Damage caused by debris and flooding took its toll on travel networks as people returned to work after the New Year holiday.
ScotRail was still unable to run services between Glasgow and Wemyss Bay and Gourock.
Operators said a replacement bus service is running from Paisley to both stations, and a train shuttle will operate between Glasgow Central and Paisley Gilmour Street calling at Cardonald, Hillington East and Hillington West.
The Dalmuir to Larkhall train services are currently withdrawn with passengers advised to travel on a service to Motherwell where replacement transport will operate to Larkhall.
Passengers were also advised of problems on the Milngavie to Motherwell line via Hamilton. Services will run between Cambuslang and Motherwell but not call Newton, Blantyre, Hamilton West, Hamilton Central and Airbles.
The Helensburgh to Edinburgh line will start at Dumbarton East until tomorrow due to structural damage to the sea wall near Cardross.
Replacement buses are running between Dumbarton East and Helensburgh Central.
In Glasgow's South Side, Crossmyloof platform 1 is closed due to an unsafe building. Services from Glasgow Central and East Kilbride and Barrhead will not stop at the station until further notice.