San Francisco is located on the west coast of the U.S. at the tip of the San Francisco Peninsula and includes significant stretches of the Pacific Ocean and San Francisco Bay within its boundaries.

Several islands are part of the city, notably Alcatraz, Treasure Island, and the adjacent Yerba Buena Island, together with small portions of Alameda Island, Angel Island, and Red Rock Island. Also included are the uninhabited Farallon Islands, 27 miles (43 km) offshore in the Pacific Ocean.

The mainland within the city limits roughly forms a seven by seven mile square (11 by 11 km), which has become a colloquialism referring to the city's shape. The San Francisco Peninsula: San Francisco and, below it, northern San Mateo County San Francisco is famous for its hills. There are more than 50 hills within city limits.

Some neighborhoods are named after the hill on which they are situated, including Nob Hill, Pacific Heights, Russian Hill, Potrero Hill, and Telegraph Hill.

Near the geographic center of the city, southwest of the downtown area, are a series of less densely populated hills. Dominating this area is Mount Sutro, the site of Sutro Tower, a large red and white radio and television transmission tower. Nearby is Twin Peaks, a pair of hills resting at one of the city's highest points and a popular overlook spot for tour groups. San Francisco's tallest hill, Mount Davidson, is 925 feet (282 m) high, and is capped with a 103 feet (31.4 m) tall cross built in 1934.

The San Andreas and Hayward Faults are responsible for much earthquake activity, even though neither passes through the city itself. It was the San Andreas Fault which slipped and caused the earthquakes in 1906 and 1989.

Minor earthquakes occur on a regular basis. The threat of major earthquakes plays a large role in the city's infrastructure development. New buildings must meet high structural standards, and older buildings and bridges must be retrofitted to comply with new building codes.

San Francisco's shoreline has grown beyond its natural limits. Entire neighborhoods such as the Marina and Hunters Point, as well as large sections of the Embarcadero sit on areas of landfill.

Treasure Island was constructed from material dredged from the bay as well as material resulting from tunneling through Yerba Buena Island during the construction of the Bay Bridge. Such land tends to be unstable during earthquakes; the resultant liquefaction causes extensive damage to property built upon it, as was evidenced in the Marina district during the 1989 Loma Prieta Earthquake.