Early fall can be a productive time to fish as deep cool water seeking fish begin to migrate back toward shallow water as temps begin to drop. However, once surface water temps drop so that the surface water is cooler than deeper water lakes experience turnover. Lakes literally exchange deep water with surface water and the results are usually chaotic for fishing. This will happen at different times for different lakes. If you become intimately familiar with a particular lake you may be able to cope with fall turnover and catch fish throughout. For the most part though it might be more advantageous to fish river systems during this time. Walleyes in particular migrate upstream during the fall and stage in areas that they would normally be found in the spring. One of the reasons they do this is because some species of minnows migrate and spawn during this time to the same locations. Walleyes are simply following the food surce.
Lake trout are more apt to be found in shallow waters but may also be scattered and difficult to find in numbers.
Large smallmouth bass become more accessible in shallow water but it will take some searching to find them. Look near areas where smallies normally spawn.
And if your looking for large pike in fall find the walleyes first. There will always be big pike hanging around.