The Massachusett people called the peninsula where Boston was established Shawmut, "place of clear waters." For generations they spent their summers in Quonehassit, as they called the harbor, fishing and farming on the islands. But between 1617 and 1619, European fishermen brought diseases that decimated the native population. When the English colonists began arriving in the 1620s and 1630s, few Native people remained on the peninsula or on the North Shore of Massachusetts Bay.

A group of English Puritans led by John Winthrop landed in Salem in June of 1630. They quickly moved on to what is now Charlestown, but the scarcity of fresh water and an abundance of mosquitoes there prompted them to keep looking for a more desirable site. They found one across a channel to the south, on the Shawmut peninsula. The Reverend William Blackstone was the only Englishman living there, and he invited Winthrop and approximately 175 of his followers to join him.

On September 17, 1630, they agreed to name the 780-acre peninsula "Boston," after the town in the southwest of England from which many of them came. The main geographic feature of the area was the Trimountain, a high ridge extending through the center of the peninsula. (Beacon Hill has been called "the sole, and greatly mutilated, remnant.") The town was built on the treeless plain between the harbor and the wooded Trimountain.

In 1634 the town bought 45 acres of the Common to use "for a trayning field . . . & the feeding of Cattell," making it the oldest public open space in the nation. Merchants established a marketplace, where the Old State House would later be built, and the first tavern opened.

The settlement was linked to the mainland by Boston Neck, a strip of land only 40 yards wide. At high tide, the Neck flooded, cutting the village off completely. One of the first things the colonists did was to set up ferries, running to both Chelsea and Charlestown. Then they established a legislative body, the General Court, as the Massachusetts legislature is still called today, noting that Boston was "the fittest place for publique meetings of any place in the Bay [colony]." Bostonians built a meetinghouse and a jail and opened the Latin School, the first public school in British North America. The bustling town quickly became the political, economic, and religious center of the Massachusetts Bay Colony.

During the first century after settlement, Boston prospered, but the population grew slowly, reaching only 16,382 by 1743. The next 50 years would see a modest increase with 18,320 inhabitants listed in the 1790 census. Even within the confines of the peninsula, there was still plenty of room.

A thriving seaport, with 40 wharves, more than a dozen shipyards, and six ropewalks, Boston was the largest town in all of British North America until the mid 1700s, when it fell behind the faster growing ports of New York and Philadelphia.

The change from a relatively homogeneous, self-contained maritime community began with the completion of the first Charles River Bridge in 1786. Over the next quarter century, three other bridges were built, and Boston quickly lost its insular character. The population more than tripled between 1790 and 1825. Tracts of vacant land were fast disappearing. As historian Walter Muir Whitehill explains, the hills of the Boston peninsula "all but vanished, and so [did] much of the water. Long before the invention of bulldozers and steam shovels, Bostonians had begun to modify their landscape in the attempt to accommodate an expanding population on the limited site that had been chosen for a wilderness village."

A city of 58,277 in 1825, by 1840 Boston had over 93,000 inhabitants. In the next decade, the population grew to almost 137,000, largely as a result of the influx of Irish immigrants. The number of Irish in Boston went from 35,000 in 1850 to 50,000 five years later – twice the entire population of Boston in 1800.

Where would all these people go? Many crammed into the increasingly crowded North End. Others moved to the South End, where fields, gardens, and large houses were giving way to streets and sewer lines. Originally intended as a middle-class neighborhood, the South End soon became almost as squalid as the North End. 

The population continued to grow; between 1868 and 1874, Boston annexed Roxbury, Dorchester, Charlestown, Brighton, and West Roxbury. The city was undergoing a dramatic physical transformation due to creation of "made land" in what became known as the Back Bay. Soon one would have to look at old maps to see traces of the early town that planted itself on the narrow Shawmut peninsula. By 1895 the Public Garden, Copley Square, Newbury Street, and Kenmore Square, all built on fill, would be part of a new Boston — the city as we know it today.