The centre of Tropical Storm Alberto made landfall at 12:30 pm (local time) near Adam's Beach, a sparsely inhabited area of western Florida, according to the National Hurricane Centre (NHC.)
The NHC had initially issued a hurricane warning for parts of Florida's Gulf of Mexico coast, but the storm failed to strengthen into the first hurricane of 2006.
Authorities nevertheless warned residents to brace for coastal storm surge flooding as the storm moves inland.
The storm also could spawn tornadoes in parts of Florida, Georgia and South Carolina, the NHC said.
Before it hit land, Alberto had maximum sustained winds of 85 kilometres per hour (50 mph.)
The wind speed was expected to weaken as the centre of the storm moves over land.
Mindful of the devastation caused by Katrina and other hurricanes last year, authorities took no chances.
On Monday they ordered the evacuation of about 20,000 people living in mobile homes and low-lying areas, and Governor Jeb Bush decreed a state of emergency, which allows him to mobilize emergency personnel and National Guard troops.
Plane crash
In the city of Tampa, a small plane slammed into a house on Monday, killing one person.
Authorities said it was unclear whether the severe weather already affecting the area played a role in the crash.
In Cuba, authorities had evacuated 28,000 people as the storm swept past the island on Monday, packing winds of almost 115 kph (70 mph.)
Eight people were injured, four homes were destroyed and 48 others damaged by a tornado at Nueva Paz, south of Havana, which was whipped up by Alberto, television reports said.
Alberto is the first Atlantic tropical storm since last year's record-smashing season of 28 named storms, 15 of which became hurricanes.
Several of the hurricanes blasted across Florida, including the season's worst, Katrina, which left 1,300 people dead and tens of thousands homeless along the Louisiana and Mississippi Gulf Coast.
The city of New Orleans is still struggling to recover and engineers have warned its levees may not withstand another Katrina-style battering.
The Atlantic hurricane season officially started on June 1 and lasts until November 30.
US weather experts are forecasting between eight to 10 hurricanes - as many as six of them major - will form in the Atlantic basin this year.