When the project is completed, pristine water from the moors will once more flow through the abbey, over three cascades and past the Palladian Temples of Fame and Piety to a lake at Studley Royal.
In monastic times, the water of the river Skell, which flows down to Ripon, was used to flush the reredorters - the latrines where the monks performed their ablutions.
Kitchen rubbish was also thrown down special disposal slots to be carried away conveniently and a lavatorium, used for ritual foot washing, drained into the river.
Hilary Lade, estate manager at Fountains Abbey, said: 'This drainage system helped to keep the monks very healthy and so they often lived into their 80s. The monks must have seemed blessed to the ordinary people living downriver in Ripon, who were lucky to live beyond their 30s.'
As the monastery expanded during the 13th century, the monks built across the river, causing it to flow through large stone tunnels under the refectory and the lay brothers' infirmary. After heavy rainfall on the surrounding fells, the waters of the Skell swept away the monks' rubbish. Over some 600 years, they also eroded the tunnels.
The National Trust, which owns the abbey, has spent about pounds 130,000 on restoring the tunnels and sluices through the property and the adjoining water garden, which was built by John Aislabie, a Chancellor of the Exchequer in the 18th century. Aislabie made a fortune out of the South Sea Bubble - inflationary stocks which he bought and sold at an opportune time. After spending a month in the Tower for his misdemeanour he retired to spend much of his fortune building the water garden at Studley Royal, landscaping it with the help of hundreds of labourers.
But after some 250 years, the powerful waters of the Skell had caused considerable damage to a rustic bridge built by Aislabie and a nearby overflow tunnel. It seemed at first that the tunnel was beyond repair and that huge concrete drainpipes would have to be installed. But Ms Lade and her staff were able to find craftsmen who understood the stone-arched tunnel and were able to repair it.
The trust has no plans to restore the reredorters, believed to have been wooden structures built into stone walls. But it is spending about pounds 50,000 on restoring the mill leat - a large, stone-reinforced ditch taking water to the mill.
This will eventually be followed by restoration of the mill itself, which had two wheels, one undershot and one overshot. 'The mill was working until the war,' Ms Lade said. 'We want to restore the mill pond and get it all working again. It's the key to controlling the level in the water garden.'
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