All trains that run between Boston and Skegness have been cancelled for the next three days.
Pictures taken by East Midlands Trains (EMT) shows how the line has been completely submerged in water.
The train service between the two towns are expected to be reinstated on Saturday morning, depending on weather.
A spokesperson for EMT said: “There has been heavy rain and flooding on the railway between Boston and Skegness.
“The flooding is still high and is expected to get higher, there is also lots of safety equipment that needs testing.”
Buses have been put in place to replace the existing services.
Commuters are also being advised to avoid travelling to or from Wainfleet, with delays of up to 90 minutes expected.