators, like muskies, that are after prey of their own in the quest to build fat stores for the coming winter. The fact that they’re willing to eat more in general during this period makes fall a prime time for targeting them throughout their range.

Baitfish then become the key ingredient to your success, and studying their habits and movements determines everything about the fall bite at hand. The challenges relating to baitfish, however, are severalfold, given that different systems have varying bait species in fluctuating supply, not to mention the effect that cover, structure, weather and resulting water temperatures can have.

Of course, there’s also the technique by which you hope to catch fish, which isn’t always as bait-related as you might suspect. From north to south, and east to west, the interplay of these various ingredients and others can just as easily make for an unproductive day on the water as much as a good one. The key is breaking down your lake, your bait and their habits in conjunction with the other variables to arrive at winning periods and patterns throughout the fall.


In the northern part of the muskie’s range, deep and rocky lakes teem with ciscoes and whitefish, both silvery snacks that fuel the largest portion of any predator’s diet in these areas. Head 100 miles south, or maybe less in some areas, and relatively shallow weed-ridden lakes hold large muskies that generally target everything from suckers to sunfish. Farther south still are reservoirs that hold muskies in great number, who focus on large runs of shallow-moving shad. The point is that muskie diets are diverse and adaptive to the system at hand, so knowing your baitfish and their behaviors reaps dividends especially when fishing far from home.

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In the north, baitfish migrations revolve around cisco and whitefish fall spawning habits, and muskies are never far behind. Guide and St. Croix Rods Pro Mike Brown brings clients to Minnesota’s famed Lake Vermilion in search of massive ’skis that fatten up on these baitfish stocks each fall. Brown said, “fish are rather unpredictable in early fall as they sit over deep mud and sand, picking off bait that are still out deep eating bugs.” Once water temps start to decline into the mid-40s, these fish concentrate shallower. “Eventually, you’ll see big schools of bait up on 10- to 20-foot reefs, popping on the surface,” he added, “that’s when you know the bite is really on.”

The farther south you go, the number of bait species increases for muskies to target, from perch, bullheads and suckers to crappies and sunfish. While most species will use existing weed cover to hide, some fish like crappies are pelagic, roaming the open basin, with muskies often just below or at least nearby. In systems with gizzard shad, muskies will often follow big schools of bait shallow, as older bait and young-of-the-year shad return shallow to find more plankton on rocky shorelines and feeder creeks.

Fall is when muskies put on the feedbag. Using imaging technology helps locate the bait and effectively fish the area. (Photo by Ron Sinfelt)


Fall is a dynamic period, as weather can dominate bait movement and ultimately predator location. The key is really paying attention to your electronics and what’s going on in the moment. Standard down sonar, down-imaging and side-imaging are helpful, but one stands out among the crowd.

“Side-imaging is chapter one of the muskie-finding bible,” said Brown, who often drives around for up to a few hours before ever wetting some braid. “I want to get a feel for what bait is where and what they’re doing,” he continued. “Up north, I’m trying to figure out if ciscoes are still on mud, or if they’re transitioning to spawning areas, and side-imaging helps me cover so much more water to hunt down those clues.” Brown targets muskies in these lakes usually later, post-turnover, as those water temps are more in line with the baitfish fall spawning run.

On weed-dominated lakes, massive milfoil beds, coontail and cabbage can all hold fish, and fall often has the usual baitfish suspects clinging off the deep end of those weeds. Although warmer temps can push northern fish into a funk by slowing down the bait spawn, those fish on weeds tend not to move as much.

“With those deep weed fish,” Brown said, “I’m looking at 14 to 18 feet or more—however deep the weedline will extend to—and I can usually count on those fish being nearby regardless of funky weather in the fall.” On southern reservoirs like Kentucky’s Cave Run, Brown has fished more feeder creek edges and shelfs with nearby main-lake depths. As cooler weather persists in fall, those fish are following big schools of gizzard shad moving shallow as they’ve depleted main-lake food sources over summer.


Presentation is still a big part of the equation. However, so too is boat control, especially as the bite moves shallower later into the fall.

“When bait is as shallow as 5 to 10 feet like it is on spawning shoals up north, you need to start two full cast-lengths away and work up onto those fish,” Brown said. “You’ll push active fish around that would otherwise be willing to eat simply by moving in too shallow.”

Brown, who prefers casting Bulldawgs, Medusas and paddle tail style swimbaits, loves to put a client on the front deck throwing while he drowns some bait on the back end of the boat. Brown said, “if I can get them throwing, that’s more my style, but as water temps drop, especially in weed-dominated lakes, the sucker bite gets going.” Here, he said, “the key is moving slow so that sucker stays deep. I see guys running and gunning too quickly during this time of year, dragging suckers behind the boat and ultimately too high in the water column for those deep fish.”

Though he’d prefer to cast on these fish, Brown breaks up client trips with a fair amount of trolling. Brown said, “not only can I give us a break from throwing big baits all day, I can be more productive on the search with side-imaging as I cover large swaths of lake and eliminate water.”

Not to mention, there’s times in October and early November where trolling is the only option. Brown continued, “air temps can be unseasonably cold in the northern reaches, and casting will freeze you up. Trolling is the only game in town then.”

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Trolling is also effective in lakes with abundant stunted panfish, where often small, suspended crappies and bluegills can be the preferred snack of fall. Midsummer crappies suspend and eventually move toward their deep wintering holes, making them easy targets for open-basin muskies that lack other good bait options. These fish are also readily visible on side-imaging, especially when they congregate later into the fall as water temps drop below 55 degrees.


Consistent wind from any direction can certainly focus bait on shorelines. This is true on reservoirs for shad, weed-dominated lakes for all species and in northern reaches for ciscoes and whitefish alike. Brown favors smaller rock and big traditional points for these kinds of conditions.

“Flat shale rock doesn’t hold as many fish as the smaller stuff I’ve found,” Brown said. “I’m looking for gravel or smaller chunk rock that feeds off of deeper points into the main lake, as these spots consistently hold fish in a good wind or otherwise.”

General weather patterns can really focus a bite as well, or scatter it. Brown said, “I’m most excited to fish gradually cooling temperatures. On years where it gets progressively colder in a steady manner, the bite just continues to get better and better. Years where it’s warm and the mercury drops off a cliff just concentrates the fall bite into a smaller window.”

Overall, there’s rarely a bad time in the fall to be chasing muskies, especially if you use your electronics to reliably place you near active bait. As fish are looking to build fat reserves, you multiply your odds greatly just by being near the favored baitfish found in any system. Don’t hesitate to fish deep into the fall either. Brown said, “there’s some incredible fishing when I can’t make 10 casts before everything freezes up.” Troll with confidence and continue the hunt for bait, as wherever you fish, fall muskies surely won’t be too far behind.

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