Up to 50,000 tonnes of raw sewage has flowed into the Thames after sewers were unable to cope with 'moderate' rain, the Environment Agency said.
Drainage solutions would cost billions of pounds
More than 600,000 tonnes were forced into the river last week leaving thousands of fish dead in the Isleworth area, west London.
The agency said the sewage entered the river near Battersea Park on Tuesday and would affect the same areas.
Thames Water said the worst pollutants had been skimmed off.
But the Environment Agency described the waste, discharged from storm tanks at the sewage treatment works, as "highly polluting".
Andrew Boyd of Thames Water said the sewage was being treated.
He added: "It's obviously regrettable that the water has to go into the Thames but we have agreed with the Environment Agency that it is better than the sewage treatment works being flooded or it backing up into the sewage system itself.
London's Victorian drainage system pushed water into the Thames instead of allowing it to flood homes and streets during the storms.
Thames Water has been working with the Environment Agency and other bodies to come up with a with a long-term solution to the problem.
They have submitted their ideas to the Department of Environment, Food and Rural Affairs and are waiting for a response.