This is a very tricky question and you will hardly find a different answer than mentioned below when you go for a search in Google. However, after doing a detailed search I found that there are no different answer than mentioned below in many of the engineering sites written by experts.
The principal function of waterstops is to prevent liquids (e.g. water), water-borne materials and solids to pass through concrete joints. In essence, it aims at providing watertightness to the drainage channel.
Besides, waterstops in drainage channels or box culverts can also serve two other purposes:
to avoid water contacting joints’ dowel bars and causing corrosion. (ii) to avoid water seeping in from the underside of drainage channels or box culverts, thereby washing in soil particles and causing voids underneath these structures and finally leading to their failure. To serve the second purpose, obviously only one waterstop is required at any depth location.
To serve the first purpose, a waterstop has to be installed on top of dowel bars to prevent water from drainage channels from leaking through. On the other hand, a waterstop has to be provided below dowel bars to avoid underground water from surging upwards.
In fact, the other way out to serve the first purpose is by using corrosion resistant bars.