Rail operator Northern said all lines between Buxton and Stockport were blocked for a time due to heavy rain flooding the railway.
A spokesperson said: "Due to signalling problems caused by flooding on the line of the route between Hazel Grove and Buxton services are unable to run in either direction."
A replacement bus service operated between Stockport and Buxton, but journey times were "significantly extended".
Trains began running again on Wednesday evening, but Northern warned that the services could still be cancelled or delayed at short notice, and advised customers to check before travelling.
Flooding also caused disruption to rail services on the Hope Valley Line between New Mills Central and Sheffield.
The wet weather led to difficult driving conditions on the roads, and the A6 between Buxton and Bakewell was shut due to the River Wye bursting its banks.
Derbyshire police said the following roads were unsafe to pass: Bridge Street, New Mills; Hyde Bank Road, New Mills; Ford Road, Whaley Bridge; Start Lane, Whaley Bridge; Hayfield Road, Birch Vale; Lightwood Road, Buxton; and the A623 Sparrowpit stretch.
The A555 Manchester Airport relief road remained closed in both directions between the Oil Terminal roundabout, heading down Woodford Road to the A34.
The National Trust estate Lyme Park in Disley also closed its doors early due to flooding and is expected to remain shut tomorrow (Thursday).