The beaches, many of which recently won Blue Flag awards for cleanliness, were closed by Thanet District Council over the weekend over health concerns.
Problems started at Margate’s Foreness Point pumping station on 30 May. Southern Water said crews had been working 24/7 to resolve the issues in the face of heavy rain.
“We are extremely sorry and disappointed by this incident,” said Southern Water’s Jon Crooke.
“We’ve been working tirelessly with the council to clean up the beach so bathers can again swim.”
Repairs on the pumping station have now been completed and a Southern Water spokesperson said the beaches may be reopened this afternoon. The Environment Agency is monitoring water quality.
Southern Water teams have also been battling sewer flooding in several parts of Sussex since Sunday night, when a month’s rainfall fell in 12 hours.
According to a statement, it appeared sites were working as they should but were simply overwhelmed by the volume of water entering the system.
The company dispatched tankers to remove stormwater and crews to clean up debris in areas including Littlehampton, Bognor, Chichester and Worthing.
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The coast is clear