Thames Water says that flood water is entering the sewers at Hambleden in Buckinghamshire and Playhatch near Reading.
A statement on the company's website said:
"Floodwater is going into our sewers. Normally our network can cope with this, but high groundwater is going into the sewers as well, tipping the balance and overwhelming the system.
"Our sewers are designed to take only wastewater from homes and businesses, not rivers and groundwater too.
"Some people have suffered horrible flooding to their properties. We are working with partner agencies and our engineers are doing all they can to help."
More top news
Three men from East London have been jailed for stealing vital life-saving equipment worth over £100,000 from fire stations.
A 19 year-old from South East London has pleaded guilty after he soiled himself and revealed where he had hidden packets of heroin.
Max Whitlock was greeted by hundreds of fans as he returned to his gym in Essex for the first time since winning double gold in Rio.