Thunderstorms account for most of the wet season rainfall in the Keys. Evaporation at the sea surface and cooling in the upper atmosphere leads to the formation of billowing cumulus clouds offshore in the morning. As the clouds move onshore throughout the day, thunderstorms can occur at anytime. They are usually short-lived and widely scattered occurring most often in the early morning. In Key West, the most thunderstorms occur in the summer, with July being the peak month.

A distinctive oceanic weather feature sometimes observed offshore of the Keys is the waterspout. Having the distinctive funnel-cloud shape characteristic of tornados, waterspouts most often form during the summer months. The most waterspouts have been observed in July. The daytime heat, high moisture, and light surface winds of summer are most conducive to waterspout formation. Waterspouts rarely last long enough to come ashore and do damage.