The earliest European settlers were Robert Barker and Dolor Davis, who settled in the vicinity of Herring Brook in 1650. Up until that time, the Wampanoag and the Massachusett were the only residents, fishing and farming along the rivers; they called the area Mattakeesett, which means "place of much fish", because of the annual springtime run of herring in the local rivers. The land was part of the Major's Purchase, a large tract of lands bought from Josias Wampatuck of the Massachusetts by a group of English investors. The area was once a part of Duxbury, before incorporating as a separate town in 1712, and was ultimately named for the town of Pembroke, Wales, the name of Brookfield being rejected because it was already in use by the town in Worcester County that still bears this name.

Most notable of the town's resources are its water resources, which include the North River and Indian Head River; its ponds, Oldham, Furnace, Great Sandy Bottom, Little Sandy Bottom, and Stetson Ponds; and Silver Lake. The town's ponds, streams and marshes are the home of herring that were prized so much that in 1741, the town began regulating the taking and preservation of the fish. The herring are celebrated each year at the town's annual "Grande Old Fish Fry".

The Pembroke Iron Works was established in 1720 and used iron dredged from the bottom of the ponds. Ice was cut from the ponds, stored in icehouses, and used in the summer months for food preservation. The ponds and streams also provided power for various mills, including grist, flour and sawmills. Later, shipbuilding and box manufacturing became important factors in the development of the town.

The town has large tracts of woodlands that provided timber for homes and industry, and provided cover for abundant wildlife. Because of its proximity to timber and location on the river, the town in its early years was known for its shipbuilding industry. The North River was the location of five shipyards – Brick Kiln Yard, Seabury Point, Job's Landing, Turner's Yard and Macy's. Between 1678 and 1871, 1,025 vessels were produced on the shores of the North River.

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