Disruptions to southside Dart and Rosslare/Gorey services are expected to continue for up to a fortnight, Iarnród Éireann said tonight.
The disruptions are due to repair work being carried out on a bridge near Landsdowne Road station, which was damaged in the flooding which hit the capital earlier this week.
At least two large trees were swept downstream by the River Dodder and became lodged under the bridge on Monday evening, causing debris to build up against it.
An inspection carried out by divers last night showed damage to the ground in the vicinity of a support pier of the bridge.
Iarnród Éireann closed the structure as a precautionary measure and is now devising a remedial works programme to repair the damage.
There will be no Dart service between Grand Canal Dock and Sydney Parade. Dublin Bus will accept rail tickets for customers affected.
Services will operate from Howth/Malahide to Grand Canal Dock, and from Sydney Parade to Greystones. Southside service will be reduced in frequency, operating every 30 minutes.
Rosslare and Gorey services will operate from Rosslare and Gorey to Bray, with bus transfers between Bray and Connolly station in Dublin.
Other commuter services which operate from Drogheda or Maynooth to Dún Laoghaire and Bray will now only operate from Drogheda/Maynooth to Pearse.
Dublin Bus will accept rail tickets for customers travelling south of Pearse Street.
Following protocols adopted after the Malahide viaduct collapse in 2009, detailed inspections are now carried as a matter of course as soon as possible after major flooding events.
A total of 21 bridges have been inspected in areas affected by flooding.
