Finally a topic that I actually know something about. I have absolutely no legal advice because I am just some backwoods girl that happened to get an amazing job in Pond Management out of pure luck. I have been doing it for 5 years now and the main thing I have learned is that as long as people don't know about it until it is done you are usually okay. The big things that will get you in trouble even before you finish the project are...
a) changing the waterway. If you create a damn to stop flow of water and divert it to your pond your in trouble.
b) adding chemicals to the water. Even ones that don't require permits like copper sulfate can cause problems.
c) building your pond in a wetland area or an environment that is ideal for endangered plants to thrive. You may have to have a professional evaluation to determine this. Most likely the local authorities already know if your property is one of the off limit areas but they won't tell you about it until you try to build. Hiring a private company for the evaluation is your best bet.
Having said all of that in my experience once a pond is up and running and supporting plant and fish life people are less likely to do anything about it. They may be angry at you, but they would have to jump through a bunch of hoops at this point to do something about it and that is more work then most people want to do.
Also be aware that once you build the pond even if it is smack dab in the middle of your property you no longer own that part of your property. The federal government owns all water and can come on your property whenever they want without notice or permission to get to it. Also if others can get to the pond by water without stepping on your property they can fish and swim and do whatever they want. In some cases you may even be held liable if anything happens to them while they are using your pond without permission.