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Every fall in NW Wisconsin, I have found big walleyes to feed on perch in deep water mud flats. The best technique I have found to land these monsters is to utilize leadcore line. Leadcore line is a large diameter nylon coated lead wire which changes colors every 10 yards. The leadcore comes in various sizes of which I prefer 18lbs test. I use a large spool level wind reel such as those from Penn to put on approximately 6 colors of leadcore. I first tie onto the reel some heavy mono line as backing then attach the leadcore. I then attach the leadcore to a small barrel swivel. I then attach about a 6ft mono leader attached to a Berkley cross-lok snap. I normally troll in about 25ft which requires about 4 1/2 colors of leadcore to reach the bottom. A factor in determining how much line is required to reach bottom is the boat speed. I try to troll between 1.8mph to 2.2mph. I use a stiff 6ft musky rod of which I replaced the tip with a roller tip to help let out the leadcore more easily.
Some of the best lures of me are small Storm Hot-N-Tots, Normark deep baby N, Jointed rapala shad raps, Cotton Cordell deep minnows, plus a few others. My favorite colors are perch, green/black herringbone, firetiger, and black.
Give leadcore line trolling a try on your next trip as the more options you are comfortable with, the higher your catch rate will be!