Evidently it’s not a problem because the chlorine kills them but still, yech! And the only way they can get in your brain is if you snort the water:

Brain-eating amoebas have taken up residence in Tucson’s water supply as recent tests have shown their presence in 12 wells.
While the discovery of the killer amoeba, known as Naegleria Fowleri, is surprising to at least one UA researcher, the microscopic bug’s presence in the Old Pueblo’s water supply doesn’t pose any health risks.
Tucson Water chlorinates its well water before distribution, killing the amoeba before the water hits taps; but the amoeba’s presence in an underground water source is surprising and is likely the result of biodegradable oil used in pumps. The amoeba is usually found in surface water such as rivers and lakes.

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Disgusting news of the day: 6 Die From Brain-Eating Amoeba in Lakes