Salmon begin decaying from the inside-out in late September and early October as they approach their spawning grounds in the tributaries of the Great Lakes. It starts with the shiny silver sides of the feisty open water Salmon fading to a dull white as they reach the pier heads, then the fish progressively turn darker until they become the black/moldy Salmon that can be seen hanging on to life in the rivers weeks after the spawn has completed.
While the color on the outside is changing, so is the color and complexity of the meat inside the Salmon. The nice pink colored meat seen on the fish in July begins to fade towards shades of gray, and the firmness of the meat starts to turn more mushy with each hour in the turbid waters of the tributaries. Now I cannot say from experience, but I can't imagine these fish tasting good. This is another reason that I have turned my focus to the Trout that run up the same stretches of river, spawn, and then return to the lake without breaking down internally.
Flow is another variable affecting when Great Lakes Trout decide to make their annual run upstream to spawn. A good rain in this time period will almost always bring numbers of fresh fish upriver. Knowing what flows will be fishable is also key in catching fish. An inch of rain may make some tributaries to dirty and fast to fish, while others may be prime. The only way to figure this out is to check the tributaries after a rain.
Another interesting variable with fall Trout is the harbors of the Great Lakes. Some Trout are stocked in the harbors rather than the tributaries, which causes these fish to show up in the harbors to spawn. Once in the harbors, some Trout will actually hang around and feed on the Gobies, Shad, spawn, and other food that can be plentiful in the harbors. Water clarity becomes the biggest variable when fishing the harbors, and can change quickly depending on the winds out on the lake. Dirty water in the harbors makes for tough fishing, while clean water can make for great fishing if there are enough fish around!