Boston was founded by wayward Puritans, who - for whatever resons - sought to get away from Plymouth. The Reverend William Blackstone was the first to settle there, building a house on what is now Beacon Hill - one of three hills that made up the Boston area - in 1624. Blackstone is also considered to be the first Christian to settle in Rhode Island. Keep in mind that this was a much thinner piece of land, as much of modern Boston lies on recently-placed landfill. Puritan settlers of the Massacusetts Bay Colony, who were on the less receptive Mishawum(Charlestown) Peninsula, eventually crossed the river and joined Blackstone's growing settlement. This was the basis of Modern Boston.
Beacon Hill was originally three hills(thus the word Tremont), two of which were leveled for real estate purposes by industrious men. One was used to fill in "the Back Bay," and the other was leveled to fill in what is now known as Charles Street at the foot of Beacon Hill, preventing the Crarles River from further encroachment. More importantly, the fill was also used to level the "West End" area and provide a stable footing for the North Station - where textiles from the City of Lowell could finally reach Boston by train. Mr. Lowell bbbuilt his first textile mill on the Charles River in the city of Waltham, but soon found more water power was needed. Investors bought a vast amount of land at the confluence of the Merrimack and Nashua Rivers, designed and built their city of canals, mills, bridges and the City was named after Lowell shortly after his passing. The Middlesex Canal had been dug from Boston to Lowell before the advent of trains, with horses pulling barges. Extremely inefficient and costly, this was used for perhaps a decade before the demolition of Trimount - leaving only Beacon Hill.