Train services from Howrah were disrupted throughout Tuesday as tracks went under water.
Officials said trains of the South Eastern Railway were more affected - because of waterlogging between Howrah and Tikiapara - than of the Eastern Railway.
"Several trains were cancelled or rescheduled, while many were delayed," an official said.
All four pairs of tracks of the South Eastern Railway, the official said, were 5ft under water.
"Five pumps have been running since last night to drain out the water but there was not much improvement in the situation till Tuesday evening because of high tide in the Hooghly," he said.
Among the trains cancelled on Wednesday are the Howrah-Barbil Jan Shatabdi Express, Howrah-Titlagarh Ispat Express, Howrah-Digha Tamralipta Express and the Santragachhi-Purulia Rupasi Bangla Express.
The trains that will start from Santragachhi instead of Howrah on Wednesday are the Faluknama Express and the Dhauli Express.
Among the trains that were cancelled on Tuesday were the Howrah-Digha Express, Howrah-Digha AC Express and the Howrah-Purulia Lalmati Express.