Eight years ago air pollution in China was the curse of the Olympics. Beijing had to spend tens of millions of dollars closing factories, banning cars and trying to engineer the weather. Air pollution was thrust on to the world stage and has stayed there ever since.

Now it’s Rio’s turn to host the Games and attention has turned to water and basic sanitation. Parts of Guanabara Bay, which will host aquatic events, are teeming with dangerous viruses and bacteria, threatening the athletes as well as the 350,000 spectators who may want a dip in the sea.

Rio has the image of a rich, beautiful city, but its crowded hospitals testify to the nightmare of its sanitation for people who must live with urban pollution every day. One in three of the more than 10 million inhabitants of the greater metropolitan area live in places that have no connection to a sewerage system, and only about half of the city’s waste is treated before entering waterways and eventually the ocean.

Not surprisingly, diarrheal diseases and childhood sickness are rife. The many rivers that flow through Rio’s sprawling urban areas into Guanabara Bay were declared biologically dead by scientists years ago and tonnes of raw sewage pour into the sea every day. There are high levels of viruses and algal blooms in the water, as well as industrial contamination and floating debris. A succession of city authorities has promised, tried and failed to clean it up.

In Beijing, a wealthy, authoritarian government could simply ban cars and close down factories for the few weeks of the Games and restart them when people went home. But sorting out basic sanitation and hygiene in crowded, chaotic Rio with its many favelas, steep slopes and a cash-strapped administration is far harder. It involves cultural change, huge costs, many different technologies and immense disruption.

To widespread community anger, only one waste treatment plant is fully in operation instead of the seven pledged by the city when it bid for the Olympics in 2007. Instead of sanitation being extended to 80% of people, as promised, vast money has been spent on highly visible cable cars, beautification and facilities for tourists and athletes rather than on basic services like waste collection and sewers. Unsurprisingly there have been protests.

There should be no excuses because Rio won its bid to host the Olympics in 2009, giving it years to make good its promises. Nevertheless, some progress has been made. When, a few years ago, the city began to realise it was falling well behind on its Olympic pledges, consultants were called in, and a myriad of solutions proposed. The World Bank, the Dutch development bank and many others all contributed ideas and money, and more than 20 separate major proposals to deal with Rio’s water pollution and solid waste challenges were accepted. A million more people are now connected to the sewers than 10 years ago and this will increase over the next decade.

But Rio is like 1,000 other cities grappling to improve its infrastructure. Rapid industrialisation, population growth and lack of money have overwhelmed local authorities all over the world. About 2.4 billion people still live without decent sanitation facilities, and the target in the millennium development goals to halve the proportion of the population without basic sanitation was missed by nearly 700 million people.

This week, Eduardo Paes, the mayor of Rio who also chairs the C40 initiative of global mayors trying to improve the environment of their cities, accepted that Guanabara Bay is not in the pristine state envisaged in 2007.

But he said the city is in a far better state than 10 years ago. Gramacho, Latin America’s largest open landfill, has been closed down, public transport extended and improved, 450km of cycle track built, CO2 emissions reduced, old neighbourhoods improved and mangroves restored.

“For every one real we have spent on the Games, we have invested five on ensuring a legacy for the city, through sustainable infrastructure, improved public transport and accessible facilities for our citizens,” he said.

Paes welcomes the international scrutiny of the city. “The process of preparing for the Games has brought attention to the issues of pollution, waste management and water usage, triggering a discussion within the city and at the state and national level,” he said.

“The Olympics are just the beginning. Politicians, journalists and citizens within Rio and across Brazil have begun to address these environmental issues in a way they never have before.”