I can see the appeal for this. We have a "typical" pool in our back yard, an indoor 25m community pool about 2 easy miles away and lot's of ponds around (one that is used for the local tris). I do my workouts at the community pool, but would love to use the pond (not allowed except during events). There are snakes and turtles and such in and around the water, but these types of animals are app to be more concerned about what you will do to it than what it will do to you. (But I'm pretty sure alligators are not like that when they are interested in feeding.)
For cleanliness if I was going to build my own pond and had the funds to make it how I wanted, I would line the pond with limestone. Limestone is a natural water cleaner. Even if you don't "filter" through the limestone, it will keep the water clean. If you look at Lake Amistad, which is almost 100% (if not 100%) limestone "lined" it is extremely clean. Lakes Travis and Possum Kingdom are two others that come to mind as being very clean because of the limestone.
You wouldn't need boulders or anything like that. You'd simply get the largest area size, but thin, "tiles" or rocks and line it. Even if you only used limestone in part of the pond (like just the bottom), it would remain cleaner.
But I think you'd need at least 3 acres for swimming or you'll need to add a recirculation/aeration system and "natural" filtration or salt filtration.
If you had a continuously flowing creek or river that you can join into, it'd be even better. Part of the flow from the creek is funneled to the pond and then back to the creek.
Sounds like a great project if you can afford it. Here's an example of a pond I found that you might consider
https://www.youtube.com/watch?v=Le-MwLETtOU.
It's not for swimming, but you can get the basic idea of what you'll have to do.
I'm sure there are many of us on ST who love to see photos of the completed pond. (Maybe you can make a video of the build and completion.)
Good luck!
Not a coach. Not a FOP Tri/swimmer/biker/runner. Barely a MOP AGer.
But I'm learning and making progress.