The Environment Agency is forecasting the River Ouse will rise to at least 4.47 metres or 14 feet seven inches, by the early hours of Tuesday morning. It has yet to say when the peak will be.
The Ouse was at 1.05 at 3.30pm today or just over three feet, and rising.
Storm Isha is expected to bring heavy rain as well as high winds.
More bad weather is expected on Tuesday and Wednesday.
The river was at 14 feet or more for five consecutive days over the New Year.
The agency has issued a flood alert, its lowest warning level, for the Upper Ouse from just south of Boroughbridge to just south of Naburn.
It has also put flood alerts on the lower and upper Nidd, the lower and upper Ure and the lower and upper Swale, all of which flow into the Ouse before it reaches York.
There are similar warnings on the lower and upper Wharfe. During the floods earlier this month, Tadcaster Bridge over the river was closed.
On Friday, the Met Office issued an amber warning for York starting at 6pm and lasting until 6am forecasting that the storm, the ninth named storm of the 2023/24 season, to bring major disruption to travel and power supplies as well as property damage.
