The microbial decomposition of nitrogen-rich organic matter in aquaculture ponds is affected by the oxic-anoxic conditions gradient at the soil-water interface as well as by resuspension practices. To investigate these interactions, the decomposition of a 49% protein fish feed was analyzed in 10 marine lab-scale systems with different exposures to aerobic and anaerobic conditions. The degree of coupling between oxic and anoxic conditions in the system had a strong effect on product accumulation and loss from the culture system. Pure oxic or anoxic conditions proved to be less favorable than mixed aerobic-anaerobic systems with respect to the metabolites accumulated in the system. Short 15-min resuspension events and a continuous alternation of oxic and anoxic conditions at 12-h time intervals proved to be the best options to minimize the accumulation of organic matter in the systems. The correct coupling of aerobic-anaerobic conditions in space and time is a key to maintain a good water quality condition for the cultured animals and also to improve the decomposition and recycling of organic matter, reducing the environmental impact from the effluents.