Clover Creek is a 50 square mile watershed located in the southeastern part of Blair County. The watershed borders the Huntingdon County line to the east and crosses into Bedford County to the south. It covers parts of three Blair County municipalities, encompassing 45% of Woodbury Township, 50% of Huston Township, and 60% of North Woodbury Township. Parts of State Game Lands 73 and 118 are located in the watershed. Land use is split almost evenly between agriculture and forested lands, with urban/suburban development accounting for a small percentage of the watershed.
Clover Creek, the tributary that gives the watershed its name, is 24.5 miles long and a popular trout fishing destination. It is also used to irrigate nearby farms. The creek originates on Tussey Mountain in Bedford County, then flows north through the watershed until it joins the Frankstown Branch of the Juniata River.