It sounds unfortunate as to how this has come about. Some comments on authorities of federal agencies. The Corps would be interested if you filled a wet land, placed fill in a navigable water way, or altered the course of a navigable waterway (section 10 and section 404). Under the dam safety program, they would also be interested if you have built a dam / impoundment where if it failed could endanger life or property down stream.
EPA would be interested in impacts caused by your activities which could pollute water or impact human health or the environment (e.g. clean water act or the National Environment Policy act, NEPA).
The fact that you do something on your property doesn't limit potential impacts to your property. Pollution of a stream or ground water, or flooding a neighbor would be of concern and would likely be covered by law.
I can't comment on your specific situation but I would go to the source and get some technical advice as to your options. Note that in many states, some of these authorities (such as NEPA) have been delegated to the state. Your worst enemy will be miss information. You should be able to get facts from the net also if you have the time to do the research.
