High frequency measurements at the seabed in a shallow semi-enclosed embayment of the Indian Ocean reveal deoxygenation of the bottom water at a rate of 40 mmol O2 m−3 d−1 when seasonal density stratification occurs. The vertical profile of dissolved oxygen below the pycnocline shows concentration decreasing at a constant rate toward the seabed suggesting a benthic sink and an associated downward flux of ∼30 mmol O2 m−2 d−1. This is closely coupled to an increase in CO2 indicative of microbial respiration. The results and nutrient history of the area suggest that the accumulation of organic material in the marine sediments have led to high sediment oxygen demand making the area extremely sensitive to reduced ventilation from the surface caused by low rates of vertical mixing. The data also shows that the existing weekly water-quality monitoring often misses the most severe events. Global warming is expected to worsen the problem with longer and more frequent stratification periods, reduced oxygen solubility and enhanced rates of microbial respiration.