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Variability of nature and composition of organic matter in the surficial sediments of mangrove and estuarine systems of Cochin were investigated. Assessment of biochemical composition and elements such as carbon, nitrogen and sulphur were employed for this. Irrespective of the higher content of total organic matter, the labile organic matter was very low in both mangrove and estuarine sediments. Concentrations of biochemical compounds were comparatively higher in mangrove sediments. Total lipids were the dominant class among labile organic compounds in both mangrove and estuarine sediments contributing 51.4% and 45.3%, respectively. Protein to carbohydrate ratio was higher in estuarine sediments when compared to mangroves, indicating low dead organic matter accumulation, probably due to the strong hydrodynamic conditions in estuaries. Correlation analysis showed that sediment texture had no significant correlation with any of the sedimentary parameters in mangroves, whereas in estuaries, it showed significant correlations with most of the sedimentary parameters. Principal component analysis indicated three different dominant processes in mangroves namely mangrove litter addition, diagenesis and other geochemical process like siltation and sorption/desorption, while in estuaries the dominant process seems to be diagenesis. [ABSTRACT FROM AUTHOR]