Up to 30mm of rainfall is expected in parts of the South East.
Rivers on flood alert were susceptible to the increased rainfall, leading to possible flooding of properties including in Berkshire, Oxfordshire, Hertfordshire, Sussex, Hampshire and the Isle of Wight, the Environment Agency said.
The agency is now urging those who may be at risk to "take steps to limit the damage a flood can cause - to themselves and to their property".
"Our area incident room has opened, we have mobilised teams across the country to check on flood defences, clear any river blockages and closely monitor river levels.
"These teams have been working around the clock to reduce the risk of flooding and will remain out in force over the coming days to remove blockages.
"We will do everything we can to warn and inform people about the risk of flooding from rivers but we cannot always prevent it, so people need to take action to prepare now."
More top news
More than 70 firefighters have been tackling a fire in a thatched cottage in Longparish, Hampshire.
Police have released CCTV footage of the last known movements of 21-year-old University of Brighton student Janet Muller.
Wednesday night's weather for the east of the region