There are several reasons why fall time shore fishing is less productive in the shallows.
1) Temperature change is more significant in the shallows. The water can be cool from evening to morning hours, but rises from mid-morning to late afternoon. This fluctuation in temperature can be quite significant. Any rainfall can also significantly cool the shallows. Fish prefers more stable temperatures, so as the weather cools and become unstable with more rainfall, fish moves for deeper water.
2) With decreasing daylight, weeds begin to die as early as mid-September. This not only remove fish habitat in the shallows, but it also depletes the oxygen level in the shallows as the weeds rot (bacteria consumes the oxygen). This pushes fish to areas where there is sufficient levels of oxygen, either other areas with green weeds, or to deeper water where oxygen level is higher and more stable.
3) With the approach of winter, fish knows that shallow areas will soon be frozen. Various fish species will move out to deeper water for that reason as well.
Notice the point here...deeper water!
This is even true for icefishing. Early in the season during first ice, you can often find fish on "shallow" flats and weedlines where there are healthy green weeds. During mid-ice season, snow cover over the ice kills a lot of the remaining vegetation in shallow water and fish will push deeper. Once late-ice approach and spring is around the corner, fish will once again move toward the shallows again. This is very evident for anyone who has fished Lake Simcoe in the winter. Perch schools are often in 6-8 FOW on first ice, then move deeper and deeper as deep as 70 FOW (I've even caught some in over 100FOW) during mid-Feb, then these fish will once again move shallower in mid-March to stage for the spring spawn. This is true for pike, walleye, and surprisingly even for whitefish (sightfishing for whitefish in less than 20 FOW is super rad!!!
Try casting to deeper water where it is close to shallow habitat where fish can move up onto the flats occassionally, but retreat to deep water when weather and temperature changes.
Also...you want to target catfish...try night time. When Michael and I took the trip a couple of weeks ago, fishing for catfish was very slow during the day. Once it got dark, it was like a switch that went off and the kitties came out to play.
. Yuck!