Much of the Back Bay and South End neighborhoods are built on reclaimed land-all of the earth from two of Boston's three original hills, the "trimount", was used as landfill material. Only Beacon Hill, the smallest of the three original hills, remains partially intact; just half of its height was cut down for landfill. The downtown area and immediate surroundings consist mostly of low-rise brick or stone buildings, with many older buildings in the Federal style. Several of these buildings mix in with modern high-rises, notably in the Financial District, Government Center, the South Boston waterfront, and Back Bay, which includes many prominent landmarks such as the Boston Public Library, Christian Science Center, Copley Square, Newbury Street, and New England's two tallest buildings: the John Hancock Tower and the Prudential Center. Near the John Hancock Tower is the old John Hancock Building with its prominent weather forecast beacon-whatever light illuminates gives an indication of weather to come: "steady blue. clear view; flashing blue, clouds are due; steady red, rain ahead; flashing red, snow instead." (In the summer, flashing red indicates instead that a Red Sox game has been rained out.) Smaller commercial areas are interspersed among single-family homes and wooden/brick multi-family row houses. Currently, the South End Historic District remains the largest surviving contiguous Victorian-era neighborhood in the U.S.

Along with downtown, the geography of South Boston was particularly impacted by the Central Artery/Tunnel (CA/T) Project (or the "Big Dig"). The unstable reclaimed land in South Boston posed special problems for the project's tunnels. In the downtown area, the CA/T Project allowed for the removal of the unsightly elevated Central Artery and the incorporation of new green spaces and open areas.

Boston Common, located near the Financial District and Beacon Hill, is the oldest public park in the U.S. Along with the adjacent Boston Public Garden, it is part of the Emerald Necklace, a string of parks designed by Frederick Law Olmsted to encircle the city. Franklin Park, which is also part of the Emerald Necklace, is the city's largest park and houses a zoo. Another major park is the Esplanade located along the banks of the Charles River. Other parks are scattered throughout the city, with the major parks and beaches located near Castle Island, in Charlestown and along the Dorchester, South Boston, and East Boston shorelines.

The Charles River separates Boston proper from Cambridge, Watertown, and the neighborhood of Charlestown. To the east lies Boston Harbor and the Boston Harbor Islands National Recreation Area. The Neponset River forms the boundary between Boston's southern neighborhoods and the city of Quincy and the town of Milton. The Mystic River separates Charlestown from Chelsea and Everett, while Chelsea Creek and Boston Harbor separate East Boston from Boston proper.