Just my theory but what I gather from reading you statement I would guess this is more about potential erosion of soil that could possibly enter into a navigable stream due to erosion from your land disturbance, which would be in the jurisdiction of the EPA or the DNR, they are extremely sensitive, especially in some areas to runoff carrying soil and other contaminants into a stream.
As an excavating contractor I deal with such every week, Another local contractor received over 30 thousand in fines for failing silt retention devices allowing a minute amount of soil contamination in a minor creek, not even a navigable one.
