Part of the railway is now used by the Chester branch of the Wirral Line, one of the two urban electric commuter rail services operated by Merseyrail on Merseyside.

A parliamentary bill authorising the merger was submitted, and it was passed on 22 July 1847, but provisions for leasing by other companies, chiefly the LNWR, were removed because of concerns about interests other than development of the docks.

[7][8] The Shrewsbury and Chester Railway had emerged from the North Wales Mineral Railway, and brought considerable volumes of minerals, chiefly coal, from Flintshire to Birkenhead; there was a triangle of lines at Chester station, enabling these trains to avoid the station.

By an act of Parliament on 1 August 1859 the BL&CJR company changed its name to the Birkenhead Railway, and the transfer of ownership took effect on 1 January 1860.

[note 1][16][6][17][18] The LNWR opened the direct line over the Mersey at Runcorn on 1 February 1868, allowing London to Liverpool trains to avoid Warrington.

This considerably shortened the transit time between Chester and Liverpool and abstracted nearly all of the passenger traffic that had gone via Birkenhead and the Mersey ferries.

[19] On 20 January 1886 the Mersey Railway opened between Liverpool James Street and Green Lane Junction in Birkenhead, where it entered on the Chester–Birkenhead line.

Much continued as before, but the transfer of bulk goods to containers, and the increasing use of road transport abstracted from the railway, which declined, as did passenger business.

As much of the goods and mineral traffic to and from Birkenhead had Manchester as its terminal, the Joint companies decided to build the Helsby branch, a straight route of nearly 9 miles (14 km).

It intersected the Shropshire Union Canal at Ellesmere Port, then a very busy dock, but no railway connection was made there.

[25][6] A branch from Hooton to Parkgate was planned, chiefly to access collieries at Neston, and potentially to develop a residential district.

[26][27] In 1881, the Joint Line directors decided to extend the railway from Parkgate to West Kirby, along a developing residential strip.

The line opened on 19 April 1886 and the passenger train service ran from Birkenhead Woodside to West Kirby, via Hooton.