Thousands of plane trees along the banks of the Canal du Midi, a Unesco heritage site, will have to be cut down because of a deadly fungus

If you want to revel in the dappled shade of the most beautiful canopy of plane trees in Europe, go now. It is likely that in 20 years' time, not one of the 42,000 trees currently stretching along the banks of the Canal du Midi, which winds from Toulouse to the Mediterranean, will still be standing. An unstoppable fungal disease has left the French state no choice but to reach for the chainsaw, bringing down the ceiling of leaves covering the nation's most romantic waterway.

The felling of these 200-year-old trees is seen as a national tragedy. Cyclists, walkers and canal-boat owners are gutted, and local politicians are panicked that the canal's Unesco heritage status will be revoked, wrecking tourism. The president, Nicolas Sarkozy, sniffing an opportunity for electioneering, has promised to heal the "sadness" and trauma and "save" the canal.

"It's heartbreaking," says Jacques Noisette of Voies Navigables de France, which runs the waterways.

Unesco is not yet threatening to withdraw the canal from its ratings. But the French authorities must prove they can quickly replant an avenue of young trees to recreate the magic of a historic waterway that dates to the reign of the Sun King, Louis XIV.

Two thousand trees along the canal have so far been hit by the microfungus Ceratocystis platani – which arrived in France via the contaminated wooden ammunition boxes of American GIs in the second world war. But the disease has been spreading steadily along the canal since it was first spotted there in 2006. It's spread through the water and perhaps by canal boats mooring and transferring the fungus between trees.

Diseased trees must be chopped down and burned, but so must the healthy ones surrounding them. By the end of this year, 1,000 trees will have been felled. Next year, 4,000 will go and the number of axings will steadily increase each year for more than a decade.

Replanting will begin at the end of this year, with a mix of new varieties of trees more resistant to the disease. But it will take 30 to 40 years to replant the famous leafy lane that runs for more than 200km through the historic heart of southern France.

• This article was amended on 28 July 2011. The original referred to the most beautiful canapé of plane trees in Europe. This has been corrected.