The brick-lined culvert that runs through the centre of Manchester's Philips Park has all the charm of an open sewer. There are no grassy banks, no fish, no reeds or other aquatic plants, no signs of life. Apart from a few broken bottles and an occasional rusting supermarket trolley, the waterway – built at the turn of the 20th century – is featureless and sterile for its entire mile-long course through the park.

The 2m-wide channel could pass for a section of the city's sewage works. In fact, this turns out to be one of the major rivers of north-west England, the Medlock. Like dozens of other natural waterways in Britain it was channelled into culverts – others were buried in tunnels – in the wake of the country's industrial expansion during Victorian and Edwardian times.

To the industrialists back then, rivers – apart from supplying water for dye works or taking away waste – were considered to be inconveniences and so were diverted, often underground. The end result was the creation of a network of lost rivers across the nation.

But now the Medlock is being reclaimed as part of a campaign that ecologists hope will return many of these lost waterways to their natural glory.

The programme has been set up as part of Britain's response to the EU Water Framework Directive which aims to breathe life back into natural waterways across the continent by 2027. Hundreds will be tackled, many of them in Britain.

In London, it is believed there are at least 20 lost rivers that were buried to allow the city to expand, for example. These include the Tyburn, Effra and Fleet. Many of these will have to remain underground, such is the extent of the capital's expansion, but a few have been rescued, including the river Quaggy, whose course was recently brought back to the surface. Since then it has become a major feature of Sutcliffe Park in Eltham, south London.

Other lost rivers targeted for restoration include the Calder in Burnley; the Salmon's Brook, a key tributary of the Lea in Enfield; and the Wensum in Norfolk. All these projects are backed by the Environment Agency which has pledged to restore 9,500 miles of river nationally with the help of other organisations.

However, it is the Medlock restoration that attracts particular attention for it is intended to be a model for other clean-ups. As part of the project, all 8 million of the bright red bricks that were used to create the river's culvert through Philips Park – one of the nation's first municipal parks – are being ripped up. These are Accrington bricks, made in Lancashire, and their kind were used for the foundations of Blackpool Tower and the Empire State Building, such was their reputation for strength. Remarkably, those dug up from the Medlock look new, despite having been immersed in running water for more than 100 years.

"The Medlock is known locally as the Red River because of those bright Accrington bricks," said Jo Fraser, of project partner the Groundwork Trust. "However, we are going to change that. We are going to turn it blue again."

The culverted River Medlock cuts through the industrial landscape of Manchester a century ago. Photograph: Environment Agency

Once the bricks are removed and concrete foundations dug up, the river will no longer be confined to a narrow channel. It will become wider and shallower and will start to meander along its own course. Weirs will be ripped up, with the result that the flow of water will slow down.Fish will be able to swim up the Medlock again and plants should start to grow on the riverbed.

Workers have already spotted brown trout and kingfishers. "We are breathing life back into dead rivers," said Oliver Southgate, of the Environment Agency.

The Medlock's brick and concrete culvert was originally built after a major flood washed away dozens of bodies from a nearby graveyard in the 1860s. The aim was to divert waters from causing similar mayhem. In fact, the culvert has only increased flood risk by accelerating the water flow. "Another key benefit of allowing the Medlock to revert to its old ways will be to improve flood management in the city," said Dave Barlow, a senior environment officer for Manchester City Council.

It is expected that the Medlock works will be completed by 2014 and the Philips Park section will slowly return to life over the next few years. The only major headache remaining then will be to find homes for those 8 million very solid, very heavy Accrington bricks it will left with left over. "We are open to offers," added Southgate.