Hi.
I know nothing about MSFS, and my first and maybe lone answer on the matter, but what I see is your water (river, polygon, whatever) is creating its own altitude (the same value probably for each of his point coords) or is using the elevation of something else (a mesh data). If I were you, I would check anything that may have something to do with both possibilities :
Where do I define the altitude of what I am drawing ? Or where do I set that each point of the polygon has its own altitude ?
What thing or process among all those options may prevent my polygon to draw/snap on ground ?
Did I specified a lower altitude somewhere ? (like I started this river near a shose, altitude 0ft, then drawn deeper inlands, but I didn't check in the options how to make the stream use local elevation instead of the 0ft I specified/used by default by my first coordinate plot)
If I can't set altitude or elevation offset, or make the thing follow terrain, am I unsing the right tool ?
What do I have to draw elevation coordinates if I had to use something else to get the river at the right elevation again ? (you should not check this until you have nothing else. Creating cliff then deleting them by setting altitude is counter productive and not at all efficient)
^^ that's how you solve a problem, by making possible all hypothesis (including those where you missed something because it's new and no one told you how to), and ruling them out one by one by checking it.
For instance, selecting the polygon gives you a bunch of options to check. But what about available options you have when you select a single coordinate point ? Or several of them ? Perhaps you have some default parameters to define via the first point of the polygon before adding/plotting the other coords ?