The "microburst," which is defined as a localized column of sinking air within a thunderstorm, struck around Bay Ridge Parkway, between 18th and 20th avenues, around 3:40 p.m.
Bensonhurst, which took the brunt of the damage, saw downed trees, damaged cars and blocked roads.
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Departures at all three major area airports also experienced delays due to the weather.
The region is expected to swelter through the first heat wave of the season later this week, with temperatures Friday soaring into the high-90s.