Lewisboro's story begins in 1731, when the eastern section of town, encompassing what is now South Salem, Lewisboro hamlet, and Vista, was settled as part of a long-disputed border territory between New York and Connecticut known as the Oblong. The western section, including today's Cross River and Goldens Bridge, developed separately as part of the 1697 Cortlandt Manor land grant.

The town's hamlets grew at different paces and for different reasons. Waccabuc was settled by the Mead family in the 1770s. Cross River grew around its own mills and, later, a stagecoach line running between New York City and Danbury. South Salem, renamed several times over the decades, from Salem to Lower Salem to South Salem, served for years as the area's commercial and civic center.

In 1840, a New York City businessman named John Lewis offered the town $10,000 to improve its schools in exchange for renaming it in his honor, and the Town of Lewisboro was born. The arrival of the railroad in the 1840s and 1850s reshaped the town's hamlets yet again, bringing new growth to Goldens Bridge and Cross River, while the New York City water supply's expanding reservoirs permanently altered the landscape around them.