More than 120 flights were axed and Eurotunnel warned of three hour delays, causing headaches for British holidaymakers heading away for Easter.
Easyjet and British Airways blamed staff absences from Covid for cancellations, while Eurotunnel said a broken down train caused delays.
However, flights in and out of Doncaster Sheffield Airport have not been impacted with all Wizz Air and TUI flights operating as normal both today and tomorrow.
Flight cancellations were down to combination of factors which had come together in "a perfect storm", Simon Calder, travel correspondent at The Independent told the BBC.
"We have got very high levels of Covid in the nation and that is affecting the transport industry. But there are also more underlying problems which go back to the start of Covid," he said.
These included a lack of staff after thousands of people left the aviation industry during the pandemic. Staff shortages have led to long queues at security and check-in.
Some passengers at Manchester Airport have missed their flights at the start of the Easter holidays as a result of queues.
There have also been complaints about extensive waits in the baggage reclaim halls.
EasyJet, one of Europe's biggest airlines, said the cancellations-which included 62 from the UK- were a small part of its schedule on Monday, which is about 1,645 flights.
It apologised and said it had tried to offset the problem by using standby crew but was forced "to make some cancellations in advance".
"As a result of the current high rates of Covid infections across Europe, like all businesses, EasyJet is experiencing higher than usual levels of employee sickness," a spokesman said.
He said affected customers had been contacted and could rebook on alternative flights or receive a voucher or refund.
About 60 British Airways flights to and from Heathrow airport were cancelled on Monday. Fifty were cancelled in advance last week but 10 flights were late notice overnight cancellations, due to Covid sickness among staff.
Eurotunnel warned motorists heading abroad to expect delays after a train "temporarily stopped" in the tunnel linking England to France.
The operator, which runs services from Folkestone to France, warned journeys could be delayed by up to three hours.