The objective of this thesis is to constrain the fundamental hydrogeological processes of a large crystalline fractured rock watershed in the Canadian Shield. The fundamental hydrogeological processes of groundwater recharge, flow and discharge are examined individually as well as holistically using a revised conceptual model. The study area is the topographically-subdued Tay River watershed in eastern Ontario where a thin veneer of soil overlies Precambrian crystalline rocks and Paleozoic sediments. Spatial scales from local-scale (100s m² to 1 km²) to watershed-scale (>100 km²) are examined. Recharge processes are defined using hydrogeological characterization, numerical simulation and isotopic, thermal and hydraulic responses to a snowmelt event. Soil thickness and bedrock transmissivity are highly heterogeneous at the local scale. Cold, 2H depleted snowmelt locally recharged the bedrock aquifer to depths of at least 20 m within two days. This rapid recharge process is localized to areas where the soil is very thin whereas slow recharge is likely widespread. The impact of lineaments on groundwater flow at the watershed-scale is examined using geomatic analysis, hydrogeological characterization, numerical simulation and fracture mapping. Lineaments are interpreted as structural features because the two principal lineament sets are oriented parallel to fracture and fault orientations. The fractured bedrock underlying lineaments generally consists of poorly connected zones of reduced permeability suggesting lineament can be barriers to recharge and flow in this setting. Natural conservative, radioactive, and thermal tracers are integrated with streamflow measurements and a steady-state advective model to delimit the discharge locations and quantify the discharge flux to lakes, wetlands, creeks and the Tay River. The groundwater discharge rate to most surface water bodies is low. Groundwater discharge is distributed across the watershed rather than localized around lineaments or zones of exposed brittle fractures. In the revised conceptual model, recharge is considered two separate processes, groundwater flow is compartmentalized and the discharge flux is considerably lower than porous media watersheds. This thesis provides a better understanding of fundamental hydrogeological processes in a large crystalline fractured rock watershed which impacts the sustainability of water resources and ecology.