While the bite is more challenging, fish are still feeding. This is a time of year to consider all variables if you know you are on fish. Depth, retrieval speed, lure action, and wind are all factors that need to be taken into account. I will change a variable much more quickly if the fish are not biting in late fall then I would in the spring or summer.
I have found that trolling in the kayak is a great way to find fish, while being able to control depth and cover lots of water in relatively short time. Rattle lures, crank baits, and swim baits allow for a variety of depths to be explored while paddling across the water. Trolling in a kayak, however, is not the most precise way to control lure speed or action.
An angler can take advantage of these variables with casting or jigging while drifting to utilize the strength of the wind. I have had nice success in the past month while drifting - using one rod to “drag” a lure (usually a crank or swim bait) while jigging or casting with another (usually an in-line spinner). This has worked well on days when the wind is not overpowering.
On the days when the wind is so strong that you spend more time repositioning then fishing, I have used one of two strategies. The first is to allow Mother Nature to work you to the wind-blown side of the water. One big advantage is this places you where the forage is as well, and that is often where you can find the fish. Another good option on a windy day is to find an area protected from the wind and work the calmer waters. While this can make for smoother paddling, it can also limit the amount of water you have available to fish. With my poor paddling skills, I often select this option instead of battling the whitecaps.
Regardless of the challenges of fishing in late fall in the Midwest, an angler can still get out and experience some success. However, soon the only way to fish with a kayak is to use it to drag an auger and tip-ups onto the ice.