Heatwave Scotland: Farmers banned from removing river water in Fife amid dry conditions
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These areas include the Tweed and the River Eden catchments.
Sepa said the current conditions are a consequence of drier weather this year, with only four of the last 12 months recording above average rainfall, and the tinder-dry conditions across Britain.
The UK’s Environment Agency said millions could face a hosepipe ban as an official drought was declared in parts of south-west England, southern, central and eastern England.
Sepa said a temporary suspension on water abstraction licences is being imposed from midnight on Saturday for the vast majority of farmers in Fife’s River Eden catchment to allow levels to recover.
Any licence suspensions for water abstractors in the Tweed area will take effect early next week, the agency said.
David Harley, of Sepa, said: “Having to impose suspensions on water abstractions underlines the severity of the conditions being experienced in the east of Scotland this summer.
“It is not a step we take lightly but the evidence is clear, and it is one we can no longer avoid.”
The main stem of the River Eden is at the second lowest level on record; only 1989 was lower, according to the Sepa data.
In the Tweed catchment in the Borders, Lyne Station recorded its fourth lowest flow in 53 years, only 2003 was lower.
Mouthbridge at Blackadder Water has dropped to its lowest flow since records began in 1974.
The combination of very low flows and high temperatures in watercourses leads to mortality of fish, invertebrates and plants.
While some parts of river ecology can recover quickly, others such as fish and plant populations can take years to recover, with some populations, such as pearl mussels, being permanently lost, Sepa warned.
The temporary restrictions are part of Scotland’s National Water Scarcity Plan, which is designed to ensure the correct balance is struck between protecting the environment and providing resource for human and economic activity during prolonged dry periods.
Sepa said suspensions are predominantly within the agriculture sector and will be imposed for the minimum time necessary.
Mr Harley added: “We’re working closely with Scottish farmers to ensure the sustainability of local water environments for all who rely on them.
“Without action, there is a substantial risk of impacts on fish populations, natural habitats and longer term damage to watercourses.
“With climate change leading to water scarcity becoming a more regular occurrence, we are also working to help businesses plan longer term for these conditions.
“We remain in continuous dialogue with sectors reliant on water and work with them all year round on ways to become more resilient, protecting the environment as well as their own operations.”
Sepa said anyone concerned about meeting licence conditions or wishing to discuss contingency measures are encouraged to contact the agency.