Waterbeach station is unstaffed, and has only basic waiting shelters on each of the two platforms. All station buildings have been demolished. The platforms are staggered on each side of a half barrier level crossing. Until electrification and the automation of the crossing, the platforms were located opposite each other.
The station is served by First Capital Connect as part of their service from London King's Cross to King's Lynn. Most services run non-stop between London and Cambridge as part of the "Cambridge Cruiser" rail service. These services use Class 365 or (occasionally) Class 317 electrical multiple units. National Express East Anglia also provides a limited service to the station, with trains running to Liverpool Street station in London.