The tracks on either side of the Christleton Tunnel, on the outskirts of Chester, regularly flood during wet weather causing delays to services and disruption to passengers.
Between Monday 12 May and Saturday 17 May, Network Rail will be upgrading drainage in the area to prevent future flooding and improve the reliability of the railway.
To complete the work, the line will be closed to all trains between Crewe and Chester, affecting Arriva Trains Wales and Virgin Trains services.
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Ian Joslin, area director for Network Rail, said: "The work in the Christleton Tunnel area will significantly improve performance on this section of line, resulting in fewer delays and a more reliable railway for passengers in the future.
"Unfortunately because of the scale of the work, there will be disruption to journeys though the area between 12 and 17 May while we carry out the improvements.
"We have worked closely with Arriva Trains Wales and Virgin Trains to minimise disruption as much as possible and I apologise for any inconvenience this essential work may cause."
A spokesman for ATW said: "There will be no Arriva Trains Wales train services running between Chester and Crewe during this work but tickets will be valid on connecting Virgin Train services between these stations or a rail replacement bus service will be available. We are advising passengers to check their journey plans before they travel and to allow extra time for their journey."
(CD/MH)
