More than 1000 people along the River Thames, west of London, were evacuated as the river broke its banks in places.
But after more than four weeks of persistent rain the ground is unable to cope with even more water and is pushing it back through street drains, home sinks and even toilets.
The Environment Agency's head of strategy, Pete Fox, said rain on one side of the country was set to affect the other side in two or three days time, with unprecedented levels of groundwater.
"Those high levels are going to maintain for weeks and cause flood risk for weeks to come yet, into March and beyond," he said. The Met Office described the weather as a multi-pronged attack with almost every pocket of the UK experiencing downpours, gales or snow.
Severe gales, large waves and high sea levels were also threatening the Dorset coast with flooding.
More than 2200 soldiers were deployed across England including Gurkhas, Nepalese fighters, brought in to erect flood barriers west of London. Sailors from HMS Collingwood were also sandbagging properties against rising Thames tides.
Chief fire and rescue adviser Peter Holland said more than 70 per cent of England's fire and rescue services were now involved in the flood and storm relief effort. More than 5000 homes have been flooded since December. Rainfall is at the highest levels for 250 years.