A fire crew from Bradford on Avon spent three hours pumping out water from the Bull Pit last night after it seeped through the newly installed flood defences.
On Thursday night, barriers were placed in the Bull Pit, which has an uneven surface, and despite efforts to block the gaps with sandbags, water still passed through.
The Environment Agency has been monitoring river levels and called the fire service when water started to breach the barriers last night. The crew from Bradford on Avon was there for three hours and left at midnight.
Yesterday a second set of barriers were set up on the opposite side of the river in Westbury Gardens, but as of this morning water has not breached the river wall.
Bristol City Council supplied both flood defences and helped put them up with the Environment Agency.
Meanwhile traffic is building up in the town due to emergency repairs to a manhole cover. Temporary traffic lights were set up outside Westbury Gardens yesterday and will remain in place until repairs take place.
Malmesbury appears to have escaped the worst last night as there have been no major reports of flooding, but the town, along with Bradford on Avon and the rest of Wiltshire, is keeping a close eye on the weather forecast.