It would be a little easier to understand if you had a diagram but I have a fair idea of what you have. As for the ducks, it's been my experience that some grass and cattails will not be a hindrance and in fact will help - especially with locating a blind or such. It would be good to have some open water. If you are already at 2 feet deep I wouldn't think you need to excavate another foot out of there, I'd leave it at 2 feet unless the water flow is such that it is difficult to maintain 2 feet. Being a gravel pit makes me think that it is primarily ground water that is filling in the main hole (if I am picturing this correctly). The levee (trust me on the spelling, I'm a Louisiana native) is probably diverting as it is placed/sitting on top of or very near the water source, hence the splitting. And being a gravel pit I wonder about the bottom surface - sand, gravel, rock, or mud? Back in Louisiana gravel pits were notorious for having false bottoms (mostly sand), slides from slopes underwater were also common and more than one have drowned as a result. With some more visual information I could help more as I am a water pump application sort of guy.
Do you know why Cajuns don't hunt elephants? Because the decoys won't fit in their pirogues!