IMHO it is unadvisable to use pond substrate in an aquarium. There are so many different organisms living in the mud that you won't have any idea what to expect. From microorganisms to macrro in egg/larval/et cetera stages and so on you run the risk of fish and plant kills without a sure idea of what caused it. Plus, you won't have a solid way of knowing what types of chemicals or other nutrients are in the soil and organic components. Pond margins are great at nutrient and chemical sequestration and accumulation

. Also, many aquatic critters can be parasitic or predatory.
Too many unknowns, and the knowns are just not very appealing to aquaria.
On the other hand, using pond substrate along with the native inhabitants, water, and so on who will have natural defenses or immunities to what ever is in there would make a great aquarium project representing that site specifically. Just don't add a lot of expensive "outsiders" to the mix.
Sounds interesting.