The Ciliwung River flows from a volcano south of the Indonesian capital, through the heart of one of the world’s most densely populated cities and almost into Jakarta Bay. Almost, because for the final mile or so of its course, the river would have to flow uphill to reach the bay.

The same is true for the rest of the half-dozen sewage-choked rivers that wind though central Jakarta. Unable to defy gravity, they’ve been redirected to canals that drain into the sea.

The reason these conduits are necessary is that Greater Jakarta, an agglomeration of 28 million people, sits on a swampy plain that has sunk 13 feet (4 meters) over the past three decades.

“Jakarta is a bowl, and the bowl is sinking,” said Fook Chuan Eng, senior water and sanitation specialist with the World Bank, who oversees a $189 million flood mitigation project for the city.

The channels of the Ciliwung and other rivers are sinking. The entire sprawl of Jakarta’s north coast - fishing ports, boatyards, markets, warehouses, fish farms, crowded slums and exclusive gated communities - it’s all sinking. Even the 40-year-old seawall that is supposed to keep the Java Sea from inundating the Indonesian capital is sinking.

Just inside the seawall sits the Muara Baru kampong, or village, that is home to more than 100,000 people. It is now at least 6 feet below sea level, and residents like Rahmawati, a mother of two small children, gaze upward from their front stoops to view the sea.

“When there’s a high tide, the ships float almost at the same height as the seawall - we can see the ships from here,” said Rahmawati, who like many Indonesians goes by one name.

Flooding from overflowing rivers and canals in the area is at least an annual event that forces Rahmawati and the rest of the kampong to evacuate to public buildings nearby. High-water marks from the last big flood, in 2013, are still visible on the walls of the kampong.

“WORST SINKING CITY”

Jakarta is sinking because of a phenomenon called subsidence. This happens when extraction of groundwater causes layers of rock and sediment to slowly pancake on top of each other.

The problem is particularly acute in Jakarta because most of its millions of residents suck water through wells that tap shallow underground aquifers. Wells also provide about a third of the needs of business and industry, according to city data.

“It’s like Swiss Cheese underneath,” the World Bank’s Fook said. “Groundwater extraction is unparalleled for a city of this size. People are digging deeper and deeper, and the ground is collapsing.”

The effect is worsened by the sheer weight of Jakarta’s urban sprawl. Economic development in recent decades has transformed the city’s traditional low-rise silhouette into a thickening forest of high-rise towers. The weight of all those buildings crushes the porous ground underneath.

Previous articles in this series have focused on rising seas, which are climbing as the warming atmosphere causes water to expand and polar ice to melt. Ocean levels have increased an average of 8 inches globally in the past century, according to the United Nations-backed Intergovernmental Panel on Climate Change.

But in many places - from metro Houston, Texas, and cities on the U.S. East Coast to the megacities of Southeast Asia - the impact of subsidence, due mainly to groundwater extraction, has been greater. Manila is sinking at a rate of around 3.5 inches a year. Ho Chi Minh City, Vietnam, is subsiding 3 inches a year, and Bangkok around an inch.

This has been happening even as populations around the world have tended to concentrate along low-lying coastal land. In 2010, an estimated 724 million people around the world lived in what researchers consider low-elevation coastal zones - coastal areas 10 meters or less above sea level. That number increased 34 percent from 538 million people in 1990, according to a Reuters analysis of data developed by the Socioeconomic Data and Applications Center at Columbia University.

The phenomenon has been most pronounced in Asia, home to the top five nations in terms of population growth in vulnerable coastal areas. In China, that population rose 29 percent to 162 million during the 20-year period; in India, the increase was 43 percent to 88 million; and in Bangladesh, it was 46 percent to 68 million.

In Indonesia, the number of people living in vulnerable coastal areas was 47.2 million - one of the highest totals in the world, and up 35 percent since 1990.

Higher seas, sinking cities and more people mean worsening impacts from storms and floods. And the frequency of these events is increasing, too. Recorded floods and severe storms in Southeast Asia have risen sixfold, from fewer than 20 from 1960 to 1969 to nearly 120 from 2000 to 2008, according to an Asian Development Bank study.

No city is subsiding faster than Jakarta. As a whole, the city is sinking an average of 3 inches a year, far outpacing the one-third inch annual rise in mean sea level in the area. The coast near Jakarta is sinking at a much greater average of six inches a year - and in some places as much as 11 inches - according to a 10-year study by a team of geodynamics experts from the Institute of Technology Bandung.

Today, 40 percent of the city is below sea level.

