Tropical Storm Alex lashed Cuba as warnings were issued for parts of the island, the Bahamas and the Florida Peninsula Friday.
In Havana, the heavy and uninterrupted rain caused street flooding, bringing traffic to a halt.
Two people have been reported dead in Havana and one person missing in Pinar del Rio.
Stores were mostly closed as few people braved the flooded streets to walk through knee-high water.
Strong downpours brought intermittent flooding but no high winds inside the low pressure area that, if it intensifies as it passes through the Gulf of Mexico, could finally advance towards Florida.
In the northern coastal town of Pinar del Rio, people rushed to secure homes, boats, and the precious tobacco crop warehoused in drying barns.
The Forecast Center at the Cuban Institute of Meteorology reported over 30 locations with a total of 4 inches (102 mm) of rain water in the center and west of the country.
Experts warned that winds aren't the hallmark of this storm, rather the saturated ground caused by heavy rains in May may bring flooding in low-lying areas with poor drainage.
The National Hurricane Center, based in Miami, specified that the storm – which will form from the remains of Hurricane Agatha in the Pacific Ocean – will be known as Alex in the Atlantic Ocean basin.
The Atlantic hurricane season started on Tuesday this week and the NOAA (National Oceanic and Atmospheric Administration) predicts an above-average hurricane activity this year — which would make it the seventh consecutive above-average hurricane season.