With forecasts of at least another week of gales and torrential rain, severe weather warnings and hundreds of flood alerts covering the entire south and south-west coasts of England, and all rail links to the West Country severed for the first time, the flood waters and the political blame game are both deepening.

Firefighters, assisted by soldiers from a nearby barracks, were working round the clock to keep the floods away from an electricity substation at Burghfield, near Reading in Berkshire, which supplies power to 40,000 homes and businesses. The power station is near the river Thames which burst its banks in several places over the weekend, closing many roads in the area.

An elderly woman was taken to hospital in Birmingham, with severe injuries, after a tree fell on the car she was travelling in.

The Somerset Levels were hit by further rainfall, with water levels rising 0.6cm (0.25in) an hour at Burrowbridge – one of two areas of the levels still covered by severe flood warnings, indicating a danger to life.

There could be a brief respite on Monday, but further rain warnings have been issued for Tuesday and Wednesday.

The Met Office's chief scientist, Dame Julia Slingo, said for the first time that climate change almost certainly lies behind this winter's torrential rains and violent storms.

As prime minister David Cameron prepared to chair a meeting of the Cobra emergency committee, communities secretary Eric Pickles offered an "unreserved" apology and said the government recognised that there should have been more dredging of the Somerset Levels.

Network Rail staff worked through the weekend to restore train links to Devon and Cornwall, after all routes to the West Country were cut through flooding, landslips and trees and other obstructions on the lines.

Dawlish: waves crash over the main Exeter to Plymouth railway line which has been closed. Photograph: Dan Kitwood/Getty Images

A landslip at Crewkerne closed the last open line to the west country. Flooding at Athelney, and between Taunton and Bridgewater – where the line was blocked by the flooded river Parret, which left the tracks resembling a causeway across a lake – shut down the other routes. The line to Cornwall was cut last week when a 30m stretch of the seawall supporting the line at Dawlish was washed away.

Network Rail said the Crewkerne line could take a week to restore, and that work at Dawlish was progressing well in six-hour shifts between high tides.

Rail replacement buses are in operation, but there will inevitably be chaos for long-distance commuters as the working week starts. First Great Western posted a warning that all direct lines were closed until further notice, and warned that journey times would be extended by at least 120 minutes to Exeter and 180 minutes to Plymouth.

Some branch lines are running within Cornwall, and between Penzance and Plymouth.

The company is discounting fares by 25% from Sunday for services that pass through the affected areas. The line between Exeter and Plymouth is not expected to reopen for at least six weeks.

In the south-east, which has mostly escaped the worst of the weather so far, there are 84 Environment Agency flood warnings and 124 flood alerts in place, covering most of the upper Thames including Windsor, Abingdon, Dorchester and parts of Oxford, and the river Wey in Guildford, and the riverside around Hampton Court Palace.

In south London a concrete pedestrian underpass at Purley Cross, near Croydon, has been turned into an emergency flood pond, to hold thousands of litres of flood water being pumped away from 400 homes and businesses and the Kenley water treatment works which supplies 46,000 properties and 116,000 people. The main flood pond overflowed on Friday night. The water table in the area has risen from its usual 25m below ground to 0.75m below.

In south Wales, where gusts of up to 80mph were recorded at Mumbles head near Swansea, both the Severn bridge and the M4 were closed for periods on Saturday and Sunday because of strong winds and traffic accidents.

Many other roads were closed by fallen trees or flooding, and a landslip closed the trainline between Abergavenny and Hereford. At one point 68,000 homes had lost electricity supplies, though most have now been reconnected.

The Ministry of Defence has placed 1,600 personnel on six hours notice to help if needed in the south.