Clarkston is located at 46°24'59" North, 117°2'38" West (46.416389, -117.043889).
According to the United States Census Bureau, the city has a total area of 2.03 mi2 (5.26 km2). 1.93 mi2 (4.99 km2) of it is land and 0.10 mi2 (0.27 km2) of it is covered by water. The total area is 5.04% water.
Clarkston is located in the Pacific Standard Time (PST) timezone, GMT-08:00. It observes Daylight Saving Time (DST).