Temporal and spatial changes in the sediment properties of a mangrove ecosystem (Cochin, southwest coast India) are presented. The region was freshwater dominated during monsoon (June–September) and seawater dominated during other two seasons. The system remained eutrophic due to the high inputs of organic matter (OM) during most part of the year. The organic-rich sediments accumulated high amount of carbohydrates (22% of OM) and proteins (11% of OM) during non-monsoon months as compared to coastal environments. Principal component analysis showed that the biochemical properties are uniformly influenced by seasonal and spatial variations. Higher concentrations of sediment protein over carbohydrate indicate an efficient mineralization leading to the non-availability of aged OM in the system. The dominance of these labile components is generally indicative of the eutrophic condition of the system.