Oxygen depletion and sulphide formation, resulting from the accumulation of organic waste, are common challenges in shrimp ponds that could result in complete harvest failure. The stage at which these circumstances occur during the shrimp growth period remains elusive, yet, knowledge of the timing of oxygen depletion and sulphide formation is essential to enable remediating actions. Here, we used an experimental shrimp pond model at different stages in the shrimp growth period to determine when oxygen depletion and sulphide production occur. Microscale depth measurements of oxygen and H2S were determined using microelectrodes to visualize their profiles at different depths of the water-sediment interface and the sediment. We evaluated the potential of different molybdate concentrations at different stages to determine the optimal conditions to suppress H2S formation. Oxygen depletion and sulphide production took place in the middle of the shrimp growth cycle in the simulated model of waste accumulation. The addition of molybdate was only effective in the early stages of the onset of oxygen depletion and H2S formation, and residual molybdate was required to ensure a continuous suppression of sulphide production. However, oxygen depletion could not be prevented and reintroduction of oxygen did not occur when molybdate was added. In conclusion, molybdate appeared to be an effective strategy to suppress H2S formation at the onset of its production in a shrimp pond bottom model.