“Jakarta is the world’s worst sinking city,” said JanJaap Brinkman, a hydrologist with the Dutch water research institute Deltares, who has spent years studying the city’s subsidence and helping devise solutions for it.

Little can be done to halt the slow upward creep of the seas. But it is possible to stop subsidence. Jakarta has regulations limiting the amount of water that can be extracted daily from licensed wells. A public-awareness campaign on television urges viewers to “save groundwater for the sake of our nation.” But enforcement is weak, and illegal wells are rife in the city.

About three-fourths of residents rely on groundwater. Many of them are refusing to connect to the piped water distribution system because it is more expensive, is not always available and sometimes looks dirty coming out of the tap.

The city has a moratorium on new mall construction, mainly to ease notorious traffic congestion, but has otherwise not tried to temper the building that weighs on the ground below.

WATERSHED MOMENT

Unable to stop itself from sinking, Jakarta has focused its attention on walling off an inevitable inundation from the sea. A February 2007 storm was literally a tipping point for moving the government to act.

A strong monsoon storm coinciding with a high tide overwhelmed ramshackle coastal defenses, pushing a wall of water from Jakarta Bay into the capital. It was the first time a storm surge from the sea had flooded the city. Nearly half of Jakarta was covered by as much as 13 feet of muddy water. At least 76 people were killed, and 590,000 were left homeless. Damage reached $544 million.

As Jakarta cleaned up, then-President Susilo Bambang Yudhoyono formed a task force to come up with a strategy to deal with more frequent flooding.

One option discussed was to move the overcrowded capital to higher elevations southeast of the city or to another island altogether, said Robert Sianipar, a top official from the Coordinating Ministry of Economic Affairs, which convened the task force. With 5,585 people per square km (0.4 square mile), Jakarta is among the 10 most densely populated cities in the world.

Another thought was simply to abandon the old city district of north Jakarta.

Both ideas were dismissed. Jakarta is the economic hub of Indonesia, contributing 20 percent of the nation’s gross domestic product. Allowing the sea to claim 40 percent of the capital city, home to nearly half of Jakarta’s population, was unthinkable, Sianipar said. “If we abandon north Jakarta, that would cost $220 billion in assets - not to count the number of people and productivity that would have to be replaced,” he said.

The group decided to focus on bolstering coastal defenses and refurbishing the crumbling flood canal system. The Dutch government offered technical assistance.

The height of the existing 20-mile seawall was raised in 2008. But as that structure slips under the waves, it offers little protection against another big storm surge, or even a moderately high spring tide. At high tide in some places, the city’s old seawall can barely be seen poking above the water’s surface, both because the sea is rising and because the wall itself is sinking into soft alluvial sediments.

The World Bank warned in a 2012 report that catastrophic floods would soon become routine in Jakarta, “resulting in severe socio-economic damage.”

The task force was still trying to decide on an overall strategy when the World Bank’s prediction came true in January 2013: Parts of the city were submerged under 6 feet of water after a heavy monsoon storm. Days later, President Yudhoyono ordered the task force to take a bolder approach.

The result was the National Capital Integrated Coastal Development Master Plan, better known as the “Giant Sea Wall” or the “Great Garuda,” for its resemblance from the air to the bird-god of Hindu mythology that is Indonesia’s national symbol. The $40 billion complex will include a 15-mile outer seawall and 17 artificial islands that will close off Jakarta Bay.

Construction of the first stage of the plan, a new 6-foot-wide inner seawall just behind the existing one, was launched on Oct. 9. The inner seawall is aimed at buying time, holding off another inundation until the new outer wall of the Great Garuda provides long-term protection.

The Great Garuda won’t, however, restore the flow of some of the sinking city’s 13 rivers and various canals into Jakarta Bay.

Some of the channels drain into floodwater retention lakes, a magnet for new migrants from outlying provinces who squat illegally around their perimeters. Pumping stations then spew the highly polluted water from these lakes the last few hundred yards into Jakarta Bay.

More and bigger such lakes will soon be needed to discharge the water of all other rivers and canals, including the large flood canals, according to the NCICD Master Plan. “You’re talking about pumping lakes up to 100 square kilometers,” said Victor Coenen, Indonesia chief representative for Dutch engineering and consulting firm Witteven+Bos, who was part of the government’s Dutch consulting team. “Where do you find room for that in a densely populated city?”

The Great Garuda would solve that problem by creating a single gigantic storage lake in Jakarta Bay, enclosed by the inner and outer seawalls and fed by pumping stations onshore. “If it comes to that, I’d prefer to have the one big black lagoon offshore,” Coenen said.

