Present study has been designed to reveal the organic matter sources (algal vs. terrestrial), trophic status, the role of diagenesis and the applicability of biogeochemical indicators in a highly urbanized tropical mangrove forest. This has been achieved through a multiproxy approach by investigating the downcore distribution of bulk elemental properties (Total organic carbon (TOC%), total nitrogen (TN%)), biochemical composition, phytopigments and total hydrolysable amino acids (THAA). Both cores have a strong increase in algal biomass in the upper more fine grained part while core C2 has higher land plant fraction in its lower part compared to C1. The THAA profile decreased downcore ranging from 6.07 to 602.93 mu mol g-1, contributing 7-53% THAA-N and 6-23% THAA-C to the sediments. Amino acids namely, serine (Ser) and tyrosine (Tyr) suggesting the contribution of fresh plankton organic matter likely by bacterial activity, while valine (Val), phenylalanine (Phe), isoleucine (Iso) and leucine (Lue) indicated more land plant derived organic matter. The surface dominance of proteins (PRT) and phaeophytin (Phaeo) pigment supporting the change from a more land plant derived organic matter to a more aquatic/marine driven productivity in the upper core sediments. Biochemical ratio (PRT/CHO >1), biopolymeric carbon (BPC), algal contribution to BPC (AL%-BPC) and degradation index (DI) indicated eutrophication related with the increase in algal organic matter. Based on mol%, amino acids viz., glycine (Gly) and alanine (Ala) were significantly enriched in downcore diagenetically reworked sediments indicating the growth of bacterial colonies and the selective preservation of bacterial biomass. Organic matter transformation from labile form into refractory character and vice versa through bacterial reworking, plays a major role in the development from oligotrophy to hypertrophy in the Cochin lagoon. The increasing urbanization have caused anthropogenic induced change in sediment composition, and recent eutrophication changed a more land plant dominated aquatic system to enhanced algal productivity.