According to the United States Census Bureau, the village has a total area of 2.2 square miles (5.6 km²), of which, 2.1 square miles (5.4 km²) of it is land and 0.1 square miles (0.2 km²) of it (3.24%) is water.
The largest active landfill in New York State, Seneca Meadows, is northeast of Waterloo in the town of Seneca Falls.