This four-year instream flow study was initiated to evaluate the hydraulics, habitat, and water quality of the North Fork Shenandoah River, Virginia, during low flow conditions. Virginia Tech in cooperation with the United States Geological Survey (USGS) collected hydraulic, fish habitat, and water quality data throughout the basin during periods of extreme drought in 1999 and 2002. This report summarizes the cumulative results, hydraulic, fish habitat, and water quality conditions in the North Fork Shenandoah River (NFSR). These results were used to establish a stepwise process for implementing aquatic conservation flow management in the NFSR basin and facilitate water use conservation measures at appropriate times during extreme droughts of the future. We applied the Instream Flow Incremental Methodology to provide a comparison of usable habitat conditions under baseline and alternative hydrologic time series corresponding to water use restrictions. Six study sites (with a total of 36 transects) were selected to characterize the mesohabitats (riffle, run, pool, and pocket run) of the entire river. Aquatic conservation thresholds were developed for three river reaches and were directly related to three long-term gauging stations: Cootes Store (mile 92 in Rockingham County), Mount Jackson (mile 70 in Shenandoah County), and Strasburg (mile 10 in Warren County).