The heavy rain that spoilt May and June looks set to stay for the rest of summer, Met Office research suggests.

Cooler sea temperatures in the Pacific Ocean prompted by the La Niña weather system, sister to El Niño, have been identified as the likely cause of summer depressions sweeping across Northern Europe.

The finding came as more rain fell over wide parts of Britain yesterday, much of it in regions trying to recover from last week’s floods, which are now estimated to have cost more than £1 billion.

Yorkshire and Lincolnshire, which suffered the worst of last Monday’s rains, escaped comparatively lightly yesterday, but the Midlands and Wales endured another soaking.

Officials at the Environment Agency were hopeful that further flooding had been avoided. They said that river levels were falling despite more rain, adding that the picture was “a lot more healthy”.

They cautioned, however, that the flood waters in Sheffield and Hull, which are still 2 feet (61cm) or more deep in parts, are likely to take the best part of a week to drain away.

Western areas from Cornwall to Scotland bore the brunt of heavy rain over the weekend, with more than an inch falling in places. A break in the relentless downpours is not forecast until Thursday.

The Church of England took a different stance to the Met Office as to cause of the floods — senior bishops said that the severe weather were a consequence of the West’s decision to ignore the Bible.

The church leaders emphasised that while the seven people who died were innocent victims, it was man-made climate change and an “arrogant” world “reaping what we have sown” that had caused the disasters of the past week.

The quantities and spread of the rain yesterday gave emergency workers a respite. Joe Giaconelli, of the Environment Agency, said: “There’s been quite a lot of heavy rain. Fortunately, it hasn’t resulted in any further floods and river levels are falling quite nicely.”

He said that there were still concerns that the rains, mainly in the West, could spread to eastern regions again and delay the clearing-up operation in flooded areas.

Four severe flood warnings remained in force for stretches of the River Don in South Yorkshire, but emergency workers coping with the floods were increasingly optimistic last night that the worst was over.

Troops and lifeboat crews, on standby in case of further heavy rain, were stood down and a spokesman at the South Yorkshire emergency control room said: “It’s certainly not getting any worse. The rains haven’t been quite as bad as they could have been.”

Trading standards officers advised people to beware of cowboy builders and workmen offering same-day repairs at reduced prices.

Flooded householders were advised to obtain three separate quotes from established tradesmen before agreeing to have work done.

Mary Dhonaum, co-ordinator of the National Flood Forum, said that cowboy builders could arrive at people’s doors “wearing spurs and yelling yee-haa”. She advised flood victims to use recommended workmen “even if it means you are displaced for longer”.

Insurers said that the cost of the damage across the country was expected to top £1 billion, with 27,000 homes and 5,000 businesses affected.

While the worst of the flooding may be over, researchers at the Met Office were holding out little hope that the rest of summer would have much in the way of blazing sunshine.

Adam Scaife, at the Met Office, said that researchers had now discovered that La Niña also played a big role in shaping British summers.

Meteorologists have become increasingly convinced of La Niña’s knock-on effect and have detected a growing signal in the Pacific that it is kicking in strongly. Their first clue was finding a mirror-image of Britain’s current weather in the southern hemisphere, where similar bands of depressions have been sweeping 45 to 55 degrees latitude, similar latitudes to Britain and Northern Europe. “To get this sort of symmetry in both hemispheres tells us that there’s something coming from the tropics, and La Niña is by far the biggest suspect,” Dr Scaife said.

Records going back more than 100 years revealed that bouts of La Niña often coincided with summer depressions sweeping across northernmost Europe.“There’s a remarkable similarity over the past four months’ forecasts and our historical analysis. If our forecast is correct, then unusually cloudy, windy conditions may continue this summer.”

La Niña’s effect changes the pattern of rain in the tropics, which ripples out through the atmosphere as giant waves that hit the jet streams in the northern and southern hemispheres. The streams are rivers of wind flowing a few miles above the Earth’s surface and help to drive weather.