To prevent the Great Garuda from looking like a great black lagoon, the city must address another huge priority - providing clean piped water to most of its citizens and setting up waste treatment facilities so the rivers and canals no longer have to function as open sewers.

“NOT A DROP TO DRINK”

Jakarta under Dutch rule was known as Batavia, styled “the Queen of the East” for its distinctive colonial architecture and tree-lined canals. Closer inspection of the coast revealed “a dismal succession of stinking mud-banks, filthy bogs and stagnant pools (that) announces to more senses than one the poisonous nature of this dreadful climate,” British writer John Joseph Stockdale observed in his 1811 book, “Island of Java.”

Then as now, “stagnant canals” functioned as open sewers and exhaled “an intolerable stench.” In the wet season, “those reservoirs of corrupted water overflow their banks in the lower part of town, and fill the lower stories of the houses where they leave behind an inconceivable quantity of slime and earth.”

Today, the city has just one small wastewater treatment plant that serves the central business district. Almost everyone uses septic tanks or dumps waste into neighborhood sewers that flow into the canal system.

The slime has mounted over the centuries in the canals, and their embankments have risen in a failing effort to contain the flood waters. The canals that flow to the sea or into the coastal retention ponds have lost up to 75 percent of their capacity, said Brinkman at Deltares.

The city is near the end of a three-year project to deepen the canals and increase the height of their walls. But the homes alongside them are often below the level of the canals now, leaving no “vertical escape” to the rooftop in a flood, he said.

A city with an extensive canal system and a tropical rainforest climate should not have a water shortage. Yet only about a quarter of Jakarta’s population is connected to the city’s piped water system. Half draw their water from wells, and the other quarter buy from vendors who get their water from both legal and illegal public wells.

Some city residents who could have access to piped water prefer to use groundwater because connection fees - a month’s minimum wage - and additional charges on the bill make it much more expensive than a backyard well.

Piped water is also unpopular because it is often filthy when it comes out of the tap. There’s a good reason for that: Half of Jakarta’s water supply comes from the basin of the Citarum River, which the Asia Development Bank has dubbed “the world’s dirtiest river.” It is so clogged with industrial and agricultural effluents and waste from the teeming settlements along its banks that it almost seems like you could walk across parts of the river.

Groundwater is hardly better. Seventy percent of the wells in the city are contaminated by the E. coli bacteria from leaking septic tanks, according to a study conducted by the city government.

The water crisis has been a boon to the increasing ranks of water vendors who drag long carts filled with 5-gallon (20-liter) jerrycans of water around the kampongs. One jerrycan costs about 500 rupiah (4 U.S. cents).

They are especially prevalent in the coastal districts, where subsidence has allowed saltwater to flow into the water table, making well water undrinkable. And in some areas along the coast, piped water is only sporadically available during the day.

The Jakarta government does not publish data on the volume of groundwater use. But the city’s new governor, Basuki Tjajaja Purnama, said illegal use of groundwater had reached “alarming levels.” He said he will start enforcing a 2008 law that imposes fines of up to 1 billion rupiah ($80,000) and jail terms of six years for those who misuse groundwater.

The concrete jungle is not only an intensive water user; it has also taken over natural drainage sites and green areas, preventing the water tables below from being recharged. Instead of seeping into the ground, monsoon rains now wash into the canals and out to the sea.

In 2009, the Ministry of Environment came up with a novel idea to restore the water tables: It issued a decree requiring homeowners and commercial buildings to store rainwater in 3-foot-deep “biopore cylinders” on their properties to absorb and store rainwater. The decree has no enforcement mechanism, and the city environment ministry could not say how many cylinders had been installed.

ON THE MOVE

The city has recently tried another tack in its water wars: evicting settlers to create green areas along the coast.

Tens of thousands of squatters occupy large swaths of the Muara Baru kampong, behind the seawall and around a retention pond, scavenging, collecting green mussels or shrimp from the dirty water, or picking up work in the boatyards.

Every year, the floods come, people evacuate to public buildings, and the kampong sinks some more. “It’s not that bad,” says Sukiman, a 41-year-old father of three and a neighbourhood chief in Muara Baru. “We can live here.”

But Muara Baru’s days appear to be numbered. The city has begun shifting the residents to create green space and to restore the Pluit retention pond, which had become clogged with garbage and waste.

Those who have a residency card may be eligible to get an apartment in new high-rise public housing projects. Those buildings, going up alongside luxury apartments and retail stores, will add to the weight pressing down on steadily subsiding land and - as with other besieged coasts around the world facing rising sea levels - only worsen the problem.