Hundreds of people were delayed at Lincoln's level crossing as dozens of trains were diverted through the city.
An extra 56 trains passed through the crossing on Saturday while Network Rail carried out engineering work on the East Coast Mainline.
Traders say they noticed a drop in footfall as shoppers were stuck at the crossing or decided to avoid the city.
Network Rail apologised for the delays and asked people to be patient. Work is also being done on Saturday 16 October.
Matt Corrigan, from the Lincoln Business Improvement Group, said the delays were affecting the city.
"There were delays for cars and vehicles and a build-up of people at the level crossing. Network Rail paid special attention to keep delays down in that area but it certainly had an impact on trade and business there," he said.
Some trains were diverted from Peterborough via Spalding and Lincoln to Newark, while others continued along the line from Lincoln via Gainsborough and on to Doncaster.
A spokeswoman from Network Rail said everything had been done to minimise disruption and that the level crossing barriers had been kept up as long as possible.
She said that delays were inevitable but the company had "a commitment to keep passengers on the railways".
The same diversions will be in place on Saturday, shoppers and residents are warned.