President Luis Guillermo Solis declared three days of mourning. Some 5,500 residents had to be evacuated.
Several towns were covered by water and mud, and small bridges collapsed.
Otto, the southernmost hurricane on record to hit Central America, made landfall in southern Nicaragua as a category-two storm on Thursday.
But it weakened rapidly and became a tropical storm as it moved into the Pacific, the US National Hurricane Center (NHC) said. At its peak, Otto had wind speeds of up to 175km/h (110mph).