The biggest problems with waterways are possible wetland restrictions (as covered by
@Ridgerunner ), flood plains, and use restrictions (such as minimum offsets). Additional problems can occur if the waterway is considered to be navigable... and surprisingly small creeks can be classified as "navigable". Part of my Grand Father's difficulties were that the stream adjoining his property was navigable. The county told him that he had to allow fisherman right-of-way river access to those walking the river bank. But because his driveway was the only road access to that part of the river (and perhaps because the county plowed partway in) he also had to allow access
through his property. That meant he had to allow strangers to enter his private drive, park on his property, and maintain a pathway for them to the river. It was basically a government-sanctioned open door to trespassers.
All that being said...
It sounds like the property you are looking at has a lot of potential,
@margali , and you have already done a considerable amount of research. I look forward to updates.