Arpley Junction is adjacent to Warrington Bank Quay Station, but is located on the goods line that passes beneath. The line used to continue to Manchester but due to structural damage on a bridge over the Ship Canal, it was truncated at Latchford Sidings in the 1980s, just past Arpley Junction to the east.
The main freight passing beneath Warrington station are coal trains to Fiddlers Ferry Power Station. These follow a complex route from Liverpool Docks. Most workings reverse at Edge Hill, before proceeding via Rainhill and Earlestown and through Bank Quay station. They then run round in Arpley Yards, before passing Arpley Junction to Latchford Sidings. They then run round again to pass Arpley once more to head to Fiddlers Ferry. Occasionally they can be routed via Widnes to Liverpool instead of via the reverse of the above route, which will entail them exiting Fiddlers Ferry, passing Arpley Junction to Latchford, running round and heading back past Arpley and Fiddlers Ferry to Speke. Generally a train will take 30-40 minutes between passing through Bank Quay on the main line to heading under the station to Fiddlers Ferry. They will take about 90-120 minutes then to return. There are usually about 3 trains operating this circuit, but are dependant on a ship arriving at Liverpool Bulk Terminal.
Other freight trains also use Latchford Sidings to reverse when Arpley Yard is busy.