I have heard of spreading 2 or 3 bales of OLD hay over the surface to clear mud. It was recommended by the fisheries biologist(s) on the Mississippi Fishing website. I talked to one Texas pond owner who told me that he cleared his one acre pond by simply adding a bale of hay that wasn't spread. Heck, I'd try that but first I'd do the jar test that Sunil recommends.

If the sand falls to the bottom and your jar does clear, it indicates that something is stirring it. I don't think gypsum will do much good if that's the problem.