The station is on the Fen Line from Cambridge to King's Lynn, which is an electrified line.
Waterbeach station has no staff, and only some basic waiting shelters on each platform. All previous station buildings have been demolished and the platforms are now staggered each side of a level crossing with half barriers. Until the line was electrified and the crossing made automatic, the platforms were opposite each other.
Before the line through Waterbeach was electrified, services did not often officially stop at Waterbeach. Since electrification, however, virtually all King's Lynn/Ely - Cambridge/London services have stopped here and passenger numbers have increased, with rail travellers in the area north of Cambridge using it as their primary station.
Trains to and from two London terminus stations travel through Waterbeach – from London Liverpool Street via the West Anglia Main Line and from London King's Cross via the East Coast Main Line.
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