This week’s fierce storms were unexpectedly hard on Delta Air Lines and its passengers.

The carrier wound up cancelling 1,200 flights over two days after waves of thunderstorms late Wednesday fouled operations at Hartsfield-Jackson International.

On Thursday thousands of travelers still waited in lines stretching through the terminal, as Delta struggled to re-set operations after planes and crews were left out of positions.

At mid-afternoon, the Federal Aviation Administration’s flight delay information website showed inbound flight delays of more than five hours as planes were held on the ground elsewhere.

The storms came in the middle of a busy spring break week. While some travelers resorted to searching for rental cars to drive home, many were already taken because of the Masters Tournament in Augusta.

“It’s been a nightmare,” said traveler Greg Hall of Roanoke, Va., who was returning from a business trip to Louisiana. His group overnighted in Atlanta after a delayed flight, then finally rented a car after Thursday morning flights were cancelled.

“It’s been kind of a fiasco … Just had to bag the airline flight,” he said.

Delta spokesman Michael Thomas said the nature of Wednesday’s storms made them harder to predict and complicated recovery. Airport ramps must be closed when lightning is close, adding to the problems.

Then, the resulting flight cancellations cascade to affect subsequent flights.

“When an airplane doesn’t fly, it means that crews aren’t getting to where they need to be,” Thomas said, also citing limits on how long crews can be on duty before a required rest period.

Many travelers were still frustrated with the fallout.

Belinda England, of Glasgow, Ky., was returning with family from a vacation in Cancun, and said their delayed flight arrived at Hartsfield-Jackson around 2 a.m. Thursday. They missed their connection home and eventually arranged to have someone drive them back to their car in Nashville.

“I’m a travel agent, and I’m very, very upset with Delta,” England said. “I know weather is not their fault, but they had ample time to get their act together.”

It was “the perfect storm — and we got caught in the middle of it,” England said.