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There were no immediate reports of fatalities in Cuba, where the government prides itself on disaster preparedness and said it had carried out evacuations totaling more than 1 million people.
Authorities warned that the floodwaters could linger for more than a day, and there was as-yet uncalculated damage to sugar cane and banana fields in central Cuba and to northern cays studded with all-inclusive resorts, potentially dealing a major blow to the country's key tourism industry.
The powerful storm ripped roofs off homes, collapsed buildings and caused floods along hundreds of miles of coastline after cutting a trail of destruction across the Caribbean. Irma has killed at least 24 people in the region, leaving officials scrambling to bring aid to shattered communities.
In Havana, home to 2 million people, central neighborhoods along the coast between the Almendares River and Havana harbor suffered the brunt of the flooding, with seawater penetrating as much as a third of a mile inland in places.
Waves as high as 20 feet continued to pound Havana, with the spray topping the lighthouse at the Morro fortress at the entrance to the bay, and Civil Defense Col. Luis Angel Macareno warned that the flooding would persist into Monday.
Emergency workers and residents boated and waded through streets littered with debris: toppled trees, downed electrical lines, roofs torn off by the winds and concrete water tanks that fell from atop homes.
Elena Villar and her mother spent the night huddling in the lobby of a building on higher ground as her home of 30 years filled with more than 6 feet of water.
"I have lost everything," she said, on the edge of tears.
Floodwaters entered the high-end Melia Cohiba and Riviera hotels, where the storm damaged the buildings, landscaping and roofing.
The waters and winds also damaged the seaside U.S. Embassy, tossing around shipping containers that sit on the compound, smashing parts of its black perimeter fence, ripping exterior panels from the building and breaking windows and doors. The embassy's flag was in tatters fluttering from its staff Sunday.
Hector Pulpito, 33, recounted a harrowing night at his job as night custodian of a parking lot that flooded five blocks from the sea in the Vedado neighborhood.
"I felt great fear. This was the worst of the storms I have been through, and the sea rose much higher," Pulpito said. "The trees were shaking. Metal roofs went flying."
State television reported severe damage to hotels on the northern cays off Ciego de Avila and Camaguey provinces.
Witnesses said a provincial museum near the eye of the storm was in ruins, and authorities in the city of Santa Clara said 39 buildings collapsed.
Communist Party newspaper Granma reported that the Jardines del Rey airport serving the northern cays was "destroyed" and posted photos to Twitter showing the shattered terminal hall littered with debris.
In Caibarien, a small coastal city about 200 miles east of Havana where many residents stayed put to ride out the storm, winds downed power lines and neighborhoods were under water.
Similar scenes played out across the Caribbean, where the storm devastated islands before setting its sights on Florida.
In St. Martin, formerly lush green hills were stripped to a brown stubble and the smell of rotting debris spread across the French Caribbean territory of 40,000 people. Irma passed through last week as a Category 5 storm.
A truck drove through damaged neighborhoods distributing water, and authorities expected to set up distribution points on Monday. Plans to do so were initially delayed by Hurricane Jose, which roared toward the region as a Category 4 storm on Saturday but turned north without doing much further harm.
"Everything has been destroyed where I work. There's nothing there," 27-year-old Manon Brunet-Vita said as she walked through the streets of Grand Case. "When I got to this neighborhood, I cried."
More than 1,000 tons of water and 85 tons of food have been shipped to the French Caribbean territories of St. Martin and St. Barts, and additional deliveries are expected, according to government officials in the nearby island of Guadeloupe.
Authorities announced the reopening of St. Martin's Marigot port and said a boat was expected to dock by Monday with a 5-ton crane capable of unloading large containers of aid.
More police and soldiers were patrolling the streets following reports of looting, and authorities set up 1,500 emergency shelters.
On the Dutch side of St. Martin, an island divided between French and Dutch control, an estimated 70% of all homes were destroyed by Irma.
Dutch Prime Minister
"Unfortunately, there are more victims to mourn," Rutte said.
With power out to much of the French Caribbean region, France's main electricity provider, EDF, said it has flown 140 tons of generators, pumps and other equipment to help St. Martin and St. Barts.
In St. Thomas, the U.S. Virgin islands, a convoy of FEMA trucks carrying water rumbled past damaged homes with sirens blaring.
William Mills, a 35-year-old security worker, said he waited in a mile-long line for gas. He said many were seeking to leave St. Thomas, but that's not an option for him.
"I'm going to stay here and tough it out," Mills said.
3:50 p.m.: This article has been updated with waves topping Havana seawall, other details.