Limestone Township was established on December 4, 1824, by the Court of Quarter Sessions of the Peace of Lycoming County.

[4] Upon arriving in present-day Limestone Township in 1789, the first settlers deemed it barren because the base of valley was covered by thickets of thorny bushes and was largely free of trees.

After the initial settlers cleared the shrubbery and planted wheat, the land was found to be quite fertile, and prices rose to $5.00 per acre.

[4] Much of the farmland in the southeastern portion of Limestone Township was purchased by the Williamsport Water Authority in the early 1900s as part of its watershed.

Visitors to the "water company" lands can see the stone remains of the early settlers homesteads spread throughout the watershed.

With the construction of this plant, the lands of the water authority were opened to the general public as a nature preserve, with limited hunting permitted at certain times of the year.

The community of Rauchtown, mostly in neighboring Clinton County, extends into the westernmost part of Limestone Township.

According to a research paper from the University of Akron, the center has been eroded, exposing carbonate rocks in the valley.

There is an average total of about 470 m (1,540 ft) of Lower to Middle Ordovician limestone and dolomite underlying the valley.

[7] Within a number of caves in this valley a new species of fish, a type of troglomorphic sculpin, was identified in 2003 by Luis Espinasa, an associate professor of biology at Marist College.