Landslides and floods are common, especially during the monsoon season between October and April, when rains lash the vast Southeast Asian archipelago.
On Monday, Indonesia's disaster agency confirmed 29 deaths and said at least 13 more people were missing after days of pounding storms on the island of Sumatra.
Some 12,000 others have been evacuated from water-logged Bengkulu province with hundreds of buildings, bridges and roads damaged.
Hardest hit was Bengkulu Tengah district, just outside of the provincial capital, where 22 people were killed along with hundreds of livestock.
Authorities have set up temporary shelters and public kitchens for the evacuees.
Meanwhile, a landslide triggered by heavy rain in Sumatra's Lampung province on Saturday killed a family of six and disrupted transportation links to neighbouring regions.
Flooding in parts of the capital Jakarta during the week killed at least two people and forced more than 2,000 to evacuate their homes.
Residents of Bogor, a satellite city of Jakarta, also had to contend with 14 pythons that were set loose from a private property due to the high waters.
Six of the snakes -- which were as long as four metres (13 feet) -- have been found, but the remaining eight remain on the loose, officials said at the weekend.
In Sumatra, authorities said that illegal coal mining was partly to blame for deadly landslides as the practice makes loose soil susceptible to slides when heavy rains hit.
"Apart from natural factors like the heavy rain,(the flooding) was also caused by human activity that destroys the environment," disaster agency head Doni Monardo told reporters in Bengkulu on Monday.
Activists have long warned deforestation from rampant mining in the province could trigger a catastrophe.
At least four major rivers in Bengkulu overflow every time it rains due to environmental damage near their banks, activists said.
"The flooding in Bengkulu was made worse by the severe damage...caused by coal mining," Ali Akbar from local environmental group Kanopi Bengkulu said in a statement.
Illegal mining was blamed for killing dozens on the island of Sulawesi in March when a makeshift mine collapsed.