Much of the trail was the original towpath for the Pennsylvania Canal that operated in the early 1800s and was known as the "continuous waterways" which linked Pittsburgh and Philadelphia.
By the 1850s, area canals became obsolete due to the rise of the Pennsylvania Railroad and its passage through the Allegheny Mountains via the Horseshoe Curve.
Much of the Lower Trail, paralleling the Frankstown Branch of the Juniata River, was part of the original towpath of the Pennsylvania Main Line Canal which operated in the mid-1800s.
Following the end of the canal era, the Pennsylvania Railroad took over the property and developed the Petersburg Branch of the PRR on this alignment.
The trail extension, from Williamsburg to Canoe Creek, was purchased by an anonymous donation for the land in 1994.
The project was made possible with a large grant from the Pennsylvania Department of Transportation, County of Blair and Frankstown Township Supervisors.