Flood damage on the line at Thackley, near Bradford, has caused delays to services from Leeds to Carlisle as trains slowed to pass through the worst affected areas.
Services are now running at normal speed but residual delays are expected into Tuesday afternoon.
Up to a month worth of rainfall has fallen in the UK today and heavy showers have battered Leeds since early this morning.
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A flood alert remains in place for the River Aire, near Hunslet, and drivers are advised to avoid low-lying roads near the river.
The Leeds flooding incident room is monitoring the situation closely.
The rain is finally expected to clear after 4pm, with sunny spells developing later in the evening.
It will remain largely dry overnight but the odd shower is possible.
What is the long term forecast for Leeds?
The Met Office forecasts a dry and clear day on Wednesday, with spells of bright sunshine.
Autumnal temperatures are expected, dropping as low as 5C overnight.
Thursday is forecast as cloudy before wind and patches of heavy rain hit Leeds overnight, as the remnants of tropical storm Lorezno arrives in the UK.
However, these downpours should only last for a few hours and the weekend is expected to be cloudy but largely dry.