Waddington is located at 44°51'51" North, 75°12'15" West (44.864444, -75.204444).
According to the United States Census Bureau, the village has a total area of 2.38 mi2 (6.16 km2). 2.17 mi2 (5.62 km2) of it is land and 0.21 mi2 (0.54 km2) of it is covered by water. The total area is 8.69% water.
Waddington is located in the Eastern Standard Time (EST) timezone, GMT-05:00. It observes Daylight Saving Time (DST).