Human activities such as mining, logging, agriculture, and residential development have degraded biological conditions in many West Virginia (USA) streams. Using benthic macroinvertebrates as biological indicators of stream condition, the West Virginia Department of Environmental Protection (WVDEP) identified streams across the State that do not meet aquatic life use designations; these streams are considered to be biologically impaired. Total Maximum Daily Loads (TMDLs) are required for all streams classified as biologically impaired, and the TMDL process mandates that stressors to the biological community are identified so that pollutants resulting from human activities can be controlled within each watershed. We used the U.S. EPAs Stressor Identification (SI) guidance (U.S. EPA, 2000) to identify and rank the probable physical, chemical, and biological stressors that have impaired the aquatic community in the Clear Fork of Coal River, West Virginia. We developed a comprehensive conceptual model to establish the causal pathways for each stressor. The conceptual model illustrates linkages between candidate causes and their biological effects based on general ecological knowledge. Stressor-response (S-R) threshold values were based on statistical analyses of statewide data. We used these analyses and thresholds to infer whether the stressor occurred at a sufficient intensity to cause biological impairments in specific portions of the watershed. We plotted and analyzed quantitative data spatially using a geo-order format. Through this method, we were able to assign relative positions of sampling locations (from downstream to upstream), along each impaired stream and its tributaries, within a subwatershed. We included watershed characteristics such as land use and soils, point-source inventories, site observations, and other evidence in these analyses to help identify stressor sources.