At least 20 people are confirmed to have died and as many 50,000 have been left homeless.
But the danger is not over, with the Indonesian weather bureau forecasting more heavy rain this week.
It says the monsoonal conditions will last into February.
Many in the city are pointing their fingers at the local and central governments, who they say have failed to maintain Jakarta's essential infrastructure and flood defences.
But Fook Cheung Eng - Senior Water and Sanitation Specialist for the World Bank in Indonesia - says progress has been made since the city's last major floods in 2007, which killed 70 people, forced 350,000 out of their homes and cost USD $900 million.
"Both the central government and Jakarta city government have made significant inroads to improve the infrastructure,"
"Last year, in 2011, the East Flood Canals (BKT) canals were completed by the central Government - that's a key piece of the Jakarta flood-management master plan. The Jakarta city Government has been shoring up the sea defences against floods over the years as well and there have been more resources put in to the maintenance of the canals. But it is a very large challenge."
Last year, the World Bank issued an 'urgent flood mitigation report', which outlined a plan to dredge the city's major floodways and canals.
The Bank also committed nearly USD $150 million to a rehabilitation plan to be managed by both central and local governments.
Nearly a year, on the physical task of dredging the canals and restoring the riverbanks is yet to begin, but Fook Cheung Eng insists progress has been made.
"... at this point, the works have not started, the governments and project-implementing agencies ... are in the stage of procuring the large dredging and embankments-repairs works," said Fook Cheung Eng.
He also says there are issues with doing these works in a city as urbanised and dense as Jakarta and that planning the works will take some time.