I agree with John B.

If your land has agricultural potential then for all intesive purposes the government agents should treat it as a farm...

If they are valuing it as "farmland", then they should let you improve it as "farmland".

Its ironic that the Corps in your area apparently wants to maintain run-off. Is there a white water rafting river or something downstream from you?

In many areas of the country you would expect that the Corps would be happy to have private ponds added to the watersheds as they would reduce erosion and flooding problems.

I think the Corps, like any government agency probably gets pulled in a lot of different directions: For example: Less erosion might improve water quality, but reduced erosion upstream might cause places like the Mississippi Delta to disapear under seawater...

Keep trying!