Abstract. The considerable impact of oxygen deficient waters on marine resources in St Helena Bay has generated interest in exploring the vulnerability of South Africa's largest and most productive bay to further deoxygenation in response to climate change. Seasonal, sub-seasonal and spatial fluctuations in bottom dissolved oxygen (DO) are examined in St Helena Bay to facilitate better interpretation of historical data. DO measurements in relation to physical, chemical and biological variables were made between November 2013 and November 2014. Alongshore bay characteristics were assessed through comparison of variables along the 50 m depth contour. A mean coefficient of variation of 0.35 provided a measure of the relative variability of near-bottom DO concentrations along this contour. Across-shelf transects captured the seasonal development of hypoxia in relation to the distribution of phytoplankton biomass. DO was lowest in autumn in the south of the bay prior to winter ventilation of the bottom waters. Exceptional dinoflagellate blooms forming extensive subsurface thin layers preceded the autumn DO minima. The development of hypoxia at inner and central stations prior to expansion beyond the boundaries of the bay provided evidence of local drawdown. Coincident with the seasonal decline of DO within the bay was an increase in macronutrient concentrations which tended to mirror DO concentrations. Indication of denitrification in the suboxic waters in the south of the bay was provided through evidence of a nitrate deficit in autumn supported by elevated nitrite concentrations. Superimposed on the seasonal decline of DO concentrations in the bottom waters were sub-seasonal events of hypoxia and anoxia linked to episodic deposition of organic matter as indicated by increases in bottom Chl a concentrations.