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."