Once again, it’s that time of year when areas of Jakarta find themselves hip-deep in water, the victims not so much of the seasonal downpours but of poor sanitation, lagging infrastructure and substandard drainage.

It is estimated that the health of as many as 5 million of Jakarta’s official 10. 1 million residents are being threatened by river water that is polluted by household and industrial waste. As many as 50,000 people die annually in Indonesia, attributed to poor sanitation and hygiene, according to a March, 2008 study by the World Bank, which estimates that as much as 6 million tonnes of human waste are released into Indonesia’s inland water bodies without treatment.

Unfortunately, Jakarta is far from alone. As cities have grown to unmanageable size in third-world countries, the problem is being compounded by climate change, which climatologists believe has increased the number of adverse weather events. Another World Bank study published in March and titled “Cities and Flooding” pointed out that over the past 18 months alone, destructive floods have hit Pakistan, Australia, South Africa, Sri Lanka, the Philippines, Brazil, Bangkok, the Mississippi River in the United States and other areas. In 2010 alone, according to the report, 178 million people were affected by floods.

As Jakarta has grown, it has become a textbook example of what happens when urbanization meets flood risk. The city’s population has continued to rise inexorably as millions of its 237 million people seek economic advancement by moving to the city. In that, it is at one with the rest of the world. In 2008, for the first time in human history, half of the world’s population lived in urban areas, with two-thirds of this in low-income and middle-income nationsThe world’s urban population is estimated to rise to 60 percent in 2030 and 70 percent in 2050 to a total of 6.2 billion, or double the projected rural population for that time, according to the World Bank study.

Jakarta catches floods as badly as anywhere, unless it’s Manila, where typhoons in the past two years have dumped massive amounts of water on low-lying areas and paralyzed the city’s administrative services, so that flood damage went unremedied for weeks, or Bangkok, where residents regularly have to wade home.

Like most other coastal cities, Jakarta was built on a flood plain because when the city was founded, water was the main method of transport. The city is criss-crossed by 13 rivers, which are silting up without dredging, which began in 2011 on three of the rivers. Some 40 percent of the city now lies below sea level, and continues to sink as subsidence continues as groundwater is sucked out for urban use. Concrete has replaced green space, so that the ability of rainwater to penetrate into the soil is lost.

But dredging the rivers is only part of the problem. In a country best by vast numbers of provincial administrations and interlocking jurisdictions not only in Jakarta but throughout the country, mitigation has to start near the rivers’ headwaters, not in the low-lying areas where the floodwaters are more difficult to control.

Hendri Bastaman, the Deputy Minister of the Indonesian Environment Ministry, told IRIN, the reporting service of the United Nations Office for the Coordination of Humanitarian Affairs, that pollution in West Java’s rivers is worsening, particularly in the Ciliwung and Citaruma areas.

“Much of the waste is dumped into rivers from households,” said Bastaman. “People are using these rivers as personal toilets. We’ve also found mercury in river water, which we suspect is coming from companies or those running small-scale mining activities close to the rivers.”

Muhammad Rez Sahib, advocacy coordinator of KRuHA, a Jakarta-based coalition of more than 30 Indonesian NGOs focusing on safe water access, also told IRIN that none of the capital’s rivers could be viewed as safe for human use.

“Even the water suppliers in Jakarta don’t use the water here because it is so polluted,” he was quoted as saying. “Instead, they use water from the Citarum River, which is also heavily polluted. Even after this water is treated it’s still unsafe to drink.” The Citarum flows north from Bandung, the capital of West Java, for approximately 300km to the Java Sea.

Safe water alternatives for poor communities are “few and far between” Sahib said. “Many will turn to use ground water, but due to a poor sewage system and open defecation, 90 percent of ground water in Jakarta is contaminated by E.coli bacteria. Many infant deaths are caused by this bacteria - E.coli is the main threat to human life from these rivers.”

Edward Carwardine, spokesperson for the UN Children’s Fund (UNICEF) in Indonesia, told IRIN that in West Java the use of “improved water” - obtained from taps, boreholes, covered wells and springs - falls below the national average, with only half of the population (approximately 20 million) able to access it.

“When families don’t have access to improved water sources, disease is much more likely,” said Carwardine. “Nearly a quarter of all deaths amongst children under five in Indonesia are caused by diarrhoeal disease.”

The World Health Organization (WHO) estimates that nationwide more than 20,000 children in this age group die every year from diarrhoea.

Dengue fever and malaria, both spread by mosquitoes that thrive in stagnant water, account for an additional 3 percent of overall child deaths, according to Carwardine, who said more focus is needed to end the widespread practice of defecating in the open.

The Environment Ministry’s Bastaman said the government is using educational campaigns to raise awareness of the dangers of unsafe water and to end defecation in rivers.

“For the Ciliwung we have a 10-year plan to restore the river’s health,” said Bastaman. “But for the Citarum, it’s impossible to get it back to the way it was prior to being polluted. The pollution is just too much.”