It lies on the Wirral Line 8 miles (13 km) north of Chester and 9+1⁄2 miles (15.3 km) south west of Liverpool Lime Street on the Merseyrail network, and is the junction of the branch from the Chester line to Ellesmere Port.

It provides a major park and ride facility for Birkenhead, Liverpool and Chester, being convenient of access from north east Wales by the A550.

Network Rail has installed a DDA compliant structure to replace the original footbridge, with lifts to all platforms; it was completed at the end of January 2011, making Hooton a wholly 'disabled friendly' station.

Improvements to the station also include new waiting rooms on platforms and fully accessible toilet facilities.

The service to Helsby has been replaced by a couple of diesel "parliamentary" services between Ellesmere Port and Warrington Bank Quay, thus no longer serving Hooton; however the platform sign at Ince & Elton still displays Hooton and Helsby as the termini.

However, in spite of some local L&NWR (later LMS) trains and locomotives, it was very much Great Western territory - situated as it is near the end of the main line which earned that railway its major profits, even though it did not serve the rather more glamorous destinations with which the GWR liked to be, and generally is, associated.

Each morning there was a train to Bournemouth (West) and a three-portion train, of green carriages provided by the Southern Region on alternate days, which travelled via Oxford and Reading to Redhill, where the Brighton portion was detached, thence to Ashford where it was split into a portion for Margate, and another for Dover, Deal and Sandwich.

Mr Parton of the Station Garage provided a taxi service with two luxurious black Packard limousines.

Hooton handled a substantial trade in railway goods and parcels; even unaccompanied dogs (crated) could be sent in the care of the Guard who would attend to their needs en route.

For a very short period during the 1970s even the sparse Sunday services between Chester and Rock Ferry stopped only at Bromborough and omitted Hooton.

The line serving it is not electrified, reverts to double track north of the road bridge, and continues northbound for some three-quarters of a mile.