Groundwater in fractured igneous and metamorphic rocks commonly occurs in near surface fractures and weathered zones, and is characterized by low yield wells. Fracture hydraulic conductivity normally decreases with depth due to decreasing fracture apertures and increasing fracture spacing. A deep fracture groundwater system in the Cuyamaca - Julian area of San Diego County is evidenced by wells that have high yields and exhibit increasing fracture hydraulic conductivity with depth. These wells are located along a structural lineament that intersects the study area, and are completed in igneous and metamorphic rocks. The vertical distribution of hydraulic conductivity in a test well indicates that a low hydraulic conductivity intermediate zone exists above a deeper high hydraulic conductivity fracture system. The average hydraulic conductivity of the intermediate zone ranges from 1 x 10-5 cm/sec to 8 x 10-5 cm/sec. This range corresponds to low to mid ranges of fractured igneous and metamorphic rocks. The average hydraulic conductivity of the deep fracture system, which comprises portions of the lower 19 meters of the 122.5 meter test well, ranges from 3 x 10-2 to 5 x 10-1 cm/sec. This range corresponds to the highest values of fractured igneous and metamorphic rocks and values found in karstic limestone. Almost 100 percent of the well yield is attributable to the deep fracture system. There are three hydrogeologic zones in the study area; 1) near surface weathered zone, or residuum, 2) low hydraulic conductivity intermediate zone, and 3) the deep fracture system. A downward vertical gradient exists from the residuum to the intermediate zone, and finally to the deep fracture system. The lateral gradient in the deep fracture zone indicates that the direction of groundwater flow in this system is to the northeast, parallel to the structural lineament. A spring and several residential and business wells are points of discharge from the deep fracture system. The source of recharge is either groundwater in the residuum basins or surface water. The geochemistry of the groundwater in the deep fracture system associated with the lineament evolves from the intermediate zone to the deep fracture system. Similarly, in the deep fracture system the water chemistry evolves from the southwest to the northeast. This is based on overall chemistry of the water and best evidenced by a linear trend in the sulfate to chloride ratios increasing from the intermediate zone to the spring discharge at the eastern terminus of the lineament. Stable hydrogen and oxygen isotopes analyses of groundwater samples collected from the intermediate zone and two samples collected from the deep fracture system indicate that the waters are isotopically similar, with an apparent shift off the meteoric water line in the samples collected from the deep fracture system. Additionally there is evidence of localized oxidation of sulfide minerals based on sulfate enrichment in groundwater samples collected from mine discharge and several springs.