During the Great Stink of 1858 so much sewage was flowing into the river Thames that Benjamin Disraeli labelled London a “Stygian pool reeking with ineffable and unbearable horror”.

It was only then, with the windows of parliament hung with lime-soaked curtains to fend off the stench, that MPs begrudgingly approved the building of the system that today still handles the capital’s waste.

And now, 150 years on, a project no less ambitious is in the pipeline. Thames Water plans to build a 32km “super sewer” to handle the raw waste that empties into the Thames today. The tunnel, big enough to fit three double-decker buses side-by-side, would be the largest in the northern hemisphere.

Even on the best estimates it will take eight years to build, cost more than £2 billion and cause huge disruption throughout the capital. Aside from the engineering complexities, it will require the approval of 13 councils and more than 30 other groups including the mayor’s office and the London Development Agency.

But to Phil Stride, head of the London Tideway Tunnels project, there is no choice but to get on with it. He said: “We have looked at other options but none of them makes sense. There is no alternative.”

When the Victorians built London’s sewer system, only 2.8m people lived in the city. Today there are nearly 8m and Thames Water expects that to grow by another 1m by 2030. Climate change, meanwhile, has led to bigger storms with heavier downpours of rain. Those twin pressures mean that more than once a week the system becomes overloaded.

To prevent sewage from backing up into the streets or gurgling up kitchen plugholes, it is released through a network of overflows straight into the Thames. Each year more than 32m tonnes of untreated sewage go into the river, enough to fill the O2 arena 15 times.

This is why Thames Water is the worst polluter among Britain’s water companies and why Britain is in violation of Europe’s Urban Wastewater Treatment Directive, which could bring fines of up to £37,000 a day. Brussels has agreed to suspend these penalties because London has a plan: the tunnel.

Other options were considered, such as using a fleet of boats called “bubblers” that would inject oxygen into the river to save marine life. The sewers could be modified to separate rain water from waste, making overflows less poisonous. Both ideas were dismissed.

“Keeping rain water and foul water separate is the preferred option but the history of London’s system going back to the 16th century means it’s not possible,” said Stride. “It would cost £15 billion to retrofit, not to mention the upheaval it would cause.”

The tunnel then is simply the least bad of several bad options but it will have to navigate a minefield of public opposition. Along the Thames there are 57 sewer overflow points. At the 34 worst offenders, Thames Water wants to drill shafts so overflow sewage drops down them into the tunnel, which will be built at a subtle incline so the water flows to the sewage works at Beckton, the largest in Europe.

Thames Water is now starting to talk about its plan publicly; it has a lot of people to get onside. Early designs indicate that the company will need to buy at least 45 sites, some as big as three football pitches, where it can drop in tunnelling machines for different sections or drill shafts to cut off the overflow sewers. All the land it is looking at is within 500 metres of either bank of the river and that means acres of waterfront property being turned into building sites. Next month it will send a small drilling rig onto the river to take more than 80 geological samples.

There is also the question of how the project will be financed. Thames Water has approached Ofwat, its regulator, to request special dispensation from the five-year financing regime because the scale is entirely different to typical water-main replacement and should be, it argues, given some insulation against the fines it would pay if its other projects overrun or come in over budget.

It will get a glimpse of what it is up against in the next couple of weeks. In addition to the main Thames tunnel, the company has much more advanced plans for a 7km tunnel from Abbey Mills on the River Lee (also known as Lea) in north London to Beckton. Newham council will meet next week to decide on the planning application for the £400m project and, if all goes well, Thames Water expects to award the contract in the winter so work can begin in the new year. Because it is shorter, in a less populated area and requires only two ground-level sites - at the tunnel’s start and end - it is far less complex.

The ultimate cost of the projects will be covered by customers. Early estimates are that annual bills will rise by £40 per household over the life of the construction. That is in addition to the rise in charges that Thames hopes to push through to cover its wider upgrade programme.

Stride admits, however, that the company has no clear idea of how much the project will ultimately cost. The last estimate of £2.2 billion for the two tunnels was made when only “1% to 2% of the design work had been done”.

The company is lobbying to get the scheme on the list of projects of “national significance”. If it does, it would fall under the remit of the Infra-structure Planning Commission, the body created by the government to streamline the planning process by taking approval for big projects out of the hands of local councils.

However, the Conservatives oppose the commission and could scrap it if they get into power. As a safeguard, Thames Water is also talking to the mayor’s office, local councils and whoever else it might need to get onside.

Stride said: “This could be the first project for the Infra-structure Planning Commission but there are questions about whether it will be around if the Conservatives come in. We are not going to put all our eggs in one basket. We are lobbying whoever can help us get on with this.”

For now, the tunnel remains the biggest project the public has not heard of, but that will soon change. Thames Water does not expect to file its planning application until 2011, so construction can begin in 2012. Just in time for the Olympics.

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