Boston is much larger than it once was. For roughly 100 years, between the early 1800s and early 1900s, the city was expanded either through land-filling projects, what some people call land making, or direct annexation of neighboring towns. Charlestown and Dorchester were once independent municipalities, both slightly older than Boston itself.
Charlestown was annexed by Boston in 1874 and Dorchester a few years earlier. The original town of Dorchester, founded in 1630, included South Boston, Hyde Park, and Mattapan. Roxbury, which once included West Roxbury, Jamaica Plain, and Roslindale, was absorbed by Boston in 1868. Brighton, with the neighborhood of Allston, was also added to Boston in the same manner.
Kenmore Square and the Fenway area were under the control of Brookline until the 1870s. During that time Brookline resisted annexation to Boston, but they did give up Kenmore Square as well as parts of Commonwealth Avenue, the latter so that Brighton would be physically connected to the rest of Boston after its annexation in 1874. Interestingly, Brookline was not a distinct municipality from Boston until 1705, so Kenmore was part of Boston in the 1600s.
The current South End, Chinatown, Bay Village, and Back Bay neighborhoods of Boston, as well as large areas of the waterfront including South Bay, Columbia Point, the Bulfinch Triangle, and the new Seaport District, are built entirely on marsh and mud flats once covered by relatively shallow water. This includes the Boston Public Garden, the part of Beacon Hill west of Charles Street, and even the land under UMass Boston and the John F. Kennedy Presidential Library and Museum.
After peeling away all of these places, each with their own long and interesting histories, what is left is the original English town of Boston, built on a peninsula that local Native Americans called Shawmut. Officially founded in September of 1630, that smaller town of Boston included a largely uninhabited West End, which was more or less at the rear of the town, including Beacon Hill and Boston Common. There was also a South End that is now the Financial District and Downtown Crossing shopping area. Finally there was the North End, which continues today as a vibrant residential and commercial part of modern Boston.