Trains are running again between Thirroul and Waterfall on the South Coast Line after earlier flooding on the tracks at various locations.
Buses continue to replace trains between Wollongong and Port Kembla.
On the Southern Highlands Line, trains have resumed between Campbelltown and Moss Vale after earlier flooding between Bowral and Mittagong, and also at Picton.
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Buses may continue to supplement some services on both lines as required.
Passengers are advised to allow extra travel time, listen to announcements and check information displays for updates as services return to normal.