Network Rail has said that it is watching groudwater levels in the Patcham area outside Brighton, which has reached 44 metres above average and may flood the railway when it touches 47 meters.
If rainfall changes significantly in the next few days it could have a major impact on the line.
The rail network is also monitoring the Adur and Mole rivers, is working closely with the Environment Agency, Southern and First Capital to restore passenger services at the earliest.
Network Rail Sussex route managing director Tim Robinson said: "We can currently run Brighton Main Line services but if the groundwater levels rise above the railway we will have to divert trains around the problem.
"For now we continue to ask passengers on this and other routes to check before they travel given the continuing bad weather, flooding and land slips we are experiencing across the region."
Network Rail said it has installed extra pumps and raised railway to protect from flooding and to maintain services as long as possible. However, train services between Oxted and Woldingham remain suspended due to a landslip at Oxted.
Southern’s managing director Chris Burchell said: "Should flooding occur in the coming days, we will ensure that we are able to respond by introducing contingency plans quickly, and making sure that our passengers are kept well informed about their travel options."
Image: Flooding in Maidenhead. Photo: courtesy of Network Rail.