The Table Mountain Group is a folded, faulted, quartzite-dominated sedimentary sequence, metamorphosed to lower greenschist facies, that forms steep mountains dominating the topography of the Western Cape and causing orographic rainfall in an otherwise semi-arid region. These quartzites are highly fractured to depths of kilometres and act as a complex aquifer system that supplies groundwater directly and indirectly, through baseflow, essential for sustaining the natural environment and human activity in the region. Hydrogen and oxygen isotope data for rain, rivers and groundwater (boreholes and springs) in the region give typical altitude effects of −1.8‰ δD/100 m and -0.33‰ δ18O/100 m, and a very strong continental effect of -30‰ δD/100 km and -4.7‰ δ18O/100 km. This allows for application of stable isotopes as natural hydrological tracers. Groundwater at several locations had stable isotope compositions different from ambient rainfall, but similar to rainfall at high altitudes in adjacent mountains, indicating recharge at high altitude. The groundwater flow is through the Skurweberg Aquifer, here defined as all three formations of the Nardouw Subgroup. Observations on the Peninsula Aquifer suggest a very well mixed aquifer, due to extensive fracturing. Potential exists to delineate groundwater protection zones, detect overabstraction and understand aquifer connectivity better by applying stable isotope hydrology to the Table Mountain Group.