Flooding of rail lines in the Haywards Heath area is subsiding and trains are now running, Southern Rail says.
All lines through Haywards Heath have now re-opened, although disruption is expected until about 09:00 BST a Southern spokesman said.
Services between London Victoria and the East and West Sussex coast were being delayed and cancelled earlier, with Thameslink and Gatwick Express services also affected.
Journeys to and from Three Bridges, Brighton and Lewes may still be delayed by up to an hour, the rail company warned.
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Thousands of commuters on one of the busiest rail routes in the South East will face major disruption next week as part of a £300m improvement project.
There will be no direct trains between London and Brighton, and Lewes or Eastbourne and the city from Saturday until 24 February.
Network Rail said surrounding services would be affected while engineers renew and upgrade the Brighton Main Line.