If you eat one bacterium, it’s likely that it will be destroyed by your body before it can reproduce or make you sick. If you eat 10^12 bacteria, they’ll start reproducing before your body can get a handle on it.
Bacteria are all over the place; you’re routinely eating, breathing, and drinking in bacteria, just not at dangerous levels. Still waters let bacteria grow to high concentrations, dangerous to hour health. Running water is constantly washing the bacteria away, so the concentration in any single unit of water is low.
The major thing you’re trying to avoid in water is harmful microorganisms, usually from animal waste and rotting flesh. Moving water will dilute things that fall in and the aeration will help decompose rotting materials. So if a deer shits in a river, you’ll probably be fine. If a deer shits in a pond, it might not be safe for weeks.
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