The hydrogeochemistry of the Lac du Bonnet granitic batholith has been determined for the region of the Whiteshell Research Area (WRA) in southeastern Manitoba, Canada. This work forms part of the geosciences studies performed for the Canadian Nuclear Fuel Waste Management Program over the period 1980–1995 by Atomic Energy of Canada Limited (AECL). Knowledge of the variation of groundwater chemistry and its causes is useful in assessing the performance and safety of a nuclear fuel waste vault located at depths of up to 1000 m in a crystalline rock formation of the Canadian Shield. Groundwaters and matrix pore fluids have been obtained by standard sampling methods from shallow piezometers in clay-rich overburden, from packer-isolated borehole zones intersecting fractures or fault zones in the bedrock, and from boreholes in unfractured rock in AECL's Underground Research Laboratory (URL). Eighty-six individual fracture groundwaters have been sampled and analysed from permeable zones in 53 boreholes drilled to depths of up to 1000 m in the Lac du Bonnet batholith. In addition, 28 groundwaters from piezometers in a large wetland area near the URL have been sampled and analysed to determine the influence of clay-rich overburden on the bedrock hydrogeochemistry. Analyses have been made for major and minor ions, pH, Eh, trace metals, and stable and radioactive isotopes, to characterise these groundwaters and relate them to their hydrogeologic regimes. Shallow groundwaters in the fractured bedrock are generally dilute (TDS <0.3 g/l), Ca–Na–HCO 3 waters and show little indication of mixing with Ca–Mg–HCO 3–SO 4 groundwater from overburden sediments. The near-modern levels of 3H and 14C, and a warm-climate 2H/ 18O signature in these groundwaters, indicates that the upper ∼200 m of fractured bedrock contains an active groundwater circulation system with a residence time of tens to hundreds of years. Deeper fracture groundwaters (200–400 m depth) in recharge areas, are more alkaline, Na–Ca–HCO 3 waters and evolve to Na–Ca–HCO 3–Cl–SO 4 waters with increasing distance along the flow path. Isotopic data indicate the presence of a glacial melt-water component suggesting that the residence times of these waters are 10 3–10 5 a. These waters form a transition zone between the upper, advective flow regime and a deeper regime in sparsely fractured rock where groundwater in fractures and fracture zones is largely stagnant. At these depths (> 500 m), Na–Ca–Cl–SO 4 waters of increasing salinity (up to 50 g/l) with depth are found and in some fractures the waters have evolved to a Ca–Na–Cl composition. Isotopic data indicate that these waters are warm-climate and pre-glacial in origin, with residence times of over 1 Ma. Pore fluids observed to drain from the unfractured rock matrix in the URL facility are almost pure Ca–Cl in composition, ∼90 g/l salinity, and have a 2H/ 18O composition displaced well to the left of the global meteoric water line, about which all other WRA groundwaters lie. This information indicates that these pore fluids have undergone prolonged water-rock interaction and have residence times of 10 1–10 3 Ma. Most of the deeper fracture groundwaters and pore fluids have low Br/Cl ratios and moderate to high δ 34S values of dissolved SO 4 which indicates that their salinity could be derived from a marine source such as the basinal sedimentary brines and evaporites to the west of the batholith. These fluids may have entered the batholith during early Paleozoic times when sedimentary rocks were deposited over the granite and were driven by a hydraulic gradient resulting from higher ground in western Canada. The hydrogeochemical data and interpretations show that below ∼500 m in the WRA, fracture-hosted groundwaters are very saline, reducing and old, and are, therefore, indicative of stagnant conditions over the period of concern for nuclear waste disposal (1 Ma). The intact rock matrix at these depths is extremely impermeable as indicated by the presence of pore fluids with unusual geochemical and isotopic characteristics. The pore fluids may represent basinal brines that have evolved geochemically and isotopically to their current composition over periods as long as 10 3 Ma.