The majority of the 50 square mile Upper Yellow Creek watershed is located in Bedford County. However, a small portion of the watershed’s headwaters are found in North Woodbury Township and Taylor Township. In the Blair County part of the watershed, agriculture is the dominant land use. Several of the watershed’s tributaries, in both Blair and Bedford counties, are listed as impaired due to excess nutrient and sediment runoff from agriculture.
Yellow Creek itself flows southwest until it joins with the Raystown Branch of the Juniata River. The creek is listed as a High Quality Cold Water Fishery, which draws fishermen to the area.