Groundwater studies in the South Fork Palouse River Basin have been unable to determine recharge sources, subsystem connectivity and flow patterns due to the discontinuity of pathways in the heterogeneous and anisotropic aquifers located in Columbia River flood basalts and interbedded sediments. Major ion, delta O-18, delta H-2, delta C-13, delta S-34 and temperature for groundwater collected from 28 wells of varying depths indicate a primary recharge source dominated by snowmelt along the eastern basin margin. This recharge can be separated into two distinct sources-a deeper and relatively less altered snowmelt signal (-17.3 parts per thousand to - 16.8 parts per thousand delta O-18, -131 parts per thousand to - 127 parts per thousand delta H-2, -12.9 parts per thousand to -10 parts per thousand delta C-13,18-23 degrees C) and a more altered signal likely derived from a shallower mixture of snowmelt, precipitation and surface water (-16.1 parts per thousand to -15.5 parts per thousand delta O-18, -121 parts per thousand to -117 parts per thousand delta H-2, -15.9 parts per thousand to -12.9 parts per thousand delta C-13, 12-19 degrees C). A mixing of the shallow and deep source waters is observed within the upper aquifer of the Grande Ronde Formation near Moscow, Idaho, which results in a homogenization of isotope ratios and geochemistry for groundwater at nearly any depth to the west of this mixing zone. This homogenized signal is prevalent in a likely primary productive zone of an intermediate depth in the overall aquifer system.