Stony Brook was first settled in the late 17th century. It was originally known by the native name Wopowog and then as Stoney Brook, with both names likely referring to the interconnected bodies of water at the hamlet's western edge. It began as a satellite community of adjacent Setauket, New York, the Town of Brookhaven's first settlement, and its land was included in the initial 1655 purchase from the native Setalcott tribe.