The U.S. hurricane center had said Sandy is expected to produce total rainfall of 6 to 12 inches across Jamaica, Haiti, Dominican Republic and eastern Cuba.
"These rains may produce life-threatening flash floods and mud slides, especially in areas of mountainous terrain," the center said.
Eastern Cuba is mountainous and home to independent and state farms growing yucca, sugar, corn, coffee and fruit, among other crops.
Fishermen on the Gulf of Guaranayabo, which Manzanillo is located, moved their boats to safer ground.
People in Manzanillo, a city of 132,000 some 465 miles (750 kilometers) east of Havana, said they were worried about the impact, particularly after a wet summer that left sub-soils saturated.
"Given the condition of my house, I don't know if it will withstand the force of a hurricane, but we are prepared," said Emiliano Lopez, a 62-year-old who lives near Manzanillo's seaside boulevard.
In Santiago, Cuba's second largest city, tourist hotels prepared by getting generators ready and closing off some outdoor spaces and pools. Guests were being kept informed, but there were no evacuations other than from the beach resorts. Heavy rain was already falling late Wednesday night.
"We're well prepared for the storm," said Mayte Cuesta, an employee of the Hotel Melia Santiago. "It will affect us, but we don't think there is any danger."
As Sandy crossed over Jamaica on Wednesday an elderly man was killed by a boulder that crashed into his clapboard house, police said. In southwestern Haiti, a woman died in the town of Camp Perrin after she was swept away by a river she was trying to cross, said Marie Alta Jean-Baptiste, head of the country's civil protection office.
Jamaican authorities closed the island's international airports and police ordered 48-hour curfews in major towns to keep people off the streets and deter looting. Cruise ships changed their itineraries to avoid the storm, which made landfall Wednesday afternoon near the capital, Kingston.