Video compression- how to prioritize one area over another?
This is an interesting question, but I don't think that you will find a good solution without changing your inputs (the video elements you are using). I'm not aware of any software that allows you to prioritize compression by area. The compressor itself usually makes all these kinds of decisions for you.

Aside from that, you said the magic (not good) word for compression: Youtube. Even if you could find a way to do the above, you basically give it all up when you upload it to Youtube, where they will run their own fixed compression algorithms that will ruin all your work.

I think there are a couple of things you can do (perhaps all of them in combination):


If you haven't already, try doing 2-pass compression, instead of one-pass. This will take longer, but the compressor will have a chance to analyze the video on the first pass, and that may possibly help improve your output a little.
Massage that water footage. If you can get rid of it completely and replace it with something else that causes less trouble, do it. If not, you can try things like:


Apply some blur (either chroma [color portion of the signal], luma [monochrome portion of the signal] or both) to the footage.
It would also help to run the water footage through a denoiser first.



Both denoising and slight blurring should help reduce the amount of bandwidth that your compressor needs to dedicate to that area of your video.