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I've read quite a lot online about bacteria you can be infected with by swimming in freshwater lakes. Anecdotally I've had friends tell me that when swimming in a lake you should keep your head over water.
In many cases, avoiding submersion isn't an option, and you're going to freestyle swim anyway. Is it common for people to use earplugs or noseplugs or anything like that? If industrial pollution isn't a particular concern where you're swimming, would you take any precautions?
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.
I suggest you go swimming in a more regular and clean swimming pool.Swimming in places that don't pay attention to the cleanliness of water can easily infect bacteria in the water, although taking protective measures can also make bacteria come into contact with you.Regular swimming pools are usually equipped with filters manufactured by regular manufacturers, which can effectively remove harmful chlorine, heavy metals, bacteria, viruses and so on. Such clean and hygienic water quality is very safe for people.This article describes the benefits of changing filter elements. You can see that the water in a regular swimming pool is much safer and healthier than that in a lake. It is better for you to go swimming in a regular swimming pool. http://www.waterfiltersfactory.com/news/benefits-of-pools-water-filter.html
