Four alerts remain in place that the Environment Agency says require "immediate action".
They are along the River Ouse at Naburn Lock and York riverside where there are residential properties. They are also at the River Swale at Kirby Wiske and Roecliffe Caravan Park near Boroughbridge.
Weather forecasters have been monitoring the situation throughout the night and predict that between 7am and 8am this morning is when the worst of the rainfall will strike as river levels expect to reach three metres. Further rainfall is expected in the area and levels are expected to continue rising throughout Wednesday.
The penstocks and flood gates near Roecliffe Caravan Park have been closed and the Flood Information Service also warns that parts of Kirby Wiske will be cut off or have limited access due to local flooding.
A service spokesperson added: "Levels are expected to reach 3m (9ft 10in) around 8am before continuing to rise throughout Wednesday. Further rainfall is expected across the catchment which is expected to keep levels high. The Foss Barrier is in operation and floodgates along the River Ouse in York will be closed in the early hours of Wednesday morning. We will continue to monitor the situation."
There are 22 other less severe flood warnings stretching from Bridlington on the east coast across to the Yorkshire Dales.