Port Jefferson was first settled in the 17th century and remained a rural community until its development as an active shipbuilding center in the mid-19th century. The village has since transitioned to a tourist-based economy. The port remains active as terminus of the Bridgeport & Port Jefferson Ferry, one of two commercial ferry lines between Long Island and Connecticut, and is supplemented by the terminus of the Long Island Rail Road's Port Jefferson Branch. It is also the center of the Greater Port Jefferson region of northwestern Brookhaven, serving as the cultural, commercial and transportation hub of the neighboring Port Jefferson Station, Belle Terre, Mount Sinai, Miller Place, Poquott, and the Setaukets.
The township is home to two renowned Research centers, Stony Brook University and Brookhaven National Laboratory. Combined these two research centers are approximately 50% of the Town's top ten employer's employee count. Tourism is also a part of the local economy. The largest traditional downtowns are located in Port Jefferson, a regional transportation hub, and Patchogue. The area has long been serviced by the Long Island Railroad and Bridgeport & Port Jefferson Ferry.
The peninsula on which the community of Belle Terre is situated has been known as Mt. Misery since the 17th century. Before Belle Terre's modern existence, the area was referred to as Mt. Misery Point. By comparison, the lower portion of the peninsula, which is currently a section of the neighboring village of Port Jefferson, was referred to as Mt. Misery Neck.
Throughout the 1700s and 1800s, the bulk of the peninsula was owned by the Strong family, who had their Oakwood estate in its Mt. Misery Neck section. The first known dwelling in contemporary Belle Terre was a shack constructed by an African-American affectionately known as Uncle Mott in the 1800s. This house was the subject of a painting by local artist William Moore Davis.