I've thought about this a little bit more and another source of your problem may be pH. This is typically usually more of a problem in spruce bogs. If your marsh is too acidic it also won't support the bacteria etc...that you need to keep your potholes from filling in. There are three possible sources for increasing acidity, surrounding vegetation, acid rain and run off from an external source (agricultural land, roads, industry etc). If your marsh is surrounded by conifers (softwoods) they may be affecting the pH.
The first thing you should do is check the pH of the marsh water with a litmus test (you should be able to buy one at a place that sells swimming pool equipment). Check it in as many places as you can, potholes that are filling in, ones that are stable, near the shore, in the middle of the pothole, on the surface and near the bottom. Ideally you want a pH that is neutral to slightly acidic, (pH of 6.7-7.0). Unfortunately this is only the water pH and in the best case scenario you would want soil and water both but you really need some sort of background in soil sciences when trying to determine soil pH.
Now this problem may be easier to fix than the dissolved oxygen content of the water. As a long term fix if you are dealing with conifers surrounding your marsh you may want to consider planting some hardwoods. In the short term if you lime the hell out of your marsh you should be able to lower the pH.
pH and oxygen levels are the first two things that occured to me when I read about your problem. There may well be other potential sources of the problem as well as alternate ways to fix them. You may want to talk to your local duck biologist, DU or Delta chapter or someone at your local university.