Residents are advised to be prepared for localised flooding as well as frequent lightning.
The county council said disruption to travel is likely with journey times expected to be increased due to the intense weather.
The amber weather warning from the Met Office advises that torrential rain should be expected, with a chance of hail.
More than 30mm of rain could fall in an hour with rainfall in excess of 50mm possible in two to three hours.
The Environment Agency has highlighted problems for parts of East Sussex and Brighton and Hove, in particular.
It is opening its incident rooms and will be tracking the weather system.
It said it is likely that if heavy rainfall does occur, fast acting rivers are likely to respond first.
Teams are out on the ground working with partners to reduce the risk of flooding and supporting local authorities who will respond to reports of surface water flooding.
There is a possibility that Flood Alerts and Flood Warnings may be issued over Wednesday night and into Thursday morning. P
eople are encouraged to know their flood risk and check the Environment Agency website for the latest information.
Ian Nunn, Environment Agency manager, said: “Thunderstorms are expected to bring heavy rain at times across the south east overnight (Wednesday) into Thursday morning, and intermittently through to Friday morning, which may lead to surface water flooding in some communities, and significant disruption to travel, particularly in parts of Kent, East Sussex and Brighton & Hove.
“There is also a risk of flooding from smaller, faster responding rivers in built-up areas.
“People are advised to check their flood risk at https://www.gov.uk/check-if-youre-at-risk-of-flooding or sign up to Floodline on 0345 988 1188.
“Also, people should stay safe by not going near or trying to drive through fast moving water. Just 30cm of floodwater is enough to move a car.’’
The weather is forecast to improve tomorrow.
For more information follow the West Sussex County Council Resilience and Emergency Team on Twitter or register for flood warnings on the Environment Agency website.
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