Cross-shelf distributions of temperature, salinity, water masses, and dissolved oxygen in St. Helena Bay revealed substantial vertical and seasonal variations. In the surface layers, nearshore and offshore temperature and salinity patterns differed, with bay-scale variability linked to upwelling dynamics and coastal processes, while the offshore region was influenced by solar insolation. Spectral analysis revealed that an annual signal prevailed at most stations, and corroborated contrasting patterns between the offshore and nearshore regions, with phase differences suggesting shoreward propagation of the offshore temperature signal. The shelf was dominated by Modified Upwelled Water (MUW) and Subantarctic Mode Water (SAMW), which comprised the primary source of upwelled water. Clear zonation of MUW was evident across the shelf, resulting from seasonal variations in locations of the oceanic and bifurcated shelf-break fronts. Dynamics within St. Helena Bay consistently differed from those further offshore, due to the influences of the shelf-break front, Cape Columbine upwelling plume, and cyclonic recirculation, which appeared to be associated with an intraannual signal with a periodicity of 3–4 months. Persistent hypoxia in the bottom waters suggested the occurrence of a permanent reservoir of Low Oxygen Water (LOW). Seasonal shoreward and offshore expansion of LOW occurred throughout the upwelling season, with maximum extent reached during summer and autumn, due to the coupled effects of advection and local phytoplankton decay. While wind mixing ventilated the water column at nearshore stations in winter, and the onset of upwelling during spring introduced oxygen-richer water from further offshore, hypoxia persisted in the center of the Bay.