This question is a hypothetical, and has to do with the notion of cheap, modular turbines that can be sunk and anchored to a specific depth in a body of water. Each would not generate much power, but collectively that might be different, and it's a possible means of giving people living on riverfront properties greater self sufficiency. But that's not the question, just the context, so it need not be addressed.
The question is: When the topmost layer of a large body of moving water freezes, and assuming the water beneath is insulated by the ice and does not freeze, does that remaining water's rate of flow (rate, not volume) differ from its rate when none of the body of water was frozen?