The Broad Top coal field in Bedford, Fulton and Huntingdon counties contains the only significant section of coal-bearing rocks in the Juniata River basin. Commercial development of coal there ran from the mid-1800's to about 1918. Much of the land in this area has been disturbed and local groundwater in some places has been seriously degraded by acid mine drainage. The Juniata's mainstem appears unaffected by acid mine drainage. The types of pollution which affect the Juniata River, fortunately, tend to be local in nature and have not yet overcome the ability of the system to handle them.
River pollution is a reflection of the ways in which the surrounding land is used.
Industrial and municipal waste disposal, and farming and yard care practices along Juniata tributaries will shape the Juniata's future. Since the late l980's, many counties in the Juniata basin have become participants in the Pennsylvania Chesapeake Bay Program, which enables farmers to receive financial help to implement water quality protection measures through their local conservation districts. Farmers in selected watersheds of the Juniata basin are currently eligible. The Juniata River may face impacts from beyond its basin, as well. A plan under review would release water from the Raystown Dam flood-control impoundment on the Raystown Branch Juniata to help maintain fresh water flowing into the Chesapeake Bay.