Samples taken by the Scottish Environment Protection Agency (Sepa) at Fife's Leven Beach and Coldingham in the Scottish Borders failed the tests, despite both stretches having been awarded the Blue Flag by Keep Scotland Beautiful for the past three years.
The charity said some samples only narrowly missed its top standard – both beaches are still expected to meet mandatory standards of the EU Bathing Water Directive and so will continue to the Scottish Seaside Award flag.
It is thought that heavy rain may have caused higher than normal bacterial readings.
Derek Robertson, chief executive of Keep Scotland Beautiful, said: "While we are all bitterly disappointed that the Blue Flag has had to be withdrawn, we are pleased that both beaches will continue to be actively managed and that Seaside Award standards will be maintained.
"We would urge people to keep visiting the beaches, and to check the most recent water quality results on the information boards or online."
Blue Flags are withdrawn if more than two of 20 planned samples fail to meet Intestinal Enterococci standards during the sampling season between June and September.
Keep Scotland Beautiful said it is working with Sepa, Scottish Borders and Fife Council to identify the causes.
Ron Smith, environment convener at Scottish Borders Council, said: "It is highly likely that these failures can be attributed to the unusually heavy rainfall we have been experiencing over the past couple of months."
Tom Adams, Levenmouth Area Committee chairman said: "The water tests at Leven beach had been carried out at a time of recent heavy downpours, which may have caused higher than normal bacterial readings.
"However, the water quality is back to high standard now but the strict criteria for the Blue Flag award means we cannot fly the Blue Flag for the rest of the season. We hope to receive a Blue Flag for Leven Beach next year."
A HIT-AND-RUN drink driver who left a pedestrian for dead has been jailed for 10 months.
Kevin Smith, 22, was left brain damaged and blind in both eyes after being struck by a van driven by John McDougall.
Paisley Sheriff Court heard the incident had resulted in catastrophic consequences for all involved.
Mr Smith now needs constant care and life for members of his family has been changed beyond all recognition.
Sentencing McDougall, Sheriff Derek Livingston said his hands had been tied as the Crown had raised the prosecution at summary level, restricting his sentencing powers.
Witnesses, one of whom told others to keep Mr Smith, who was also under the influence of alcohol, from staggering back on to Paisley Road in Barrhead, East Renfrewshire, last September, watched as McDougall's van, travelling at excessive speed, struck him.
The pedestrian was catapulted over the vehicle's windscreen and on to its roof before sliding over the rear end and landing on the ground.
Those who rushed to his aid as the van sped off saw blood coming from his ears and feared the worst. Mr Smith was taken by ambulance to hospital and found to have multiple fractures and severe brain damage.
In the weeks which followed he went blind, suffered a major seizure and contracted meningitis.
Earlier this year a consultant said he had "lost all of his independence and his situation seemed unlikely to change," said depute fiscal Frank Clarke, who added: "Kevin requires day-to-day assistance."
The court was told that beforehand he had been a healthy young man who enjoyed life.
Mr Clarke said: "Now he is mentally impaired, unable to care for himself and is disorientated in time, place and person. He has no knowledge of his situation.
He stressed he was attempting to give a fair narration and conceded Mr Smith's conduct on the day played a contributory part. However he said McDougall had been impaired due to alcohol, was not paying proper attention and was driving at excessive speed.
McDougall, formerly of Craighead Way, Barrhead, and now of Cross Street, Paisley, Renfrewshire, admitted driving carelessly and while twice over the legal drink-drive limit, failing to keep a proper lookout, striking Mr Smith to his severe injury and danger of life, and failing to stop and provide his details.
Defence lawyer John McGuire admitted there was very little he could say in mitigation.
McDougall, 32, had seen Mr Smith stepping in front of him too late and was unable to avoid him. He panicked and drove on instead of stopping.
Mr McGuire said: "He is horrified and deeply remorseful. He expresses sorrow over the dreadful consequences and wishes to publicly apologise. This will live with him for the rest of his life."
McDougall, it was stated, is currently serving a four-month jail term imposed at Kilmarnock Sheriff Court following a domestic incident involving a girlfriend.
Sentencing him to a further jail term and banning him from the road for five years, Sheriff Livingston said: "Your drove on this occasion with twice the legal limit of alcohol and hit this poor unfortunate man, then drove off instead of stopping to help him.
"The circumstances here are tragic. If you had not driven that night, this would not have happened."
Referring to the jail term imposed, he added: "It is 10 months reduced from 12 due to your early guilty plea. The reason is I cannot impose any more as this charge has been brought on summary complaint which restricts my powers."
Members of Mr Smith's family who had been in court left in distress.
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