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This is the same lake that I grew up just one block away from, constantly wrinkling my nose at the smell, and concerned that if one single drop of lakewater got on me I might melt, mutate or grow an extra limb. E.coli bacteria is the main threat, washing into the lake after heavy rains from sources like agricultural run-off and overflowing storm drains. True, the bacteria can cause ear, eye and nose infections or (only if enough lake water is swallowed) more severe gastrointestinal problems.
The reality? Your sandwich is more likely to make you sick than swimming in Lake Ontario!
Lake Ontario has some of the safest beaches in the world, many adhering to the standards of the internationally recognized Blue Flag program. Beaches along the Niagara Peninsula are monitored (daily for the most popular, weekly for others) by the Niagara Region's public health department with signs posted informing bathers of the water quality. When signs are posted "unfit" for swimming its because E. coli bacteria have passed a Ontario standard threshold of 100 counts / 100 millilitres which is still less than half of (or twice as stringent as) the 235 counts / 100 millilitres that the US Federal Government deems safe.
Decades of contrary opinions are hard to ignore but these days you're far more likely to hear stories about E.coli poisoning caused by sandwich meat, tomatoes or mixed salad greens than you are horror stories of swimming in Lake Ontario. Sure, I wouldn't recommend hitting up the beach the day after a large rainstorm .. but with the long broiling weeks of sun we've had, why wouldn't you make use of Ontario's under-appreciated assets?
If you're still wary - make sure to rinse off afterwords with a shower, don't drink the water & avoid sandwiches at all costs.