Earlier the NWS office in Miami said between 6 and 11 inches of rain fell on some areas.
A Flood Watch was in effect for South Florida late Saturday afternoon and included parts of Broward, Miami-Dade and Palm Beach counties.
A tropical storm watch was also in effect for the northwestern Bahamas.
The disturbance is unlikely to become the first named storm of the Atlantic hurricane season before it finishes crossing Florida Saturday, the NHC said.
“The disturbance is expected to become a tropical storm off the East Coast of Florida by (Saturday night), and some strengthening is forecast tonight through Monday as the system moves farther away from Florida over the western Atlantic,” the NHC said.
Some locations could see up to 15 inches before the end of Saturday; Miami had 11 inches by 9 a.m. The NHC added “considerable flash and urban flooding is expected” across this region.
“Over the past few hours, a weather station at Fowey Rocks near Miami, Florida reported sustained winds of 46 mph and a wind gust of 56 mph,” the NHC said.
A tropical storm warning means tropical storm conditions are possible.
Airlines canceled 841 flights on Friday amid multiple storm systems, FlightAware data showed.
US airlines warned disruptions at the Florida airports would last through the weekend.
CNN’s Gene Norman and Greg Wallace contributed to this report.
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