There is definitely a difference in temperature based on lake size and depth. Keuka, Canandaigua, and Skaneatles will be the warmest with Cayuga coming next and Seneca bringing up the rear, so to speak.
The lakes are generally swimmable from late June through early September. If you are coming this summer, however, the lakes are cooler than usual due to the very cold summer we have had so far. Typically I would say water temp in Canandaigua lake, where I live would be as follows on a normal summer:
late June in the high 60s
July in the low 70s
August in the mid or high 70s
September in the low 70s or high 60s
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