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To answer your question, yes you can find water moccasins (or "cottonmouths") in Missouri streams.
However, you should not be worried. They do not have a nasty temperment. I'm an avid enjoyer of Missouri streams, and have been for many years, but have never had a problem with poisonous snakes in the rivers. They seldom have any interest in people, and I've swam right by them before (by accident, of course) and we've left each other alone. If you happen to see one (they swim on the top of the water), simply swim away and they will leave you alone.
As far as pollutes lakes/rivers, it depends on which ones you visit. Most of the streams further out in the Ozarks are very clean. Only a few are polluted.
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