I have a creek that we are putting a 48in metal pipe in. would it be possible to use 2X6 or heavy plywood to stop the pipe up and flood the area? if I use 2X6's I could put handles on each one and pull them off or add them individually as I want to lower or raise it.

Should work with no problem. I did that before on a 1A pond in order to raise an lower the water level...

You can the the 2X6 with the tongue and groove in PT. They work great.