The hydrogeology of the Lac du Bonnet batholith at the Whiteshell Research Area (WRA) in southeastern Manitoba has been studied extensively. Although the general structure of the batholith is well known, its near-surface structure is less well known because of the overburden. Consequently, the precise locations of groundwater discharge from deep fractures into local surface water remain uncertain. Deep groundwater in the WRA is highly enriched with radiogenic He from the decay of natural U and Th ([He] is up to 50 mL∙L−1). Surface waters normally equilibrate with atmospheric He and contain a standard [He] of 47 nL∙L−1. We hypothesized that areas of deep groundwater discharge from the Lac du Bonnet batholith should be characterized by elevated aqueous He concentrations. We surveyed Boggy Creek and Boggy Lake at the WRA in the late winter of 1989 for such He anomalies. In Boggy Creek, three significant anomalies were identified, whereas in Boggy Lake several were found, the largest occupying the southeast quarter of the 80 ha lake. All the He anomalies were closely associated with the mapped or projected locations of faults in the underlying granite. A calculation of the total mass of excess He trapped under winter ice in Boggy Lake suggests that the total volume of deep groundwater seepage is small.