Seasonally stratified shelf seas are amongst the most biologically productive on the planet. A consequence is that the deeper waters can become oxygen deficient in late summer. Predictions suggest global warming will accelerate this deficiency. Here we integrate turbulence timeseries with vertical profiles of water column properties from a seasonal stratified shelf sea to estimate oxygen and biogeochemical fluxes. The profiles reveal a significant subsurface chlorophyll maximum and associated mid-water oxygen maximum. We show that the oxygen maximum supports both upward and downwards O2 fluxes. The upward flux is into the surface mixed layer, whilst the downward flux into the deep water will partially off-set the seasonal O2 deficit. The results indicate the fluxes are sensitive to both the water column structure and mixing rates implying the development of the seasonal O2 deficit is mediated by diapcynal mixing. Analysis of current shear indicate that the downward flux is supported by tidal mixing, whilst the upwards flux is dominated by wind driven near-inertial shear. Summer storminess therefore plays an important role in the development of the seasonal deep water O2 deficit.