Heavy rainfall has caused overflowing sewers to pollute a chalk stream.
Chiltern Chalk Streams said Thames Water had been "pumping screened sewage" into the River Misbourne near Amersham, Buckinghamshire.
Thames Water said its sewers were "struggling to cope" and it was deemed a category 1 pollution event by the Environment Agency.
Affinity Water has stopped taking water from a nearby borehole "as a precautionary measure".
However, Affinity Water said while there was "no impact to the quality" of people's water supply it would continue to monitor the situation.
Singer and environmental campaigner Feargal Sharkey, who has been highly critical of water companies, said on X, formally called Twitter: "Thames Water's sewage network is so badly maintained, sewage is leaking out contaminating surrounding groundwater. The same groundwater Affinity Water relies upon to supply customers."
Affinity Water said it was a "water only company" which provided "high quality drinking water to our customers".
"We do not manage or process wastewater or sewage," it said.
The River Misbourne is 16 miles (27km) long and flows through Great Missenden, Amersham, Chalfont St Giles and Chalfont St Peter. It is one of eight major chalk streams running through the Chiltern hills.
Chiltern Chalk Streams, which works to protect them, said on X that "the Misbourne is in a terrible state" due to "groundwater contamination".
Thames Water said "excessively heavy rain in our region" since the start of 2024 meant that "groundwater and river levels are very high and the ground is saturated".
It said its system was designed "to allow overflows to [the] river where there is no other alternative", to prevent wastewater backing up into people's homes.
"Although we regard any discharge of untreated sewage as unacceptable, and are working hard to make them unnecessary, this will take time," the company added.
The water company said it was installing large temporary pumps to create space in the sewers to get them back working normally.
An Environment Agency spokesman said officers were "closely monitoring the issue for any impact to the environment" and the issue was caused by "significant recent rainfall" leading to "flooded sewers".
"We have instructed Thames Water and Affinity Water to take action to manage sewage overflowing from manholes in the Misbourne Valley," the agency said.