Hi,
Some things I would do in your situation might be to give the polygon a fill but make it very transparent so it doesn't interfere too much with everything else that's going on. If that's not possible having thick but transparent boundaries may also decrease how distracting the boundaries are while still being visible. I would also consider making the other features in the map which are not the focus of the display much lighter and also more transparent so the most important data stands out best.
If you can, editing the boundaries so they don't fall in the middle of the river would look a little nicer and easier to see.
I'm definitely no expert but I hope I gave you a few ideas to play with!