The River Derwent near the North Yorkshire town remained up to five metres above its normal levels on Friday (Jan 22) evening.
Some 27 pumps were used yesterday in a multi-agency relief operation from North Yorkshire County Council, Ryedale District Council, North Yorkshire Fire and Rescue, the Environment Agency, and Yorkshire Water.
According to the Environment Agency, levels at 17.1ft (5.24 metres) were the highest they have ever reached since records began.
The water was so high that it reached the underside of County Bridge in the town centre, which remained closed for a second day following Storm Christoph.
A flood warning remained in place last night in Malton, as well as one at Mill Beck in nearby Norton.
The Morrisons car park in the town centre was closed to most cars, with just 20 spaces not submerged under flood water.
A small number of properties on the town’s Castlegate flooded yesterday, leaving residents only able to watch as crews tried to mitigate the damage.
No further rain is expected in the town over the weekend but there are concerns that heavy rain next week may pose further challenges in Malton and across the county.
Richard Flinton, chair of the North Yorkshire Local Resilience Forum, said: “This has been a massive effort, bringing together the expertise and resources of various agencies.
“It is a challenging situation and it remains fragile, but the combined operation is working well and the operation will continue.
“I thank all those from all the agencies involved who have been on the ground around the clock working tirelessly to protect these communities.”