If you're swimming from a public beach or park, the first thing you should do is find out if/where water quality test results are posted. There are generally higher E.coli readings after heavy rains or when waves churn the sediment from the bottom, and they can also be higher downwind from river and stream outlets. Beaches just a few miles apart can have vastly different bacteria levels due to these factors, so it's good to be aware of them.
I'm probably more on the cautious side, since I always wear goggles and (usually) earplugs if I'm planning to be submerged, but it's as much for comfort as anything else. I might consider plugging my nose if I lived in a warmer region, but in places similar to the deep South of the United States, you're probably in much more danger from alligators and snakes while swimming in fresh water than a 1-in-10-million deadly amoeba.
Respecting the local hazards and using any available resources to stay up-to-date on the water quality is probably much more effective than any personal precaution you could take.