Yes, you can use a trolling motor on a pontoon boat to help it move through shallow water. The trolling motor will provide enough power to get the boat through the shallows without trouble. Remember that when using a trolling motor, you'll need to adjust the trim of the outboard engine to achieve the desired depth. Make sure to choose a trolling motor compatible with your pontoon boat. You don't want to overload your boat with too much weight, so be sure to select an appropriate motor for your vessel. With the right equipment, you should easily navigate even the shallowest waters.