According to the United States Census Bureau, the city has a total area of 75.4 km² (29.1 mi²). 70.4 km² (27.2 mi²) of it is land and 5.0 km² (1.9 mi²) of it (6.63%) is water. Boca Raton is a 'principal city' (as defined by the Census Bureau) of the South Florida metropolitan area. Like most south Florida cities, Boca Raton has a water table that does not permit building basements, but there are several high points in the city, such as Bibletown located at 4th Avenue and the aptly named "High Street." The highest point in this area is the guard shack at Camino Gardens, which is 24 ft above sea level. The Boca Raton Hotel's Beach Club rests at 23 ft above sea level.

Several small tunnels run under roads in Boca, but the roads are built up several feet at these locations, or are located on dunes. Several of these tunnels are under State Road A1A at Spanish River Park, from the west side of the road where parking is available to beachgoers, to the east side of the road, which is where the beach is located. A1A is already higher than the surrounding land here due to sand dunes formed by erosion and other natural features.