Passengers were advised to check journey planners ahead of travelling and allow extra time to complete journeys.
National Rail provided a list of expected changes but said other short notice changes and delays were also likely.
Journey planners were due to be updated by 22:00 GMT on Sunday, it added.
People who want to delay their journey until Tuesday will be able to use Monday-dated tickets on Southern, Thameslink and Gatwick Express services, National Rail said.
Southern services between Reigate and London Victoria and between Redhill and Tonbridge in Kent will run normally.
Network Rail originally scheduled the work to take place over three weekends in January, external, with further dates planned in February, March and May.
Work was planned over winter to protect the line during peak tourism season, Network Rail said.