The prolonged drought between 1999 and 2002 drew attention in Clarke County, Virginia, to the quantity and sustainability of its groundwater resources. The groundwater flow systems of the county are complex and are controlled by the extremely folded and faulted geology that underlies the county. A study was conducted between October 2002 and October 2008 by the U.S. Geological Survey, in cooperation with Clarke County, Virginia, to describe the hydrogeology and groundwater availability in the county and to establish a long-term water monitoring network. The study area encompasses approximately 177 square miles and includes the carbonate and siliciclastic rocks of the Great Valley section of the Valley and Ridge Physiographic Province and the metamorphic rocks of the Blue Ridge Physiographic Province (Blue Ridge). High-yielding wells generally tend to cluster along faults, within lineament zones, and in areas of tight folding throughout the county. Water-bearing zones are generally within 250 feet (ft) of land surface; however, median depths are slightly deeper for the hydrogeologic units of the Blue Ridge than for those of the Great Valley section of the county. Total water-level fluctuations between October 2002 and October 2008 ranged from 2.86 to 87.84 ft across the study area, with an average of 24.15 ft. Generally, water-level fluctuations were greatest near hydrologic divides, in isolated elevated areas, and in the Opequon Creek Basin. Seasonally, water-level highs occur in the early spring at the end of the major groundwater recharge period and lows occur in late autumn when evapotranspiration rates begin to decrease. An overall downward trend in water levels between 2003 and 2008, which closely follows a downward trend in annual precipitation over the same period, was observed in a majority of wells in the Great Valley and in some of the wells in the Blue Ridge. Water-level fluctuations in the Blue Ridge tend to follow current meteorological conditions, and seasonal highs and lows tend to shift in response to the current conditions. Springs generally are present along faults and fold axes, and discharges for the study period ranged from dry to 10 cubic feet per second. A similar downward trend in discharges correlates with the trend in water levels and is indicative of an aquifer system that, over time, drains to a base level controlled by springs and streams. Point discharge from springs can occur as the start of flows of streams and creeks, along banks, and as discrete discharge through streambeds in the Great Valley. For the most part, streams, creeks, and rivers in the Great Valley function as aqueducts. Springs in the Blue Ridge have relatively low discharge rates, have small drainage areas, and are susceptible to current meteorological conditions. Estimates of effective groundwater recharge from 2001 to 2007 ranged from 6.4 to 23.0 inches per year (in/yr) in the Dry Marsh Run and Spout Run Basins with averages of 11.6 and 11.9 in/yr, respectively. Base flow accounted for between 80 and 97 percent of mean streamflow and averaged about 90 percent in these basins. The high base-flow index values (percent of streamflow from base flow) in the Dry Marsh Run and Spout Run Basins indicate that groundwater is the dominant source of streamflow during both wet and drought conditions. Between 46 and 82 percent of the precipitation that fell on the Dry Marsh Run and Spout Run Basins from 2001 to 2007 was removed by evapotranspiration, and an average of approximately 30 percent of the precipitation reached the water table as effective recharge. The high permeability of the rocks and low relief in these basins are not conducive for runoff; therefore, on average, only about 3 to 4 percent of the precipitation becomes runoff. Groundwater flow systems in the county are extremely vulnerable to current climatic conditions. Successive years of below-average effective recharge cause declines in water levels, spring discha