A study was conducted to examine the variation in fish farm sediment quality with varying organic carbon input in the form of feed. In order to elucidate the seasonal variation in farm sediment quality, relation between seasonal organic carbon input, temperature and sediment quality was studied. The sediment ignition loss, redox potential and acid volatile sulfide sulfur (AVS‐S) content showed a correlation with annual organic carbon input. The seasonal AVS‐S content showed a significant correlation with the seasonal organic carbon input as well as temperature. Multiple regression analysis revealed that both of these factors explicated 80% of the seasonal variation in AVS‐S content. Although redox conditions of the sediment could also be correlated with both the organic carbon input and temperature, the latter seemed to have a greater control. Thus, the farm sediment quality could be directly related to the annual organic carbon input to the fish farm under similar hydrographic conditions. Acid volatile sulfide sulfur content exhibited a significant correlation with both the annual as well as the seasonal organic carbon input. Therefore, AVS‐S content proved to be a fairly simple and better indicator for monitoring the fish farm environment for effective farm management and sustainable aquaculture. Importance of size of pellets as a factor affecting the feed input‐sediment quality relation is also demonstrated in the present study.