Two of the victims were children whose home was destroyed by a mudslide triggered by the storm.
The third victim was a 56-year-old woman who perished when she attempted to drive from her riverfront home to another dwelling to find shelter.
Cities across the state reported damage to roads, bridges, utility lines and crops.
Carlotta left an estimated 4 to 8 inches of rainfall across parts of southern Mexico, according to the U.S. National Hurricane Center.
Carlotta, the third named storm of the Pacific hurricane season, passed to the north of Mexico's largest oil refinery, the 330,000 barrel-per-day Salina Cruz installation, which remained open and unaffected.
Hurricane Carlotta Track
Satellite Loop Data: CIMSS