I know question had been around a couple of months, but it sounds interesting and here is my input.
I could think of a bunch of ways to do an intake, but to me the bigger issue is how you are going to handle conveyance. How is the water going to go from the intake through the dam? I assume there is a dam of some sort. How much water are you talking about? How far below minimum pool do you need to withdraw the water? If it is pump driven, you should be able to do some kind of prefab intake and sink or drive it into place and run the lines over the dam, or maybe run them through the dam above your low water line.
I am used to big stuff, we would cofferdam (yes you can build high cofferdams) and do everything in the dry. If you had to do it underwater and it was pretty big and gravity driven, I would tunnel a regulating outlet through a solid embankment, build a gate chamber with rock trap, then tunnel the intake mouth close to the reservoir and do a wet tap. If you need trash racks, build an intake and sink it in place over the new inlet. Very expensive, twould be a lot cheaper to just drain the reservoir.
Again, the solution would really depend on how much flow we are talking about.