The alert area covers the Lower River Wharfe and tributaries from Ilkley to upstream of Ulleskelf.
It comes as river levels have risen as a result of snow which fell at the weekend melting and also additional rainfall that is forecast for overnight.
The government's flood warning service says that flooding of property, roads and farmland is possible tomorrow (Wednesday) and added that areas most at risk are low lying land and roads.
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It said: "Our incident response staff are closely monitoring the forecast."
Motorists are also being asked to plan driving routes to avoid low lying roads near rivers, which may be flooded.