By 2025, estimates from the Inter-governmental Panel on Climate Change show, sea levels would have risen by only about 5cm.
But Mr Brinkman said that Jakarta, which spans a plain between coast and mountains, will be between 40cm and 60cm lower than it is now.
The study shows that without better defences, the sea will reach the presidential palace, which is around 5km inland, in 2025 as well as completely inundate Jakarta's historic old city.
Dec 6 that year will see the tidal cycle reaching its highest point, but Mr Brinkman warned that there are likely to be plenty of floods before then.
He blamed the swelling city's over-development, which is compressing the land it is built on, for the looming predicament.
The problem has been exacerbated by factories, hotels and wealthy residents drilling deep-water bores to bypass the city's shambolic water grid, sucking out the groundwater and causing further subsidence.
Around 40 per cent of Jakarta's population is not connected to the water grid, said Mr Achmad Lanti, the city's water regulator.
Jakarta privatised its water supply in 1997 in the hope of improving services, but Mr Lanti said the two foreign operators had failed to live up to pledges to deliver water to 75 per cent of the population by last year.
The shortage leaves many residents with limited options: Buy water at an inflated price, dig for it or steal it.
Around half of the water from the city's pipes disappears through a combination of leaks and theft, Mr Lanti said.
The World Bank has called for a halt to deep groundwater extraction, and the city administration has raised the price of groundwater. But there has been little progress so far.
Mr Brinkman said: 'If you do nothing about the groundwater problem, parts of Jakarta will sink 5m (by 2025).'
A glimpse of the future can be seen in the shacks of Muara Baru, where the city's northern limit meets the sea, and where flood levels late last year reached up to 2m.
The slum is bordered by just the kind of high-rise towers, luxury homes and mega- malls that are pushing the area into the sea.
'Sometimes (those who steal) are only individuals, sometimes they form a kind of organised crime, what I call a water mafia,' said Mr Lanti.
The waste-filled canal that runs up to the edge of Muara Baru shows the effects of the city's chaotic development.
Big buildings have taken over natural drainage sites, while human waste and rubbish clog waterways, causing freshwater floods that surge up from the ground during the rainy season.
The drainage system built by the Dutch who once ruled Jakarta is unable to cope with its rapid growth, said Mr Hongjoo Hahm, the top infrastructure specialist at the World Bank in Indonesia.
'Every year we get floods,' he said.
'The scale of the floods (the Dutch) said would happen every 25 years, we are seeing every year now.'
BY 2025, sea levels would have risen by only about 5cm, according to estimates by the Inter-governmental Panel on Climate Change.
But Jakarta will be between 40cm and 60cm lower than it is now, said Mr Jan Jaap Brinkman, an engineer with Dutch consultancy Delft Hydraulics.
The city will be submerged by sea water, come Dec 6, 2025 - when the tidal cycle is at its highest point. But Mr Brinkman warned there are likely to be plenty of floods before then.
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