Groundwater recharge and discharge were studied in a gneissic terrain with minimal glacial overburden at a well-instrumented field site adjacent to a 1.2km section of the Tay River, near Perth, Ontario, Canada. Seven 31–56m-deep monitoring wells were constructed, characterized, and sampled for ¹⁸O and ²H. Each well was first hydraulically tested using a 1.77m straddle packer system and then instrumented with multi-level piezometers. Detailed fracture mapping and electrical conductivity surveys were conducted in a 1.2km section of the river to identify potential groundwater discharge points. Groundwater, surface water and precipitation (rain and snow) samples were collected to measure δ²H and δ¹⁸O during and following several storm events, and during baseflow conditions. Results showed that groundwater flow in the upper 30–40m of bedrock is dominated by a few horizontal fractures which are weakly connected by sparsely-arranged vertical fractures. Values of δ²H and δ¹⁸O indicate that precipitation does not directly influence the isotopic signature of river water and deep groundwater during a rain event. Recharge is localized and rapid where overburden is thin, however, it does not penetrate deeply into the flow system at this site. There is no hydraulic or isotopic evidence that groundwater discharges into the river over the study section, thus most of the groundwater underflows the river at this location. Flow in this reach, and likely in the bulk of the river, is controlled by an upstream dam and by surface water runoff. The results of this study suggest that the use of traditional methods for water budgeting based on equivalent porous media are highly inappropriate for this crystalline bedrock setting.