Passengers rescued from a flood-hit train became stuck near the scene on a second train that came to rescue them.
The 14:34 service from London to Nottingham was stopped because of a landslip near Corby, Northamptonshire.
East Midlands Trains said coaches had been sent to collect the passengers.
Elsewhere, the RAF was called in to help block a break in a river bank causing severe flooding at Wainfleet All Saints, Lincolnshire.
One hundred people had to be evacuated. The county council said the river breach presented a “risk to residents”.
Asst Ch Cons Shaun West of Lincolnshire Police said the RAF helicopter crews would be working during the night.
Passengers on the London to Nottingham train were transferred to a second train which stopped alongside, but that could not leave the area because of flooding.
In a statement East Midland Trains said: “The second train is now also at a standstill due to flooding near the tunnel.
“We are now working closely with Network Rail, the British Transport Police and the emergency services to carry out a safe evacuation of this train.”
It said the train had been diverted on to the flooded line because of trespassing on its usual route.
Lincolnshire County Council issued guidance to residents in Wainfleet which included advice on not using domestic toilets as this would add “pressure to the system”.
The Environment Agency has issued dozens of flood warning and alerts across the country.
The majority were across the Midlands and North West, although they extended as far as Northumberland and Christchurch in Dorset.
The River Steeping also burst its banks at Thorpe St Peter near Skegness, Lincolnshire, on Wednesday night.
Lincolnshire County Council said the equivalent of two months’ rain had fallen in the area in two days.
Jean Hart, who has lived in the town for 40 years, said it was the worst flooding she had ever seen.
“To see our house under water is absolutely horrendous,” she said.
“The whole of my house is completely devastated.
“Last night when we got back here I didn’t realise I was just sobbing, but I didn’t even know I was crying to be honest.”
Emergency services have rescued her tortoise Mr T from her home, and she had earlier been reunited with her cat Aurora.
Rail services between Skegness and Boston are suspended until Saturday due to flooding, while Merseyrail has cancelled some trains on the Chester and Ellesmere Port lines because of water on the tracks at Hooton.
Music fans have been leaving the “Drownload” Festival at Donington Park early because of the soggy ground and mud.
Motorists including a minibus of Indian tourists became trapped at Lambley, near Nottingham, overnight and were taken in by local residents.
Resident Malcolm Bamford said: “We had two in our house and the neighbours had three, and then there was a group of about eight Indian tourists in a little tiny bus and they all wanted to use the toilet.”
In Derby, Oakwood Infant and Nursery school will now be closed until Monday because of flood damage.
National Rail Enquiries said heavy rain had flooded the tracks between Whitlocks End, near Solihull, and Stratford-upon-Avon.
Chillingham in Northumberland had 73mm of rainfall over a 28-hour period – more than the 66.4mm average for the whole of June.
Elsewhere, Waddington in Lincolnshire saw nearly 40mm fall over a period of 14 hours, while over the same period Coleshill in Warwickshire had 30mm fall and 31mm was seen at Astwood Bank, Worcestershire.