The Susquehanna River Basin Commission (SRBC) conducted a survey in the Morgan Run Watershed from November 2003 to September 2004 as part of the Year-2 small watershed study in the West Branch Susquehanna River Subbasin. The Year-1 survey was conducted in the West Branch Susquehanna Subbasin from July to November 2002 (LeFevre, 2003). Through this Year-1 survey, SRBC determined that the largest source of impairment in the West Branch Subbasin was abandoned mine drainage (AMD), and a large portion of the abandoned mine lands (AML) were concentrated in the western part of the subbasin. Based on these findings from the Year-1 survey and input from state and local government officials and watershed organizations, SRBC decided to conduct its Year-2 study in the Morgan Run Watershed, which is heavily impacted by AMD. The goal of this Year-2 study was to provide chemical, biological, and habitat information to the state and local government officials, watershed organizations, local citizens, and other interested parties. The ultimate goal is to have a Total Maximum Daily Load (TMDL) and restoration plan developed and implemented for the Morgan Run Watershed. The Year-2 survey included quarterly water chemistry samples and flow measurements, and spring and summer sampling and assessment of macroinvertebrates, fish, and habitat.