High winds and heavy rain left many roads and railway lines in Devon impassable today.
Parts of the Westcountry were last night urged to "be prepared" as the Environment Agency issued dozens of flood alerts.
Some trains between the region and London were cancelled because of flooding on the line near Exeter.
The Met Office is forecasting up to three inches (80mm) of rain for parts of the South West, as well as South East, Midlands and North East, over the next 48 hours.
Amber warnings are in place until 4pm today.
The Environment Agency has already put out several flood alerts, and said further warnings are likely to be issued for river and surface water flooding elsewhere.
"We are expecting heavy rain in the South West in the next couple of days and this might lead to some flooding," Nick Moore, from the Environment Agency, said.
"We strongly urge people to sign up to flood warnings, keep a close eye on local weather forecasts and be prepared for the possibility of flooding.
"We also ask that people stay safe, by staying away from swollen rivers and not attempting to drive through floodwater. The Environment Agency already has teams out on the ground checking on flood defences and clearing any blockages in order to reduce the risk of flooding as much as possible."
Yesterday afternoon flood alerts, meaning flooding is possible, were issued for the rivers Yealm, Plym, Lynher, Seaton and Tavy.
They were also issued for the Lower Tamar and rivers Torridge, Clyst, Culm, Otter, Sid, Exe, Axe, Dart and the South Devon coast.
The Environment Agency said it was likely that more serious flood warnings, meaning that flooding is expected, would be issued over the next three days.
This morning police urged drivers to avoid the A3052 at Stafford Cross, Colyton in East Devon after a diesel spill on the road.
The spill started at the Three Horseshoes junction with Putts Corner towards Boswell Cross.
The spillage was reported to police at around 7.15am and road closures were put in place.
Police also dealt with a number of minor collisions in the area.
Flooding left the A373 at Honiton is just about passable in both directions between the Winneford Lane junction in and the Broad Road junction in Cullompton.
Diversions were put in place through Exeter via the A30 and M5 in both directions.
A multi-vehicle accident and a fuel spillage has blocked the A3052 in Sidford between Fortescue Road and B3172. The road is closed in both directions and there are long delays.
Difficult driving conditions have been reported on the A30 at Lifton around Polson due to rain and surface water.
Wolseley Road in Plymouth was flooded in both directions between A3064 Weston Mill Drive and B3396 Milehouse Road.
Windmill Road on the A3072 at Holsworthy was flooded but just passable both ways between Waterloo Road and Moor View.
Devon and Somerset Fire Service said it had responded to dozens of reports of flooding, mainly between 6am and 10am today.
Severe flooding was reported in the Guildhall Lane and Gramball Lane area of Wedmore, near Wells, Somerset due to a swollen river – with water up to 3ft deep in some properties.
Flooding led to several vehicles stuck in floodwater on the A361 at Greinton, leading to the temporary closure of the road.
There was also a vehicle reported stuck in floodwater on the Shurton to Hinkley Point road, Storgursey.
Two people were also rescued from a car stuck in floodwater at Curry Mallet, Taunton, the fire service said.
Flood Line is on 0845 988 1188.