Cage culture in estuaries and backwater systems is augmented as an additional source of income among the coastal population. However, the growing popularity of cage culture has resulted in its expansion to a greater level. Hence the present study was carried out to identify the impacts associated with cage culture on the water quality, sediment characteristics, macrobenthic abundance, and the community structure of the fishing island Pizhala on the southwest coast of India on a seasonal scale. The sample was taken from six stations near the cage (<1m) and two reference stations (200-300 m away). The study revealed significant variation in the water quality between the seasons. The DO concentration during pre-monsoon (PRM) had considerable variation between the cage sites and reference sites (RF). The sediment organic carbon in cage sites was consistently higher than the RF irrespective of the season. The RF sites had higher species diversity than the cage sites contributed mainly by sensitive organisms like amphipods. The feeding guild analysis revealed a higher abundance of sub-surface deposit feeders (SSDF) and surface deposit feeders in the cage sites corresponding to an increase in the sediment organic carbon concentration.