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Joss Bay is one of the beaches closed for swimming
More sewage has been pumped into the sea off the Thanet coast.
Southern Water's station at Foreness Point had been working normally throughout yesterday after it was cleared of the debris which caused a major spill last week.
But the site - which is running below capacity while repairs are made to the pumps - could not handle the heavy rainfall in the afternoon.
Southern Water manager Jon Crooke said: “At 5pm yesterday, heavily diluted and screened wastewater was released into the sea through our long sea outfall which goes 2km out to sea.
“This continued to prevent the works from flooding and to protect homes in the catchment.
“This wastewater, which was heavily diluted with rainwater, was screened to remove non-biodegradable debris.
“There won’t be the scenes we saw earlier in the week of debris on the beach as this has been removed by the screens on site.
“The Environment Agency and Thanet District Council were informed and we are working with them to resolve this as soon as we can.
“Our priority at the moment is to ensure that the beach is thoroughly cleaned and that the pumping station is repaired.
“Once this is completed we will carry out a full investigation to find out what happened and what can be done to reduce the risk of it happening again.”
A clean-up of Thanet's beaches is still continuing after last week's major sewage spill. Thanet District Council has temporarily closed them to all swimmers as a precaution.
Mike Humber, engineering technical services manager at Thanet, said: "Thanet has a large number of award-winning Blue Flag beaches, that's something we take very seriously and we want to maintain the quality of those beaches."
A machine is being used to clear the sand, while a team of around 20 people are working in shifts to remove debris.
The Environment Agency is regularly testing the water quality, however it could take several days for results to come back.
Mr Humber added: "They (the clean-up team) are making very good progress and working very long hours and we will continue to do that after every tide to minimise levels of material on the beach.
"What we're concerned with is making sure that before we lift this closure of the beaches for bathing, the water quality is safe for people."