Storm Ciara battered the region over the weekend, bringing heavy downpours and gale force winds of up to 80mph.
In York, the River Ouse is more than 3.5m higher than its normal levels. City officials expect water levels to continue rising until five o'clock on Tuesday morning.
Anticipating the highest water levels since the 2015 floods, City of York Council said their preparations would ensure residents and businesses could get on with "business as usual".
- Cllr Paula Widdowson from City of York Council said the lessons of 2015 had been learnt and emergency services and staff from the Environment Agency were working "beautifully together".
As flood waters recedes in other parts of North Yorkshire, there is still disruption across the region's travel networks.
LNER, which operates the East Cost Mainline, warned of "major disruption across the rail network due to Storm Ciara yesterday with many services cancelled or suspended due to damage or flooding."
The operator also warned that services to London would be exceptionally busy and passengers should expect to stand for part or all of journey.
Overall, the North East escaped the worst of the storm, which grounded hundreds of flights and forced the closure of major motorways and roads elsewhere in the country.
- In County Durham, High Force waterfall is closed to visitors because of the strong winds.
However, in parts of Northumberland and Teesside, more a month's worth of rain fell in less than 24 hours, leading to pockets of flooding.
- In Kirk Hammerton, North Yorkshire, horses waded through a flooded field.
All the main rail operators ran a reduced timetable on Sunday and advised against all but essential travel.
Trains that did leave on time were forced to travel at half their normal speed, with some journeys between the North East and London taking up to six hours.
Gail and Matthew Rich from Newcastle were among the travellers caught up in the disruption. Their two daughters have a rare genetic condition called Batten disease, which requires weekly trips to London for treatment at Great Ormond Street Hospital. The family praised rail staff for their customer service during the disruption.
Wintry weather is expected over the coming days, with the Met Office issuing yellow warnings for parts of Northumberland and North Yorkshire.
- A spokesperson for the Environment Agency said: