The worst-hit country was Guatemala, where officials say at least 82 people died. Nine were killed in El Salvador and at least eight in Honduras.
Storm Agatha swept in from the Pacific Ocean on Saturday, bringing torrential rains that added to disruption caused by a volcano erupting in Guatemala.
The storm is dissipating but more heavy rain is forecast for the next few days.
Man carries bottles through flood in Guatemala
A state of emergency has been declared in three countries
Rescue workers have been clearing debris from roads to reach cut-off communities.
Many areas have not been reached and the number of dead is expected to rise. In Guatemala, where Agatha made landfall on Saturday, at least 53 people were reported missing.
Parts of Guatemala have received their highest rainfall in more than 60 years, according to the country's President Alvaro Colom, who said more than 3ft (1m) of rain fell in some areas.
"Many places are cut off but it appears the weather will improve a bit today and we will be able to airlift supplies to those places. The road network is badly damaged," President Colom said at a news conference on Sunday.
Nearly 112,000 people have been evacuated from their homes across Guatemala, officials said.
Guatemala, El Salvador and Honduras have all declared emergencies in an attempt to increase immediate aid and resources.
Agatha - the first named storm of the Pacific hurricane season - also hit southern Mexico.
The storm is dissipating over the mountains of western Guatemala - but emergency workers have warned residents to expect heavy rain for several more days.
Devastation
A mudslide devastated an entire neighbourhood in the Guatemalan town of San Antonio Palopo, 90 miles (150km) south-east of the capital.
"There was a mudslide that wiped out homes, trees and everything in its path," a witness told local radio.
In Quetzaltenango, 125 miles (200km) west of the capital, Guatemala City, a boulder came loose and crushed a house, killing four people, including two children.
In El Salvador rains triggered at least 140 landslides in which President Mauricio Funes said nine people had died.
"Although the storm appears to be diminishing in intensity, the situation across the country remains critical," he said.
Officials in Honduras, where several regions have been put under a state of emergency, said there had been at least eight storm-related deaths.
The storm has also complicated efforts to clear up ash from the Pacaya volcano in southern Guatemala, which began erupting on Thursday.
Guatemala's main airport has been closed while workers clear the runways.
A state of emergency declared because of the volcanic eruption has been extended across the country.
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