Saybrook Colony formally joined Connecticut in 1644. The portion of the original colony east of the Connecticut River was set off as a separate town in 1665. The site of the present village of Deep River was said to have been owned by John, Nathaniel, and Philip Kirtland in 1723. The village of Winthrop was said to have been settled by Baptists as early as 1729. In the early to mid-19th century, various portions of Saybrook broke off as separate towns, starting from Chester in 1836 to Old Saybrook in 1854. In 1947, the town of Saybrook changed its name to "Deep River", matching the name of the town center village.