I'm not a fish expert, so I contacted an IDNR fisheries biologist on this one. Here is his response:
The fish parasites are most likely black spot or yellow grubs, the two most common fish parasites in Illinois. There is really no treatment for either one. Black spot has a life cycle requiring snails as an initial host, fish as an intermediate host, and birds as the terminal host. Black spot can reach elevated levels due to a large snail population. Snail populations can be reduced, thus reducing the black spot outbreak, by stocking fish that are known to eat snails. In this area, the species of choice is the redear sunfish. Yellow grubs are also very common in this area. They also require fish-eating birds (Great blue herons, usually) to complete their life cycle. I have not heard of anybody accomplishing this, but it may be feasible to reduce the yellow grub population by deterring access to the pond by fish-eating birds. Otherwise, they are pretty much stuck with it. Neither parasite is harmful to humans, and the fish is safe to eat as the parasites are "cooked-out" in preparation. If the parasite infection has become severe to the point of destroying tissue, evidenced by red bloody decaying meat, the infected areas may be cut out and discarded prior to consumption.
