Well,I don't doubt the vegetation issue, and unfortunately, from the sound of things you will probably have your hands full in this regard. A shallow pond, fed with agricultural runoff, will more than likely suffer more than an average share of vegetation problems.
I also wonder about the effects of cropland runoff on a future fish population.... do you know if there are fish in it now? Either way, working with a pond is like building a house...you start with the foundation and work your way up. Verifying the depth would still be my first step..it all kind of hinges on that in my book.