Santee is located at 32°50'17" North, 116°58'22" West (32.838056, -116.972778).
According to the United States Census Bureau, the city has a total area of 16.28 mi2 (42.16 km2). 16.06 mi2 (41.59 km2) of it is land and 0.22 mi2 (0.57 km2) of it is covered by water. The total area is 1.35% water.
Santee is located in the Pacific Standard Time (PST) timezone, GMT-08:00. It observes Daylight Saving Time (DST).