The River Wharfe burst its banks in a number of places as it surged through Ilkley, Otley and Pool, north of Leeds. It said services between Leeds and Huddersfield, Leeds and Shipley and Skipton and Settle were running at reduced speeds because of the conditions.
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A spokesman said the risk remains highest for Cumbria, parts of Lancashire and western parts of North Yorkshire and West Yorkshire.
“Clearance work will continue throughout the day with several roads still closed”.
The council set up a reception centre at Kendal Town Hall for anyone who has nowhere else to go and said military personnel could be used to help with flood defence.
Both Egremont and Kendal, the two areas that were most at risk, suffered minor disruption with a small number of evacuations from properties.
The Environmental Agency has issued amber weather warnings, the most severe warning possible.
Natural Resources Wales has 21 flood alerts in place across Wales on Saturday with two higher level flood warnings on the River Vyrnwy.
The Northumberland, Durham and Tees incident room was opened after predictions of heavy rainfall falling on already saturated ground and the threat of flooding to properties from rivers.
“Further heavy, persistent rain is expected throughout Sunday and into Monday, and river levels remain extremely high and are continuing to rise in places”.
“Partner agencies have worked together tirelessly over the past 24 hours in order to take precautionary action as initial indications suggested that areas such as Egremont and Kendal were at risk of severe flooding”.
Natural Resources Wales said it was keeping a close eye on the Dyfi, Elwy, Conwy and Vyrnwy catchments in particular.
The Environment Agency has issued severe flood warnings – indicating a risk to life – in northern England.
“Working with local authorities, the Enviornment Agency and other emergency services, people will have to keep in touch with their local community contacts and take the advice that’s given”.
The spokesman said Environment Agency teams are out maintaining flood defences, preparing temporary barriers, deploying sandbags along riverbanks, clearing river blockages, monitoring water levels and sending out warnings.
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Many northern parts of the country are already saturated after days of wet and windy weather. The Highlands and Islands were worst hit by gusts of 84mph while the rest of the United Kingdom experienced thundery showers as a result of Britain’s first named storm.
