Marlboro is located at 41°36'20" North, 73°58'18" West (41.605556, -73.971944).
According to the United States Census Bureau, the city has a total area of 3.35 mi2 (8.68 km2). 2.76 mi2 (7.16 km2) of it is land and 0.59 mi2 (1.52 km2) of it is covered by water. The total area is 17.51% water.
Marlboro is located in the Eastern Standard Time (EST) timezone, GMT-05:00. It observes Daylight Saving Time (DST).