The Waterworks were located in the Southern end of Isla Nublar, near the volcanic steam fields. The waterworks were made of concrete, were mostly used to control flooding in the southern flatlands. Most of this structure was underground, and there is an indication of an entrance to the structure from the beach. Ellie Sattler realized that the Velociraptors were hiding in the southern end of the island, partly due to the warmth from the steam fields. On her request, Tim Murphy brought up the schematics and plans for the Waterworks from a terminal in the Visitors’ Center. The Velociraptors had made their nest in the waterworks, the entrance is from a hole in the steam fields.
Jurassic Park by Michael Crichton page 373, 376,386(First Edition, Thirty-Fourth printing)