By his own admission, sediment settles into his pond, so the water flowing out of the pond has less sediment than the water flowing in, so even if the flow rate has equalized (which is not guaranteed), he's changed the quality of the water flowing through. That could be a good thing or a bad thing, depending on what that sediment did downstream. Sediment can act as a fertilizer, so the potential for harm exists.
You would hope, but the neighbors could be several miles away. He could even be not aware of some of them.
Tributaries of navigable water do fall under federal control.