Sat, 29 Dec 2012 17:05 UTC
Some suburbs in the capital already go underwater when there is a big tide but the problem is expected to get even worse.
Jakarta is sinking by up to 10 centimetres a year and Indonesia's national disaster centre says with oceans rising, large parts of the city, including the airport, will be inundated by 2030.
Flooding and high tides are already causing problems for some residents in the city of 10 million people.
Kartoyo's roadside food stall is swimming in about 30 centimetres of water.
"It has been easier," he said.
"This kind of flood is manageable but hopefully it won't get higher."
"The people here before, they couldn't even go to the market because of the flood and the children couldn't go to school."
In 2009 the council built a small sea wall, but the ocean still pushes its way up through the drains and into homes.
But while some suburbs still go under and the roads are rivers, residents across town have the opposite problem.
Juriah lives next to a new development, one of the many pushing skywards as Indonesia's economy booms, but the water supply to her suburb has disappeared.
"Because the development project next door sucks up all the water, the water stopped since the project started - about three months ago. That's what caused it I think," she said.
"I use a small water pump, and no water flows.
"In the beginning there was a little water but in the end it just stopped."
As developers suck up the watertable it dries out and the city slumps into the empty cavity.
"From our observations, since the 1960s the ground water has declined around 30 metres," the head of water resources at Indonesia's energy and mineral resources ministry, Dodid Murdohardono, said.
"The decline of ground water causes pressure in the groundwater lining and that's why Jakarta is sinking."
Sutopo Purwo Nugroho, an expert hydrologist with the National Disaster Mitigation Agency, says if the problem is not remedied, it could have massive consequences.
"If this continues, the area will have permanent flooding will increase especially with the additional increase of sea level in Jakarta Bay or the Java Sea, which is around seven millimetres per year," he said.
"If our efforts aren't fast enough compared to the causes, more than five million people could be affected."
The city's given itself less than 20 years to sort it out.
To curb the twin problems of the city sinking and the ground water drying up, the government's attempting to restrict the amount industries can take.
"And in the next 30 years the government of Jakarta plans to build a giant dam around Jakarta Bay to anticipate the increased sea levels, tidal waves and land subsidence," Mr Nugroho said.
"If the land sinking isn't resolved, then there will be widespread tidal waves that would cause more extensive flooding in Jakarta."