I'm sure many people can guess this without having to read the article but, yes, the E coli is present due to faeces being discharged into the river:
River Action said the testing locations suggested the source of pollution is from Thames Water discharging sewage directly into the river and its tributaries. It said this was based on publicly available data which showed that the water company had discharged sewage into the Greater London area of the River Thames for 1,914 hours from the start of 2024 up to 26 March.