Train services were disrupted following two separate landslips in Stockport and Tameside.
Services were temporarily suspended between Manchester Victoria and Huddersfield following the incident near Mossley.
Rose Hill station in Stockport was also shut due to a landslip.
The incidents came after Storm Christoph brought 24 hours of heavy rainfall to the region.
Manchester Piccadilly Twitter account posted about the incident in Mossley around midday, saying: "Services are cancelled from # ManchesterVictoria to # Huddersfield due to a landslip.
"Staff are working hard to resolve this issue."
At 1.20pm, Transpennine Express tweeted that the incident had been resolved.
However, delays are still expected.
The post read: "Following a landslip in the Mossley area, the line has now re-opened.
"Train services are now able to run between Huddersfield and Stalybridge, however delays can still be expected."
Rose Hill station was temporarily closed.
TfGM warned that booked services would terminate at Marple Station.
It has since been reopened and services have resumed.
There was further disruption to railway services elsewhere as downpours caused flooding in some parts of Greater Manchester.
Rail provider Northern said there was disruption to a number of services across the network, as they advised people not to travel in the North West.
There were delays and cancellations to services between Sheffield and Manchester Piccadilly .
The Liverpool to Manchester route via Warrington Central was also closed around 1.30pm due to flooding.
