The Met Office's yellow warning - in place until 2pm on Wednesday (September 3) - stated that heavy rain 'may cause travel disruption and flooding in places'. A thunderstorm warning is also in place for other parts of the UK - from London northwards.
The Environment Agency has issued a flood forecast.
This read: "Local flooding is probable from surface water today (Wednesday) across parts of England.
"Land, roads and some properties could flood and there could be travel disruption.
"Local flooding is possible but not expected from surface water across parts of England on Thursday.
"Properties may flood and there may be travel disruption."
Six flood alerts are in place across the UK but, as of 12pm on Wednesday, there are none in the South East.
However, a yellow warning from the Met Office means 'flooding of a few homes and businesses is possible'.
The government agency added: "Some interruption to power supplies and other services is possible.
"Spray and flooding on roads probably making journey times longer.
"Bus and train services probably affected with journey times taking longer."
The Met Office said heavy rain and strong winds will move northeast through the first part of Wednesday, 'followed by heavy showers and some thunderstorms'. These are expected to become 'more isolated through the afternoon'.
The forecast read: "Rainfall totals widely 20-30 mm, but some places could see 40-60 mm within a period of six to nine hours.
"Coastal gales are likely for a time, especially along English Channel coasts."
People in the warning area are advised to 'give yourself the best chance of avoiding delays' by checking road conditions if driving, or bus and train timetables and amending your travel plans if necessary.
The Met Office added: "Check if your property could be at risk of flooding. If so, consider preparing a flood plan and an emergency flood kit.
"Be prepared for weather warnings to change quickly: when a weather warning is issued, the Met Office recommends staying up to date with the weather forecast in your area."