The Susquehanna River Basin Commission (SRBC) conducted a survey of the Juniata Subbasin from June to November 2004. This survey was part of SRBCs Subbasin Survey Program, which is funded in part through the United States Environmental Protection Agency (USEPA). This program consists of two-year assessments in each of the six major subbasins on a rotating schedule. Included in this report are details of the Year-1 survey, which entailed point-in-time samples of the water quality, macroinvertebrate community, and habitat in the major tributaries and areas of interest throughout the Juniata River Subbasin. The Year-2 survey will be a more intensive study in the Morrison Cove area, which has been identified as a highly agricultural and potentially stressed groundwater area. Previous surveys of the Juniata Subbasin were conducted in 1985 and 1995. A comparison of the 1995 data and the present results are included in this report.