The section west of Ellesmere Port has been part of the Merseyrail network since 1994. This part of the line is electrified. There are no longer through train services to Liverpool's city centre via Birkenhead.
A branch at Helsby connected the line to the former West Cheshire Railway to Northwich via Mouldsworth Junction. The line closed in 1991 and tracks were lifted in 1995.
Passenger services
Former services
Services previously used to operate from Hooton to Helsby. This service was relatively frequent (every half-hour until 1993), operating via Ellesmere Port. It was withdrawn after the line was electrified west of Ellesmere Port. Station signs at Ince and Elton railway station still display signage relating to services to/from Hooton.
In 2008 Quinn Glass was planning expansion and wanted to serve their 205 acres (0.83 km2; 0.320 sq mi) site at Elton which outputs 1.2 billion glass containers per year for the food and beverage industry[9] near the Ince & Elton railway station by rail. Network Rail Route Strategy states that Quinn Glass is interested in additional passenger and freight services on this line. It is also thought that planning permission requires Quinn Glass to maximise upon existing public transport links.[10] A trial service ran on 7 April 2011 and a twice-weekly service every Wednesday and Friday commenced on 13 April 2011.[11][12] Those services were operated by Freightliner Heavy Haul and transported sand from Sibelco's Middleton Towers Quarry in Middleton, Norfolk.[13][14][15][16][17][18]
At present the sand is transported by road the final five miles to the Quinn Glass plant from a former Cawoods siding in Ellesmere Port beside the Manchester Ship Canal, south of Manisty Wharf, but from November 2011 trains were due to begin using a dedicated terminal at the plant itself.[11][19][20] It was announced during this month that construction work had been delayed due to the discovery of a badger sett on the proposed site. Completion of the new line was set back to the end of June 2012 with a reported total cost of more than £2 million.[21] In November 2012 it emerged that Quinn Glass had broken a planning condition requiring the rail terminal to be operational by November 2011.[22] The company cited additional demands by Network Rail and the Environment Agency's decision to switch off the Frodsham Marshes pumping stations as causes of delay. Quinn Glass have since been granted an extended period by Cheshire West and Chester council during which to complete the project.[23]
Stations
Hooton; opened October or November 1840; still open;
Sutton; opened 1 July 1863; renamed Little Sutton 1886; still open;
Overpool; opened 15 August 1988; still open;
Whitby Locks; opened 1 July 1863; renamed Ellesmere Port 1870; still open;
Stanlow & Thornton; opened 23 December 1940 for refinery workers; opened to public 24 February 1941; (service suspended since 3 February 2022)
Ince; opened 1 July 1863; renamed Ince and Elton 1884; still open;
West Cheshire Junction; divergence of line to Mouldsworth;
Helsby; opened September 1852; still open;
Three of the four stations between Helsby and Ellesmere Port are unstaffed. Two of them, Ellesmere Port and Ince and Elton, are accessible for those in wheelchairs. Stanlow and Thornton and Helsby both have footbridges as their only means of exit. Facilities at Ince and Elton and Stanlow and Thornton are basic, comprising little more than covered waiting areas and timetable information. Ellesmere Port has full ticket-selling capabilities, including a Ticket Vending Machine and a staffed ticket office, along with real-time information displays and help points. Helsby has real-time information displays and a Ticket Vending Machine.