Muskego is located at 42°54'20" North, 88°8'18" West (42.905833, -88.138611).
According to the United States Census Bureau, the city has a total area of 35.88 mi2 (92.93 km2). 31.23 mi2 (80.87 km2) of it is land and 4.66 mi2 (12.06 km2) of it is covered by water. The total area is 12.98% water.
Muskego is located in the Central Standard Time (CST) timezone, GMT-06:00. It observes Daylight Saving Time (DST).