Here is a Pond Boss thread directly about transferring parasites.
Scroll down to the second post. (Bill Cody was giving me advice in a PM thread, but he let me post it to the forum.)
Transferring ParasitesThe thread then goes on to discussing how to exclude wading birds from forage and grow-out ponds - which obviously is NOT applicable to your situation of a duck marsh.
I do have some guys around me that run duck marshes/ponds. It is usually below their main pond, so they let it dry every year and then fill it at the right time for the plants to be perfect for duck season.