Emergency services said a 54-year-old woman, who had been driving, managed to escape from the vehicle after it got stuck in "5ft of fast-flowing" water near Newbury in West Berkshire.
The 52-year-old man, who was a passenger in the vehicle, was pronounced dead at the scene in Compton Wood, Hampshire.
Inspector Jon Snook said: "We believe the car drove into the ford from the Hampshire side where it appears as though it was swept downstream and became submerged.
"On arrival, we co-ordinated a rescue operation with the fire service to try and free the man. Unfortunately, he was pronounced dead at the scene.
"We know that the ford was flooded and we are now conducting an investigation to establish the exact circumstances of this incident and will be preparing a file for the coroner."
Police also said the woman was taken to Basingstoke and North Hampshire Hospital, where she was being treated for shock.
It comes as rain and wind continue to wreak havoc in many parts of the country and high rivers from the weekend rain pose a danger to property.
The Met Office says this month has been the UK's wettest April since records began in 1910.
At least 36 flood warnings and 152 flood alerts are in place, with localised flooding expected in parts of southern and eastern England, the Midlands and Wales.
A spokeswoman for the Environment Agency (EA) said three incident rooms had been set up in the Midlands, while a further incident room was set up for the Wessex area in the south.
She said: "It's not unusual to experience heavy downpours and some flooding - mainly of farmland - at this time of year, but we're continuing to closely monitor the forecast and rainfall particularly in areas along the rivers Severn, Teme and Avon, including Worcestershire, Shropshire, Herefordshire and Gloucestershire.
"Environment Agency teams are out on the ground continuing a close watch on river levels as well as checking defences and clearing any potential blockages to reduce the risk of flooding."
The heavy rain has caused the cancellation of the Badminton Horse Trials in Gloucestershire, which were due to start on Friday.
Organisers admitted the decision was taken as there was no realistic chance of the ground drying out in time for the event.
Among the towns worst hit by the downpours are Taunton, in Somerset, and Tewkesbury, in Gloucestershire, which was devastated by flooding five years ago.
Midlands correspondent David Crabtree is in Tewkesbury, which he said was under more than two foot of water.
"In places there was around 2.2 inches of rainfall, which is well above the average," he said.
"People in some places are preparing with sandbags to make sure that the water doesn't get into their homes.
"I have to say, (the water) is still rising. We do hear that more rainfall is on the way.
"The Environment Agency say this above-average rainfall does help in terms of trying to alleviate drought conditions that are still in force here, but we'll need similar kinds of rainfall over the next few months to get out of that situation."
More than 1,800 households in Tewkesbury were forced to move out of their homes and into temporary accommodation by torrential rainfall in 2007.
The latest downpours come at the end of a particularly wet week for England and Wales, in which 42mm (1.7in) of rain fell in the South East and 55mm (2.2in) in the South West, which has now had 166% of the average rainfall for April.
Many areas at risk of floods are currently in a state of drought, which is gripping the South East, East Anglia, the Midlands, the South West and south and east Yorkshire after two unusually dry winters in a row.
While some parts of Britain can hope for a reprieve today, the South West shows no sign of drying up with the wet weather set to continue.
Sky News weather presenter Joanna Robinson said: "Most other places will dry up, but southwest Britain will stay wet and windy, with gusts up to 60mph."
Thousands of homes were left without power in Wales over the weekend.
Around 1,200 homes in South Wales still have no electricity.
Earlier many homes were cut off in the West Midlands, as well as 2,000 in the South West, electricity supplier Western Power said.