Of course all areas/states are different but in areas where water isn't fought over, properly developing ponds and wetlands is usually supported and encouraged. There are correct ways to do it and there are wrong ways. The Feds or the EPA would be the least of my worries in this area. The key here is to stay away from running water and existing wetland habitats when locating a pond.
If a person is willing to follow some sensible rules, they can avoid a lot of problems. It's always the folks who think they know better, or have a constitutional right to be ignorant, that get themselves into trouble in these cases.