Rail operators told commuters to expect delays and longer journey times, and drivers were warned to expect hazardous driving conditions due to the weather.
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Some train journeys were cancelled or delayed more than 15 minutes, and airports also reported delays as they encouraged travellers to check their flight status.
The Met Office issued a yellow warning for fog for the East Midlands, East of England, London and South East England, South West England and West Midlands.
It warned the public and emergency responders of severe or hazardous weather which has a potential to cause danger to life or widespread disruption.
The Met Office said: "Dense fog patches will affect parts of eastern, central and southern England this morning.
"We aware of the potential for difficult driving conditions with slower journey times.
The yellow warning was in effect until 10am.
The Met Office added: "Fog patches have formed again overnight, with visibility reduced to 50m in places.
"Much of this denser fog will clear by mid-morning, though a few patches may linger into early afternoon."
Complicating matters even further for rail commuters was a nationwide fault affecting real-time information systems.
Trains may be incorrectly shown as delayed, said South West Trains.
Woolwich ferry service was suspended due to heavy fog, said Transport for London.
British Airways said fog was disrupting flights at Heathrow, Gatwick and City airports.
Stansted Airport said it was experiencing "slight delays".
It was the second straight day air travellers faced delays as foggy conditions also caused problems on Sunday.
Passengers were told to check with the airline they were flying with to find out if their flight was affected.