Flooded signalling equipment has led to disruption for rail commuters travelling between Brighton and London.
Southern said high ground water levels at Patcham, near Preston Park, had led to flooding over the weekend.
Services from Brighton were diverted via Lewes to Haywards Heath, with rail replacement buses running between Brighton and Hassocks.
Southern later said trains were running again but with a heavily amended service.
Beach huts destroyed
Gatwick Express services operated normally between London Victoria and Gatwick Airport.
However, peak services during the morning and evening were not running between Brighton and Gatwick.
Rail services were also disrupted on Saturday after high winds and heavy rain hit the South East overnight causing trees to fall across some tracks.
Across Sussex nearly 2,000 homes were left without power, while an electricity sub-station under the land end of Brighton Pier suffered flood damage.
The storm also destroyed some beach huts on Hove seafront and caused sea water flooding to the Sea Life Centre in Brighton and the arches by Brighton Pier, known as the Artist's Quarter.